replaced all subData. with survData.

ICON-in-R · Nov 9, 2023 · 0d40e0a · 0d40e0a
1 parent 789e609
commit 0d40e0a
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Showing 43 changed files with 1,658 additions and 1,648 deletions.
diff --git a/R/check_study_data.R b/R/check_study_data.R
@@ -1,31 +1,31 @@
 
 #
-check_study_data <- function(subDataHR = NA,
-                             subDataMed = NA,
-                             subDataBin = NA,
+check_study_data <- function(survDataHR = NA,
+                             survDataMed = NA,
+                             survDataBin = NA,
                              countData  = NA,
                              contsData  = NA,
                              binData = NA) {
 
-  if (any(!is.na(subDataHR))) {
+  if (any(!is.na(survDataHR))) {
     hr_col_names <- c("tx", "base", "study", "Lmean", "Lse", "multi_arm")
-    hr_missing_cols <- !all(hr_col_names %in% names(subDataHR))
+    hr_missing_cols <- !all(hr_col_names %in% names(survDataHR))
 
     if (hr_missing_cols)
       stop("HR data set is missing columns", call. = FALSE)
   }
 
-  if (any(!is.na(subDataBin))) {
+  if (any(!is.na(survDataBin))) {
     bin_col_names <- c("tx", "base", "study", "BinN", "BinR")
-    bin_missing_cols <- !all(bin_col_names %in% names(subDataBin))
+    bin_missing_cols <- !all(bin_col_names %in% names(survDataBin))
 
     if (bin_missing_cols)
       stop("Binary data set is missing columns", call. = FALSE)
   }
 
-  if (any(!is.na(subDataMed))) {
+  if (any(!is.na(survDataMed))) {
     med_col_names <- c("tx", "base", "study", "medN", "medR", "median")
-    med_missing_cols <- !all(med_col_names %in% names(subDataMed))
+    med_missing_cols <- !all(med_col_names %in% names(survDataMed))
 
     if (med_missing_cols)
       stop("Median data set is missing columns", call. = FALSE)

diff --git a/R/data.R b/R/data.R
@@ -13,7 +13,7 @@
 #'   \item{Lse}{Standard error of log hazard ratio}
 #'   \item{multi_arm}{Multi-arm trial indicator: 0/1}
 #' }
-"subDataHR"
+"survDataHR"
 
 
 #' Study survival binary outcome data
@@ -28,7 +28,7 @@
 #'   \item{BinR}{Count of number of events}
 #'   \item{BinN}{Total sample size}
 #' }
-"subDataBin"
+"survDataBin"
 
 
 #' Study median time to event
@@ -44,7 +44,7 @@
 #'   \item{medN}{Sample size}
 #'   \item{medR}{Sample size/2 as estimated number of events}
 #' }
-"subDataMed"
+"survDataMed"
 
 
 #' Binary data

diff --git a/R/load_input_data.R b/R/load_input_data.R
@@ -22,14 +22,14 @@ load_input_data <- function(is_med,
              header = TRUE,
              as.is = TRUE)
 
-  subDataBin <-
+  survDataBin <-
     if (is_bin) {
       read.csv(paste0(file_name, "bin.csv"),
                header = TRUE,
                as.is = TRUE)
     } else {NA}
 
-  subDataMed <-
+  survDataMed <-
     if (is_med) {
       read.csv(paste0(file_name, "med.csv"),
                header = TRUE,
@@ -38,7 +38,7 @@ load_input_data <- function(is_med,
     } else {NA}  
 
   list(subData = subData,
-       subDataMed = subDataMed,
-       subDataBin = subDataBin)
+       survDataMed = survDataMed,
+       survDataBin = survDataBin)
 }
 
diff --git a/R/make_report.R b/R/make_report.R
@@ -38,19 +38,19 @@
 #' 
 #' file_name <- here::here(file.path("inst", "extdata", "survdata_"))
 #' 
-#' subDataHR <-
+#' survDataHR <-
 #'   read.csv(paste0(file_name, "hr_test.csv"),
 #'            header = TRUE,
 #'            as.is = TRUE)
 #' 
-#' subDataBin <-
+#' survDataBin <-
 #'   tryCatch(
 #'     read.csv(paste0(file_name, "bin_test.csv"),
 #'              header = TRUE,
 #'              as.is = TRUE),
 #'     error = function(e) NA)
 #' 
-#' subDataMed <-
+#' survDataMed <-
 #'   tryCatch(
 #'     read.csv(paste0(file_name, "med_test.csv"),
 #'              header = TRUE,
@@ -59,9 +59,9 @@
 #'     error = function(e) NA)
 #' 
 #' nma_model <-
-#'   new_NMA(subDataHR = subDataHR,
-#'           subDataMed = subDataMed,
-#'           subDataBin = subDataBin,
+#'   new_NMA(survDataHR = survDataHR,
+#'           survDataMed = survDataMed,
+#'           survDataBin = survDataBin,
 #'           bugs_params = bugs_params,
 #'           is_random = RANDOM,
 #'           data_type = data_type,

diff --git a/R/new_NMA.R b/R/new_NMA.R
@@ -7,9 +7,9 @@
 #' the passed data sets. If none given then all of the supplied
 #' data are assumed.
 #' 
-#' @param subDataHR Hazard ratio input data frame. Optional
-#' @param subDataMed Median time input data frame. Optional
-#' @param subDataBin Survival binary data input data frame. Optional
+#' @param survDataHR Hazard ratio input data frame. Optional
+#' @param survDataMed Median time input data frame. Optional
+#' @param survDataBin Survival binary data input data frame. Optional
 #' @param binData Binary data input data frame. Optional
 #' @param countData Count data input data frame. Optional
 #' @param contsData Continuous data input data frame. Optional
@@ -27,9 +27,9 @@
 #' @return
 #' @export
 #'
-new_NMA <- function(subDataHR = NA,
-                    subDataMed = NA,
-                    subDataBin = NA,
+new_NMA <- function(survDataHR = NA,
+                    survDataMed = NA,
+                    survDataBin = NA,
                     binData = NA,
                     countData = NA,
                     contsData = NA,
@@ -43,9 +43,9 @@ new_NMA <- function(subDataHR = NA,
                     endpoint) {
 
   data_lookup <-
-    c(subDataHR = "hr_data",
-      subDataMed = "med_data",
-      subDataBin = "surv_bin_data",
+    c(survDataHR = "hr_data",
+      survDataMed = "med_data",
+      survDataBin = "surv_bin_data",
       binData = "bin_data",
       countData = "count_data",
       contsData = "conts_data")
@@ -55,7 +55,7 @@ new_NMA <- function(subDataHR = NA,
               several.ok = TRUE)
 
   nma_datasets <-
-    tibble::lst(subDataHR, subDataMed, subDataBin,
+    tibble::lst(survDataHR, survDataMed, survDataBin,
                 binData, countData, contsData)
 
   # use all provided data

diff --git a/R/new_NMA_dir.R b/R/new_NMA_dir.R
@@ -13,12 +13,12 @@ new_NMA_dir <- function(data_dir = ".") {
 
   analysis_filename <- reference$file[reference$type == "analysis"]
   bugs_filename <- reference$file[reference$type == "bugs"]
-  subDataHR_filename <- reference$file[reference$type == "subData"]
-  subDataBin_filename <- reference$file[reference$type == "subDataBin"]
-  subDataMed_filename <- reference$file[reference$type == "subDataMed"]
+  survDataHR_filename <- reference$file[reference$type == "subData"]
+  survDataBin_filename <- reference$file[reference$type == "survDataBin"]
+  survDataMed_filename <- reference$file[reference$type == "survDataMed"]
 
   subData <-
-    read.csv(fs::path(data_dir, subDataHR_filename),
+    read.csv(fs::path(data_dir, survDataHR_filename),
              stringsAsFactors = FALSE,
              header = TRUE,
              as.is = TRUE)
@@ -37,17 +37,17 @@ new_NMA_dir <- function(data_dir = ".") {
     keyval_as_list %>% 
     validate_analysis_param
 
-  subDataBin <-
-    if (length(subDataBin_filename) != 0) {
-      read.csv(fs::path(data_dir, subDataBin_filename),
+  survDataBin <-
+    if (length(survDataBin_filename) != 0) {
+      read.csv(fs::path(data_dir, survDataBin_filename),
                stringsAsFactors = FALSE,
                header = TRUE,
                as.is = TRUE)
     } else {NA}
 
-  subDataMed <-
-    if (length(subDataMed_filename) != 0) {
-      read.csv(fs::path(data_dir, subDataMed_filename),
+  survDataMed <-
+    if (length(survDataMed_filename) != 0) {
+      read.csv(fs::path(data_dir, survDataMed_filename),
                stringsAsFactors = FALSE,
                header = TRUE,
                as.is = TRUE) %>% 
@@ -57,8 +57,8 @@ new_NMA_dir <- function(data_dir = ".") {
   NMA_params <- 
     c(analysis_params,
       list(subData = subData,
-           subDataBin = subDataBin,
-           subDataMed = subDataMed,
+           survDataBin = survDataBin,
+           survDataMed = survDataMed,
            bugs_params = bugs_params))
 
   do.call(new_NMA, NMA_params)

diff --git a/R/plotNetwork.R b/R/plotNetwork.R
@@ -2,7 +2,7 @@
 #' Plot network diagram
 #'
 #' @param dat List of study data, including subData
-#'  and possibly subDataBin and subDataMed
+#'  and possibly survDataBin and survDataMed
 #' @param usecurve Which line to use? Logical 
 #' @param ... Additional arguments
 #' @export
@@ -23,7 +23,7 @@ plotNetwork <- function(dat,
 plotNetwork.default <- function(dat,
                                 usecurve = FALSE,
                                 ...) {
-  keep_dat <- names(dat) %in% c("subDataBin", "subDataMed", "binData")  #, "subDataHR"
+  keep_dat <- names(dat) %in% c("survDataBin", "survDataMed", "binData")  #, "survDataHR"
   study_data <- dat[keep_dat]
 
   for (i in seq_along(study_data)) {

diff --git a/R/plots_and_tables.R b/R/plots_and_tables.R
@@ -2,7 +2,7 @@
 #' Write to file multiple NMA plots and tables
 #'
 #' @param dat ist of study data, including subData
-#'  and possibly subDataBin and subDataMed
+#'  and possibly survDataBin and survDataMed
 #' @param res_bugs BUGS output
 #' @param effectParam Effect parameter names; string
 #' @param labels Labels
@@ -110,7 +110,7 @@ plots_and_tables <- function(dat,
     append = TRUE,
     col.names = NA)
 
-  if (all(!is.na(dat$subDataBin))) {
+  if (all(!is.na(dat$survDataBin))) {
 
     file_name <- paste0("data_", label, "_bin.csv")
     dataFileLocBin <- file.path(folder, "data", file_name)
@@ -129,14 +129,14 @@ plots_and_tables <- function(dat,
       col.names = NA)
 
     write.table(
-      dat$subDataBin,
+      dat$survDataBin,
       file = dataFileLocBin,
       sep = ",",
       append = TRUE,
       col.names = NA)
   }
 
-  if (all(!is.na(dat$subDataMed))) {
+  if (all(!is.na(dat$survDataMed))) {
 
     file_name <- paste0("data_", label, "_med.csv")
     dataFileLocMed <- file.path(folder, "data", file_name)
@@ -154,7 +154,7 @@ plots_and_tables <- function(dat,
       col.names = NA)
 
     write.table(
-      dat$subDataMed,
+      dat$survDataMed,
       file = dataFileLocMed,
       sep = ",",
       append = TRUE,