adding tests

NAMESPACE

@@ -32,6 +32,7 @@ export(lyt_to_side_by_side)
 export(lyt_to_side_by_side_two_data)
 export(mutate_actarm)
 export(na_replace)
+export(null_report)
 export(orange_format)
 export(perc_perc)
 export(ph_with_img)

R/null_report.R

@@ -0,0 +1,41 @@
+#' Null report
+#'
+#' @author Thomas Neitmann (`neitmant`)
+#' @export
+#'
+#' @details
+#' This will create a null report similar as STREAM does. You can use
+#' it inside output functions as shown in the example below.
+#'
+#' @examples
+#' library(dplyr)
+#' library(filters)
+#' data <- list(
+#'   adsl = eg_adsl,
+#'   adae = eg_adae %>% mutate(AREL = "")
+#' )
+#'
+#' null_report()
+#'
+#' ## An example how to use the `null_report()` inside an output function
+#' t_ae <- function(datasets) {
+#'   trt <- "ACTARM"
+#'   anl <- semi_join(
+#'     datasets$adae,
+#'     datasets$adsl,
+#'     by = c("STUDYID", "USUBJID")
+#'   )
+#'
+#'   return(null_report())
+#' }
+#'
+#' data %>%
+#'   apply_filter("SER_SE") %>%
+#'   t_ae()
+#'
+null_report <- function() {
+  rtable(
+    header = " ",
+    rrow("", "Null Report: No observations met the reporting criteria for inclusion in this output.")
+  )
+}

R/save_output.R

@@ -11,7 +11,8 @@
 #'
 #' @examples
 #' library(dplyr)
-#' adsl <- eg_adsl %>% filter(SAFFL == "Y") %>%
+#' adsl <- eg_adsl %>%
+#'   filter(SAFFL == "Y") %>%
 #'   mutate(TRT01P = factor(TRT01P, levels = c("A: Drug X", "B: Placebo")))
 #' output_dir <- tempdir()
 #' t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY")) %>%

R/t_ae_slide.R

@@ -49,8 +49,9 @@ t_ae_slide <- function(adsl, adae, arm = "TRT01A",
     return(null_report())
   } else {
     lyt <- build_table_header(adsl, arm,
-                              split_by_study = split_by_study,
-                              side_by_side = side_by_side)
+      split_by_study = split_by_study,
+      side_by_side = side_by_side
+    )
 
     lyt <- lyt %>%
       split_rows_by(

R/t_dm_slide.R

@@ -17,12 +17,13 @@
 #' generate_slides(out1, "dm.pptx")
 #'
 #' out2 <- t_dm_slide(adsl, "TRT01P", c("SEX", "AGE", "RACE", "ETHNIC", "COUNTRY"),
-#'                    split_by_study = TRUE)
+#'   split_by_study = TRUE
+#' )
 #' print(out2)
 #'
 t_dm_slide <- function(adsl,
                        arm = "TRT01P",
-                       vars = c("AGEGR1", "SEX", "RACE", "BECOG", "BBMI"),
+                       vars = c("AGE", "SEX", "RACE"),
                        stats = c("median", "range", "count_fraction"),
                        split_by_study = FALSE,
                        side_by_side = NULL) {
@@ -39,8 +40,10 @@ t_dm_slide <- function(adsl,
   adsl1 <- adsl %>%
     select(all_of(c("STUDYID", "USUBJID", arm, vars, extra)))
 
-  lyt <- build_table_header(adsl1, arm, split_by_study = split_by_study,
-                            side_by_side = side_by_side)
+  lyt <- build_table_header(adsl1, arm,
+    split_by_study = split_by_study,
+    side_by_side = side_by_side
+  )
 
   lyt <- lyt %>%
     analyze_vars(
@@ -55,7 +58,6 @@ t_dm_slide <- function(adsl,
   result <- lyt_to_side_by_side(lyt, adsl1, side_by_side)
 
   if (is.null(side_by_side)) {
-
     # adding "N" attribute
     arm <- col_paths(result)[[1]][1]
 

R/util.R

@@ -669,29 +669,12 @@ lyt_to_side_by_side_two_data <- function(lyt, anl, alt_counts_df, side_by_side =
   return(result)
 }
 
-#' Checker of data frame display per patient (or not)
-#'
-#' @param pp per patient
-#' @param colname name of column
-if_display_pp <- function(pp, colname = FALSE) {
-  if (!pp) {
-    if (!colname) {
-      return("USUBJID")
-    }
-    return("Patient ID")
-  }
-  return(NULL)
-}
 
 do_call <- function(fun, ...) {
   args <- list(...)
   do.call(fun, args[intersect(names(args), formalArgs(fun))])
 }
 
-strip_NA <- function(input) {
-  return(input[which(input != "NA")])
-}
-
 
 build_table_header <- function(anl,
                                arm,
@@ -722,7 +705,5 @@ build_table_header <- function(anl,
 
 
 get_version_label_output <- function() {
-   NULL
+  NULL
 }
-
-

tests/testthat.R

@@ -0,0 +1,3 @@
+pkg_name <- "autoslider.core"
+library(testthat)
+test_check(pkg_name, reporter = ParallelProgressReporter$new())