Initial kmg01_1

.gitignore

@@ -3,12 +3,10 @@
 .RData
 .Ruserdata
 .DS_Store
-InputVads.Rdata
-t_ae_ctc_SE.out
-t_ae_ctc_ATEZOREL_SENBX.out
 inst/doc
 docs
 temp
 *.bak
 .Renviron
 .Rprofile
+.vscode

DESCRIPTION

@@ -80,6 +80,7 @@ Collate:
     'egt05_qtcat.R'
     'ext01.R'
     'gen_args.R'
+    'kmg01.R'
     'lbt01.R'
     'lbt04.R'
     'lbt05.R'

NAMESPACE

@@ -54,6 +54,7 @@ export(aet10_1_pre)
 export(args_ls)
 export(assert_all_tablenames)
 export(assert_colnames)
+export(assert_only_one_paramcd)
 export(chevron_g)
 export(chevron_l)
 export(chevron_t)
@@ -150,6 +151,10 @@ export(get_preprocess)
 export(gg_list)
 export(grob_list)
 export(h_format_dec)
+export(kmg01_1)
+export(kmg01_1_main)
+export(kmg01_1_post)
+export(kmg01_1_pre)
 export(lbt01_1)
 export(lbt01_1_lyt)
 export(lbt01_1_main)

R/ael01_nollt.R

@@ -99,7 +99,9 @@ ael01_nollt_1_post <- function(tlg, ...) {
 #' @export
 #'
 #' @examples
-#' run(ael01_nollt_1, syn_data, new_lbls = list(AETERM = "Investigator-Specified\n Adverse Event Term"))
+#' run(ael01_nollt_1, syn_data, new_lbls = list(
+#'   AETERM = "Investigator-Specified\n Adverse Event Term"
+#' ))
 ael01_nollt_1 <- chevron_l(
   main = ael01_nollt_1_main,
   preprocess = ael01_nollt_1_pre,

R/assertions.R

@@ -167,3 +167,18 @@ assert_subset_suggest <- function(x, choices) {
 
   stop(msg, call. = FALSE)
 }
+
+
+#' Check to have only one PARAMCD in the analysis dataset
+#' @param param_val (`character`) value of PARAMCD
+#' @export
+assert_only_one_paramcd <- function(param_val) {
+  unique_param_val <- unique(param_val)
+  if (length(unique_param_val) > 1) {
+    stop(paste0(
+      "More than one parameters:",
+      toString(unique_param_val),
+      ", only one suppose to have."
+    ))
+  }
+}

R/kmg01.R

@@ -0,0 +1,137 @@
+# kmg01_1 ----
+
+#' @describeIn kmg01_1 Main TLG Function
+#'
+#' @details
+#'  * No overall value.
+#'
+#' @inheritParams gen_args
+#' @param dataset (`string`) the name of a table in the `adam_db` object.
+#' @param x_name (`string`) the name of the x-axis.
+#' @param y_name (`string`) the name of the x-axis.
+#' @param show_statis (`flag`) should the summary statistic table be displayed.
+#' @param show_censor (`flag`) should the censor flag be displayed.
+#' @param pval_method (`string`) should the censor flag be displayed.
+#' @param ties (`string`) should the censor flag be displayed.
+#' @param conf_level (`numeric`) should the censor flag be displayed.
+#' @param position_coxph (`numeric`) x and y positions for plotting survival::coxph() model.
+#' @param position_surv_med (`numeric`) x and y positions for plotting annotation table estimating
+#'   median survival time per group.
+#' @param line_col (`list`) describing the colors to use for the lines or a named `list`
+#'  associating values of `arm_var` with color names.
+#'
+#' @note
+#'  * `adam_db` object must contain the table specified by `dataset` with the columns specified by  `arm_var`.
+#'
+#' @return a list of `ggplot` objects.
+#' @export
+kmg01_1_main <- function(adam_db,
+                         dataset = "adtte",
+                         arm_var = "ARM",
+                         x_name = "Time (Days)",
+                         y_name = "Survival Probability",
+                         show_statis = TRUE,
+                         show_censor = TRUE,
+                         pval_method = "wald",
+                         ties = "exact",
+                         conf_level = 0.95,
+                         position_coxph = c(0, 0.05),
+                         position_surv_med = c(0.9, 0.9),
+                         line_col = as.list(nestcolor::color_palette()),
+                         ...) {
+  anl <- adam_db[[dataset]]
+  assert_colnames(anl, "PARAMCD")
+  assert_only_one_paramcd(anl$PARAMCD)
+  checkmate::assert_string(x_name)
+  checkmate::assert_string(y_name)
+  checkmate::assert_flag(show_statis)
+  checkmate::assert_flag(show_censor)
+
+  line_col <- unlist(line_col)
+  checkmate::assert_character(line_col, null.ok = TRUE)
+
+  assert_colnames(anl, "AVAL")
+  variables <- list(tte = "AVAL", is_event = "is_event", arm = arm_var)
+
+
+  if (!is.null(names(line_col))) {
+    color_lvl <- sort(unique(anl[[arm_var]]))
+    col <- line_col[as.character(color_lvl)]
+
+    if (anyNA(col)) {
+      missing_col <- setdiff(color_lvl, names(col))
+      stop(paste("Missing color matching for", toString(missing_col)))
+    }
+
+    col <- unname(col)
+  } else {
+    col <- line_col
+  }
+
+  g_km(
+    df = anl,
+    variables = variables,
+    censor_show = show_censor,
+    xlab = x_name,
+    ylab = y_name,
+    annot_surv_med = !show_statis,
+    annot_coxph = show_statis,
+    control_coxph_pw = control_coxph(pval_method = pval_method, ties = ties, conf_level = conf_level),
+    position_coxph = position_coxph,
+    position_surv_med = position_surv_med
+  )
+}
+
+#' @describeIn kmg01_1 Preprocessing
+#'
+#' @inheritParams kmg01_1_main
+#'
+#' @export
+kmg01_1_pre <- function(adam_db, dataset = "adtte", ...) {
+  assert_all_tablenames(adam_db, c("adsl", dataset))
+  assert_colnames(adam_db[[dataset]], "CNSR")
+
+  adam_db[[dataset]] <- adam_db[[dataset]] %>%
+    mutate(is_event = .data$CNSR == 0)
+
+  adam_db
+}
+
+#' @describeIn kmg01_1 Postprocessing
+#'
+#' @inheritParams gen_args
+#'
+#' @export
+kmg01_1_post <- function(tlg, ...) {
+  tlg
+}
+
+# `kmg01_1` Pipeline ----
+
+#' `KMG01` Kaplan-Meier Plot 1.
+#'
+#'
+#' @include chevron_tlg-S4class.R
+#' @export
+#'
+#' @examples
+#' library(dplyr)
+#' library(dunlin)
+#'
+#' col <- list(
+#'   "A: Drug X" = "black",
+#'   "B: Placebo" = "blue",
+#'   "C: Combination" = "gray"
+#' )
+#'
+#' syn_data2 <- log_filter(syn_data, PARAMCD == "OS", "adtte")
+#' run(kmg01_1, syn_data2, dataset = "adtte", line_col = col)
+#'
+#' syn_data3 <- log_filter(syn_data, PARAMCD == "AEREPTTE", "adaette")
+#' run(kmg01_1, syn_data3, dataset = "adaette")
+kmg01_1 <- chevron_g(
+  main = kmg01_1_main,
+  preproces = kmg01_1_pre,
+  postprocess = kmg01_1_post,
+  adam_datasets = c("adsl")
+)

_pkgdown.yaml

@@ -80,6 +80,7 @@ reference:
       - egt05_qtcat_1
       - ext01_1
       - ext01_2
+      - kmg01_1
       - lbt01_1
       - lbt04_1
       - lbt05_1
@@ -108,6 +109,7 @@ reference:
       - h_format_dec
       - gg_list
       - grob_list
+      - assert_only_one_paramcd
 
   - title: Non-exported Documented Functions for Packagage Developers
     contents:

inst/WORDLIST

@@ -2,22 +2,21 @@ ADEG
 ADaM
 AESI
 CTCAE
-gg
-gg_list
 Hoffmann
+Kaplan
 NCI
 PARAMCD
 Postprocessing
-postprocessing
-preprocess
 Pre
 Repo
-SSO
+Rua
 TLG
 TLGs
+coxph
+de
 funder
+postprocessing
 pre
+preprocess
 repo
 reproducibility
-de
-Rua