From d3b5f4f0caeb6dde9db57a3261150ac37e5d1e74 Mon Sep 17 00:00:00 2001
From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com>
Date: Wed, 31 Jul 2024 12:22:03 -0400
Subject: [PATCH] added more explicit HTTR retrieval (#9)

---
 .github/workflows/R-CMD-check.yaml            | 59 +++++++++++++++++++
 Syndemics/.Rbuildignore                       |  1 +
 Syndemics/NAMESPACE                           |  5 +-
 Syndemics/R/Syndemics-package.R               | 10 ++++
 Syndemics/R/fetch_sas.R                       |  2 +-
 .../{respond_outputs.R => loadOutputFiles.R}  |  0
 ..._inputs.R => respond_inputManipulations.R} |  0
 Syndemics/man/Syndemics-package.Rd            | 11 ++++
 Syndemics/man/formula_corr.Rd                 |  6 +-
 Syndemics/man/formula_list.Rd                 |  2 +-
 Syndemics/man/is.formula.Rd                   |  2 +-
 11 files changed, 89 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 Syndemics/R/Syndemics-package.R
 rename Syndemics/R/{respond_outputs.R => loadOutputFiles.R} (100%)
 rename Syndemics/R/{respond_inputs.R => respond_inputManipulations.R} (100%)
 create mode 100644 Syndemics/man/Syndemics-package.Rd

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..bc2eb2d
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,59 @@
+# 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: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+        with: 
+          working-directory: Syndemics
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with: 
+          working-directory: Syndemics
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          working-directory: Syndemics
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: Syndemics
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: Syndemics
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/Syndemics/.Rbuildignore b/Syndemics/.Rbuildignore
index e13c405..31e3754 100644
--- a/Syndemics/.Rbuildignore
+++ b/Syndemics/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^\.github$
diff --git a/Syndemics/NAMESPACE b/Syndemics/NAMESPACE
index ae9e28c..880be6f 100644
--- a/Syndemics/NAMESPACE
+++ b/Syndemics/NAMESPACE
@@ -10,10 +10,13 @@ export(loadOutputFiles)
 export(new_block)
 export(replace_vals)
 import(data.table)
-import(httr)
 importFrom(MASS,glm.nb)
 importFrom(ggcorrplot,ggcorrplot)
 importFrom(ggplot2,theme)
+importFrom(httr,GET)
+importFrom(httr,config)
+importFrom(httr,content)
+importFrom(httr,stop_for_status)
 importFrom(stats,as.formula)
 importFrom(utils,combn)
 importFrom(utils,read.csv)
diff --git a/Syndemics/R/Syndemics-package.R b/Syndemics/R/Syndemics-package.R
new file mode 100644
index 0000000..364ffee
--- /dev/null
+++ b/Syndemics/R/Syndemics-package.R
@@ -0,0 +1,10 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom httr config
+#' @importFrom httr content
+#' @importFrom httr GET
+#' @importFrom httr stop_for_status
+## usethis namespace: end
+NULL
diff --git a/Syndemics/R/fetch_sas.R b/Syndemics/R/fetch_sas.R
index d3d421d..f7d725f 100644
--- a/Syndemics/R/fetch_sas.R
+++ b/Syndemics/R/fetch_sas.R
@@ -1,7 +1,7 @@
 #' MA DPH PHDW Script Pull
 #' Fetches most recent .SAS files for MA DPH work and saves them to a SAS/ subdirectory
 #'
-#' @import httr
+#' @importFrom httr GET stop_for_status content config
 #'
 #' @export
 fetch_sas <- function(){
diff --git a/Syndemics/R/respond_outputs.R b/Syndemics/R/loadOutputFiles.R
similarity index 100%
rename from Syndemics/R/respond_outputs.R
rename to Syndemics/R/loadOutputFiles.R
diff --git a/Syndemics/R/respond_inputs.R b/Syndemics/R/respond_inputManipulations.R
similarity index 100%
rename from Syndemics/R/respond_inputs.R
rename to Syndemics/R/respond_inputManipulations.R
diff --git a/Syndemics/man/Syndemics-package.Rd b/Syndemics/man/Syndemics-package.Rd
new file mode 100644
index 0000000..cfbf72b
--- /dev/null
+++ b/Syndemics/man/Syndemics-package.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Syndemics-package.R
+\docType{package}
+\name{Syndemics-package}
+\alias{Syndemics}
+\alias{Syndemics-package}
+\title{Syndemics: A collection of miscellaneous functions created for internal use with the Boston Medical Center Syndemics lab}
+\description{
+The Syndemics Lab is a research unit with Boston Medical Center. Our primary work involves dynamic simulations for predicting and analyzing opioid use disorder, HIV, and HEP-CE. This package is a collection of commonly used workflow functionalizations serving analytic purposes.
+}
+\keyword{internal}
diff --git a/Syndemics/man/formula_corr.Rd b/Syndemics/man/formula_corr.Rd
index 39964e6..25bd652 100644
--- a/Syndemics/man/formula_corr.Rd
+++ b/Syndemics/man/formula_corr.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internalTools_crc.R
+% Please edit documentation in R/internal_crcTools.R
 \name{formula_corr}
 \alias{formula_corr}
 \title{Internal function to create a formula based on correlation among databases listed in \code{CRC}}
 \usage{
-formula_corr(corr_matrix, threshold, freq.column)
-
 formula_corr(corr_matrix, threshold, freq.column)
 }
 \arguments{
@@ -16,8 +14,6 @@ formula_corr(corr_matrix, threshold, freq.column)
 \item{freq.column}{frequency column, e.g. N_ID}
 }
 \description{
-Internal function to create a formula based on correlation among databases listed in \code{CRC}
-
 Internal function to create a formula based on correlation among databases listed in \code{CRC}
 }
 \keyword{internal}
diff --git a/Syndemics/man/formula_list.Rd b/Syndemics/man/formula_list.Rd
index 54d38f0..73b5c00 100644
--- a/Syndemics/man/formula_list.Rd
+++ b/Syndemics/man/formula_list.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internalTools_crc.R
+% Please edit documentation in R/internal_crcTools.R
 \name{formula_list}
 \alias{formula_list}
 \title{Generates All Possible Combination of Interaction Terms
diff --git a/Syndemics/man/is.formula.Rd b/Syndemics/man/is.formula.Rd
index 300fe87..41092d9 100644
--- a/Syndemics/man/is.formula.Rd
+++ b/Syndemics/man/is.formula.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/internalTools_crc.R
+% Please edit documentation in R/internal_crcTools.R
 \name{is.formula}
 \alias{is.formula}
 \title{Formula Objects