update to 0.2.0 [skip vbump] (#22)

- [x] - requirement #0.15 'Format of xx.xx (xx.xx, xx.xx)' is not
covered by any test
- [x] - requirement #0.27 'Refactor active arm' is not covered by any
test
- [x] - requirement #0.31 'Format of (xx%, xx%)' is not covered by any
test
- [x] - requirement #0.36 'survival proportion afun' is not covered by
any test
- [x] - requirement #0.40 'Generate flextable for preview first page' is
not covered by any test
- [x] - requirement #0.53 'Format of xx.xx (xx.x)' is not covered by any
test

---------

Signed-off-by: Joe Zhu <[email protected]>

DESCRIPTION

@@ -1,9 +1,10 @@
 Type: Package
 Package: autoslider.core
 Title: Slide Automation for Tables, Listings and Figures
-Version: 0.1.0.9004
+Version: 0.2.0
 Authors@R: c(
-    person("Joe", "Zhu", , "[email protected]", role = c("cre", "aut")),
+    person("Joe", "Zhu", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0001-7566-2787")),
     person("Heng", "Wang", role = "aut"),
     person("Yinqi", "Zhao", role = "aut"),
     person("Bo", "Ci", role = "aut"),

NAMESPACE

@@ -47,7 +47,6 @@ export(preprocess_t_ds)
 export(purple_format)
 export(read_spec)
 export(red_format)
-export(s_proportion_1)
 export(s_surv_time_1)
 export(save_output)
 export(save_output.autoslider_error)

NEWS.md

@@ -1,4 +1,4 @@
-# autoslider.core 0.1.0.9004
+# autoslider.core 0.2.0
 
 ### New features
 

R/util.R

@@ -113,7 +113,7 @@ trim_perc <- function(x, output) {
 #' @return formatted values
 #' @export
 perc_perc <- function(x, output) {
-  paste0(round(x[1] * 100, 1), "% (", round(x[2] * 100, 1), "%)")
+  paste0(new_round(x[1] * 100, 0), "% (", new_round(x[2] * 100, 0), "%)")
 }
 
 #' Format of xx.xx (xx.xx, xx.xx)
@@ -123,7 +123,7 @@ perc_perc <- function(x, output) {
 #' @return formatted values
 #' @export
 format_3d <- function(x, output) {
-  paste0(round(x[1], 2), " (", round(x[2], 2), ", ", round(x[3], 2), ")")
+  paste0(new_round(x[1], 2), " (", new_round(x[2], 2), ", ", new_round(x[3], 2), ")")
 }
 
 
@@ -175,7 +175,6 @@ s_surv_time_1 <- function(df, .var, is_event, control = control_surv_time()) {
 #' @param long flag
 #' @return A function suitable for use in rtables::analyze() with element selection,
 #' reformatting, and relabeling performed automatically.
-#' @export
 s_proportion_1 <- function(x, conf_level = 0.95,
                            method = c(
                              "waldcc", "wald", "clopper-pearson",

inst/WORDLIST

@@ -95,3 +95,4 @@ tlg
 yaml
 yml
 yyyy
+ORCID

tests/testthat/_snaps/helper_functions.md

@@ -0,0 +1,26 @@
+# Test some functions in helper_functions.R
+
+    Code
+      mutate_actarm(adsl)
+    Output
+      # A tibble: 400 x 63
+         STUDYID   USUBJID  SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
+         <chr>     <chr>    <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
+       1 AB12345-1 AB12345~ id-128 CHN-3     32 YEARS M     ASIAN HISPA~ CHN     Y    
+       2 AB12345-2 AB12345~ id-262 CHN-15    35 YEARS M     BLAC~ NOT H~ CHN     N    
+       3 AB12345-1 AB12345~ id-378 RUS-3     30 YEARS F     ASIAN NOT H~ RUS     N    
+       4 AB12345-2 AB12345~ id-220 CHN-11    26 YEARS F     ASIAN NOT H~ CHN     N    
+       5 AB12345-1 AB12345~ id-267 CHN-7     40 YEARS M     ASIAN NOT H~ CHN     N    
+       6 AB12345-2 AB12345~ id-201 CHN-15    49 YEARS M     ASIAN NOT H~ CHN     Y    
+       7 AB12345-1 AB12345~ id-45  USA-1     34 YEARS F     ASIAN NOT H~ USA     N    
+       8 AB12345-2 AB12345~ id-261 USA-1     32 YEARS F     ASIAN NOT H~ USA     N    
+       9 AB12345-1 AB12345~ id-173 NGA-11    24 YEARS F     BLAC~ NOT H~ NGA     N    
+      10 AB12345-2 AB12345~ id-307 CHN-1     24 YEARS M     ASIAN NOT H~ CHN     Y    
+      # i 390 more rows
+      # i 52 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
+      #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
+      #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
+      #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
+      #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
+      #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, ...
+

tests/testthat/_snaps/slides_preview.md

@@ -0,0 +1,46 @@
+# Test slides preview
+
+    Code
+      ret$header$dataset
+    Output
+        V1        V2         V3             V4           V5
+      1    A: Drug X B: Placebo C: Combination All Patients
+
+---
+
+    Code
+      ret$body$dataset
+    Output
+                                                V1          V2          V3
+      1                                        Sex                        
+      2                                          F    79 (59%)  82 (61.2%)
+      3                                          M    55 (41%)  52 (38.8%)
+      4                                        Age                        
+      5                                     Median       33.00       35.00
+      6                                  Min - Max 21.0 - 50.0 21.0 - 62.0
+      7                                       Race                        
+      8                                      ASIAN  68 (50.7%)    67 (50%)
+      9                  BLACK OR AFRICAN AMERICAN  31 (23.1%)  28 (20.9%)
+      10                                     WHITE  27 (20.1%)  26 (19.4%)
+      11          AMERICAN INDIAN OR ALASKA NATIVE      8 (6%)   11 (8.2%)
+      12                                  MULTIPLE           0    1 (0.7%)
+      13 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER           0    1 (0.7%)
+      14                                     OTHER           0           0
+      15                                   UNKNOWN           0           0
+                  V4          V5
+      1                         
+      2     70 (53%) 231 (57.8%)
+      3     62 (47%) 169 (42.2%)
+      4                         
+      5        35.00       34.00
+      6  20.0 - 69.0 20.0 - 69.0
+      7                         
+      8   73 (55.3%)   208 (52%)
+      9   32 (24.2%)  91 (22.8%)
+      10  21 (15.9%)  74 (18.5%)
+      11    6 (4.5%)   25 (6.2%)
+      12           0    1 (0.2%)
+      13           0    1 (0.2%)
+      14           0           0
+      15           0           0
+

tests/testthat/test-formats.R

@@ -0,0 +1,30 @@
+testthat::test_that("new_round function", {
+  da1 <- data.frame(
+    raw = seq(0, 1, 0.0005),
+    r = unlist(lapply(seq(0, 1, 0.0005) * 100, new_round, digits = 1))
+  )
+  expect_true(all(table(da1$r[2:2001]) == 2))
+
+  da2 <- data.frame(
+    raw = seq(0, 1, 0.00005),
+    r = unlist(lapply(seq(0, 1, 0.00005) * 100, new_round, digits = 2))
+  )
+  expect_true(all(table(da2$r[2:20001]) == 2))
+})
+
+
+testthat::test_that("xx.xx (xx.xx)", {
+  expect_identical(trim_perc(c(10, 0.6375)), "10 (63.75)")
+})
+
+testthat::test_that("xx.xx (xx.x)", {
+  expect_identical(trim_perc1(c(10, 0.6375)), "10 (63.8)")
+})
+
+testthat::test_that("(xx\\%, xx\\%)", {
+  expect_identical(perc_perc(c(0.2, 0.6375)), "20% (64%)")
+})
+
+testthat::test_that("xx.xx (xx.xx, xx.xx)", {
+  expect_identical(format_3d(c(10, 0.6375, 0.2413)), "10 (0.64, 0.24)")
+})

tests/testthat/test-helper_functions.R

@@ -0,0 +1,4 @@
+test_that("Test some functions in helper_functions.R", {
+  testthat::expect_no_error(mutate_actarm(adsl))
+  testthat::expect_snapshot(mutate_actarm(adsl))
+})

tests/testthat/test-slides_preview.R

@@ -0,0 +1,7 @@
+test_that("Test slides preview", {
+  adsl <- eg_adsl
+  out <- t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE"))
+  expect_no_error(ret <- out %>% slides_preview())
+  expect_snapshot(ret$header$dataset)
+  expect_snapshot(ret$body$dataset)
+})