knitr::opts_chunk$set(cache = FALSE)
resFiles <- list.files("outputs/") for (fileName in resFiles) { load(paste0("outputs/", fileName)) }
library(VSURF)
toys
datadata(toys)
randomForest
set.seed(556264) toysRF <- VSURF(toys$x, toys$y)
summary(toysRF) save(toysRF, file = "outputs/toysRF.Rdata")
ranger
set.seed(475073) toysRg <- VSURF(toys$x, toys$y, RFimplem = "ranger")
summary(toysRg) save(toysRg, file = "outputs/toysRg.Rdata")
randomForest
ncores <- 24
set.seed(364693, kind = "L'Ecuyer-CMRG") toysRFPara <- VSURF(toys$x, toys$y, parallel = TRUE, clusterType = "FORK", ncores = ncores)
summary(toysRFPara) save(toysRFPara, file = "outputs/toysRFPara.Rdata")
ranger
set.seed(850162, kind = "L'Ecuyer-CMRG") toysRgPara <- VSURF(toys$x, toys$y, RFimplem = "ranger", parallel = TRUE, clusterType = "FORK", ncores = ncores)
summary(toysRgPara) save(toysRgPara, file = "outputs/toysRgPara.Rdata")
set.seed(289817) toysRgParaInter <- VSURF(toys$x, toys$y, RFimplem = "ranger", parallel = TRUE, clusterType = "ranger", ncores = ncores)
summary(toysRgParaInter) save(toysRgParaInter, file = "outputs/toysRgParaInter.Rdata")
spam
datadata("spam", package = "kernlab") set.seed(9146301) levels(spam$type) <- c("ok", "spam") yTable <- table(spam$type) indApp <- c(sample(1:yTable[2], yTable[2]/2), sample((yTable[2] + 1):nrow(spam), yTable[1]/2)) spamApp <- spam[indApp, ] spamTest <- spam[-indApp, ]
ncores <- 32
spamThres <- VSURF_thres(type~., spamApp, parallel = TRUE, ncores = ncores, clusterType="FORK") save(spamThres, file = "outputs/spamThres.Rdata")
spamThres$comput.time
spamRgThres <- VSURF_thres(type~., spamApp, parallel = TRUE, ncores = ncores, clusterType="FORK", RFimplem = "ranger") save(spamRgThres, file = "outputs/spamRgThres.Rdata")
spamRgThres$comput.time
spamRgThresParaRg <- VSURF_thres(type~., spamApp, parallel = TRUE, ncores = ncores, clusterType = "ranger", RFimplem = "ranger") save(spamRgThresParaRg, file = "outputs/spamRgThresParaRg.Rdata")
spamRgThresParaRg$comput.time
spamInterp <- VSURF_interp(type~., spamApp, vars = spamThres$varselect.thres, parallel = TRUE, ncores = ncores, clusterType = "FORK") save(spamInterp, file = "outputs/spamInterp.Rdata")
spamInterp$comput.time
spamRgInterp <- VSURF_interp(type~., spamApp, vars = spamThres$varselect.thres, parallel = TRUE, ncores = ncores, clusterType = "FORK", RFimplem = "ranger") save(spamRgInterp, file = "outputs/spamRgInterp.Rdata")
spamRgInterp$comput.time
spamRgInterpParaRg <- VSURF_interp(type~., spamApp, vars = spamThres$varselect.thres, parallel = TRUE, ncores = ncores, clusterType = "ranger", RFimplem = "ranger") save(spamRgInterpParaRg, file = "outputs/spamRgInterpParaRg.Rdata")
spamRgInterpParaRg$comput.time
spamRbInterp <- VSURF_interp(type~., spamApp, vars = spamThres$varselect.thres, parallel = TRUE, ncores = ncores, clusterType = "FORK", RFimplem = "Rborist") save(spamRbInterp, file = "outputs/spamRbInterp.Rdata")
spamRbInterp$comput.time
spamRbInterpParaRb <- VSURF_interp(type~., spamApp, vars = spamThres$varselect.thres, parallel = TRUE, ncores = ncores, clusterType = "Rborist", RFimplem = "Rborist") save(spamRbInterpParaRb, file = "outputs/spamRbInterpParaRb.Rdata")
spamRbInterpParaRb$comput.time
spamPred <- VSURF_pred(type~., spamApp, err.interp = spamInterp$err.interp, varselect.interp = spamInterp$varselect.interp) save(spamPred, file = "outputs/spamPred.Rdata")
spamPred$comput.time
spamRgPred <- VSURF_pred(type~., spamApp, err.interp = spamInterp$err.interp, varselect.interp = spamInterp$varselect.interp, RFimplem = "ranger") save(spamRgPred, file = "outputs/spamRgPred.Rdata")
spamRgPred$comput.time
spamRgPredParaRg <- VSURF_pred(type~., spamApp, err.interp = spamInterp$err.interp, varselect.interp = spamInterp$varselect.interp, RFimplem = "ranger", num.threads = ncores) save(spamRgPredParaRg, file = "outputs/spamRgPredParaRg.Rdata")
spamRgPredParaRg$comput.time
spamRbPred <- VSURF_pred(type~., spamApp, err.interp = spamInterp$err.interp, varselect.interp = spamInterp$varselect.interp, RFimplem = "Rborist") save(spamRbPred, file = "outputs/spamRbPred.Rdata")
spamRbPred$comput.time
spamRbPredParaRb <- VSURF_pred(type~., spamApp, err.interp = spamInterp$err.interp, varselect.interp = spamInterp$varselect.interp, RFimplem = "Rborist", nThread = ncores) save(spamRbPredParaRb, file = "outputs/spamRbPredParaRb.Rdata")
spamRbPredParaRb$comput.time
vac18
datadata("vac18", package = "mixOmics") geneExpr <- vac18$genes stimu <- vac18$stimulation ncores <- 3
randomForest
vacRF <- VSURF(x = geneExpr, y = stimu, parallel = TRUE, ncores = ncores, clusterType = "FORK")
summary(vacRF) save(vacRF, file = "outputs/vacRF.Rdata")
ranger
vacRgThres <- VSURF_thres(x = geneExpr, y = stimu, parallel = TRUE, ncores = ncores, RFimplem = "ranger", clusterType = "FORK")
vacRgThres$comput.time save(vacRgThres, file = "outputs/vacRgThres.Rdata")
vacRgInterp <- VSURF_interp(x = geneExpr, y = stimu, parallel = TRUE, ncores = ncores, RFimplem = "ranger", clusterType = "FORK", vars = vacRF$varselect.thres)
vacRgInterp$comput.time save(vacRgInterp, file = "outputs/vacRgInterp.Rdata")
vacRgPred <- VSURF_pred(x = geneExpr, y = stimu, RFimplem = "ranger", varselect.interp = vacRF$varselect.interp, err.interp = vacRF$err.interp)
vacRgPred$comput.time save(vacRgPred, file = "outputs/vacRgPred.Rdata")
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