processing maps, intended use vignette, introduction vignette

Co-authored-by: benoit <[email protected]> Co-authored-by: Adrian Waddell <[email protected]>
insightsengineering · Dec 9, 2021 · 7b4ef11 · 7b4ef11
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -24,14 +24,16 @@ Imports:
     rlang,
     rtables,
     tidyr,
-    tibble
+    tibble,
+    methods
 Suggests:
     DiagrammeR,
     DiagrammeRsvg,
     knitr,
     rmarkdown,
     scda,
-    scda.2021
+    scda.2021,
+    purrr
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ export(aet03_1)
 export(aet03_1_lyt)
 export(aet04_1)
 export(aet04_1_lyt)
+export(append_to_pmap)
 export(assert_colnames)
 export(bol_YN)
 export(cut_by_group)
@@ -28,10 +29,14 @@ export(ext01_2_lyt)
 export(lbt01_1)
 export(lbt01_1_lyt)
 export(pivot_wider_labels)
+export(pmap_row)
+export(preprocess_data)
+export(remove_tlg_pmap)
 export(reorder_levels_params)
 export(std_deco)
-export(std_filter)
-export(std_mutate)
+export(std_filter_fun)
+export(std_mutate_fun)
+export(std_pmap)
 export(syn_test_data)
 export(var_labels_for)
 import(dm)
@@ -45,7 +50,9 @@ importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(magrittr,"%>%")
+importFrom(methods,is)
 importFrom(rlang,sym)
 importFrom(rtables,var_labels)
+importFrom(stats,setNames)
 importFrom(tibble,tribble)
 importFrom(tidyr,pivot_wider)
diff --git a/R/aet02.R b/R/aet02.R
@@ -22,11 +22,7 @@
 #' library(rtables)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adae)
-#'
-#' db <- db %>%
-#'   (std_filter("aet02_1"))() %>%
-#'   (std_mutate("aet02_1"))()
+#'   preprocess_data("aet02_1")
 #'
 #' aet02_1(adam_db = db) %>% head(15)
 #'
@@ -96,7 +92,6 @@ aet02_1 <- function(adam_db,
 #' @param lbl_AEBODSYS (`string`) text label for AEBODSYS.
 #' @param lbl_AEDECOD (`string`) text label for AEDECOD.
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -180,11 +175,8 @@ aet02_1_lyt <- function(armvar = .study$armvar,
 #' library(rtables)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adae)
+#'    preprocess_data("aet02_2")
 #'
-#' db <- db %>%
-#'   (std_filter("aet02_2"))() %>%
-#'   (std_mutate("aet02_2"))()
 #'
 #' aet02_2(db) %>% head(15)
 #'
@@ -255,7 +247,6 @@ aet02_2 <- function(adam_db,
 #' @param lbl_AEHLT (`string`) text label for AEHLT.
 #' @param lbl_AEDECOD (`string`) text label for AEDECOD.
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -356,11 +347,7 @@ aet02_2_lyt <- function(armvar = .study$armvar,
 #' library(dm)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adae)
-#'
-#' db <- db %>%
-#'   (std_filter("aet02_3"))() %>%
-#'   (std_mutate("aet02_3"))()
+#'    preprocess_data("aet02_3")
 #'
 #' aet02_3(adam_db = db) %>% head()
 #'
@@ -406,7 +393,6 @@ aet02_3 <- function(adam_db,
 #'
 #' @param lbl_AEDECOD (`string`) text label for AEDECOD.
 #'
-#' @return
 #' @export
 #'
 #' @examples

diff --git a/R/aet03.R b/R/aet03.R
@@ -24,11 +24,7 @@
 #' library(rtables)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adae)
-#'
-#' db <- db %>%
-#'   (std_filter("aet03_1"))() %>%
-#'   (std_mutate("aet03_1"))()
+#'    preprocess_data("aet03_1")
 #'
 #' aet03_1(db)
 #' aet03_1(db, lbl_overall = "All Patients")
@@ -94,15 +90,16 @@ aet03_1 <- function(adam_db,
 #' @param lbl_AEDECOD (`string`) text label for AEDECOD.
 #' @param severity_grade (`vector of strings`) describing the severity levels present in the data set.
 #'
-#' @return
 #' @export
 #'
 #' @examples
-#' aet03_1_lyt(armvar = "ACTARM",
-#'  lbl_AEBODSYS = "Body System or Organ Class",
-#'  lbl_AEDECOD = "Dictionary-Derived Term",
-#'  lbl_overall = NULL,
-#'  deco = std_deco("AET03"))
+#' aet03_1_lyt(
+#'   armvar = "ACTARM",
+#'   lbl_AEBODSYS = "Body System or Organ Class",
+#'   lbl_AEDECOD = "Dictionary-Derived Term",
+#'   lbl_overall = NULL,
+#'   deco = std_deco("AET03")
+#' )
 aet03_1_lyt <- function(armvar = .study$armvar,
                         lbl_AEBODSYS = "",
                         lbl_AEDECOD = "",

diff --git a/R/aet04.R b/R/aet04.R
@@ -23,11 +23,7 @@
 #' library(rtables)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adae)
-#'
-#' db <- db %>%
-#'   (std_filter("aet03_1"))() %>%
-#'   (std_mutate("aet03_1"))()
+#'    preprocess_data("aet03_1")
 #'
 #' aet04_1(db)
 #' aet04_1(db, prune_0 = FALSE)
@@ -103,7 +99,6 @@ aet04_1 <- function(adam_db,
 #' @param lbl_AEDECOD (`string`) text label for AEDECOD.
 #' @param group_grades (`list`) putting in correspondence severity levels and labels.
 #'
-#' @return
 #' @export
 #'
 #' @examples

diff --git a/R/dmt01.R b/R/dmt01.R
@@ -23,15 +23,9 @@
 #' @examples
 #'
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl)
-#'
-#' db <- db %>%
-#'   (std_filter("dmt01_1"))() %>%
-#'   (std_mutate("dmt01_1"))()
-#'
+#'    preprocess_data("dmt01_1")
 #'
 #' dmt01_1(db, summaryvars = c("AGE", "RACE", "SEX", "BWGHTSI"))
 #' dmt01_1(db, summaryvars = c("AGE", "RACE", "SEX"), lbl_overall = NULL)
@@ -82,7 +76,6 @@ dmt01_1 <- function(adam_db,
 #' @param summaryvars (`vector of strings`) variables summarized in demographic table.
 #' @param summaryvars_lbls (`vector of strings`) labels corresponding to the analyzed variables.
 #'
-#' @return
 #' @export
 #'
 #' @examples

diff --git a/R/dst01.R b/R/dst01.R
@@ -45,24 +45,18 @@ check_dst01_1_args <- function(reason, status, status_treatment) {
 #' @examples
 #'
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl)
-#'
-#' db <- db %>%
-#'   (std_filter("dst01_1"))() %>%
-#'   (std_mutate("dst01_1"))()
+#'    preprocess_data("dst01_1")
 #'
 #' dst01_1(db)
 #'
-#'
 dst01_1 <- function(adam_db,
                     armvar = .study$armvar,
                     status_var = "EOSSTT",
                     disc_reason_var = .study$disc_reason_var,
-                    lbl_overall = .study$lbl_overall,
                     prune_0 = TRUE,
+                    lbl_overall = .study$lbl_overall,
                     deco = std_deco("DST01"),
                     .study = list(
                       armvar = "ARM",
@@ -134,7 +128,6 @@ dst01_1 <- function(adam_db,
 #' @details Since the two parts of the tables are pruned differently, the layout function returns a list of layouts,
 #'   which allows the tables to be constructed and pruned separately before binding.
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -223,14 +216,9 @@ dst01_1_lyt <- function(armvar = .study$armvar,
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl)
-#'
-#' db <- db %>%
-#'   (std_filter("dst01_2"))() %>%
-#'   (std_mutate("dst01_2"))()
+#'    preprocess_data("dst01_2")
 #'
 #' dst01_2(db)
 #' dst01_2(db, lbl_overall = NULL)
@@ -310,7 +298,6 @@ dst01_2 <- function(adam_db,
 #' @details Since the two parts of the tables are pruned differently, the layout function returns a list of layouts,
 #'   which allows the tables to be constructed and pruned separately before binding.
 #'
-#' @return
 #' @export
 #'
 #' @examples
@@ -403,14 +390,9 @@ dst01_2_lyt <- function(armvar = .study$armvar,
 #'
 #' @examples
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl)
-#'
-#' db <- db %>%
-#'   (std_filter("dst01_3"))() %>%
-#'   (std_mutate("dst01_3"))()
+#'    preprocess_data("dst01_3")
 #'
 #' dst01_3(db)
 #' dst01_3(db, lbl_overall = NULL)
@@ -516,7 +498,6 @@ dst01_3 <- function(adam_db,
 #' @param ongoing_lbl (`string`) associated with ongoing treatment and found in the columns given by `status_treatment`.
 #'   By Default `ONGOING.
 #'
-#' @return
 #' @export
 #'
 #' @examples

diff --git a/R/ext01.R b/R/ext01.R
@@ -22,14 +22,9 @@
 #' @examples
 #'
 #' library(dm)
-#' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adex)
-#'
-#' db <- db %>%
-#'   (std_filter("ext01_1"))() %>%
-#'   (std_mutate("ext01_1"))()
+#'    preprocess_data("ext01_1")
 #'
 #' ext01_1(db)
 #'
@@ -70,7 +65,6 @@ ext01_1 <- function(adam_db,
 #' @param summaryvars `(string)` the name of the variable to be analyzed. By default `"AVAL"`.
 #' @param summaryvars_lbls `(string)` the label associated with the analyzed variable.
 #'
-#' @return
 #' @export
 #'
 ext01_1_lyt <- function(armvar = .study$armvar,
@@ -121,11 +115,7 @@ ext01_1_lyt <- function(armvar = .study$armvar,
 #' library(dplyr)
 #'
 #' db <- syn_test_data() %>%
-#'    dm_select_tbl(adsl, adex)
-#'
-#' db <- db %>%
-#'   (std_filter("ext01_2"))() %>%
-#'   (std_mutate("ext01_2"))()
+#'    preprocess_data("ext01_2")
 #'
 #' ext01_2(db)
 #'
@@ -170,7 +160,6 @@ ext01_2 <- function(adam_db,
 #' @param summaryvars (`string`) the name of the variable to be analyzed. By default `"AVAL"`.
 #' @param summaryvars_lbls (`string`) the label associated with the analyzed variable.
 #'
-#' @return
 #' @export
 #'
 ext01_2_lyt <- function(armvar = .study$armvar,

diff --git a/R/gen_args.R b/R/gen_args.R
@@ -1,45 +1,21 @@
 
 #' General Argument Name Convention
 #'
-#' @param adam_db (`dm`) object containing the adam Datasets.
+#' @param adam_db (`dm`) object containing the ADaM datasets
 #' @param armvar (`character`) variable used for column splitting
 #' @param deco (`character`) decoration with `title`, `subtitles` and `main_footer` content
 #' @param lbl_overall (`character`) label used for overall column, if set to `NULL` the overall column is omitted
 #' @param prune_0 (`logical`) remove 0 count rows
 #' @param .study (`list`)  with default values for the arguments of the function
-#' @param ad_bl (`data.frame`) subject baseline Dataset with one row per patient
-#' @param adsl (`data.frame`) Subject Level Analysis Dataset
-#' @param adeg (`data.frame`) ECG Analysis Dataset
-#' @param adae (`data.frame`) Adverse Events Analysis Dataset
-#' @param adcm (`data.frame`) Concomitant Medications Analysis Dataset
-#' @param admh (`data.frame`) Medical History Analysis Dataset
-#' @param aag (`data.frame`) Adverse Event Grouping Defs Dataset
-#' @param advs (`data.frame`) Vital Signs Analysis Dataset
-#' @param adlb (`data.frame`) Laboratory Analysis Dataset
-#' @param adex (`data.frame`) Exposure Analysis Dataset
-#' @param adsub (`data.frame`) Subcategory Analysis Dataset
-#' @param adrs (`data.frame`) Response Analysis Dataset
-#' @param adtte (`data.frame`) Time to Event Analysis Dataset
-#' @param adhy (`data.frame`) Hy's Law Analysis Dataset
-#' @param adsaftte (`data.frame`) Safety Time to Event Analysis Dataset
-#' @param addv (`data.frame`) Protocol Deviations Analysis Dataset
-#' @param adcssrs (`data.frame`) C-SSRS Analysis Dataset
-#' @param adqlqc (`data.frame`) EORTC QLQ-C30 V3 Analysis Dataset
-#' @param acg (`data.frame`) Concomitant Med. Grouping Defs Dataset
-#' @param adic (`data.frame`) Interval Censoring Analysis Dataset
-#'
+#' @param tlgfname (`character`) function name of tlg-function
+#' @param pmap ('data frame') preprocessing map, see `std_pmap` for the required format
 #' @param group (`list of lists`) for group-dependent data binning
 #'
-#' @param group nest list for group-dependent data binning
-#'
-#' @details the following arguments are better provided through the study object:
-#'   - lbl_overall
-#'   - armvar
+#' @details the following arguments are better provided through the study object: `lbl_overall`, `armvar`.
 #'
 gen_args <- function(
-  adam_db, armvar, lbl_overall, prune_0, deco, .study,
-  ad_bl, adsl, adeg, adae, adcm, admh, aag, advs, adlb, adex, adsub, adrs, adtte,
-  adhy, adsaftte, addv, adcssrs, adqlqc, acg, adic, group
+  adam_db, armvar, lbl_overall, prune_0, deco, .study, group,
+  tlgfname, pmap
 ) {
   NULL
 }