Package: peperr 1.7

peperr: Parallelised Estimation of Prediction Error

Designed for prediction error estimation through resampling techniques, possibly accelerated by parallel execution on a compute cluster. Newly developed model fitting routines can be easily incorporated. Methods used in the package are detailed in Porzelius Ch., Binder H. and Schumacher M. (2009) <doi:10.1093/bioinformatics/btp062> and were used, for instance, in Porzelius Ch., Schumacher M. and Binder H. (2011) <doi:10.1007/s00180-011-0236-6>.

Authors:Christine Porzelius [aut], Harald Binder [aut], Frederic Bertrand [cre]

peperr_1.7.tar.gz
peperr_1.7.zip(r-4.7)peperr_1.7.zip(r-4.6)peperr_1.7.zip(r-4.5)
peperr_1.7.tgz(r-4.6-x86_64)peperr_1.7.tgz(r-4.6-arm64)peperr_1.7.tgz(r-4.5-x86_64)peperr_1.7.tgz(r-4.5-arm64)
peperr_1.7.tar.gz(r-4.7-arm64)peperr_1.7.tar.gz(r-4.7-x86_64)peperr_1.7.tar.gz(r-4.6-arm64)peperr_1.7.tar.gz(r-4.6-x86_64)
peperr_1.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
peperr/json (API)
NEWS

# Install 'peperr' in R:
install.packages('peperr', repos = c('https://fbertran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fbertran/peperr/issues

Pkgdown/docs site:https://fbertran.github.io

On CRAN:

Conda:

5.02 score 2 stars 1 packages 29 scripts 782 downloads 4 mentions 52 exports 5 dependencies

Last updated from:049242a6ad. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK147
linux-devel-x86_64OK159
source / vignettesOK199
linux-release-arm64OK141
linux-release-x86_64OK143
macos-release-arm64OK86
macos-release-x86_64OK200
macos-oldrel-arm64OK81
macos-oldrel-x86_64OK184
windows-develOK127
windows-releaseOK131
windows-oldrelOK108
wasm-releaseOK115

Exports:aggregation.brieraggregation.misclassaggregation.pmpeccomplexity.cv.glmnetcomplexity.cv.grpsurvcomplexity.cv.ncvsurvcomplexity.cv.penalizedcomplexity.cvrisk.mboostcomplexity.cvSGL.coxcomplexity.fusedLASSOcomplexity.ipec.CoxBoostcomplexity.LASSOcomplexity.mincv.CoxBoostcomplexity.oob.rfsrccomplexity.ripec.CoxBoostextract.funfit.CoxBoostfit.coxphfit.fusedLASSOfit.glmnetfit.grpsurvfit.LASSOfit.mboost.coxphfit.ncvsurvfit.penalizedfit.rfsrcfit.SGL.coxipecpeperrperrPLLPLL.CoxBoostPLL.coxnetPLL.coxphPLL.grpsurvPLL.mboost_coxphPLL.ncvsurvPLL.penfitPLL.SGL_coxpmpecpredictProbpredictProb.CoxBoostpredictProb.coxnetpredictProb.coxphpredictProb.grpsurvpredictProb.mboost_coxphpredictProb.ncvsurvpredictProb.penfitpredictProb.rfsrcpredictProb.SGL_coxpredictProb.survfitresample.indices

Dependencies:latticeMatrixsnowsnowfallsurvival

Readme and manuals

Help Manual

Help pageTopics
Determine the Brier score for a fitted modelaggregation.brier
Determine the missclassification rate for a fitted modelaggregation.misclass
Determine the prediction error curve for a fitted modelaggregation.pmpec
Complexity selection helpers for penalized backendscomplexity.cv.penalized complexity.fusedLASSO complexity.LASSO
Interface function for CoxBoost complexity selection via integrated prediction error curvescomplexity.ipec.CoxBoost complexity.ripec.CoxBoost
Interface for CoxBoost selection of the optimal number of boosting steps via cross-validationcomplexity.mincv.CoxBoost
Extract functions, libraries and global variables to be loaded onto a compute clusterextract.fun
Interface function for fitting a CoxBoost modelfit.CoxBoost
Interface function for fitting a Cox proportional hazards modelfit.coxph
glmnet Cox backendcomplexity.cv.glmnet fit.glmnet PLL.coxnet predictProb.coxnet
grpreg grouped Cox backendcomplexity.cv.grpsurv fit.grpsurv PLL.grpsurv predictProb.grpsurv
mboost Cox backendcomplexity.cvrisk.mboost fit.mboost.coxph PLL.mboost_coxph predictProb.mboost_coxph
ncvreg survival backendcomplexity.cv.ncvsurv fit.ncvsurv PLL.ncvsurv predictProb.ncvsurv
Penalized backend fitting wrappersfit.fusedLASSO fit.LASSO fit.penalized
randomForestSRC survival backendcomplexity.oob.rfsrc fit.rfsrc predictProb.rfsrc
Sparse-group-lasso Cox backendcomplexity.cvSGL.cox fit.SGL.cox PLL.SGL_cox predictProb.SGL_cox
Integrated prediction error curveipec
Parallelised Estimation of Prediction Errorpeperr
Prediction error estimatesperr
Generic function for extracting the predictive partial log-likelihoodPLL
Predictive partial log-likelihood for a CoxBoost model fitPLL.CoxBoost
Predictive partial log-likelihood for Cox poportional hazards modelPLL.coxph
Predictive partial log-likelihood for penalized Cox modelsPLL.penfit
Plot method for peperr objectplot.peperr
Calculate prediction error curvespmpec
Generic function for extracting predicted survival probabilitiespredictProb
Extract predicted survival probabilities from a CoxBoost fitpredictProb.CoxBoost
Extract predicted survival probabilities from a coxph objectpredictProb.coxph
Predicted survival probabilities for penalized Cox modelspredictProb.penfit
Extract predicted survival probabilities from a survfit objectpredictProb.survfit
Generation of indices for resampling Procedureresample.indices