runTC_usingRscript: Function for running test sets per algorithm per marker with...

In RIbench: Benchmark Suite for Indirect Methods for RI Estimation

Function for running test sets per algorithm per marker with calling Rscript for each test set

Description

Function for running test sets per algorithm per marker with calling Rscript for each test set

Usage

runTC_usingRscript(
  biomarker = NULL,
  algoName = "myOwnAlgo",
  algoFunction = "estimateModel",
  sourceFiles = NULL,
  libs = NULL,
  params = NULL,
  decimals = FALSE,
  ris = FALSE,
  RIperc = c(0.025, 0.975),
  tableTCs = NULL,
  outputDir = NULL,
  inputDir = NULL,
  timeLimit = 14400,
  subsetDef = "all",
  verbose = TRUE,
  showWarnings = FALSE,
  ...
)

Arguments

biomarker	(character) specifying the biomarker for which the algorithm should calculate RIs
algoName	(character) specifying the name of the algorithm that is evaluated
algoFunction	(character) specifying the name of the function needed for estimating RIs
sourceFiles	(list) containing all source files needed for executing the algorithm
libs	(list) containing all libraries needed for executing the algorithm
params	(list) with additional parameters needed for calling algoFunction
decimals	(logical) indicating whether the algorithm needs the number of decimal places (TRUE) or not (FALSE, default)
ris	(logical) indicating whether only percentiles and no model is estimated
RIperc	(numeric) value specifying the percentiles, which define the reference interval
tableTCs	(data.frame) with the information about the simulated test sets
outputDir	(character) specifying the outputDir: Results will be stored in outputDir/Results/algo/biomarker
inputDir	(character) specifying the inputDir: Data files should be stored in inputDir/Data/biomarker
timeLimit	(integer) specifying the maximum amount of time in seconds allowed to execute one single estimation (default: 14400 sec (4h))
subsetDef	(character) describing the specified subset of all test sets the algorithm is applied to, used for naming the progress file
verbose	(logical) indictaing if the progress counter should be shown (default: TRUE)
showWarnings	(logical) indicating whether warnings from the call to the indirect method/algorithm should be shown (default: FALSE)
...	additional arguments to be passed to the method

Value

(data frame) containing information about the test sets where the algorithm terminated the R session or failed to report a result

Author(s)

Tatjana Ammer [e-mail]

RIbench documentation built on Nov. 28, 2022, 1:11 a.m.