checking redcap dd drug codes

2021-10-15_tom_dup_drug_prefix.R

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+# Description: 
+# Author: Haley Hunter-Zinck
+# Date: 
+
+# setup ----------------------------
+
+tic = as.double(Sys.time())
+
+library(glue)
+library(dplyr)
+library(synapser)
+synLogin()
+
+# synapse
+synid_file_dd <- "syn25468849"
+
+# parmaeters
+drug_name <- "Irinotecan"
+oth_drug_names <- c("Fluorouracil", "Irinotecan Hydrochloride", "Leucovorin Calcium")
+
+# functions ----------------------------
+
+#' Download and load data stored in csv or other delimited format on Synapse
+#' into an R data frame.
+#' 
+#' @param synapse_id Synapse ID
+#' @version Version of the Synapse entity to download.  NA will load current
+#' version
+#' @param set Delimiter for file
+#' @param na.strings Vector of strings to be read in as NA values
+#' @param header TRUE if the file contains a header row; FALSE otherwise.
+#' @param check_names TRUE if column names should be modified for compatibility 
+#' with R upon reading; FALSE otherwise.
+#' @return data frame
+get_synapse_entity_data_in_csv <- function(synapse_id, 
+                                           version = NA,
+                                           sep = ",", 
+                                           na.strings = c("NA"), 
+                                           header = T,
+                                           check_names = F) {
+
+  if (is.na(version)) {
+    entity <- synGet(synapse_id)
+  } else {
+    entity <- synGet(synapse_id, version = version)
+  }
+
+  data <- read.csv(entity$path, stringsAsFactors = F, 
+                   na.strings = na.strings, sep = sep, check.names = check_names,
+                   header = header)
+  return(data)
+}
+
+# read ----------------------------
+
+dd <- get_synapse_entity_data_in_csv(synid_file_dd)
+
+# specific drug ----------------------------
+
+drugs_str <- unlist(dd %>% 
+  filter(`Variable / Field Name` == "drugs_drug_1") %>%
+  select(`Choices, Calculations, OR Slider Labels`))
+
+drugs <- strsplit(x = strsplit(x = drugs_str, split = "\\|")[[1]], split = ", ")
+
+res <- unlist(lapply(drugs, 
+       function(x, pattern) {return(grepl(pattern = pattern, x = x[2]))}, 
+       pattern = drug_name))
+
+print(drugs[which(res)])
+
+# find codes for drugs ----------------------
+
+for (oth_drug in oth_drug_names) {
+  res <- unlist(lapply(drugs, 
+                       function(x, pattern) {return(grepl(pattern = pattern, x = x[2]))}, 
+                       pattern = oth_drug))
+
+  print(glue("{oth_drug}: {drugs[which(res)][[1]][1]}"))
+}
+
+# close out ----------------------------
+
+toc = as.double(Sys.time())
+print(glue("Runtime: {round(toc - tic)} s"))