Nothing
library(npde)
cat("Running tests for the main computational functions\n")
data(theopp)
data(simtheopp)
xbase1<-autonpde(namobs=theopp,namsim=simtheopp,boolsave=FALSE)
# Cholesky decomposition
xbase1<-autonpde(namobs=theopp,namsim=simtheopp, iid=1,ix=3,iy=4,imdv=0,icens=0,icov=0,boolsave=TRUE,type.graph="eps",
namsav="base1",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky", cens.method="omit",units=list(x="hr",y="mg/L"))
# Decorrelation through the inverse method
xbase2<-autonpde(namobs=theopp,namsim=simtheopp, iid=1,ix=3,iy=4,imdv=0,icens=0,icov=0,boolsave=TRUE,type.graph="eps",
namsav="base2",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="inverse", cens.method="omit",units=list(x="hr",y="mg/L"))
idx<-xbase1@data@not.miss
ytest1<-max(abs(xbase1@results@res$pd[idx]-xbase2@results@res$pd[idx]))
if(zapsmall(ytest1)==0) cat("Cholesky/inverse method: same pd, test successful\n") else cat("Problem with xbase1/xbase2\n")
####### With censoring
dat3<-theopp
vec<-rep(1,dim(dat3)[1])
loq<-2
vec[!is.na(dat3$Conc) & dat3$Conc>=loq]<-0
dat3$Conc[!is.na(dat3$Conc) & vec==1]<-loq
sex<-ifelse(dat3$Wt>70,"M","F")
dat3<-cbind(dat3,Sex=sex,MDV=rep(0,dim(dat3)[1]),cens=vec)
dat4<-dat3
dat4$ipred<-dat4$Conc*(1+rnorm(dim(dat4)[1],0,0.1))
# Removing censored data
xcens1<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),boolsave=TRUE,type.graph="eps",namsav="cens1",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky",cens.method="omit")
##### Imputing pd for censored data
## default method (cdf)
xcens2<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),boolsave=TRUE,type.graph="eps",namsav="cens2",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky",cens.method="cdf")
## method ipred (automatic detection of ipred)
xipred<-autonpde(namobs=dat4,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),boolsave=TRUE,type.graph="eps", namsav="ipred1",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky",cens.method="ipred")
## method loq
xloq<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),boolsave=TRUE,type.graph="eps",namsav="loq1",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky",cens.method="loq")
## method ypred
xypred<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),boolsave=TRUE,type.graph="eps",namsav="ypred1",calc.pd=TRUE,calc.npde=TRUE,verbose=FALSE,method="cholesky",cens.method="ypred")
# Automatic column recognition
# xdetect<-autonpde(namobs=dat4,namsim=simtheopp,icov=c(5,6), namsav="idetect"))
# Without all defaults
xcens1.bis<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),namsav="cens1.bis",cens.method="omit")
xcens2.bis<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),namsav="cens2.bis")
idx<-(dat3$MDV==0 & dat3$cens==0)
ytest1<-max(abs(xcens1@results@res$pd[idx]-xcens1.bis@results@res$pd[idx]))
ytest2<-max(abs(xcens2@results@res$pd[idx]-xcens2.bis@results@res$pd[idx]))
ytest3<-max(abs(xcens2@results@res$pd[idx]-xipred@results@res$pd[idx]))
if(zapsmall(ytest1+ytest2+ytest3)==0) cat("Test with censoring successful \n") else cat("Different results, check defaults\n")
cat("Testing gof.test function\n")
gof.test(xbase1)
gof.test(xcens2)
ygof<-gof.test(xcens2,which="pd",covsplit=TRUE)
print(ygof)
gof.test(xcens2,which="pd",sample=TRUE)
cat("End of tests for the main computational functions\n")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.