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## BART: Bayesian Additive Regression Trees
## Copyright (C) 2018 Robert McCulloch and Rodney Sparapani
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
## You should have received a copy of the GNU General Public License
## along with this program; if not, a copy is available at
## https://www.R-project.org/Licenses/GPL-2
mc.mbart2 <- function(
x.train, y.train,
x.test=matrix(0,0,0), type='lbart',
ntype=as.integer(
factor(type,
levels=c('wbart', 'pbart', 'lbart'))),
sparse=FALSE, theta=0, omega=1,
a=0.5, b=1, augment=FALSE, rho=NULL,
xinfo=matrix(0,0,0), usequants=FALSE,
rm.const=TRUE,
k=2, power=2, base=0.95,
##sigest=NA, sigdf=3, sigquant=0.90, lambda=NA,
tau.num=c(NA, 3, 6)[ntype],
offset=NULL, ##w=rep(1, length(y.train)),
ntree=c(200L, 50L, 50L)[ntype], numcut=100L,
ndpost=1000L, nskip=100L,
keepevery=c(1L, 10L, 10L)[ntype],
printevery=100L, transposed=FALSE,
hostname=FALSE,
mc.cores = 2L, nice = 19L, seed = 99L
)
{
if(.Platform$OS.type!='unix')
stop('parallel::mcparallel/mccollect do not exist on windows')
RNGkind("L'Ecuyer-CMRG")
set.seed(seed)
parallel::mc.reset.stream()
if(type=='wbart' || is.na(ntype))
stop("type argument must be set to either 'pbart' or 'lbart'")
cats <- unique(sort(y.train))
K <- length(cats)
if(K<2)
stop("there must be at least 2 categories")
L <- length(offset)
if(!(L %in% c(0, K)))
stop(paste0("length of offset argument must be 0 or ", K))
if(!transposed) {
temp = bartModelMatrix(x.train, numcut, usequants=usequants,
xinfo=xinfo, rm.const=rm.const)
x.train = t(temp$X)
numcut = temp$numcut
xinfo = temp$xinfo
## if(length(x.test)>0)
## x.test = t(bartModelMatrix(x.test[ , temp$rm.const]))
if(length(x.test)>0) {
x.test = bartModelMatrix(x.test)
x.test = t(x.test[ , temp$rm.const])
}
rm.const <- temp$rm.const
rm(temp)
}
mc.cores.detected <- detectCores()
if(mc.cores>mc.cores.detected) mc.cores <- mc.cores.detected
mc.ndpost <- ceiling(ndpost/mc.cores)
for(i in 1:mc.cores) {
parallel::mcparallel({psnice(value=nice);
mbart2(x.train=x.train, y.train=y.train,
x.test=x.test,
type=type, ntype=ntype,
sparse=sparse, theta=theta, omega=omega,
a=a, b=b, augment=augment, rho=rho,
xinfo=xinfo, usequants=usequants,
rm.const=rm.const,
k=k, power=power, base=base,
tau.num=tau.num,
offset=offset,
ntree=ntree, numcut=numcut,
ndpost=mc.ndpost, nskip=nskip,
keepevery=keepevery,
printevery=printevery, transposed=TRUE,
hostname=hostname)},
silent=(i!=1))
## to avoid duplication of output
## capture stdout from first posterior only
}
post.list <- parallel::mccollect()
post <- post.list[[1]]
if(mc.cores==1 | attr(post, 'class')!='mbart2') return(post)
else {
if(class(rm.const)[1]!='logical') post$rm.const <- rm.const
post$ndpost <- mc.cores*mc.ndpost
p <- nrow(x.train[ , post$rm.const])
if(length(rm.const)==0) rm.const <- 1:p
post$rm.const <- rm.const
old.text <- paste0(as.character(mc.ndpost), ' ', as.character(ntree),
' ', as.character(p))
old.stop <- nchar(old.text)
for(j in 1:K)
post$treedraws$trees[[j]] <- sub(old.text,
paste0(as.character(post$ndpost), ' ',
as.character(ntree), ' ',
as.character(p)),
post$treedraws$trees[[j]])
keeptestfits <- length(x.test)>0
for(i in 2:mc.cores) {
post$yhat.train <- rbind(post$yhat.train,
post.list[[i]]$yhat.train)
post$prob.train <- rbind(post$prob.train,
post.list[[i]]$prob.train)
if(keeptestfits) {
post$yhat.test <- rbind(post$yhat.test,
post.list[[i]]$yhat.test)
post$prob.test <- rbind(post$prob.test,
post.list[[i]]$prob.test)
}
for(j in 1:K) {
post$varcount[[j]] <- rbind(post$varcount[[j]],
post.list[[i]]$varcount[[j]])
post$varprob[[j]] <- rbind(post$varprob[[j]],
post.list[[i]]$varprob[[j]])
post$treedraws$trees[[j]] <- paste0(post$treedraws$trees[[j]],
substr(post.list[[i]]$treedraws$trees[[j]], old.stop+2,
nchar(post.list[[i]]$treedraws$trees[[j]])))
}
}
post$prob.train.mean <- apply(post$prob.train, 2, mean)
if(keeptestfits) post$prob.test.mean <- apply(post$prob.test, 2, mean)
for(j in 1:K) {
post$varcount.mean[j, ] <- apply(post$varcount[[j]], 2, mean)
post$varprob.mean[j, ] <- apply(post$varprob[[j]], 2, mean)
}
attr(post, 'class') <- 'mbart2'
return(post)
}
}
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