Last updated on 2018-04-16 13:47:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0 | 8.67 | 60.94 | 69.61 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 2.0 | 6.76 | 46.72 | 53.48 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 2.0 | 84.18 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0 | 81.54 | WARN | |||
| r-devel-windows-ix86+x86_64 | 2.0 | 18.00 | 104.00 | 122.00 | WARN | |
| r-devel-osx-x86_64 | 2.0 | WARN | ||||
| r-patched-linux-x86_64 | 2.0 | 9.17 | 50.64 | 59.81 | ERROR | |
| r-patched-solaris-x86 | 2.0 | 107.40 | WARN | |||
| r-release-linux-x86_64 | 2.0 | 4.34 | 70.32 | 74.66 | NOTE | |
| r-release-windows-ix86+x86_64 | 2.0 | 13.00 | 79.00 | 92.00 | NOTE | |
| r-release-osx-x86_64 | 2.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 2.0 | 8.00 | 84.00 | 92.00 | NOTE |
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-osx-x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.0
Check: top-level files
Result: NOTE
Non-standard file/directory found at top level:
‘doc’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.0
Check: dependencies in R code
Result: NOTE
Packages in Depends field not imported from:
‘mclust’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.0
Check: R code for possible problems
Result: NOTE
File ‘npde/R/zzz.R’:
.onLoad calls:
packageStartupMessage(" Loading library npde, version 2.0, August 2012\n please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr\n")
See section ‘Good practice’ in '?.onAttach'.
autonpde: no visible global function definition for ‘new’
aux.plot.dist: no visible global function definition for ‘rnorm’
aux.plot.dist: no visible global function definition for ‘runif’
aux.plot.dist: no visible global function definition for ‘qnorm’
aux.plot.dist: no visible binding for global variable ‘quantile’
aux.plot.dist: no visible global function definition for ‘polygon’
aux.plot.dist: no visible global function definition for ‘lines’
aux.plot.dist: no visible global function definition for ‘points’
aux.plot.dist: no visible global function definition for ‘abline’
aux.plot.hist: no visible global function definition for ‘rnorm’
aux.plot.hist: no visible global function definition for ‘runif’
aux.plot.hist: no visible global function definition for ‘hist’
aux.plot.hist: no visible binding for global variable ‘quantile’
aux.plot.hist: no visible global function definition for ‘rect’
aux.plot.hist: no visible global function definition for ‘segments’
aux.plot.hist: no visible global function definition for ‘dnorm’
aux.plot.hist: no visible global function definition for ‘lines’
aux.plot.hist: no visible global function definition for ‘abline’
aux.scatter: no visible global function definition for ‘polygon’
aux.scatter: no visible global function definition for ‘lines’
aux.scatter: no visible binding for global variable ‘quantile’
aux.scatter: no visible global function definition for ‘points’
aux.scatter: no visible global function definition for ‘abline’
aux.scatter.box: no visible global function definition for ‘boxplot’
aux.scatter.box: no visible global function definition for ‘abline’
calcnpde: no visible global function definition for ‘cov’
calcnpde.sim: no visible global function definition for ‘cov’
compute.bands: no visible global function definition for ‘rnorm’
compute.bands: no visible global function definition for ‘runif’
compute.bands: no visible binding for global variable ‘quantile’
compute.bands: no visible global function definition for ‘qnorm’
compute.bands.true: no visible binding for global variable ‘quantile’
compute.vpc.pi : <anonymous>: no visible global function definition for
‘quantile’
computenpde.loq: no visible global function definition for ‘runif’
computenpde.loq: no visible global function definition for ‘qnorm’
computenpde.omit: no visible global function definition for ‘runif’
computenpde.omit: no visible global function definition for ‘qnorm’
computepd.cdf: no visible global function definition for ‘runif’
computepd.omit: no visible global function definition for ‘runif’
computepd.replace: no visible global function definition for ‘runif’
default.npde.plots: no visible global function definition for ‘par’
dist.pred.sim: no visible global function definition for ‘runif’
dist.pred.sim: no visible global function definition for ‘qnorm’
gof.test.NpdeObject: no visible global function definition for ‘qnorm’
gof.test.NpdeObject: no visible global function definition for ‘runif’
gof.test.NpdeObject: no visible global function definition for ‘anova’
gof.test.NpdeObject: no visible global function definition for ‘lm’
gof.test.NpdeObject: no visible global function definition for
‘kruskal.test’
gof.test.NpdeObject: no visible global function definition for
‘cor.test’
gof.test.NpdeObject: no visible global function definition for
‘quantile’
gof.test.NpdeRes: no visible global function definition for ‘qnorm’
gof.test.numeric: no visible global function definition for ‘var’
gof.test.numeric: no visible global function definition for ‘sd’
gof.test.numeric: no visible global function definition for ‘t.test’
gof.test.numeric: no visible global function definition for
‘wilcox.test’
gof.test.numeric: no visible global function definition for ‘ks.test’
gof.test.numeric: no visible global function definition for
‘shapiro.test’
gof.test.numeric: no visible global function definition for ‘pchisq’
npde: no visible global function definition for ‘new’
npde.binning: no visible global function definition for ‘quantile’
npde.binning: no visible global function definition for ‘Mclust’
npde.plot.data: no visible global function definition for ‘par’
npde.plot.data: no visible global function definition for ‘points’
npde.plot.data: no visible global function definition for ‘lines’
npde.plot.data: no visible global function definition for ‘abline’
npde.plot.dist: no visible global function definition for ‘par’
npde.plot.dist: no visible global function definition for ‘qnorm’
npde.plot.dist: no visible global function definition for ‘quantile’
npde.plot.loq: no visible global function definition for ‘par’
npde.plot.loq: no visible binding for global variable ‘quantile’
npde.plot.loq: no visible global function definition for ‘polygon’
npde.plot.loq: no visible global function definition for ‘lines’
npde.plot.scatter: no visible global function definition for ‘par’
npde.plot.scatter: no visible global function definition for ‘qnorm’
npde.plot.scatter: no visible global function definition for ‘quantile’
npde.plot.vpc: no visible global function definition for ‘par’
npde.plot.vpc: no visible binding for global variable ‘quantile’
npde.plot.vpc: no visible global function definition for ‘polygon’
npde.plot.vpc: no visible global function definition for ‘lines’
npde.plot.vpc: no visible global function definition for ‘points’
npde.plot.vpc: no visible global function definition for ‘abline’
npdeData: no visible global function definition for ‘new’
npdeSimData: no visible global function definition for ‘new’
pdemenu: no visible global function definition for ‘read.table’
plot.NpdeData: no visible global function definition for ‘par’
plot.NpdeData: no visible global function definition for ‘points’
plot.NpdeData: no visible global function definition for ‘lines’
plot.NpdeData: no visible global function definition for ‘abline’
plot.NpdeObject: no visible global function definition for ‘par’
plot.NpdeRes: no visible global function definition for ‘par’
plot.NpdeRes: no visible global function definition for ‘qqnorm’
plot.NpdeRes: no visible global function definition for ‘qqline’
plot.NpdeRes: no visible global function definition for ‘hist’
plot.NpdeRes: no visible global function definition for ‘dnorm’
plot.NpdeRes: no visible global function definition for ‘lines’
plot.NpdeRes: no visible global function definition for ‘abline’
plot.NpdeRes: no visible global function definition for ‘qnorm’
plot.NpdeRes: no visible global function definition for ‘qqplot’
plot.NpdeRes: no visible global function definition for ‘segments’
[<-,NpdeData: no visible global function definition for ‘validObject’
[<-,NpdeObject: no visible global function definition for ‘validObject’
[<-,NpdeRes: no visible global function definition for ‘validObject’
[<-,NpdeSimData: no visible global function definition for
‘validObject’
initialize,NpdeData: no visible global function definition for
‘validObject’
initialize,NpdeObject: no visible global function definition for ‘new’
initialize,NpdeObject: no visible global function definition for
‘validObject’
npde.graphs,NpdeObject: no visible global function definition for
‘postscript’
npde.graphs,NpdeObject: no visible global function definition for
‘jpeg’
npde.graphs,NpdeObject: no visible global function definition for ‘png’
npde.graphs,NpdeObject: no visible global function definition for ‘pdf’
npde.graphs,NpdeObject: no visible global function definition for
‘dev.off’
npde.save,NpdeObject: no visible global function definition for
‘write.table’
read.npdeData,NpdeData: no visible global function definition for
‘read.table’
read.npdeData,NpdeData: no visible global function definition for
‘head’
read.npdeData,NpdeData: no visible global function definition for
‘validObject’
read.npdeSimData,NpdeSimData: no visible global function definition for
‘read.table’
read.npdeSimData,NpdeSimData: no visible global function definition for
‘head’
read.npdeSimData,NpdeSimData: no visible global function definition for
‘validObject’
show,NpdeObject: no visible global function definition for ‘show’
Undefined global functions or variables:
Mclust abline anova boxplot cor.test cov dev.off dnorm head hist jpeg
kruskal.test ks.test lines lm new par pchisq pdf png points polygon
postscript qnorm qqline qqnorm qqplot quantile read.table rect rnorm
runif sd segments shapiro.test show t.test validObject var
wilcox.test write.table
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "postscript")
importFrom("graphics", "abline", "boxplot", "hist", "lines", "par",
"points", "polygon", "rect", "segments")
importFrom("methods", "new", "show", "validObject")
importFrom("stats", "anova", "cor.test", "cov", "dnorm",
"kruskal.test", "ks.test", "lm", "pchisq", "qnorm",
"qqline", "qqnorm", "qqplot", "quantile", "rnorm", "runif",
"sd", "shapiro.test", "t.test", "var", "wilcox.test")
importFrom("utils", "head", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-osx-x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.0
Check: Rd line widths
Result: NOTE
Rd file 'dist.pred.sim.Rd':
\examples lines wider than 100 characters:
# defaults to computing the pd and npde for 100 simulated datasets (in the theophylline example, this uses all the simulated datasets)
Rd file 'virload.Rd':
\examples lines wider than 100 characters:
plot(Log_VL~Time,data=virload,xlab="Time (d)",ylab="Viral loads, base 10 logarithmic scale (cp/mL)")
plot(Log_VL~Time,data=virload50,xlab="Time (d)",ylab="Viral loads, base 10 logarithmic scale (cp/mL)")
These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/data/gannet/ripley/R/packages/tests-clang/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘stats’
All declared Imports should be used.
Packages in Depends field not imported from:
‘mclust’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/data/gannet/ripley/R/packages/tests-devel/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See 'd:/Rcompile/CRANpkg/local/3.5/npde.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Flavor: r-devel-windows-ix86+x86_64
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-devel-osx-x86_64
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-patched-linux-x86_64
Version: 2.0
Check: tests
Result: ERROR
Running ‘test_NpdeLib.R’ [8s/10s]
Running the tests in ‘tests/test_NpdeLib.R’ failed.
Complete output:
> library(npde)
Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Loading library npde, version 2.0, August 2012
please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
> cat("Running tests for the main computational functions\n")
Running tests for the main computational functions
>
> data(theopp)
> data(simtheopp)
>
> xbase1<-autonpde(namobs=theopp,namsim=simtheopp,boolsave=FALSE)
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.0668 (SE= 0.095 )
variance= 1.074 (SE= 0.14 )
skewness= 0.511
kurtosis= 0.2912
---------------------------------------------
Statistical tests
t-test : 0.481
Fisher variance test : 0.55
SW test of normality : 0.00273 **
Global adjusted p-value : 0.00819 **
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> # 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,decorr.method="cholesky", cens.method="omit",units=list(x="hr",y="mg/L"))
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.0668 (SE= 0.095 )
variance= 1.074 (SE= 0.14 )
skewness= 0.511
kurtosis= 0.2912
---------------------------------------------
Statistical tests
t-test : 0.481
Fisher variance test : 0.55
SW test of normality : 0.00273 **
Global adjusted p-value : 0.00819 **
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> # 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,decorr.method="inverse", cens.method="omit",units=list(x="hr",y="mg/L"))
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= -0.03046 (SE= 0.096 )
variance= 1.099 (SE= 0.14 )
skewness= 0.1654
kurtosis= 0.9206
---------------------------------------------
Statistical tests
t-test : 0.751
Fisher variance test : 0.435
SW test of normality : 0.000461 ***
Global adjusted p-value : 0.00138 **
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> 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")
Cholesky/inverse method: same pd, test successful
>
> ####### 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,decorr.method="cholesky",cens.method="omit")
---------------------------------------------
Distribution of npde :
nb of obs: 105
mean= 0.1126 (SE= 0.098 )
variance= 1.009 (SE= 0.14 )
skewness= 0.4966
kurtosis= 0.3645
---------------------------------------------
Statistical tests
t-test : 0.254
Fisher variance test : 0.911
SW test of normality : 0.0085 **
Global adjusted p-value : 0.0255 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> ##### 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,decorr.method="cholesky",cens.method="cdf")
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.1318 (SE= 0.095 )
variance= 1.077 (SE= 0.14 )
skewness= 0.5094
kurtosis= 0.02638
---------------------------------------------
Statistical tests
t-test : 0.167
Fisher variance test : 0.535
SW test of normality : 0.00415 **
Global adjusted p-value : 0.0125 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> ## 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,decorr.method="cholesky",cens.method="ipred")
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.2398 (SE= 0.1 )
variance= 1.246 (SE= 0.16 )
skewness= 0.5116
kurtosis= -0.17
---------------------------------------------
Statistical tests
t-test : 0.0203 *
Fisher variance test : 0.0712 .
SW test of normality : 0.000395 ***
Global adjusted p-value : 0.00118 **
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> ## 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,decorr.method="cholesky",cens.method="loq")
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.2463 (SE= 0.1 )
variance= 1.259 (SE= 0.16 )
skewness= 0.4722
kurtosis= -0.2501
---------------------------------------------
Statistical tests
t-test : 0.0177 *
Fisher variance test : 0.0587 .
SW test of normality : 0.000901 ***
Global adjusted p-value : 0.0027 **
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> ## 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,decorr.method="cholesky",cens.method="ypred")
Warning: Censoring method ypred unavailable, switching to default method (cdf)
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.07868 (SE= 0.097 )
variance= 1.121 (SE= 0.15 )
skewness= 0.4596
kurtosis= 0.1645
---------------------------------------------
Statistical tests
t-test : 0.417
Fisher variance test : 0.348
SW test of normality : 0.00547 **
Global adjusted p-value : 0.0164 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> # 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")
---------------------------------------------
Distribution of npde :
nb of obs: 105
mean= 0.1126 (SE= 0.098 )
variance= 1.009 (SE= 0.14 )
skewness= 0.4966
kurtosis= 0.3645
---------------------------------------------
Statistical tests
t-test : 0.254
Fisher variance test : 0.911
SW test of normality : 0.0085 **
Global adjusted p-value : 0.0255 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> xcens2.bis<-autonpde(namobs=dat3,namsim=simtheopp,iid=1,ix=3,iy=4, imdv=7,icens=8,icov=c(5,6),namsav="cens2.bis")
---------------------------------------------
Distribution of npde :
nb of obs: 120
mean= 0.09821 (SE= 0.098 )
variance= 1.155 (SE= 0.15 )
skewness= 0.4114
kurtosis= 0.05261
---------------------------------------------
Statistical tests
t-test : 0.319
Fisher variance test : 0.237
SW test of normality : 0.00355 **
Global adjusted p-value : 0.0107 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
---------------------------------------------
>
> 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")
Test with censoring successful
>
> cat("Testing gof.test function\n")
Testing gof.test function
>
> gof.test(xbase1)
Error in UseMethod("gof.test") :
no applicable method for 'gof.test' applied to an object of class "NpdeObject"
Calls: gof.test -> gof.test
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
See ‘/home/ripley/R/packages/tests32/npde.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Flavor: r-patched-solaris-x86