catalogue of files in repo
==> clean.summary.R <==
clean.summary <- function(arg1, warn=TRUE){
##takes output of summary() and returns an html table with median(iqr) for continuous (numeric) variables
==> fix.peak.labels.R <==
fix.peak.labels <- function(arg1) {
#takes a vector of strings of metabolite/peak names (that were altered by R's makenames())
#and fixes names to match the format in data sheets
==> ham.dist.R <==
ham.dist <- function(arg1) {
##function ham.dist computes all pairwise hamming distances among the columns of arg1, a matrix
==> parseSlurmNodeList.R <==
parseSlurmNodeList<- function(arg1) {
#parses SLURM_NODELIST environment variable into a list of nodes (i.e. to be passed to makePSOCKcluster() or h2o.init())
==> uniqueEl.R <==
uniqueEl <- function(arg1) {
##computes the number of unique elements in a pair of sets, for all pairs of columns in a matrix
==> permimp <==
customized version of permimp to support parallel processing on SLURM
modifications were made to /R/doPermimp.R, DESCRIPTION, NAMESPACE, and MD5
to build, use: R CMD build permimp --no-build-vignettes
==> compile_met_info_and_results.R <==
compile variable information and results, save for graphing, calculate correlation for variable importance rankings
==> cpi.R <==
cpi.R measure cpi using custom parallel permimp on hpc cluster
==> plot_tune_results.R <==
graph tune results
==> regressions.R <==
regressions for validation cohort
==> rf_tune.R <==
rf hyperparameter search/tune
==> clustergram_code.m <==
code to reproduce clustergram
==> roc_coords.csv <==
contains coordinates for ROC curves
==> met_info.sav <==
contains classical permutation importance and conditional permutation importance as described in paper
can be read into R using haven::read_sav("met_info.sav")
==> tune.results.csv <==
contains results of tuning process for random forests with all variables
==> tune.results.refined.csv <==
contains results of tuning process for random forests with refined variable profile
==> lasso.results.csv <==
contains results of lasso tuning procedure