758 improve null report

DESCRIPTION

@@ -81,6 +81,7 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Collate:
+    'report_null.R'
     'utils.R'
     'chevron_tlg-S4class.R'
     'ael01_nollt.R'

NAMESPACE

@@ -171,7 +171,6 @@ export(mng01)
 export(mng01_main)
 export(mng01_pre)
 export(nocoding)
-export(null_listing)
 export(null_report)
 export(outcome_rule)
 export(pdt01)
@@ -210,6 +209,7 @@ export(rspt01_pre)
 export(run)
 export(script_funs)
 export(set_section_div)
+export(std_postprocessing)
 export(ttet01)
 export(ttet01_main)
 export(ttet01_post)

NEWS.md

@@ -2,6 +2,8 @@
 
 * Add `AEL02`, `AEL03` templates.
 * Modify the post processing of `MHT01` to allow multiple `row_split_var`.
+* Improve the `report_null` method to facilitate the creation of null reports
+* Export the `std_postprocessing` function to simplify post processing logic.
 
 # chevron 0.2.6
 

R/ael01_nollt.R

@@ -45,21 +45,6 @@ ael01_nollt_pre <- function(adam_db,
   adam_db
 }
 
-#' @describeIn ael01_nollt Postprocessing
-#'
-#' @inheritParams gen_args
-#' @returns the postprocessing function returns an `rlistings` object or an `ElementaryTable` (null report).
-#'
-ael01_nollt_post <- function(tlg, ...) {
-  if (is(tlg, "list")) {
-    if (length(tlg) == 0) tlg <- null_report
-  } else {
-    if (nrow(tlg) == 0) tlg <- null_report
-  }
-
-  tlg
-}
-
 #' `AEL01_NOLLT` Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
 #'
 #' @include chevron_tlg-S4class.R
@@ -69,6 +54,5 @@ ael01_nollt_post <- function(tlg, ...) {
 #' run(ael01_nollt, syn_data)
 ael01_nollt <- chevron_l(
   main = ael01_nollt_main,
-  preprocess = ael01_nollt_pre,
-  postprocess = ael01_nollt_post
+  preprocess = ael01_nollt_pre
 )

R/aet01.R

@@ -171,7 +171,7 @@ aet01_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET01` Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.

R/aet01_aesi.R

@@ -213,7 +213,7 @@ aet01_aesi_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET01_AESI` Table 1 (Default) Adverse Event of Special Interest Summary Table.

R/aet02.R

@@ -105,7 +105,7 @@ aet02_post <- function(tlg, row_split_var = "AEBODSYS", prune_0 = TRUE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET02` Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.

R/aet03.R

@@ -138,7 +138,7 @@ aet03_post <- function(tlg, prune_0 = TRUE, ...) {
       scorefun = cont_n_allcols
     )
   if (prune_0) tlg <- trim_rows(tlg)
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET03` Table 1 (Default) Advert Events by Greatest Intensity Table 1.

R/aet04.R

@@ -156,7 +156,7 @@ aet04_post <- function(tlg, prune_0 = TRUE, ...) {
   tlg <- tlg %>%
     tlg_sort_by_vars(c("AEBODSYS", "AEDECOD"), score_all_sum, decreasing = TRUE)
   if (prune_0) tlg <- trim_rows(tlg)
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET04` Table 1 (Default) Adverse Events by Highest `NCI` `CTACAE` `AE` Grade Table 1.

R/aet05.R

@@ -115,7 +115,7 @@ aet05_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `AET05` Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.

R/aet10.R

@@ -99,7 +99,7 @@ aet10_post <- function(tlg, atleast = 0.05, ...) {
     )
   )
 
-  std_postprocess(tlg_prune)
+  std_postprocessing(tlg_prune)
 }
 
 #' `AET10` Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.

R/cfbt01.R

@@ -204,7 +204,7 @@ cfbt01_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `CFBT01` Change from Baseline By Visit Table.

R/chevron_tlg-S4class.R

@@ -1,4 +1,5 @@
 #' @include utils.R
+#' @include report_null.R
 
 # Chevron_tlg ----
 
@@ -141,7 +142,7 @@ methods::setValidity("chevron_simple", function(object) {
 #'
 chevron_t <- function(main = function(adam_db, ...) build_table(basic_table(), adam_db[[1]]),
                       preprocess = function(adam_db, ...) adam_db,
-                      postprocess = report_null,
+                      postprocess = std_postprocessing,
                       ...) {
   res <- .chevron_t(
     main = main,
@@ -166,7 +167,7 @@ chevron_t <- function(main = function(adam_db, ...) build_table(basic_table(), a
 #'
 chevron_l <- function(main = function(adam_db, ...) data.frame(),
                       preprocess = function(adam_db, ...) adam_db,
-                      postprocess = function(tlg, ...) tlg,
+                      postprocess = std_postprocessing,
                       ...) {
   res <- .chevron_l(
     main = main,
@@ -195,7 +196,7 @@ chevron_l <- function(main = function(adam_db, ...) data.frame(),
 #'
 chevron_g <- function(main = function(adam_db, ...) ggplot2::ggplot(),
                       preprocess = function(adam_db, ...) adam_db,
-                      postprocess = function(tlg, ...) tlg,
+                      postprocess = std_postprocessing,
                       ...) {
   res <- .chevron_g(
     main = main,

R/cmt01a.R

@@ -122,7 +122,7 @@ cmt01a_post <- function(
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `CMT01A` Concomitant Medication by Medication Class and Preferred Name.

R/coxt01.R

@@ -129,7 +129,7 @@ coxt01_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `COXT01` (Default) Cox Regression Model Table.

R/dmt01.R

@@ -115,7 +115,7 @@ dmt01_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `DMT01` Table 1 (Default) Demographics and Baseline Characteristics Table 1.

R/dst01.R

@@ -170,7 +170,7 @@ dst01_post <- function(tlg, prune_0 = TRUE, ...) {
     tlg <- tlg %>%
       smart_prune()
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' DST01 Table 1 (Default) Patient Disposition Table 1.

R/dtht01.R

@@ -180,7 +180,7 @@ dtht01_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `DTHT01` Table 1 (Default) Death Table.

R/egt02.R

@@ -97,7 +97,7 @@ egt02_pre <- function(adam_db, ...) {
 #' @export
 #'
 egt02_post <- function(tlg, ...) {
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `EGT02` ECG Abnormalities Table.

R/egt03.R

@@ -156,7 +156,7 @@ egt03_pre <- function(adam_db, ...) {
 egt03_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) tlg <- smart_prune(tlg)
 
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `EGT03` Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.

R/egt05_qtcat.R

@@ -160,7 +160,7 @@ egt05_qtcat_pre <- function(adam_db, ...) {
 #'
 egt05_qtcat_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) tlg <- smart_prune(tlg)
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `EGT05_QTCAT` ECG Actual Values and Changes from Baseline by Visit Table.

R/ext01.R

@@ -135,7 +135,7 @@ ext01_pre <- function(adam_db,
 #'
 ext01_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) tlg <- smart_prune(tlg)
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `EXT01` Exposure Summary Table.

R/lbt04.R

@@ -163,7 +163,7 @@ lbt04_pre <- function(adam_db, ...) {
 #' @export
 #'
 lbt04_post <- function(tlg, ...) {
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `LBT04` Laboratory Abnormalities Not Present at Baseline Table.

R/lbt05.R

@@ -130,7 +130,7 @@ lbt05_post <- function(tlg, prune_0 = FALSE, ...) {
     }
   }
 
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `LBT05` Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

R/lbt06.R

@@ -141,7 +141,7 @@ lbt06_post <- function(tlg, prune_0 = FALSE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `LBT06` Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.

R/lbt07.R

@@ -166,7 +166,7 @@ lbt07_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) {
     tlg <- smart_prune(tlg)
   }
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `LBT07` Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.

R/lbt14.R

@@ -138,7 +138,7 @@ lbt14_pre <- function(adam_db,
 #'
 lbt14_post <- function(tlg, prune_0 = TRUE, ...) {
   if (prune_0) tlg <- tlg %>% trim_rows()
-  std_postprocess(tlg)
+  std_postprocessing(tlg)
 }
 
 #' `LBT14` Laboratory Test Results Shift Table – Highest `NCI-CTCAE` Grade Post-Baseline by

R/mht01.R

@@ -118,7 +118,7 @@ mht01_post <- function(tlg, row_split_var = "MHBODSYS", prune_0 = TRUE, ...) {
       scorefun = score_occurrences
     )
 
-  std_postprocess(tbl_sorted)
+  std_postprocessing(tbl_sorted)
 }
 
 #' `MHT01` Medical History Table.

R/pdt01.R

@@ -131,7 +131,7 @@ pdt01_post <- function(tlg, prune_0 = TRUE, dvcode_var = "DVDECOD", dvterm_var =
       scorefun = score_occurrences
     )
 
-  std_postprocess(tbl_sorted)
+  std_postprocessing(tbl_sorted)
 }
 
 #' `pdt01` Major Protocol Deviations Table.

R/pdt02.R

@@ -139,7 +139,7 @@ pdt02_post <- function(tlg, prune_0 = TRUE, dvreas_var = "DVREAS", dvterm_var =
       scorefun = score_occurrences
     )
 
-  std_postprocess(tbl_sorted)
+  std_postprocessing(tbl_sorted)
 }
 
 #' `pdt02` Major Protocol Deviations Related to Epidemic/Pandemic Table.