Merge pull request #41 from Merck/DEVR-3462function-for-baseline-char…

…acteristics-table-by-subgroup

Fix the functions for baseline characteristics table by subgroup and re-generate the tables

R/format_base_char_subgroup.R

@@ -91,7 +91,7 @@ format_base_char_subgroup <- function(
   #  tbl <- tbl[, -which(names(tbl) %in% rm_tot)]
   #}
 
-  outdata$tbl <- tbl |> dplyr::arrange(order)
+  outdata$tbl <- tbl[order(tbl$order),]
   outdata$display <- display
   outdata$display_stat <- display_stat
   outdata

R/rtf_base_char_subgroup.R

@@ -64,15 +64,8 @@ rtf_base_char_subgroup <- function(
 
   out_all <- outdata$out_all
   tbl <- outdata$tbl
-
-  #Add empty line before stats summary section
-  tbl<- tbl |> 
-    dplyr::mutate(split = cumsum(ifelse(tolower(name) == outdata$display_stat[1], 1, 0))) |>
-    dplyr::group_by(split) |> 
-    dplyr::group_modify(.f = ~dplyr::add_row(.data = .,
-                               name = "", var_label= tbl[tolower(tbl$name) == outdata$display_stat[1],]$var_label))
-
-  tbl1 <- tbl[!names(tbl) %in% c("order","split")]
+
+  tbl1 <- tbl[!names(tbl) %in% c("order")]
   tgroup <- outdata$group
   sgroup <- outdata$subgroup
   if (outdata$display_subgroup_total) tgroup <- c(tgroup, "Total")

vignettes/baseline-character.Rmd

@@ -119,7 +119,7 @@ outdata$tbl
 outdata |> rtf_base_char(
   source = "Source: [CDISCpilot: adam-adsl]",
   path_outdata = tempfile(fileext = ".Rdata"),
-  path_outtable = "base_char.rtf"
+  path_outtable = "outtable/base0char.rtf"
 )
 ```
 
@@ -205,7 +205,7 @@ raw datasets. Key arguments are:
 - `subgroup_var`: a character value of subgroup variable name in observation data saved in meta$data_observation.
 - `subgroup_header`: a character vector for column header hierarchy. The first element will be the first level header and the second element will be second level header.
 
-```{r, eval = FALSE}
+```{r}
 outdata <- prepare_base_char_subgroup(
   meta,
   population = "apat",
@@ -218,22 +218,22 @@ outdata <- prepare_base_char_subgroup(
 
 The output dataset contains commonly used statistics within each `subgroup_var`.
 
-```{r, eval = FALSE}
+```{r}
 outdata$out_all$`Placebo`
 outdata$out_all$`High Dose`
 outdata$out_all$`Low Dose`
 ```
 
 The information about subgroup saved with `outdata$group` and `outdata$subgroup`.
 
-```{r, eval = FALSE}
+```{r}
 outdata$group
 outdata$subgroup
 ```
 
 `n_pop`: participants in population within each `subgroup_var`.
 
-```{r, eval = FALSE}
+```{r}
 outdata$out_all$`Placebo`$n
 outdata$out_all$`High Dose`$n
 outdata$out_all$`Low Dose`$n
@@ -243,7 +243,7 @@ outdata$out_all$`Low Dose`$n
 
 `format_base_char_subgroup` to prepare analysis dataset before generate RTF output
 
-```{r, eval = FALSE}
+```{r}
 tbl <- format_base_char_subgroup(outdata)
 head(tbl$tbl)
 ```
@@ -252,12 +252,11 @@ head(tbl$tbl)
 
 `rtf_base_char_subgroup` to generate RTF output
 
-```{r, warning=FALSE, eval = FALSE}
-outdata |>
-  format_base_char_subgroup() |>
+```{r, warning=FALSE}
+outdata <- format_base_char_subgroup(outdata) |>
   rtf_base_char_subgroup(
     source = "Source:  [CDISCpilot: adam-adsl]",
     path_outdata = tempfile(fileext = ".Rdata"),
-    path_outtable = "base_char_subgroup.rtf"
+    path_outtable = "outtable/base0charsubgroup.rtf"
   )
 ```