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utils: Add sma_load_data()

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This function loads the data and adjust some wrong column types. It
shoulb be used from all other scripts to load the data. It the same
source data for all following calculations.
The data is stored inside a 'tibble' from the 'tidyverse' package.
This commit is contained in:
Jens Sauer 2020-11-16 12:24:20 +01:00
parent fdd17c0c71
commit f919a31527
1 changed files with 46 additions and 0 deletions
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utils.R
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@ -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)
}