Merge branch 'load-function'

* load-function:
  README: List tidyverse as used package
  survival: Use new data load function
  utils: Add sma_load_data()

README.md

@@ -1,2 +1,6 @@
 secMalASCT statistical analysis
 ===============================
+
+R packages used
+---------------
+* tidyverse

survival.R

@@ -6,7 +6,7 @@
 library(survival)
 source("utils.R")
 
-secmal <- read.csv2("current.csv", header=TRUE)
+secmal <- sma_load_data("current.csv")
 
 # Setup survival object
 surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)

utils.R

@@ -3,6 +3,8 @@
 # License: GPL version 3
 # Jens Mathis Sauer (c) 2020
 
+library(tidyverse)
+
 #
 # Write plot to filename
 #
@@ -27,3 +29,47 @@ sma_plot_file <- function(fname, ftype, title_list, legend_list, fun, ...) {
 	# hide "null device 1" in garbage
 	garbage <- dev.off()
 }
+
+#
+# Load secMalASCT data
+#
+# This loads the secMalASCT data from a CSV file and adjusts some
+# columns to the correct type.
+#
+sma_load_data <- function(file) {
+	sma <- as_tibble(read.csv(file, header = TRUE))
+
+	# Type adjustments
+	sma$follow_up_multi <- as.logical(sma$follow_up_multi)
+	sma$nicotin_history <- as.logical(sma$nicotin_history)
+	sma$relapse_treatment_asct <- as.logical(sma$relapse_treatment_asct)
+	sma$relapse_treatment_chemotherapy <- as.logical(sma$relapse_treatment_chemotherapy)
+	sma$relapse_treatment_radiotherapy <- as.logical(sma$relapse_treatment_radiotherapy)
+	sma$relapse_treatment_surgery <- as.logical(sma$relapse_treatment_surgery)
+
+	sma$pre_rt <- as.logical(sma$pre_rt)
+	sma$pre_rt_type <- as.factor(sma$pre_rt_type)
+	sma$post_rt <- as.logical(sma$post_rt)
+	sma$post_rt_type <- as.factor(sma$post_rt_type)
+
+	sma$pre_alkylating_agents <- as.logical(sma$pre_alkylating_agents)
+	sma$pre_topoisomerase <- as.logical(sma$pre_topoisomerase)
+	sma$pre_anthracyclines <- as.logical(sma$pre_anthracyclines)
+
+	sma$peri_alkylating_agents <- as.logical(sma$peri_alkylating_agents)
+	sma$peri_topoisomerase <- as.logical(sma$peri_topoisomerase)
+	sma$peri_anthracyclines <- as.logical(sma$peri_anthracyclines)
+
+	sma$post_alkylating_agents <- as.logical(sma$post_alkylating_agents)
+	sma$post_topoisomerase <- as.logical(sma$post_topoisomerase)
+	sma$post_anthracyclines <- as.logical(sma$post_anthracyclines)
+
+	sma$maintenance_treatment <- as.logical(sma$maintenance_treatment)
+	sma$maintenance_treatment_time <- as.integer(sma$maintenance_treatment_time)
+	sma$maintenance_treatment_type <- as.factor(sma$maintenance_treatment_type)
+
+	sma$thalidomid <- as.logical(sma$thalidomid)
+	sma$bortezomib <- as.logical(sma$bortezomib)
+
+	return(sma)
+}