From e6673cb0ab599bcd9d91d87c6515040ba5957a3e Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Fri, 28 Oct 2022 16:48:58 -0700 Subject: [PATCH 01/59] Create ADCC GTL and Luciferase templates. --- .../GTL/adcc-gtl-biological-endpoints.Rmd | 12 ++++++++++ .../methods-adcc/GTL/adcc-gtl-lab-methods.Rmd | 13 ++++++++++ .../GTL/adcc-gtl-statistical-methods.Rmd | 24 +++++++++++++++++++ .../adcc-luc-biological-endpoints.Rmd | 15 ++++++++++++ .../Luciferase/adcc-luc-lab-methods.Rmd | 17 +++++++++++++ .../adcc-luc-statistical-methods.Rmd | 18 ++++++++++++++ 6 files changed, 99 insertions(+) create mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd create mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd create mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd create mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd create mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd create mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd new file mode 100644 index 00000000..2ddc9036 --- /dev/null +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd @@ -0,0 +1,12 @@ +--- +title: "biological-endpoints" +output: html_document +date: '2022-10-26' +--- + + + + +# Biological Endpoints + +ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measures percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd new file mode 100644 index 00000000..388d9eb4 --- /dev/null +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd @@ -0,0 +1,13 @@ +--- +title: "lab-methods" +output: html_document +date: '2022-10-26' +--- + + + + +# Lab Methods +ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which is the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8%. + +The monoclonal antibody Synagis and a cocktail of HIV-1 monoclonal Abs (A32, 2G12, CH44, and 7B2) were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd new file mode 100644 index 00000000..c77a5543 --- /dev/null +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd @@ -0,0 +1,24 @@ +--- +title: "statistical-methods" +output: html_document +date: '2022-10-27' +--- + + + +# Statistical Methods + +## Graphical analysis + +Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depict the response rate for each antigen as a point on an individual spoke. + +Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connect each participant at each time point. + +Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represents a response magnitude value (x) and the y-axis represents the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displays the average MB across all subjects in that group. + +Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). + + +## Statistical tests + +Response rates were calculated with Wilson's confidence intervals. Response magnitude analyses included responders and non-responders. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 24]). diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd new file mode 100644 index 00000000..768fb1e0 --- /dev/null +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd @@ -0,0 +1,15 @@ +--- +title: "biological-endpoints" +output: html_document +date: '2022-10-27' +--- + + + + +# Biological endpoints + +ADCC-mediated antibody responses were measured using the ADCC luciferase assay from serum specimens obtained at weeks [insert timepoint] corresponding to [insert timepoint] weeks after the late-boost vaccination. + +The ADCC luciferase assay tests the reactivity of antibodies induced from the participant's serum against Infectious Molecular Clone (IMC)-infected target cells ([insert IMCs]) by measuring percent reduction in Relative +Luminescence Units (RLUs) over a series of dilutions of the serum. diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd new file mode 100644 index 00000000..404620f0 --- /dev/null +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd @@ -0,0 +1,17 @@ +--- +title: "lab-methods" +output: html_document +date: '2022-10-28' +--- + + + + +# Lab Methods +CEM.NKR~CCR5~ cells [@trkola1999cell] were +used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). + +Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. + +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). + diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd new file mode 100644 index 00000000..fc7a7c8f --- /dev/null +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd @@ -0,0 +1,18 @@ +--- +title: "statistical-methods" +output: html_document +date: '2022-10-28' +--- + + + +# Statistical Methods + +## Statistical tests + +Two-sided 95% confidence intervals ($\alpha$ = 0.05) for binomial proportions of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. + +## Graphical analysis + +Response rates were plotted, with accompanying Wilson score confidence intervals, for each group, IMC, and study time point. Distributions of response magnitude were plotted for each group, IMC, and study time point with boxplots superimposed on the distribution of responders. The mid-line of the box denotes the median of the distribution and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). To show response trend over time, line plots of response magnitude were plotted by study group and IMC across time points. Boxplots were superimposed on the distributions of durability AUC. + From 0b97318623efe8ec38893844d2693c0b2a15069e Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Mon, 31 Oct 2022 14:54:13 -0700 Subject: [PATCH 02/59] Update ADCC GTL lab methods. --- .../methods-adcc/GTL/adcc-gtl-lab-methods.Rmd | 2 +- .../methods-adcc/ICABA/icaba-lab-methods.Rmd | 11 +++++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd index 388d9eb4..49ba7f60 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd @@ -8,6 +8,6 @@ date: '2022-10-26' # Lab Methods -ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which is the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8%. +ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which is the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8\%. The monoclonal antibody Synagis and a cocktail of HIV-1 monoclonal Abs (A32, 2G12, CH44, and 7B2) were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd new file mode 100644 index 00000000..d62f8f57 --- /dev/null +++ b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd @@ -0,0 +1,11 @@ +--- +title: "icaba-lab-methods" +output: html_document +date: '2022-10-31' +--- + +# Lab Methods + +The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells are incubated with 1:100 dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells are subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells are stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab are defined as live, p24 positive, and FITC positive. Final results are reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. + + From 302d7131532d7498a93085790ef037ba187e75fb Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Thu, 3 Nov 2022 17:12:01 -0700 Subject: [PATCH 03/59] Create templates for ICABA lab-methods,statistical-methods,biological-endpoints. --- .../ICABA/icaba-biological-endpoints.Rmd | 8 ++++++++ .../methods-adcc/ICABA/icaba-lab-methods.Rmd | 2 +- .../ICABA/icaba-statistical-methods.Rmd | 13 +++++++++++++ .../Luciferase/adcc-luc-statistical-methods.Rmd | 7 +++---- 4 files changed, 25 insertions(+), 5 deletions(-) create mode 100644 inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd create mode 100644 inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd diff --git a/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd b/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd new file mode 100644 index 00000000..0d7ab5cb --- /dev/null +++ b/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd @@ -0,0 +1,8 @@ +--- +title: "icaba-biological-endpoints" +output: html_document +date: '2022-11-03' +--- + +# Biological Endpoints +Plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells were measured using Infected Cell Antibody Binding Assay (ICABA) from specimens obtained at [insert visit]. ICABA responses were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd index d62f8f57..00771a2e 100644 --- a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd +++ b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd @@ -6,6 +6,6 @@ date: '2022-10-31' # Lab Methods -The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells are incubated with 1:100 dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells are subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells are stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab are defined as live, p24 positive, and FITC positive. Final results are reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. +The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells are incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells are subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells are stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab are defined as live, p24 positive, and FITC positive. Final results are reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd new file mode 100644 index 00000000..eac0c030 --- /dev/null +++ b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd @@ -0,0 +1,13 @@ +--- +title: "icaba-statistical-methods" +output: html_document +date: '2022-11-02' +--- + +# Statistical Methods + +## Graphical analysis + +Distributions of response magnitudes will be plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box). + +## Statistical tests diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd index fc7a7c8f..a188d853 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd @@ -8,11 +8,10 @@ date: '2022-10-28' # Statistical Methods -## Statistical tests - -Two-sided 95% confidence intervals ($\alpha$ = 0.05) for binomial proportions of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. - ## Graphical analysis Response rates were plotted, with accompanying Wilson score confidence intervals, for each group, IMC, and study time point. Distributions of response magnitude were plotted for each group, IMC, and study time point with boxplots superimposed on the distribution of responders. The mid-line of the box denotes the median of the distribution and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). To show response trend over time, line plots of response magnitude were plotted by study group and IMC across time points. Boxplots were superimposed on the distributions of durability AUC. +## Statistical tests + +Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. From 00ec518adea0e47fba7594258d7d609fa78256b7 Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Fri, 4 Nov 2022 12:03:59 -0700 Subject: [PATCH 04/59] Update icaba templates. --- .../methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd | 2 +- .../methods-adcc/ICABA/icaba-statistical-methods.Rmd | 4 ++-- .../methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd index c77a5543..30adf0a3 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd @@ -21,4 +21,4 @@ Distributions of durability (area under the durability curve) were plotted with ## Statistical tests -Response rates were calculated with Wilson's confidence intervals. Response magnitude analyses included responders and non-responders. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 24]). +Response rates were calculated with Wilson's confidence intervals. Response magnitudes were summarized with median, minimum, and maximum. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 24]). diff --git a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd index eac0c030..278dc77b 100644 --- a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd @@ -7,7 +7,7 @@ date: '2022-11-02' # Statistical Methods ## Graphical analysis - -Distributions of response magnitudes will be plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box). +Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box). ## Statistical tests +Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998]. Response magnitudes were summarized with median, minimum, and maximum. diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd index a188d853..fbb02ea2 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd @@ -14,4 +14,4 @@ Response rates were plotted, with accompanying Wilson score confidence intervals ## Statistical tests -Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. +Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. Response magnitudes were summarized with median, minimum, and maximum. From fe90f70a08665b3dbcc5cece77cfb5b02fc187c7 Mon Sep 17 00:00:00 2001 From: ruizhw19 <96448001+ruizhw19@users.noreply.github.com> Date: Thu, 10 Nov 2022 13:08:55 -0800 Subject: [PATCH 05/59] Update icaba-statistical-methods.Rmd --- inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd index 278dc77b..ba160bb9 100644 --- a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd @@ -10,4 +10,4 @@ date: '2022-11-02' Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box). ## Statistical tests -Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998]. Response magnitudes were summarized with median, minimum, and maximum. + From 7ee3c8a5ddfe2b089a62dab7ff7176e7f5d85453 Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Fri, 9 Dec 2022 10:13:12 -0800 Subject: [PATCH 06/59] update. --- inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd index 404620f0..15d657e1 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd @@ -13,5 +13,5 @@ used as targets for ADCC luciferase assays after infection with the infectious m Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold [Adjust if different] serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). From 299b6e485cdfc7477dd788dd6a3158f8c454c710 Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Tue, 3 Jan 2023 14:14:58 -0800 Subject: [PATCH 07/59] update luciferase biological endpoints. --- .../methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd index 768fb1e0..c7eccb1e 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd @@ -9,7 +9,7 @@ date: '2022-10-27' # Biological endpoints -ADCC-mediated antibody responses were measured using the ADCC luciferase assay from serum specimens obtained at weeks [insert timepoint] corresponding to [insert timepoint] weeks after the late-boost vaccination. +ADCC-mediated antibody responses were measured using the ADCC luciferase assay from serum specimens obtained at weeks [insert timepoint] corresponding to [insert timepoint] weeks. The ADCC luciferase assay tests the reactivity of antibodies induced from the participant's serum against Infectious Molecular Clone (IMC)-infected target cells ([insert IMCs]) by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum. From b47159c0f59faeb8b12d822b46e48319ac88a516 Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Tue, 3 Jan 2023 14:47:10 -0800 Subject: [PATCH 08/59] update methods past tense. --- .../methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd | 2 +- inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd | 2 +- .../methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd | 8 ++++---- inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd | 2 +- .../methods-adcc/ICABA/icaba-statistical-methods.Rmd | 2 +- .../Luciferase/adcc-luc-biological-endpoints.Rmd | 2 +- .../Luciferase/adcc-luc-statistical-methods.Rmd | 4 ++-- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd index 2ddc9036..cbfc7e9e 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd @@ -9,4 +9,4 @@ date: '2022-10-26' # Biological Endpoints -ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measures percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. +ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd index 49ba7f60..c8ef1393 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd @@ -8,6 +8,6 @@ date: '2022-10-26' # Lab Methods -ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which is the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8\%. +ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8\%. The monoclonal antibody Synagis and a cocktail of HIV-1 monoclonal Abs (A32, 2G12, CH44, and 7B2) were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd index 30adf0a3..d4ada222 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd @@ -10,13 +10,13 @@ date: '2022-10-27' ## Graphical analysis -Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depict the response rate for each antigen as a point on an individual spoke. +Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. -Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connect each participant at each time point. +Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. -Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represents a response magnitude value (x) and the y-axis represents the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displays the average MB across all subjects in that group. +Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. -Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). +Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). ## Statistical tests diff --git a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd index 00771a2e..7d37ea0a 100644 --- a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd +++ b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd @@ -6,6 +6,6 @@ date: '2022-10-31' # Lab Methods -The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells are incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells are subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells are stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab are defined as live, p24 positive, and FITC positive. Final results are reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. +The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells were incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells were subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells were stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab were defined as live, p24 positive, and FITC positive. Final results were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd index ba160bb9..06ef3d84 100644 --- a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd @@ -7,7 +7,7 @@ date: '2022-11-02' # Statistical Methods ## Graphical analysis -Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box). +Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). ## Statistical tests diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd index c7eccb1e..5f296449 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd @@ -11,5 +11,5 @@ date: '2022-10-27' ADCC-mediated antibody responses were measured using the ADCC luciferase assay from serum specimens obtained at weeks [insert timepoint] corresponding to [insert timepoint] weeks. -The ADCC luciferase assay tests the reactivity of antibodies induced from the participant's serum against Infectious Molecular Clone (IMC)-infected target cells ([insert IMCs]) by measuring percent reduction in Relative +The ADCC luciferase assay tested the reactivity of antibodies induced from the participant's serum against Infectious Molecular Clone (IMC)-infected target cells ([insert IMCs]) by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum. diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd index fbb02ea2..69b487ba 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd @@ -10,8 +10,8 @@ date: '2022-10-28' ## Graphical analysis -Response rates were plotted, with accompanying Wilson score confidence intervals, for each group, IMC, and study time point. Distributions of response magnitude were plotted for each group, IMC, and study time point with boxplots superimposed on the distribution of responders. The mid-line of the box denotes the median of the distribution and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers denote the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). To show response trend over time, line plots of response magnitude were plotted by study group and IMC across time points. Boxplots were superimposed on the distributions of durability AUC. +Response rates were plotted, with accompanying Wilson score confidence intervals, for each group, IMC, and study time point. Distributions of response magnitude were plotted for each group, IMC, and study time point with boxplots superimposed on the distribution of responders. The mid-line of the box denoted the median of the distribution and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). To show response trend over time, line plots of response magnitude were plotted by study group and IMC across time points. Boxplots were superimposed on the distributions of durability AUC. ## Statistical tests -Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which is preferred when there is a small sample size. Response magnitudes were summarized with median, minimum, and maximum. +Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which was preferred when there was a small sample size. Response magnitudes were summarized with median, minimum, and maximum. From 9944eeb9598a2a16d52f093fc00e397620be5274 Mon Sep 17 00:00:00 2001 From: Ruizhe Wu Date: Fri, 13 Jan 2023 15:48:47 -0800 Subject: [PATCH 09/59] update lab methods, statistical methods, biological endpoints. --- inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd | 4 +--- .../methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd | 6 +++++- .../Luciferase/adcc-luc-biological-endpoints.Rmd | 5 +---- .../Luciferase/adcc-luc-statistical-methods.Rmd | 7 +++++-- 4 files changed, 12 insertions(+), 10 deletions(-) diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd index c8ef1393..c56cf585 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd @@ -8,6 +8,4 @@ date: '2022-10-26' # Lab Methods -ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. The analyses in the data focused on the readouts indicated in the statistical methods. Peak activity less than 0\% was set to 0\%. A positive response was defined as peak activity greater than or equal to 8\%. - -The monoclonal antibody Synagis and a cocktail of HIV-1 monoclonal Abs (A32, 2G12, CH44, and 7B2) were used as negative and positive controls, respectively. +ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd index d4ada222..994e8616 100644 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd @@ -21,4 +21,8 @@ Distributions of durability (area under the durability curve) were plotted with ## Statistical tests -Response rates were calculated with Wilson's confidence intervals. Response magnitudes were summarized with median, minimum, and maximum. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 24]). +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. + +Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). + +Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd index 5f296449..b880f732 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd @@ -9,7 +9,4 @@ date: '2022-10-27' # Biological endpoints -ADCC-mediated antibody responses were measured using the ADCC luciferase assay from serum specimens obtained at weeks [insert timepoint] corresponding to [insert timepoint] weeks. - -The ADCC luciferase assay tested the reactivity of antibodies induced from the participant's serum against Infectious Molecular Clone (IMC)-infected target cells ([insert IMCs]) by measuring percent reduction in Relative -Luminescence Units (RLUs) over a series of dilutions of the serum. +The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd index 69b487ba..4a2c06f7 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd @@ -10,8 +10,11 @@ date: '2022-10-28' ## Graphical analysis -Response rates were plotted, with accompanying Wilson score confidence intervals, for each group, IMC, and study time point. Distributions of response magnitude were plotted for each group, IMC, and study time point with boxplots superimposed on the distribution of responders. The mid-line of the box denoted the median of the distribution and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). To show response trend over time, line plots of response magnitude were plotted by study group and IMC across time points. Boxplots were superimposed on the distributions of durability AUC. +Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). +Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. ## Statistical tests +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. +Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). -Two-sided 95% confidence intervals ($\alpha$ = 0.05) of positive responders were calculated using Wilson's method [@agresti_approximate_1998], which was preferred when there was a small sample size. Response magnitudes were summarized with median, minimum, and maximum. +Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. From b652eb29c3452eff62d60378bbc57af923ef594a Mon Sep 17 00:00:00 2001 From: Cassidy Kornfeld <141687424+ckornfeld1@users.noreply.github.com> Date: Mon, 14 Aug 2023 13:51:12 -0700 Subject: [PATCH 10/59] Update adcc-luc-biological-endpoints.Rmd edited to match HVTN ADCC-Luc template --- .../methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd index b880f732..8db5bb53 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd @@ -9,4 +9,4 @@ date: '2022-10-27' # Biological endpoints -The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). +The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. From 35d914639bbf45b2da5f2ff0b3c14130ae153625 Mon Sep 17 00:00:00 2001 From: Cassidy Kornfeld <141687424+ckornfeld1@users.noreply.github.com> Date: Mon, 14 Aug 2023 14:02:35 -0700 Subject: [PATCH 11/59] Update adcc-luc-lab-methods.Rmd added last paragraph to align with HVTN template --- .../methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd index 15d657e1..eb4d4fe6 100644 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd @@ -8,10 +8,11 @@ date: '2022-10-28' # Lab Methods -CEM.NKR~CCR5~ cells [@trkola1999cell] were -used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). +CEM.NKR~CCR5~ cells [@trkola1999cell] were used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold [Adjust if different] serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). +In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absense of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. + From f44dd65ae48f52e0dec6ebb472cdc84f5bada1ba Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Mon, 8 Jul 2024 15:17:28 -0700 Subject: [PATCH 12/59] delete repeat files between GTL and luciferase. add commits from main. --- .../GTL/adcc-gtl-biological-endpoints.Rmd | 12 -------- .../methods-adcc/GTL/adcc-gtl-lab-methods.Rmd | 11 -------- .../GTL/adcc-gtl-statistical-methods.Rmd | 28 ------------------- .../adcc-luc-biological-endpoints.Rmd | 12 -------- .../Luciferase/adcc-luc-lab-methods.Rmd | 18 ------------ .../adcc-luc-statistical-methods.Rmd | 20 ------------- 6 files changed, 101 deletions(-) delete mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd delete mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd delete mode 100644 inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd delete mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd delete mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd delete mode 100644 inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd deleted file mode 100644 index cbfc7e9e..00000000 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-biological-endpoints.Rmd +++ /dev/null @@ -1,12 +0,0 @@ ---- -title: "biological-endpoints" -output: html_document -date: '2022-10-26' ---- - - - - -# Biological Endpoints - -ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd deleted file mode 100644 index c56cf585..00000000 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-lab-methods.Rmd +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: "lab-methods" -output: html_document -date: '2022-10-26' ---- - - - - -# Lab Methods -ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. diff --git a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd deleted file mode 100644 index 994e8616..00000000 --- a/inst/templates/methods-adcc/GTL/adcc-gtl-statistical-methods.Rmd +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: "statistical-methods" -output: html_document -date: '2022-10-27' ---- - - - -# Statistical Methods - -## Graphical analysis - -Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. - -Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. - -Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. - -Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). - - -## Statistical tests - -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. - -Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). - -Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd deleted file mode 100644 index 8db5bb53..00000000 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-biological-endpoints.Rmd +++ /dev/null @@ -1,12 +0,0 @@ ---- -title: "biological-endpoints" -output: html_document -date: '2022-10-27' ---- - - - - -# Biological endpoints - -The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd deleted file mode 100644 index eb4d4fe6..00000000 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-lab-methods.Rmd +++ /dev/null @@ -1,18 +0,0 @@ ---- -title: "lab-methods" -output: html_document -date: '2022-10-28' ---- - - - - -# Lab Methods -CEM.NKR~CCR5~ cells [@trkola1999cell] were used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). - -Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. - -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold [Adjust if different] serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). - -In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absense of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. - diff --git a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd b/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd deleted file mode 100644 index 4a2c06f7..00000000 --- a/inst/templates/methods-adcc/Luciferase/adcc-luc-statistical-methods.Rmd +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: "statistical-methods" -output: html_document -date: '2022-10-28' ---- - - - -# Statistical Methods - -## Graphical analysis - -Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). -Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. - -## Statistical tests -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. -Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). - -Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. From 5fc74dd799e62a7efd6f0dac735f48af29428a79 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Mon, 8 Jul 2024 15:21:22 -0700 Subject: [PATCH 13/59] add combined ADCC GTL-luc lab methods, bio endpts, stats endpts --- .../GTL-Luc/adcc-biological-endpoints.Rmd | 17 ++++++++ .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 22 ++++++++++ .../GTL-Luc/adcc-statistical-methods.Rmd | 42 +++++++++++++++++++ 3 files changed, 81 insertions(+) create mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd create mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd create mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd new file mode 100644 index 00000000..1955348c --- /dev/null +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd @@ -0,0 +1,17 @@ +--- +title: "biological-endpoints" +output: html_document +date: '2022-10-26' +--- + + + + +# Biological Endpoints GTL + +ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. + +# Biological endpoints Luciferase + +The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. + diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd new file mode 100644 index 00000000..cc9eff4c --- /dev/null +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd @@ -0,0 +1,22 @@ +--- +title: "lab-methods" +output: html_document +date: '2022-10-26' +--- + + + + +# Lab Methods GTL + +ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. + +# Lab Methods Luciferase + +CEM.NKR~CCR5~ cells [@trkola1999cell] were used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). + +Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. + +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold [Adjust if different] serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). + +In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absense of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd new file mode 100644 index 00000000..8dcdd0ee --- /dev/null +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd @@ -0,0 +1,42 @@ +--- +title: "statistical-methods" +output: html_document +date: '2022-10-27' +--- + + + +# Statistical Methods GTL + +## Graphical analysis + +Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. + +Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. + +Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. + +Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). + + +## Statistical tests + +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. + +Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). + +Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). + +# Statistical Methods Luciferase + +## Graphical analysis + +Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). +Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. + +## Statistical tests +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. +Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). + +Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. + From cacf083285dbc5aba00f7493177c0a6490699b59 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 08:46:43 -0700 Subject: [PATCH 14/59] add HVTN to the two other options for ADCC background section --- .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd index cc9eff4c..50473e81 100644 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd @@ -9,7 +9,15 @@ date: '2022-10-26' # Lab Methods GTL -ADCC-mediated antibody responses were measured by ADCC GranToxiLux (GTL) [@Pollara2011] and tested against [insert antigens]. Participant sera were incubated with effector cells and gp120-coated target cells and ADCC was quantified as net percent granzyme B activity, which was the percent of target cells positive for GranToxiLux (GTL) detected by flow cytometry. For each subject at each timepoint, percent granzyme B activity was measured at [#] dilution levels: [insert dilution levels] for each antigen. +note to self: decided to pull over the lab methods from HVTN word for word + + + + + + + + # Lab Methods Luciferase From 6a264c42618b6a29a76c56bb6438c981046217ed Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 09:04:40 -0700 Subject: [PATCH 15/59] erase old writing and add HVTN template writing --- .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 33 ++++++++++++------- 1 file changed, 22 insertions(+), 11 deletions(-) diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd index 50473e81..a2a403c4 100644 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd @@ -1,7 +1,9 @@ --- title: "lab-methods" -output: html_document -date: '2022-10-26' +output: + pdf_document: default + html_document: default +date: "2022-10-26" --- @@ -9,22 +11,31 @@ date: '2022-10-26' # Lab Methods GTL -note to self: decided to pull over the lab methods from HVTN word for word +The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described *[1]*. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola *[2]*. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. - +ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. + + - - - - # Lab Methods Luciferase -CEM.NKR~CCR5~ cells [@trkola1999cell] were used as targets for ADCC luciferase assays after infection with the infectious molecular clones ([insert IMCs]). +We utilized a modified version of a previously published ADCC luciferase procedure *[1, 2]*. Briefly, CEM.NKRCCR5 cells *[3]* were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: +Complete IMC name Accession Number Abbreviated name Vaccine Match +[Full name, as uploaded by lab] [provided by lab] [SRA-derived abbreviated name shown in tables and figures] [if a mix of matched and unmatched IMCs were tested, indicate here which were matched] Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold [Adjust if different] serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200 [Adjust if dilutions are different]. Co-cultures were incubated for 6 hours at $37 ^{\circ} C$ in $5\% \text{ CO}_2$. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = 100 * (RLU of target and effector well– RLU of test well)/(RLU of target and effector well). +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. -In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absense of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. +In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. + + + + + + + + + From 601fe3a5ae87e732c897b9d867642c434d34111b Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 10:00:39 -0700 Subject: [PATCH 16/59] update bibliography for adcc combined lab methods sections. update latex from word doc origin --- inst/templates/bibliography.bib | 23 ++++++++++++++++++- .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 17 ++------------ 2 files changed, 24 insertions(+), 16 deletions(-) diff --git a/inst/templates/bibliography.bib b/inst/templates/bibliography.bib index f54d604a..29732011 100644 --- a/inst/templates/bibliography.bib +++ b/inst/templates/bibliography.bib @@ -371,7 +371,7 @@ @article{Newton2004 } @article{Pollara2014, - author = {Pollara, J., Bonsignori, M. et al.}, + author = {Pollara, J. and Bonsignori, M. and Moody, A. M. and Liu, P. S. and Alam, M. and Hwang, K.K. and Gurley, T. and Kozink, D. M. and Armand, L. C. and Marshall, D. J. and Whitesides, J. F. and Kaewkungwal, J. and Nitayaphan, S. and Pitisuttithum, P. and Rerks-Ngarm, S. and Robb, M. L. and O'Connell, R. J. and Kim, J. H. and Michael, N. L. and Montefiori, D. C. and Tomaras, G. D. and Liao, H. X., and Haynes, B. F. and Ferrari, G.}, title = {HIV-1 vaccine-induced C1 and V2 Env-specific antibodies synergize for increased antiviral activities.}, journal = {J Virol.}, year = {2014}, @@ -379,6 +379,15 @@ @article{Pollara2014 pages = {7715-26} } +@article{Fisher2019, + author = {Fisher, L. and Zinter, M. and Stanfield-Oakley, S. and Carpp, L.N. and Edwards, R.W. and Denny, T. and Moodie, Z. and Laher, F. and Bekker, L.G. and McElrath, M.J. and Gilbert, P.B.}, + year = {2019}, + title = {{Vaccine-induced antibodies mediate higher antibody-dependent cellular cytotoxicity after interleukin-15 pretreatment of natural killer effector cells.}}, + journal = {{Frontiers in Immunology}}, + volume = {10}, + pages = {2741} +} + @article{Sambor2014, author = {Sambor, A. et al.}, title = {Establishment and maintenance of a PBMC repository for functional cellular studies in support of clinical vaccine trials.}, @@ -397,6 +406,16 @@ @article{Pollara2011 pages = {603-12} } +@article{Trkola1999, + author = {Trkola, A. and Matthews, J. and Gordon, C. and Ketas, T. and Moore, J. P.}, + title = {{A Cell Line Based Neutralization Assay for Primary Human Immunodeficiency Virus Type 1 Isolates That Use Either the CCR5 or the CXCR4 Coreceptor.}}, + year = {1999}, + journal = {{Journal of Virology}}, + volume = {73}, + number = {11}, + pages = {8966-8974} +} + @article{tomaras_polyclonal_2011, title = {Polyclonal B cell responses to conserved neutralization epitopes in a subset of HIV-1-infected individuals}, volume = {85}, @@ -457,3 +476,5 @@ @Manual{rlang year = {2020}, url = {https://www.R-project.org/} } + + diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd index a2a403c4..ca25559e 100644 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd @@ -11,17 +11,13 @@ date: "2022-10-26" # Lab Methods GTL -The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described *[1]*. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola *[2]*. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. +The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. - - - - # Lab Methods Luciferase -We utilized a modified version of a previously published ADCC luciferase procedure *[1, 2]*. Briefly, CEM.NKRCCR5 cells *[3]* were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: +We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014, @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: Complete IMC name Accession Number Abbreviated name Vaccine Match [Full name, as uploaded by lab] [provided by lab] [SRA-derived abbreviated name shown in tables and figures] [if a mix of matched and unmatched IMCs were tested, indicate here which were matched] @@ -30,12 +26,3 @@ Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. - - - - - - - - - From 057383c3c481bcc1e9fff38af3a87d71fdafbc44 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 10:59:20 -0700 Subject: [PATCH 17/59] move files to follow convention. change R/template file to include adcc --- R/template.R | 10 ++--- .../GTL-Luc/adcc-biological-endpoints.Rmd | 17 -------- .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 28 ------------- .../GTL-Luc/adcc-statistical-methods.Rmd | 42 ------------------- .../ICABA/icaba-biological-endpoints.Rmd | 8 ---- .../methods-adcc/ICABA/icaba-lab-methods.Rmd | 11 ----- .../ICABA/icaba-statistical-methods.Rmd | 13 ------ 7 files changed, 5 insertions(+), 124 deletions(-) delete mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd delete mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd delete mode 100644 inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd delete mode 100644 inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd delete mode 100644 inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd delete mode 100644 inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd diff --git a/R/template.R b/R/template.R index 0ffb1d9c..fd401d0e 100644 --- a/R/template.R +++ b/R/template.R @@ -105,7 +105,7 @@ use_bib <- function(study_name) { #' #' @param report_name name of the file (character) #' @param path path of the file within the active project -#' @param report_type "empty", "generic", "bama", or "nab" +#' @param report_type "empty", "generic", "bama", "nab", or "adcc" #' #' @export #' @@ -119,9 +119,9 @@ use_bib <- function(study_name) { #' } use_visc_report <- function(report_name = "PT-Report", path = ".", - report_type = c("empty", "generic", "bama", "nab")) { + report_type = c("empty", "generic", "bama", "nab", "adcc")) { - stopifnot(report_type %in% c("empty", "generic", "bama", "nab")) + stopifnot(report_type %in% c("empty", "generic", "bama", "nab", "adcc")) if (report_type == "empty") { rmarkdown::draft( @@ -178,7 +178,7 @@ challenge_visc_report <- function(report_name) { #' used in PT reports: statistical-methods.Rmd, lab-methods.Rmd, #' and biological-endpoints.Rmd #' -#' @param assay "bama" or "generic" +#' @param assay "generic", "bama", "nab" or "adcc" #' @param path path within the active project #' #' @export @@ -187,7 +187,7 @@ challenge_visc_report <- function(report_name) { #' \dontrun{ #' use_visc_methods(path = "bama/BAMA-PT-Report", assay = "bama") #' } -use_visc_methods <- function(path = ".", assay = c("generic", "bama", "nab")) { +use_visc_methods <- function(path = ".", assay = c("generic", "bama", "nab", "adcc")) { pkg_ver <- utils::packageVersion("VISCtemplates") diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd deleted file mode 100644 index 1955348c..00000000 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-biological-endpoints.Rmd +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: "biological-endpoints" -output: html_document -date: '2022-10-26' ---- - - - - -# Biological Endpoints GTL - -ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. - -# Biological endpoints Luciferase - -The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. - diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd deleted file mode 100644 index ca25559e..00000000 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: "lab-methods" -output: - pdf_document: default - html_document: default -date: "2022-10-26" ---- - - - - -# Lab Methods GTL - -The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. - -ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. - -# Lab Methods Luciferase - -We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014, @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: -Complete IMC name Accession Number Abbreviated name Vaccine Match -[Full name, as uploaded by lab] [provided by lab] [SRA-derived abbreviated name shown in tables and figures] [if a mix of matched and unmatched IMCs were tested, indicate here which were matched] - -Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. - -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. - -In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd deleted file mode 100644 index 8dcdd0ee..00000000 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd +++ /dev/null @@ -1,42 +0,0 @@ ---- -title: "statistical-methods" -output: html_document -date: '2022-10-27' ---- - - - -# Statistical Methods GTL - -## Graphical analysis - -Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. - -Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. - -Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. - -Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). - - -## Statistical tests - -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. - -Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). - -Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). - -# Statistical Methods Luciferase - -## Graphical analysis - -Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). -Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. - -## Statistical tests -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. -Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). - -Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. - diff --git a/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd b/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd deleted file mode 100644 index 0d7ab5cb..00000000 --- a/inst/templates/methods-adcc/ICABA/icaba-biological-endpoints.Rmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: "icaba-biological-endpoints" -output: html_document -date: '2022-11-03' ---- - -# Biological Endpoints -Plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells were measured using Infected Cell Antibody Binding Assay (ICABA) from specimens obtained at [insert visit]. ICABA responses were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd deleted file mode 100644 index 7d37ea0a..00000000 --- a/inst/templates/methods-adcc/ICABA/icaba-lab-methods.Rmd +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: "icaba-lab-methods" -output: html_document -date: '2022-10-31' ---- - -# Lab Methods - -The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells were incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells were subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells were stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab were defined as live, p24 positive, and FITC positive. Final results were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. - - diff --git a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd b/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd deleted file mode 100644 index 06ef3d84..00000000 --- a/inst/templates/methods-adcc/ICABA/icaba-statistical-methods.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: "icaba-statistical-methods" -output: html_document -date: '2022-11-02' ---- - -# Statistical Methods - -## Graphical analysis -Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). - -## Statistical tests - From 947775c0e43cb8ac4f09b747b56ade9758dd2746 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 11:01:50 -0700 Subject: [PATCH 18/59] move files to follow convention 2 --- .../adcc-biological-endpoints.Rmd | 17 ++++++++ .../methods-adcc/adcc-lab-methods.Rmd | 28 +++++++++++++ .../methods-adcc/adcc-statistical-methods.Rmd | 42 +++++++++++++++++++ .../icaba-biological-endpoints.Rmd | 8 ++++ .../methods-icaba/icaba-lab-methods.Rmd | 11 +++++ .../icaba-statistical-methods.Rmd | 13 ++++++ 6 files changed, 119 insertions(+) create mode 100644 inst/templates/methods-adcc/adcc-biological-endpoints.Rmd create mode 100644 inst/templates/methods-adcc/adcc-lab-methods.Rmd create mode 100644 inst/templates/methods-adcc/adcc-statistical-methods.Rmd create mode 100644 inst/templates/methods-icaba/icaba-biological-endpoints.Rmd create mode 100644 inst/templates/methods-icaba/icaba-lab-methods.Rmd create mode 100644 inst/templates/methods-icaba/icaba-statistical-methods.Rmd diff --git a/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd new file mode 100644 index 00000000..1955348c --- /dev/null +++ b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd @@ -0,0 +1,17 @@ +--- +title: "biological-endpoints" +output: html_document +date: '2022-10-26' +--- + + + + +# Biological Endpoints GTL + +ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. + +# Biological endpoints Luciferase + +The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. + diff --git a/inst/templates/methods-adcc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/adcc-lab-methods.Rmd new file mode 100644 index 00000000..ca25559e --- /dev/null +++ b/inst/templates/methods-adcc/adcc-lab-methods.Rmd @@ -0,0 +1,28 @@ +--- +title: "lab-methods" +output: + pdf_document: default + html_document: default +date: "2022-10-26" +--- + + + + +# Lab Methods GTL + +The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. + +ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. + +# Lab Methods Luciferase + +We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014, @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: +Complete IMC name Accession Number Abbreviated name Vaccine Match +[Full name, as uploaded by lab] [provided by lab] [SRA-derived abbreviated name shown in tables and figures] [if a mix of matched and unmatched IMCs were tested, indicate here which were matched] + +Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. + +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. + +In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd new file mode 100644 index 00000000..8dcdd0ee --- /dev/null +++ b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd @@ -0,0 +1,42 @@ +--- +title: "statistical-methods" +output: html_document +date: '2022-10-27' +--- + + + +# Statistical Methods GTL + +## Graphical analysis + +Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. + +Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. + +Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. + +Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). + + +## Statistical tests + +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. + +Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). + +Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). + +# Statistical Methods Luciferase + +## Graphical analysis + +Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). +Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. + +## Statistical tests +Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. +Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). + +Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. + diff --git a/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd b/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd new file mode 100644 index 00000000..0d7ab5cb --- /dev/null +++ b/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd @@ -0,0 +1,8 @@ +--- +title: "icaba-biological-endpoints" +output: html_document +date: '2022-11-03' +--- + +# Biological Endpoints +Plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells were measured using Infected Cell Antibody Binding Assay (ICABA) from specimens obtained at [insert visit]. ICABA responses were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-icaba/icaba-lab-methods.Rmd b/inst/templates/methods-icaba/icaba-lab-methods.Rmd new file mode 100644 index 00000000..7d37ea0a --- /dev/null +++ b/inst/templates/methods-icaba/icaba-lab-methods.Rmd @@ -0,0 +1,11 @@ +--- +title: "icaba-lab-methods" +output: html_document +date: '2022-10-31' +--- + +# Lab Methods + +The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells were incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells were subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells were stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab were defined as live, p24 positive, and FITC positive. Final results were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. + + diff --git a/inst/templates/methods-icaba/icaba-statistical-methods.Rmd b/inst/templates/methods-icaba/icaba-statistical-methods.Rmd new file mode 100644 index 00000000..06ef3d84 --- /dev/null +++ b/inst/templates/methods-icaba/icaba-statistical-methods.Rmd @@ -0,0 +1,13 @@ +--- +title: "icaba-statistical-methods" +output: html_document +date: '2022-11-02' +--- + +# Statistical Methods + +## Graphical analysis +Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). + +## Statistical tests + From b7d6b5d72bcd29b78e762c17112a5d5aeedde49f Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 11 Jul 2024 12:32:35 -0700 Subject: [PATCH 19/59] modify bib file. tested it and it runs when in the adcc folder. --- inst/templates/bibliography.bib | 10 +++++----- .../methods-adcc/GTL-Luc/adcc-lab-methods.Rmd | 3 --- .../methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd | 1 - 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/inst/templates/bibliography.bib b/inst/templates/bibliography.bib index 29732011..0f824501 100644 --- a/inst/templates/bibliography.bib +++ b/inst/templates/bibliography.bib @@ -382,8 +382,8 @@ @article{Pollara2014 @article{Fisher2019, author = {Fisher, L. and Zinter, M. and Stanfield-Oakley, S. and Carpp, L.N. and Edwards, R.W. and Denny, T. and Moodie, Z. and Laher, F. and Bekker, L.G. and McElrath, M.J. and Gilbert, P.B.}, year = {2019}, - title = {{Vaccine-induced antibodies mediate higher antibody-dependent cellular cytotoxicity after interleukin-15 pretreatment of natural killer effector cells.}}, - journal = {{Frontiers in Immunology}}, + title = {{V}accine-induced antibodies mediate higher antibody-dependent cellular cytotoxicity after interleukin-15 pretreatment of natural killer effector cells.}, + journal = {{F}rontiers in {I}mmunology}, volume = {10}, pages = {2741} } @@ -399,7 +399,7 @@ @article{Sambor2014 @article{Pollara2011, author = {Pollara, J., Hart, L. et al.}, - title = {High-throughput quantitative analysis of HIV-1 and SIV-specific ADCC-mediating antibody responses.}, + title = {{H}igh-throughput quantitative analysis of {HIV}-1 and {SIV}-specific {ADCC}-mediating antibody responses.}, journal = {Cytometry A.}, year = {2011}, volume = {79(8)}, @@ -408,9 +408,9 @@ @article{Pollara2011 @article{Trkola1999, author = {Trkola, A. and Matthews, J. and Gordon, C. and Ketas, T. and Moore, J. P.}, - title = {{A Cell Line Based Neutralization Assay for Primary Human Immunodeficiency Virus Type 1 Isolates That Use Either the CCR5 or the CXCR4 Coreceptor.}}, + title = {{A} {C}ell {L}ine {B}ased {N}eutralization {A}ssay for {P}rimary {H}uman {I}mmunodeficiency {V}irus {T}ype 1 {I}solates {T}hat {U}se {E}ither the {CCR}5 or the {CXCR}4 {C}oreceptor.}, year = {1999}, - journal = {{Journal of Virology}}, + journal = {{J}ournal of {V}irology}, volume = {73}, number = {11}, pages = {8966-8974} diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd index ca25559e..08c3dd2f 100644 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-lab-methods.Rmd @@ -1,8 +1,5 @@ --- title: "lab-methods" -output: - pdf_document: default - html_document: default date: "2022-10-26" --- diff --git a/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd index 8dcdd0ee..ee266f0d 100644 --- a/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/GTL-Luc/adcc-statistical-methods.Rmd @@ -1,6 +1,5 @@ --- title: "statistical-methods" -output: html_document date: '2022-10-27' --- From 0e4d8d6bb7dc989ddfbdf6d592b3969f31f71dbf Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Mon, 15 Jul 2024 14:59:13 -0700 Subject: [PATCH 20/59] modify wording of ADCC templates per current HVTN as of july 15 2024 --- .../adcc-biological-endpoints.Rmd | 7 +-- .../methods-adcc/adcc-lab-methods.Rmd | 2 +- .../methods-adcc/adcc-statistical-methods.Rmd | 45 +++++++++++-------- 3 files changed, 30 insertions(+), 24 deletions(-) diff --git a/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd index 1955348c..6ab066f4 100644 --- a/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd @@ -1,7 +1,5 @@ --- title: "biological-endpoints" -output: html_document -date: '2022-10-26' --- @@ -9,9 +7,8 @@ date: '2022-10-26' # Biological Endpoints GTL -ADCC-mediated antibody responses were measured using GranToxiLux (GTL) ADCC assays from specimens obtained at [insert visit, e.g., weeks 0 (before boost), 2 (2 weeks post-boost), 12 (12 weeks post-boost), and 24 (24 weeks post-boost)]. [#] antigens ([insert antigens]) were tested in the GTL assay. The first [#] antigens tested were vaccine-matched and the [#] antigens was tested to evaluate heterologous Clade C responses. The GTL ADCC assay measured percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. +ADCC-mediated antibody responses were measured using Luciferase GranToxiLux (GTL) assays from specimens obtained at *[describe visits; include visit number, timepoint in weeks or months, and relation to SPA. E.g. week 26 (2 weeks post-4th vaccination, visit 10)]*. The GTL ADCC assay measures percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. Endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of *[number of antigens]* HIV-1 antigens representing *[include description of viruses: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the responses against HIV-1 subtypes]*. # Biological endpoints Luciferase -The ADCC luciferase assay tested the presence of vaccine-induced antibody responses in serum samples collected from the study participants against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs) over a series of dilutions of the serum (@103389fimmu201902741). (Biological?) endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of [number of IMCs] HIV-1 IMC expressing Env representing [include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the response against HIV-1 subtypes]. - +ADCC-mediated antibody responses were measured using Luciferase ADCC assays from specimens obtained at *[describe visits; include visit number, timepoint in weeks or months, and relation to SPA. E.g. week 26 (2 weeks post-4th vaccination, visit 10)]*. The Luciferase ADCC assay tests reactivity against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs), reported as percentage specific killing. Endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of *[number of IMCs]* HIV-1 IMC expressing Env representing *[include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the responses against HIV-1 subtypes]*. diff --git a/inst/templates/methods-adcc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/adcc-lab-methods.Rmd index 08c3dd2f..9d9ceb3b 100644 --- a/inst/templates/methods-adcc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-lab-methods.Rmd @@ -8,7 +8,7 @@ date: "2022-10-26" # Lab Methods GTL -The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50. Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. +The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50 (1:50, 1:250, 1:1250, 1:6250, 1:31250, and 1:156250). Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. diff --git a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd index ee266f0d..9fd6cbec 100644 --- a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd @@ -1,41 +1,50 @@ --- title: "statistical-methods" -date: '2022-10-27' --- -# Statistical Methods GTL +## Statistical Endpoints GTL -## Graphical analysis +### Peak activity -Response rates were plotted for each antigen at each time point. Response rates were also plotted on radar plots, which depicted the response rate for each antigen as a point on an individual spoke. +Peak net percent granzyme B activity defined as the maximum activity across the six dilution levels ("peak activity"). Peak activity less than 0\% is set to 0\%. -Distributions of peak and AUTC across time were plotted for each antigen with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). Lines connected each participant at each time point. +### AUC -Individual sample-specific magnitude-breadth (MB) curve curves were plotted where the x-axis represented a response magnitude value (x) and the y-axis represented the fraction of antigens or isolates with response magnitudes less than x. In addition to the individual sample-specific curves, the group-specific curve displayed the average MB across all subjects in that group. +Area under the net percent granzyme B activity vs log10 (dilution) curve is ("AUC") calculated using the trapezoidal rule, setting any net percent granzyme B activity below 0\% to 0\%. -Distributions of durability (area under the durability curve) were plotted with superimposed box plots. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). +### Response call +A positive response is defined as peak activity greater than or equal to 8\%. Tables show positive response rates and corresponding 95\% confidence intervals calculated by the Wilson score method [@AgCo1998], as well as summary statistics among positive responders and both responders and non-responders [update as needed; must have a table of summary statistics for the same population as comparisons described below]. -## Statistical tests -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. +## Statistical Endpoints Luciferase + +### Percent loss + +Percent loss Luciferase activity was averaged over wells within participant, timepoint, and dilution. Baseline-subtracted percent loss activity was calculated for each dilution as baseline activity subtracted from post-baseline activity. Negative values were truncated at zero. + +### Peak percent loss -Within each treatment group, response rates and response magnitudes between the timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). +Baseline-subtracted peak percent (\%) loss Luciferase activity was defined as the maximum baseline-subtracted activity across the six dilution levels. -Response magnitude tests required at least four positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. Durability, as defined by change in response magnitude, was measured using area under the AUTC curve from peak to the final durability time point ([insert final time point, e.g., week 48]). +### AUC -# Statistical Methods Luciferase +Nonparametric partial Area under the baseline-subtracted curves ("pAUC"), calculated using the trapezoidal rule on three dilutions of the baseline-subtracted curves, setting baseline-subtracted loss Luciferase activity less than 0\% to zero. + +### Response call + +A response is defined as positive if the peak baseline-subtracted \% loss Luciferase activity greater than or equal to 10\% for either the 1:50 or 1:200 dilution. + +# Statistical Methods GTL and Luciferase ## Graphical analysis -Response rates were plotted for each treatment group and time point with corresponding 95% two-sided Wilson score confidence intervals. Distributions of response magnitudes were plotted for each treatment group and time point with box plots superimposed on the distribution of responders. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). -Line plots of response magnitudes were plotted for each group to show response trends for each subject over time. +Plots of peak activity and AUC show both response rates and the distribution of magnitude. Positive responses are indicated by dots color-coded by treatment group, and negative responses by gray triangles. A boxplot is superimposed on the distribution, including only positive responses. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers that extend from the top and bottom of the box extend to the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box) or if no value meets this criterion, to the data extremes. -## Statistical tests -Response rates and magnitudes were summarized by timepoints. Pairwise comparisons of response rates between groups at each timepoint was conducted using Barnard's exact test (two-sided, alpha = 0.05) (@Lyderson2009; @Suissa1985). Pairwise comparisons of response magnitudes between groups at each timepoint was conducted using the Wilcoxon rank-sum test (two-sided, alpha = 0.05) among positive responders. -Within each treatment group, response rates and response magnitudes between the two timepoints were compared using the McNemar's Test and Wilcoxon signed-rank test respectively (two-sided, alpha = 0.05). +*[If working with durability data and calculating fold change from peak, be sure to specify direction of difference, e.g. $\text{log10(durability visit)} - \text{log10(peak visit)}$.]* -Response magnitude tests required at least four [Adjust if different] positive responders in at least one of the treatment groups being compared. If at least four responders were detected among all dose levels, global tests for response magnitude would be performed using the Kruskal-Wallis test (approximate distribution, alpha = 0.05) (@Hothorn2008). If the global test was significant, then the pairwise dose group comparisons would be performed among the treatment groups. Censored measurements below the assay quantification limit were treated as ties with ties handled using the Wilcoxon rank-sum exact method. +## Statistical tests +*[If statistical tests are used to compare responses, describe here. Follow protocol and assay specific SAP, converting the language to past tense. Generally, response rates are compared between groups using Barnard's test, and response are compared using Wilcoxon rank sum tests. Typically, two sets of magnitude comparisons are done: restricted to positive responders only, and all data i.e. positive and nonresponders.]* From 3e3511108653d27afefaa6bed483f0aa47ffa6c5 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Mon, 15 Jul 2024 15:05:49 -0700 Subject: [PATCH 21/59] add adcc to use_visc_methods and use_visc_report --- man/use_visc_methods.Rd | 4 ++-- man/use_visc_report.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/man/use_visc_methods.Rd b/man/use_visc_methods.Rd index 57a6cd2f..7b059b9d 100644 --- a/man/use_visc_methods.Rd +++ b/man/use_visc_methods.Rd @@ -6,14 +6,14 @@ \usage{ use_visc_methods( path = ".", - assay = c("generic", "bama", "nab"), + assay = c("generic", "bama", "nab", "adcc"), interactive = TRUE ) } \arguments{ \item{path}{path within the active project} -\item{assay}{"bama" or "generic"} +\item{assay}{"generic", "bama", "nab" or "adcc"} \item{interactive}{TRUE by default. FALSE is for non-interactive unit testing only.} diff --git a/man/use_visc_report.Rd b/man/use_visc_report.Rd index b8f0799c..e1ada0cf 100644 --- a/man/use_visc_report.Rd +++ b/man/use_visc_report.Rd @@ -7,7 +7,7 @@ use_visc_report( report_name = "PT-Report", path = ".", - report_type = c("empty", "generic", "bama", "nab"), + report_type = c("empty", "generic", "bama", "nab", "adcc"), interactive = TRUE ) } @@ -16,7 +16,7 @@ use_visc_report( \item{path}{path of the file within the active project} -\item{report_type}{"empty", "generic", "bama", or "nab"} +\item{report_type}{"empty", "generic", "bama", "nab", or "adcc"} \item{interactive}{TRUE by default. FALSE is for non-interactive unit testing only.} From 3d5e590f20451c42cc13ea8d7467ad255b2a5314 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Tue, 23 Jul 2024 15:38:58 -0700 Subject: [PATCH 22/59] Update README.md example report_name --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 650d8858..486b4e3c 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ Use a VISC Report: ``` r use_visc_report( - report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file + report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file path = "BAMA", # the path within the active directory, usually the name of the assay report_type = "bama" # "empty", "generic", "bama", or "nab" ) From ffd2ae114a5ff1adcdbfef619822a6e3ea538954 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Tue, 23 Jul 2024 15:41:04 -0700 Subject: [PATCH 23/59] Update using_pdf_and_word_template.Rmd example report name --- vignettes/using_pdf_and_word_template.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/vignettes/using_pdf_and_word_template.Rmd b/vignettes/using_pdf_and_word_template.Rmd index fdd522ff..a6cd73bd 100644 --- a/vignettes/using_pdf_and_word_template.Rmd +++ b/vignettes/using_pdf_and_word_template.Rmd @@ -21,7 +21,7 @@ To use a VISC report template, run: ```{r eval=FALSE} use_visc_report( - report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file + report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file path = "BAMA", # the path within the active directory, usually the name of the assay report_type = "bama" # "empty", "generic", "bama", or "nab" ) @@ -33,9 +33,9 @@ example above, this structure looks like: ``` |- BAMA/ -| +- VDCnnn_BAMA_PT_Report_statusifapplicable/ -| +- BAMA-PT-Report.Rmd # VISC report template -| +- methods/ # folder with "child" .Rmd documents +| +- VDCnnn_BAMA_PTreport_interim_blinded/ +| +- VDCnnn_BAMA_PTreport_interim_blinded.Rmd # VISC report template +| +- methods/ # folder with "child" .Rmd documents | +- biological-endpoints.Rmd | +- lab-methods.Rmd | +- statistical-methods.Rmd From 67ac8c3c36aa0b14aaea588ef9a29c693274dd6b Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Tue, 23 Jul 2024 15:44:28 -0700 Subject: [PATCH 24/59] Update use_visc_report.R naming conventions for PT reports --- R/use_visc_report.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/use_visc_report.R b/R/use_visc_report.R index b59879d2..e8dc0fdf 100644 --- a/R/use_visc_report.R +++ b/R/use_visc_report.R @@ -119,7 +119,7 @@ use_bib <- function(study_name) { #' report_type = "bama" #' ) #' } -use_visc_report <- function(report_name = "PT-Report", +use_visc_report <- function(report_name = "PTreport", path = ".", report_type = c("empty", "generic", "bama", "nab"), interactive = TRUE) { @@ -159,10 +159,10 @@ challenge_visc_report <- function(report_name, interactive = TRUE) { continue <- usethis::ui_yeah(" Creating a new VISC PT Report called {report_name}. At VISC, we use a naming convention for PT reports: - 'VDCnnn_assay_PT_Report_statusifapplicable' - where 'statusifapplicable' distinguishes blinded reports, - HIV status, or something that distinguishes a type/subset - of a report. + 'VDCnnn_assay_PTreport_status_blindingifapplicable' + where 'status' should be either 'interim' or 'final' + and 'blindingifapplicable' should be either 'blinded' + or 'unblinded' (applicable to interim reports only). 'VDC' is the PI name and 'nnn' is the study number. Would you like to continue?") From 31868c7e06adb756cb837437922076cec29d09e6 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Tue, 23 Jul 2024 15:49:23 -0700 Subject: [PATCH 25/59] Update NEWS.md with report naming practices --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/NEWS.md b/NEWS.md index 2914331a..74e0626d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # VISCtemplates (development version) +* Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd + # VISCtemplates 1.3.0 Bug Fixes From b609e0b53d2efc198106cfbc1c6b2be59601bab5 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Tue, 23 Jul 2024 17:18:34 -0700 Subject: [PATCH 26/59] update documentation for use_visc_report() --- man/use_visc_report.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/use_visc_report.Rd b/man/use_visc_report.Rd index b8f0799c..e9ce1df9 100644 --- a/man/use_visc_report.Rd +++ b/man/use_visc_report.Rd @@ -5,7 +5,7 @@ \title{Use a VISC Report Template} \usage{ use_visc_report( - report_name = "PT-Report", + report_name = "PTreport", path = ".", report_type = c("empty", "generic", "bama", "nab"), interactive = TRUE From 4af743dd5d47385551b6c9d394e2573158056f74 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 30 Jul 2024 15:16:06 -0700 Subject: [PATCH 27/59] bump to devel version --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ea0fd1e3..26e755f8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: VISCtemplates Title: Tools for writing reproducible reports at VISC -Version: 1.3.2 +Version: 1.3.2.9000 Authors@R: person(given = "Jimmy", family = "Fulp", diff --git a/NEWS.md b/NEWS.md index cfba8694..30d7cad2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# VISCtemplates (development version) + # VISCtemplates 1.3.2 Bug Fix From a189dd045b8b0b6f4c49b295f75b30b632c88669 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Thu, 1 Aug 2024 06:35:53 -0700 Subject: [PATCH 28/59] provide default CRAN mirror if missing in knitr R session --- R/report_functions.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/R/report_functions.R b/R/report_functions.R index 82abc557..3f16de03 100644 --- a/R/report_functions.R +++ b/R/report_functions.R @@ -15,7 +15,10 @@ install_load_cran_packages <- function(packages) { stop(paste0("The package ", package, " must be installed through GitHub: https://github.com/FredHutch/", package, ".git")) } else { - utils::install.packages(package) + # provide a default CRAN mirror if missing (e.g. in knitr R session) + repos <- getOption("repos") + if ("@CRAN@" %in% repos) repos <- "https://cloud.r-project.org/" + utils::install.packages(package, repos = repos) # install.packages() installs packages from the repository identified in # options('repos'), which is CRAN by default. To change this # setting, edit your .Rprofile. To view a list of available CRAN From a6a80d1197095dd14d46013a669655af5d940eb7 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 1 Aug 2024 16:14:16 -0700 Subject: [PATCH 29/59] update functions to include adcc as a report type option --- DESCRIPTION | 2 +- man/use_visc_methods.Rd | 4 ++-- man/use_visc_report.Rd | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fa881134..fd448b0b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,7 +30,7 @@ Imports: Encoding: UTF-8 URL: https://github.com/FredHutch/VISCtemplates BugReports: https://github.com/FredHutch/VISCtemplates/issues -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) Suggests: knitr, diff --git a/man/use_visc_methods.Rd b/man/use_visc_methods.Rd index c22ced63..cf7fabfd 100644 --- a/man/use_visc_methods.Rd +++ b/man/use_visc_methods.Rd @@ -4,12 +4,12 @@ \alias{use_visc_methods} \title{Use template files for methods sections in PT reports} \usage{ -use_visc_methods(path = ".", assay = c("generic", "bama", "nab")) +use_visc_methods(path = ".", assay = c("generic", "bama", "nab", "adcc")) } \arguments{ \item{path}{path within the active project} -\item{assay}{"bama" or "generic"} +\item{assay}{"generic", "bama", "nab" or "adcc"} } \description{ Creates a "methods" directory that contains 3 "child" R Markdown documents diff --git a/man/use_visc_report.Rd b/man/use_visc_report.Rd index 54c16706..ed593ba9 100644 --- a/man/use_visc_report.Rd +++ b/man/use_visc_report.Rd @@ -7,7 +7,7 @@ use_visc_report( report_name = "PT-Report", path = ".", - report_type = c("empty", "generic", "bama", "nab") + report_type = c("empty", "generic", "bama", "nab", "adcc") ) } \arguments{ @@ -15,7 +15,7 @@ use_visc_report( \item{path}{path of the file within the active project} -\item{report_type}{"empty", "generic", "bama", or "nab"} +\item{report_type}{"empty", "generic", "bama", "nab", or "adcc"} } \description{ This function creates a template R Markdown file for a VISC report. From ea0cf015e9b0ea704f2447f85c846b696c3fbdc5 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 1 Aug 2024 17:04:04 -0700 Subject: [PATCH 30/59] replace percent loss luc with percent specific killing --- inst/templates/methods-adcc/adcc-lab-methods.Rmd | 2 +- inst/templates/methods-adcc/adcc-statistical-methods.Rmd | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/inst/templates/methods-adcc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/adcc-lab-methods.Rmd index 9d9ceb3b..9a882ac4 100644 --- a/inst/templates/methods-adcc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-lab-methods.Rmd @@ -20,6 +20,6 @@ Complete IMC name Accession Number Abbreviated name Vaccine Match Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific loss Luciferase activity = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific killing = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd index 9fd6cbec..439c97bc 100644 --- a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd @@ -23,19 +23,19 @@ A positive response is defined as peak activity greater than or equal to 8\%. Ta ### Percent loss -Percent loss Luciferase activity was averaged over wells within participant, timepoint, and dilution. Baseline-subtracted percent loss activity was calculated for each dilution as baseline activity subtracted from post-baseline activity. Negative values were truncated at zero. +Percent specific killing was averaged over wells within participant, timepoint, and dilution. Baseline-subtracted percent loss activity was calculated for each dilution as baseline activity subtracted from post-baseline activity. Negative values were truncated at zero. ### Peak percent loss -Baseline-subtracted peak percent (\%) loss Luciferase activity was defined as the maximum baseline-subtracted activity across the six dilution levels. +Baseline-subtracted peak percent (\%) specific killing was defined as the maximum baseline-subtracted activity across the six dilution levels. ### AUC -Nonparametric partial Area under the baseline-subtracted curves ("pAUC"), calculated using the trapezoidal rule on three dilutions of the baseline-subtracted curves, setting baseline-subtracted loss Luciferase activity less than 0\% to zero. +Nonparametric partial Area under the baseline-subtracted curves ("pAUC"), calculated using the trapezoidal rule on three dilutions of the baseline-subtracted curves, setting baseline-subtracted percent specific killing less than 0\% to zero. ### Response call -A response is defined as positive if the peak baseline-subtracted \% loss Luciferase activity greater than or equal to 10\% for either the 1:50 or 1:200 dilution. +A response is defined as positive if the peak baseline-subtracted \% specific killing activity greater than or equal to 10\% for either the 1:50 or 1:200 dilution. # Statistical Methods GTL and Luciferase From 380bef67c05228a89edd471a726f19b037b69d01 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Thu, 1 Aug 2024 17:18:31 -0700 Subject: [PATCH 31/59] removing icaba files from ADCC branch. include in separate PR. --- .../methods-icaba/icaba-biological-endpoints.Rmd | 8 -------- inst/templates/methods-icaba/icaba-lab-methods.Rmd | 11 ----------- .../methods-icaba/icaba-statistical-methods.Rmd | 13 ------------- 3 files changed, 32 deletions(-) delete mode 100644 inst/templates/methods-icaba/icaba-biological-endpoints.Rmd delete mode 100644 inst/templates/methods-icaba/icaba-lab-methods.Rmd delete mode 100644 inst/templates/methods-icaba/icaba-statistical-methods.Rmd diff --git a/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd b/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd deleted file mode 100644 index 0d7ab5cb..00000000 --- a/inst/templates/methods-icaba/icaba-biological-endpoints.Rmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: "icaba-biological-endpoints" -output: html_document -date: '2022-11-03' ---- - -# Biological Endpoints -Plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells were measured using Infected Cell Antibody Binding Assay (ICABA) from specimens obtained at [insert visit]. ICABA responses were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. diff --git a/inst/templates/methods-icaba/icaba-lab-methods.Rmd b/inst/templates/methods-icaba/icaba-lab-methods.Rmd deleted file mode 100644 index 7d37ea0a..00000000 --- a/inst/templates/methods-icaba/icaba-lab-methods.Rmd +++ /dev/null @@ -1,11 +0,0 @@ ---- -title: "icaba-lab-methods" -output: html_document -date: '2022-10-31' ---- - -# Lab Methods - -The measurement of plasma Ab binding to HIV-1 envelope expressed on the surface of infected cells is conducted using flow-cytometry-based indirect surface staining according to methods similar to those previously described (@pmid21543485; @pmid28593989). Briefly, mock infected and HIV-1 BG505 Infectious Molecular Clones-infected CEM.NKRCCR5 cells were incubated with 1:100[adjust if using different dilutions] dilutions of plasma samples of interest for 2h at 37°C, then stained with a vital dye (Live/Dead Aqua) to exclude dead cells from analysis. The cells were subsequently washed, and permeabilized using BD Cytofix/Cytoperm solution. After an additional wash, cells were stained with FITC-conjugated goat-anti-Rhesus IgG polyclonal antisera to detect binding of the plasma Ab, and PE-conjugated anti-HIV-1 p24 Ab (RD1) to identify infected cells. Cells positive for binding NHP plasma Ab were defined as live, p24 positive, and FITC positive. Final results were reported as percent of FITC positive cells and FITC MFI among the viable p24 positive events after subtracting the background observed for the prevaccination samples. - - diff --git a/inst/templates/methods-icaba/icaba-statistical-methods.Rmd b/inst/templates/methods-icaba/icaba-statistical-methods.Rmd deleted file mode 100644 index 06ef3d84..00000000 --- a/inst/templates/methods-icaba/icaba-statistical-methods.Rmd +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: "icaba-statistical-methods" -output: html_document -date: '2022-11-02' ---- - -# Statistical Methods - -## Graphical analysis -Distributions of response magnitudes were plotted for each time point and antigen with box plots superimposed on the distributions. The mid-line of the box denoted the median and the ends of the box denoted the $25^{th}$ and $75^{th}$ percentiles. The whiskers denoted the most extreme data points that were no more than 1.5 times the interquartile range (i.e., height of the box). - -## Statistical tests - From 8b214b4a60be9cf1992db4833f139f0f5c1d734b Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Fri, 2 Aug 2024 10:13:39 -0700 Subject: [PATCH 32/59] test knit adcc report template --- tests/testthat/helpers.R | 2 +- tests/testthat/test-use_visc_report.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/helpers.R b/tests/testthat/helpers.R index 7b4b460b..fd91cba3 100644 --- a/tests/testthat/helpers.R +++ b/tests/testthat/helpers.R @@ -15,7 +15,7 @@ #' @return Side effects only. test_knit_report <- function(report_type, outfile_ext){ stopifnot( - report_type %in% c('generic', 'empty', 'bama', 'nab'), + report_type %in% c('generic', 'empty', 'bama', 'nab', 'adcc'), outfile_ext %in% c('pdf', 'docx') ) report_name <- paste(report_type, outfile_ext, 'report', sep = '_') diff --git a/tests/testthat/test-use_visc_report.R b/tests/testthat/test-use_visc_report.R index 8141b5aa..00914d76 100644 --- a/tests/testthat/test-use_visc_report.R +++ b/tests/testthat/test-use_visc_report.R @@ -18,7 +18,7 @@ # succeed, they will be in a snapshots artifact. Hopefully soon this will be # changed to always have the latter behavior regardless of test success. local({ - for (report_type in c('generic', 'empty', 'bama', 'nab')){ + for (report_type in c('generic', 'empty', 'bama', 'nab', 'adcc')){ for (output_ext in c('pdf', 'docx')){ test_knit_report(report_type, output_ext) } From 90fa50e4afef5da36a4f08f8604af0548852683b Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Fri, 2 Aug 2024 16:21:27 -0700 Subject: [PATCH 33/59] change separation between references to semi-colon per PR feedback --- inst/templates/methods-adcc/adcc-lab-methods.Rmd | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/inst/templates/methods-adcc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/adcc-lab-methods.Rmd index 9a882ac4..e7c8ee58 100644 --- a/inst/templates/methods-adcc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-lab-methods.Rmd @@ -1,6 +1,5 @@ --- title: "lab-methods" -date: "2022-10-26" --- @@ -14,7 +13,7 @@ ADCC is quantified as net percent granzyme B activity, which is the percent of t # Lab Methods Luciferase -We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014, @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: +We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014; @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: Complete IMC name Accession Number Abbreviated name Vaccine Match [Full name, as uploaded by lab] [provided by lab] [SRA-derived abbreviated name shown in tables and figures] [if a mix of matched and unmatched IMCs were tested, indicate here which were matched] From 69a379c42384e53f177676b70b7e4fdc293d0ae2 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Thu, 8 Aug 2024 12:41:30 -0700 Subject: [PATCH 34/59] README.md instead of README.Rmd --- R/use_visc_report.R | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/R/use_visc_report.R b/R/use_visc_report.R index b59879d2..2932f2fb 100644 --- a/R/use_visc_report.R +++ b/R/use_visc_report.R @@ -16,6 +16,21 @@ use_visc_readme <- function(study_name, save_as = "README.Rmd") { data = list(study_name = study_name), package = "VISCtemplates" ) + # knit the md from the Rmd on request of SRA team + rmarkdown::render( + usethis::proj_path('README.Rmd'), + quiet = TRUE + ) + # remove Rmd at request of SRA team; they just manually edit the *.md + # so the Rmd file merely clutters their working directory + unlink( + usethis::proj_path( + paste0( + 'README', + c('.Rmd', '.html') + ) + ) + ) } #' Create a VISC docs directory with template files From 1e227e09f8bc3abce235712cd58822cabb5059cb Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Fri, 9 Aug 2024 10:12:56 -0700 Subject: [PATCH 35/59] news update --- NEWS.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/NEWS.md b/NEWS.md index 30d7cad2..73c84890 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # VISCtemplates (development version) +Other improvements +* create_visc_project() now discards README.Rmd after knitting template to README.md (#223) + # VISCtemplates 1.3.2 Bug Fix From 892e2f333d0e93fd074fd64246f825558a414c46 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Fri, 9 Aug 2024 11:09:17 -0700 Subject: [PATCH 36/59] add unit tests for README changes --- tests/testthat/test-create_visc_project.R | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 tests/testthat/test-create_visc_project.R diff --git a/tests/testthat/test-create_visc_project.R b/tests/testthat/test-create_visc_project.R new file mode 100644 index 00000000..1d943285 --- /dev/null +++ b/tests/testthat/test-create_visc_project.R @@ -0,0 +1,15 @@ +test_that("create_visc_project works", { + # creates ephemeral directory that will be deleted upon function exit + temp_dir <- withr::local_tempdir() + create_visc_project(temp_dir, interactive = FALSE) + # check that proper README files got rendered and deleted + expect_true( + file.exists(file.path(temp_dir, 'README.md')) + ) + expect_false( + file.exists(file.path(temp_dir, 'README.Rmd')) + ) + expect_false( + file.exists(file.path(temp_dir, 'README.html')) + ) +}) From c5e2362b20a5f73bfbbe20170d5963f647fa41ef Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Fri, 9 Aug 2024 14:49:42 -0700 Subject: [PATCH 37/59] news update --- NEWS.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/NEWS.md b/NEWS.md index 79a0c097..8e54d76a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # VISCtemplates (development version) +Bug fixes +* Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218) + Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) * Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd From d73e69649f236790a7319f9ac7ed951576ded79e Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 9 Aug 2024 15:54:05 -0700 Subject: [PATCH 38/59] latex template fix to allow flextable to render tables --- inst/rmarkdown/templates/visc_report/resources/template.tex | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/inst/rmarkdown/templates/visc_report/resources/template.tex b/inst/rmarkdown/templates/visc_report/resources/template.tex index 67980e15..f041eb9e 100644 --- a/inst/rmarkdown/templates/visc_report/resources/template.tex +++ b/inst/rmarkdown/templates/visc_report/resources/template.tex @@ -20,6 +20,11 @@ \usepackage{threeparttable} % provides a scheme for tables that have a structured (foot)note section, after the caption \usepackage{threeparttablex} % provides the functionality of the threeparttable package to tables created using the longtable package +% needed for flextable to work +\usepackage{hhline} +\newlength\Oldarrayrulewidth +\newlength\Oldtabcolsep + % being able to set emphasis for entire table row \newcommand\setrow[1]{\gdef\rowmac{#1}#1\ignorespaces} \newcommand\clearrow{\global\let\rowmac\relax} From 8b0663f0cc6e7b3f42b1731cd1105fb0cd596a81 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 9 Aug 2024 15:57:30 -0700 Subject: [PATCH 39/59] Update NEWS.md --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 8e54d76a..beb97ecc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ Bug fixes * Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218) +* Update template.tex so that flextable package can be used to create tables in PDF documents (#226) Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) From 669e44b967c2bb97113a29ed056a115b7d817d44 Mon Sep 17 00:00:00 2001 From: Gabrielle Lemire <43865993+lemireg@users.noreply.github.com> Date: Wed, 21 Aug 2024 11:15:46 -0700 Subject: [PATCH 40/59] incorporate Bhavesh's comments on PR. some comments still outstanding to review with Alicia before adding. --- .../methods-adcc/adcc-biological-endpoints.Rmd | 6 +++--- inst/templates/methods-adcc/adcc-lab-methods.Rmd | 12 ++++++++---- .../methods-adcc/adcc-statistical-methods.Rmd | 6 +++--- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd index 6ab066f4..11c979b3 100644 --- a/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd +++ b/inst/templates/methods-adcc/adcc-biological-endpoints.Rmd @@ -5,10 +5,10 @@ title: "biological-endpoints" -# Biological Endpoints GTL +## Biological Endpoints GTL -ADCC-mediated antibody responses were measured using Luciferase GranToxiLux (GTL) assays from specimens obtained at *[describe visits; include visit number, timepoint in weeks or months, and relation to SPA. E.g. week 26 (2 weeks post-4th vaccination, visit 10)]*. The GTL ADCC assay measures percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. Endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of *[number of antigens]* HIV-1 antigens representing *[include description of viruses: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the responses against HIV-1 subtypes]*. +ADCC-mediated antibody responses were measured using GranToxiLux (GTL) assays from specimens obtained at *[describe visits; include visit number, timepoint in weeks or months, and relation to SPA. E.g. week 26 (2 weeks post-4th vaccination, visit 10)]*. The GTL ADCC assay measures percent Granzyme B activity, defined as the percentage of antigen-coated target cells positive for proteolytically active Granzyme B out of the total viable target cell population. Endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of *[number of antigens]* HIV-1 antigens representing *[include description of viruses: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the responses against HIV-1 subtypes]*. -# Biological endpoints Luciferase +## Biological endpoints Luciferase ADCC-mediated antibody responses were measured using Luciferase ADCC assays from specimens obtained at *[describe visits; include visit number, timepoint in weeks or months, and relation to SPA. E.g. week 26 (2 weeks post-4th vaccination, visit 10)]*. The Luciferase ADCC assay tests reactivity against Infectious Molecular Clone (IMC)-infected target cells by measuring percent reduction in Relative Luminescence Units (RLUs), reported as percentage specific killing. Endpoints are the response rate and magnitude of ADCC-mediated antibody responses against a panel of *[number of IMCs]* HIV-1 IMC expressing Env representing *[include description of IMCs: those included in the vaccine product (vaccine-matched), Env matched in clade to vaccine products, and other Env to identify the breadth of the responses against HIV-1 subtypes]*. diff --git a/inst/templates/methods-adcc/adcc-lab-methods.Rmd b/inst/templates/methods-adcc/adcc-lab-methods.Rmd index e7c8ee58..80c13499 100644 --- a/inst/templates/methods-adcc/adcc-lab-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-lab-methods.Rmd @@ -5,13 +5,17 @@ title: "lab-methods" -# Lab Methods GTL +## Lab Methods GTL -The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. Effector cells were PBMCs obtained from a HIV-seronegative donor with heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50 (1:50, 1:250, 1:1250, 1:6250, 1:31250, and 1:156250). Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. +The qualified GranToxiLux Antibody-Dependent Cell-Mediated Cytotoxicity (GTL-ADCC) assay was performed as previously described [@Pollara2014]. Target cells were a clonal isolate of the CEM.NKRCCR5 CD4+ T-cell line (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: from Dr. Alexandra Trkola [@Trkola1999]. These cells were coated with recombinant gp120s representing the HIV-1 envelopes of the subtype [specify subtype and antigens, e.g. C (TV1 and 1086c)]. + +Effector cells were peripheral blood mononuclear cells (PBMCs) obtained from a HIV-seronegative donor heterozygous for Fc$\gamma$R3A at position 158 (158F/V). PBMCs were obtained by leukapheresis to collect enough cells for completion of the study with a single donation, minimizing potential effector cell population variability effects on the study outcome. + +PBMCs were used at an effector cell to target cell ratio of 30:1. Serum samples were tested after five-fold serial dilutions starting at 1:50 (1:50, 1:250, 1:1250, 1:6250, 1:31250, and 1:156250). Each plate has one standardized positive control in duplicate and one standardized negative control in duplicate. ADCC is quantified as net percent granzyme B activity, which is the percent of target cells positive for GTL (an indicator of granzyme B uptake) minus the percent of target cells positive for GTL when incubated with effector cells in the absence of a source of antibodies. Flow cytometry is used to quantify the frequency of granzyme B positive cells. -# Lab Methods Luciferase +## Lab Methods Luciferase We utilized a modified version of a previously published ADCC luciferase procedure [@Pollara2014; @Fisher2019] . Briefly, CEM.NKRCCR5 cells [@Trkola1999] were used as targets for ADCC luciferase assays after infection by one of the following HIV-1 [vaccine-matched, if all IMCs are vaccine-matched; if not, indicate match in table below] IMCs: Complete IMC name Accession Number Abbreviated name Vaccine Match @@ -19,6 +23,6 @@ Complete IMC name Accession Number Abbreviated name Vaccine Match Peripheral blood mononuclear cells (PBMCs) were obtained from a HIV-seronegative donor by leukapheresis and cryopreserved until the day of the assay. After thawing and overnight resting in RPMI 1640 supplemented with antibiotics, $10\%$ fetal bovine serum (R10), and 10 ng/mL of IL-15, the PBMCs were used as effector cells at an effector-to-target ratio of 30:1. -Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, and 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific killing = $100 * \frac{\text{RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. +Target and effector cells were plated in white 96-well half-area plates and co-cultured with 4-fold serial dilutions of trial participant serum starting at the 1:50 dilution. For each sample, percent specific killing was measured in duplicate at dilutions of 1:50, 1:200, 1:800, 1:3200, 1:12800, and 1:51200. Co-cultures were incubated for 6 hours at $37^{\circ}$C in $5\%$ CO2. The final readout was the reduction of luminescence intensity generated by the presence of residual intact target cells that had not been lysed by the effector population in the presence of ADCC-mediating serum antibodies. The percentage of killing was calculated using the formula: percent specific killing = $100 * \frac{\text{(RLU of target and effector well– RLU of test well)}}{\text{RLU of target and effector well}}$. In this analysis, the Relative Luminescence Units (RLU) of the target plus effector wells represents spontaneous lysis in the absence of any source of antibody and is used to calculate background activity. The monoclonal antibody [insert antibody name from lab study plan, e.g. Synagis] and a cocktail of HIV-1 monoclonal antibodies [insert antibody names from lab study plan, e.g. (A32, 2G12, CH44, and 7B2)] were used as negative and positive controls, respectively. diff --git a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd index 439c97bc..cd0130dd 100644 --- a/inst/templates/methods-adcc/adcc-statistical-methods.Rmd +++ b/inst/templates/methods-adcc/adcc-statistical-methods.Rmd @@ -12,7 +12,7 @@ Peak net percent granzyme B activity defined as the maximum activity across the ### AUC -Area under the net percent granzyme B activity vs log10 (dilution) curve is ("AUC") calculated using the trapezoidal rule, setting any net percent granzyme B activity below 0\% to 0\%. +Area under the net percent granzyme B activity ("AUC") versus log$_{10}$ (dilution) curve is calculated using the trapezoidal rule, setting any net percent granzyme B activity below 0\% to 0\%. ### Response call @@ -35,13 +35,13 @@ Nonparametric partial Area under the baseline-subtracted curves ("pAUC"), calcul ### Response call -A response is defined as positive if the peak baseline-subtracted \% specific killing activity greater than or equal to 10\% for either the 1:50 or 1:200 dilution. +A response is defined as positive if the baseline-subtracted percent (\%) specific killing activity is greater than or equal to 10\% for either the 1:50 or 1:200 dilutions. # Statistical Methods GTL and Luciferase ## Graphical analysis -Plots of peak activity and AUC show both response rates and the distribution of magnitude. Positive responses are indicated by dots color-coded by treatment group, and negative responses by gray triangles. A boxplot is superimposed on the distribution, including only positive responses. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers that extend from the top and bottom of the box extend to the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box) or if no value meets this criterion, to the data extremes. +Plots of peak activity and AUC show both response rates and the distribution of magnitude. Positive responses are indicated by dots color-coded by treatment group, and negative responses by gray triangles. A boxplot is superimposed on the distribution of positive responses. The mid-line of the box denotes the median and the ends of the box denote the $25^{th}$ and $75^{th}$ percentiles. The whiskers that extend from the top and bottom of the box extend to the most extreme data points that are no more than 1.5 times the interquartile range (i.e., height of the box) or if no value meets this criterion, to the data extremes. *[If working with durability data and calculating fold change from peak, be sure to specify direction of difference, e.g. $\text{log10(durability visit)} - \text{log10(peak visit)}$.]* From 06b45d2351721448d3b7c4e7cda17be50324416a Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 23 Aug 2024 15:57:17 -0400 Subject: [PATCH 41/59] add .aux, .toc, .lof, .lot, and .out to default gitignore --- R/use_visc_gitignore.R | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/R/use_visc_gitignore.R b/R/use_visc_gitignore.R index 02b082c4..b0ab4ba4 100644 --- a/R/use_visc_gitignore.R +++ b/R/use_visc_gitignore.R @@ -36,6 +36,11 @@ use_visc_gitignore <- function(directory = ".") { "Thumbs.db", # files from Latex "*.log", + "*.aux", + "*.toc", + "*.lof", + "*.lot", + "*.out", "**/figure-latex/*.pdf", "**/figure-docx/*.pdf", "*.zip" From 336c72c2de4dbf37f748b5aa613cc0fc2e6b1ca7 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 23 Aug 2024 15:58:48 -0400 Subject: [PATCH 42/59] add cache files to gitignore --- R/use_visc_gitignore.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/use_visc_gitignore.R b/R/use_visc_gitignore.R index b0ab4ba4..cf9ffc83 100644 --- a/R/use_visc_gitignore.R +++ b/R/use_visc_gitignore.R @@ -43,7 +43,9 @@ use_visc_gitignore <- function(directory = ".") { "*.out", "**/figure-latex/*.pdf", "**/figure-docx/*.pdf", - "*.zip" + "*.zip", + # cache files + "*_cache/" ), directory = directory ) From f5ce71c1cf96e0b4b5e9d266add6319477f301b9 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 23 Aug 2024 16:00:00 -0400 Subject: [PATCH 43/59] add smbdelete files to gitignore --- R/use_visc_gitignore.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/use_visc_gitignore.R b/R/use_visc_gitignore.R index cf9ffc83..96d39a8f 100644 --- a/R/use_visc_gitignore.R +++ b/R/use_visc_gitignore.R @@ -45,7 +45,9 @@ use_visc_gitignore <- function(directory = ".") { "**/figure-docx/*.pdf", "*.zip", # cache files - "*_cache/" + "*_cache/", + # other + ".smbdelete*" ), directory = directory ) From 64d30db88b177314a0426b2a529619db400bc94d Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 23 Aug 2024 16:04:24 -0400 Subject: [PATCH 44/59] Update NEWS.md --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index beb97ecc..35b19028 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,6 +7,7 @@ Bug fixes Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) * Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd +* Add auxiliary files to template .gitignore (.aux, .toc, .lof, .lot, .out, cache files, and .smbdelete files) # VISCtemplates 1.3.2 From c6beac05ee48a22f68cc25a64b338e0f441984f0 Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Fri, 23 Aug 2024 18:55:56 -0400 Subject: [PATCH 45/59] add PR numbers to NEWS.md --- NEWS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 35b19028..0f10eaed 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,8 +6,8 @@ Bug fixes Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) -* Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd -* Add auxiliary files to template .gitignore (.aux, .toc, .lof, .lot, .out, cache files, and .smbdelete files) +* Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd (#202) +* Add auxiliary files to template .gitignore (.aux, .toc, .lof, .lot, .out, cache files, and .smbdelete files) (#230) # VISCtemplates 1.3.2 From 528578443c4cba5ef4b21b678b0acc0d4230be4b Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Wed, 4 Sep 2024 16:11:51 -0700 Subject: [PATCH 46/59] remove Marie from template acknowledgements --- inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd index f069abac..13f5ba0e 100644 --- a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd @@ -398,7 +398,7 @@ kable( The authors thank the following individuals for their invaluable contributions to this report. From [insert group name or affiliation, for example: the CAVIMC/Duke team] we thank [insert individual names, and roles here, for example: Kelli Greene and Hongmei Gao (Experimental Design, Data Interpretation, Study Management); Nicole Yates (Scientific Research Laboratory Manager) and Sheetal Sawant (Biostatistician)]. -From Fred Hutch Cancer Center, we also thank [insert names and roles here, for example: Ratana Som (SCHARP Lab Data Manager); Marie Vendettuoli and Valeria Duran (SCHARP Statistical Programmers); and Lindsey Mwoga and Drienna Holman (VISC Project Management)]. +From Fred Hutch Cancer Center, we also thank [insert names and roles here, for example: Ratana Som (SCHARP Lab Data Manager); Valeria Duran (SCHARP Statistical Programmer); and Lindsey Mwoga and Drienna Holman (VISC Project Management)]. Note: names may be listed in bullet point format instead of paragraph format if that helps with readability, for example: From f044cdcd90e8b1b0ea459bbd155d04a1fd5cef3b Mon Sep 17 00:00:00 2001 From: Kellie MacPhee Date: Wed, 4 Sep 2024 16:13:29 -0700 Subject: [PATCH 47/59] Update NEWS.md --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 0f10eaed..763cac52 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,6 +8,7 @@ Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) * Update PT report naming practices to the format VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd (#202) * Add auxiliary files to template .gitignore (.aux, .toc, .lof, .lot, .out, cache files, and .smbdelete files) (#230) +* Update names in template acknowledgements section (#234) # VISCtemplates 1.3.2 From 602ef11f74bd8ca69c13ec957fe7cedb41d71ea7 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 29 Oct 2024 09:56:44 -0700 Subject: [PATCH 48/59] clean up invalid default ORCID generated by usethis --- R/create_visc_project.R | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/R/create_visc_project.R b/R/create_visc_project.R index 44a48671..a947a1a9 100644 --- a/R/create_visc_project.R +++ b/R/create_visc_project.R @@ -33,7 +33,15 @@ create_visc_project <- function(path, interactive = TRUE){ usethis::create_package( path = path, rstudio = TRUE, - open = interactive + open = interactive, + # fields override for usethis 3.0.0 ORCID placeholder, errors out in R 4.5 + # https://github.com/r-lib/usethis/issues/2059 + fields = list( + `Authors@R` = paste0( + "person(\"First\", \"Last\", email = \"first.last", + "@example.com\", role = c(\"aut\", \"cre\"))" + ) + ) ) # must set active project otherwise it is From 7babeaf7b7af53f496f191a3adbf36903988a6e0 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 29 Oct 2024 09:58:31 -0700 Subject: [PATCH 49/59] document() whitespace --- man/use_visc_methods.Rd | 1 - 1 file changed, 1 deletion(-) diff --git a/man/use_visc_methods.Rd b/man/use_visc_methods.Rd index 07c4a937..7b059b9d 100644 --- a/man/use_visc_methods.Rd +++ b/man/use_visc_methods.Rd @@ -17,7 +17,6 @@ use_visc_methods( \item{interactive}{TRUE by default. FALSE is for non-interactive unit testing only.} - } \description{ Creates a "methods" directory that contains 3 "child" R Markdown documents From 7467986ff1d6708c14f52c0173a0c6675af981d6 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 29 Oct 2024 10:03:29 -0700 Subject: [PATCH 50/59] clearer wording --- R/create_visc_project.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/create_visc_project.R b/R/create_visc_project.R index a947a1a9..15699ae2 100644 --- a/R/create_visc_project.R +++ b/R/create_visc_project.R @@ -34,7 +34,7 @@ create_visc_project <- function(path, interactive = TRUE){ path = path, rstudio = TRUE, open = interactive, - # fields override for usethis 3.0.0 ORCID placeholder, errors out in R 4.5 + # fields override for usethis 3.0.0 ORCID placeholder that errored in R 4.5 # https://github.com/r-lib/usethis/issues/2059 fields = list( `Authors@R` = paste0( From 2cf97a98adde488d7ca13b1f6e97260215f2e586 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 29 Oct 2024 10:41:08 -0700 Subject: [PATCH 51/59] news update --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 763cac52..a948f587 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,6 +3,7 @@ Bug fixes * Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218) * Update template.tex so that flextable package can be used to create tables in PDF documents (#226) +* Clean up invalid ORCID placeholder generated by usethis 3.0.0 that threw error on R version 4.5.x (#248) Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) From a5d417f2d29d8376f2ca565c788818cd6291ab9c Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Thu, 31 Oct 2024 10:19:54 -0700 Subject: [PATCH 52/59] prevent error during interactive knits when old value was NULL --- inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd | 2 +- inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd index b1cd3703..aed0db24 100644 --- a/inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/visc_empty/skeleton/skeleton.Rmd @@ -61,7 +61,7 @@ opts_chunk$set(cache = FALSE, out.extra = "", fig.pos = "H") # fig.align argument is not supported in Word (align in template docx) -if (knitr::opts_knit$get('rmarkdown.pandoc.to') == 'latex'){ +if (get_output_type() == 'latex'){ opts_chunk$set(fig.align = "center") } diff --git a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd index 13f5ba0e..4d6a10f0 100644 --- a/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd @@ -65,7 +65,7 @@ opts_chunk$set(cache = FALSE, out.extra = "", fig.pos = "H") # fig.align argument is not supported in Word (align in template docx) -if (knitr::opts_knit$get('rmarkdown.pandoc.to') == 'latex'){ +if (get_output_type() == 'latex'){ opts_chunk$set(fig.align = "center") } From 68a701c56220f7014c5ea191b84f8ccf55c4f7b9 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Thu, 31 Oct 2024 11:20:24 -0700 Subject: [PATCH 53/59] update NEWS --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index a948f587..bc7877c8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,7 @@ Bug fixes * Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218) * Update template.tex so that flextable package can be used to create tables in PDF documents (#226) * Clean up invalid ORCID placeholder generated by usethis 3.0.0 that threw error on R version 4.5.x (#248) +* Fix error when running skeleton.Rmd file interactively (#249) Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) From 6d4df5df5be5dc9311fa9a3e4d411ac68c7e2581 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Wed, 6 Nov 2024 11:30:42 -0800 Subject: [PATCH 54/59] add usethis-generated test coverage yml --- .github/workflows/test-coverage.yaml | 61 ++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 00000000..98822609 --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,61 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: test-coverage.yaml + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package From 32f40052b51784dc9d94ef220ee449a33384706a Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Wed, 6 Nov 2024 11:32:33 -0800 Subject: [PATCH 55/59] add badges and rebuild readme.md --- README.Rmd | 5 +++++ README.md | 8 +++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/README.Rmd b/README.Rmd index 1b084511..0fbf79ba 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,6 +13,11 @@ knitr::opts_chunk$set( ) ``` + +[![R-CMD-check](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/FredHutch/VISCtemplates/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCtemplates) + + # VISCtemplates The goal of VISCtemplates is to: diff --git a/README.md b/README.md index 486b4e3c..bfac33be 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,11 @@ + + +[![R-CMD-check](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FredHutch/VISCtemplates/actions/workflows/R-CMD-check.yaml) +[![Codecov test +coverage](https://codecov.io/gh/FredHutch/VISCtemplates/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCtemplates) + # VISCtemplates @@ -66,7 +72,7 @@ Use a VISC Report: ``` r use_visc_report( - report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file + report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file path = "BAMA", # the path within the active directory, usually the name of the assay report_type = "bama" # "empty", "generic", "bama", or "nab" ) From b19f8eb73d8d63dbcf1bbfb0960c7bdd70eee7f7 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Wed, 6 Nov 2024 11:35:33 -0800 Subject: [PATCH 56/59] VISCtemplates modifications for standard test-coverage yml --- .github/workflows/test-coverage.yaml | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 98822609..7222284e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master] + branches: [main, master, develop] pull_request: - branches: [main, master] + branches: [main, master, develop] name: test-coverage.yaml @@ -19,6 +19,17 @@ jobs: steps: - uses: actions/checkout@v4 + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-tinytex@v2 + + - name: Preinstall required latex packages + run: > + tlmgr install + lastpage morefloats parskip pdflscape textpos multirow lipsum + fancyhdr colortbl soul setspace relsize makecell threeparttable + threeparttablex environ trimspaces + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true From 58487db3aae81ccf963e94d8e243ec21b7d8283d Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Wed, 6 Nov 2024 14:06:17 -0800 Subject: [PATCH 57/59] not really needed since already testing way back to 4.0.4 --- .github/workflows/R-CMD-check.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9309e32c..984a1335 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -22,7 +22,6 @@ jobs: - {os: windows-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - {os: ubuntu-latest, r: '4.0.4', pandoc-version: '2.11.4'} env: From 0c2661a57ebcd28fd307caadfa8fe58e271311e0 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Wed, 4 Dec 2024 19:24:02 -0800 Subject: [PATCH 58/59] README.md had been edited instead of README.Rmd. Re-building from Rmd. --- README.Rmd | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 0fbf79ba..81944b4a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -81,7 +81,7 @@ Use a VISC Report: ```{r eval=FALSE} use_visc_report( - report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file + report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file path = "BAMA", # the path within the active directory, usually the name of the assay report_type = "bama" # "empty", "generic", "bama", or "nab" ) diff --git a/README.md b/README.md index bfac33be..9664956d 100644 --- a/README.md +++ b/README.md @@ -72,7 +72,7 @@ Use a VISC Report: ``` r use_visc_report( - report_name = "VDCnnn_BAMA_PT_Report_statusifapplicable", # the name of the report file + report_name = "VDCnnn_BAMA_PTreport_interim_blinded", # the name of the report file path = "BAMA", # the path within the active directory, usually the name of the assay report_type = "bama" # "empty", "generic", "bama", or "nab" ) From 1264b0bc949f08253dda2082f9b2cb8357c6db60 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 10 Dec 2024 08:27:16 -0800 Subject: [PATCH 59/59] more informative error message for visc_load_pdata() --- NEWS.md | 1 + R/visc_load_pdata.R | 8 +++++++- tests/testthat/test-visc_load_pdata.R | 2 +- 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index a948f587..5d81e258 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,7 @@ Bug fixes * Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218) * Update template.tex so that flextable package can be used to create tables in PDF documents (#226) * Clean up invalid ORCID placeholder generated by usethis 3.0.0 that threw error on R version 4.5.x (#248) +* Include pdata object name and data package name in visc_load_pdata() error message (#252) Other improvements * create_visc_project() now discards README.Rmd after knitting template to README.md (#223) diff --git a/R/visc_load_pdata.R b/R/visc_load_pdata.R index 918495b9..3c07a0d2 100644 --- a/R/visc_load_pdata.R +++ b/R/visc_load_pdata.R @@ -75,7 +75,13 @@ visc_load_pdata <- function(.data, lazyLoad(filebase = system.file(file.path('data', 'Rdata'), package = pkg_name), envir = pdata_env) } else { - stop('Unable to find data object file') + stop( + sprintf( + "Unable to find data object '%s' in package '%s'", + pdata_name, + pkg_name + ) + ) } } diff --git a/tests/testthat/test-visc_load_pdata.R b/tests/testthat/test-visc_load_pdata.R index d7ad9d1b..5f57c6d7 100644 --- a/tests/testthat/test-visc_load_pdata.R +++ b/tests/testthat/test-visc_load_pdata.R @@ -78,7 +78,7 @@ test_that("visc_load_pdata works", { '3ccb5b0aaa74fe7cfc0d3ca6ab0b5cf3' ) }), - "Unable to find data object file" + "Unable to find data object.*" ) }) })