diff --git a/utils.R b/utils.R index 7d7bc48..c8c6105 100644 --- a/utils.R +++ b/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) +}