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## Copyright (C) 2021-2022 Rodney A. Sparapani
## This file is part of nftbart.
## nft.R
## nftbart 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.
## nftbart 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, see <http://www.gnu.org/licenses/>.
## Author contact information
## Rodney A. Sparapani: rsparapa@mcw.edu
## for code maintainability, nft is just a wrapper of nft2
nft = function(## data
x.train, times, delta=NULL,
x.test=matrix(nrow=0, ncol=0),
rm.const=TRUE, rm.dupe=TRUE,
##edraws2=matrix(nrow=0, ncol=0),
##zdraws2=matrix(nrow=0, ncol=0),
##impute.bin=NULL, impute.prob=NULL,
## multi-threading
tc=getOption("mc.cores", 1), ##OpenMP thread count
##MCMC
nskip=1000, ndpost=2000,
nadapt=1000, adaptevery=100,
chv = NULL,
method="spearman", use="pairwise.complete.obs",
pbd=c(0.7, 0.7), pb=c(0.5, 0.5),
stepwpert=c(0.1, 0.1), probchv=c(0.1, 0.1),
minnumbot=c(5, 5),
## BART and HBART prior parameters
ntree=c(50, 10), numcut=100, xicuts=NULL,
power=c(2, 2), base=c(0.95, 0.95),
## f function
fmu=NA, k=5, tau=NA, dist='weibull',
## s function
total.lambda=NA, total.nu=10, mask=NULL,
## survival analysis
K=100, events=NULL, TSVS=FALSE,
## DPM LIO
drawDPM=1L,
alpha=1, alpha.a=1, alpha.b=0.1, alpha.draw=1,
neal.m=2, constrain=1,
m0=0, k0.a=1.5, k0.b=7.5, k0=1, k0.draw=1,
a0=3, b0.a=2, b0.b=1, b0=1, b0.draw=1,
## misc
na.rm=FALSE, probs=c(0.025, 0.975), printevery=100,
transposed=FALSE, pred=FALSE
)
{
res=nft2(## data
xftrain=x.train, xstrain=x.train,
times=times, delta=delta,
xftest=x.test,
xstest=x.test,
rm.const=rm.const, rm.dupe=rm.dupe,
##edraws2=edraws2, zdraws2=zdraws2,
## multi-threading
tc=tc, ##OpenMP thread count
##MCMC
nskip=nskip, ndpost=ndpost,
nadapt=nadapt, adaptevery=adaptevery,
chvf = chv, chvs = chv,
method=method, use=use,
pbd=pbd, pb=pb,
stepwpert=stepwpert, probchv=probchv,
minnumbot=minnumbot,
## BART and HBART prior parameters
ntree=ntree, numcut=numcut,
xifcuts=xicuts, xiscuts=xicuts,
power=power, base=base,
## f function
fmu=fmu, k=k, tau=tau, dist=dist,
## s function
total.lambda=total.lambda, total.nu=total.nu, mask=mask,
## survival analysis
K=K, events=events, TSVS=TSVS,
## DPM LIO
drawDPM=drawDPM,
alpha=alpha, alpha.a=alpha.a, alpha.b=alpha.b,
alpha.draw=alpha.draw, neal.m=neal.m, constrain=constrain,
m0=m0, k0.a=k0.a, k0.b=k0.b, k0=k0, k0.draw=k0.draw,
a0=a0, b0.a=b0.a, b0.b=b0.b, b0=b0, b0.draw=b0.draw,
## misc
na.rm=na.rm, probs=probs, printevery=printevery,
transposed=transposed, pred=pred
)
attr(res, 'class') <- 'nft'
res$x.train=res$xftrain
res$xftrain=NULL
res$xstrain=NULL
res$xicuts=res$xifcuts
res$xifcuts=NULL
res$xiscuts=NULL
np=length(res$xftest)
if(np>0) {
res$x.test=res$xftest
res$xftest=NULL
res$xstest=NULL
}
return(res)
}
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