BenchmarkRvsCpp: A log-likelihood calculation time comparison for different...
In PCMBaseCpp: Fast Likelihood Calculation for Phylogenetic Comparative Models

A log-likelihood calculation time comparison for different numbers of traits and option-sets

BenchmarkRvsCpp(ks = c(1, 2, 4, 8), includeR = TRUE,
  includeTransformationTime = TRUE, optionSets = NULL,
  includeParallelMode = TRUE, doProf = FALSE,
  RprofR.out = "RprofR.out", RprofCpp.out = "RprofCpp.out",
  verbose = FALSE)

`ks`	a vector of positive integers, denoting different numbers of traits. Default: `c(1, 2, 4, 8)`.
`includeR`	logical (default TRUE) indicating if likelihood calculations in R should be included in the benchmark (can be slow).
`includeTransformationTime`	logical (default TRUE) indicating if the time for `PCMApplyTransformation` should be included in the benchmark.
`optionSets`	a named list of lists of PCM-options. If NULL (the default) the option set is set to `DefaultBenchmarkOptions(k, includeParallelMode)` for each `k` in `ks` (see the code in `PCMBaseCpp:::DefaultBenchmarkOptions`).
`includeParallelMode`	logical (default TRUE) indicating if the default optionSet should include parallel execution modes, i.e. setting the option PCMBase.Lmr.mode to 21 instead of 11. This argument is taken into account only with the argument `optionSets` set to NULL (the default).
`doProf`	logical indicating if profiling should be activated (see Rprof from the utils R-package). Default: FALSE. Additional arguments to Rprof can be specified by assigning lists of arguments to the options 'PCMBaseCpp.ArgsRprofR' and 'PCMBaseCpp.ArgsRprofCpp'. The default values for both options is `list(append = TRUE, line.profiling = TRUE)`.
`RprofR.out`	character strings indicating Rprof.out files for the R and Cpp implementations; ignored if doProf is FALSE. Default values: 'RprofR.out' and 'Rprofcpp.out'.
`RprofCpp.out`	character strings indicating Rprof.out files for the R and Cpp implementations; ignored if doProf is FALSE. Default values: 'RprofR.out' and 'Rprofcpp.out'.
`verbose`	logical indicating if log-messages should be printed to the console during the benchmark. Default FALSE.

a data.table for results similar to the data.table returned from MiniBenchmarkRvsCpp with additional columns for k, option-set and the type of model.

PCMBaseCpp documentation built on March 23, 2020, 1:06 a.m.