Package: survcomp 1.63.0

Benjamin Haibe-Kains

survcomp: Performance Assessment and Comparison for Survival Analysis

Assessment and Comparison for Performance of Risk Prediction (Survival) Models.

Authors:Benjamin Haibe-Kains [aut, cre], Markus Schroeder [aut], Catharina Olsen [aut], Christos Sotiriou [aut], Gianluca Bontempi [aut], John Quackenbush [aut], Samuel Branders [aut], Zhaleh Safikhani [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
survcomp/json (API)

# Install 'survcomp' in R:

install.packages('survcomp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

mainz7g - Subset of MAINZ dataset containing gene expression, annotations and clinical data.
nki7g - Subset of NKI dataset containing gene expression, annotations and clinical data.
transbig7g - Subset of the TRANSBIG dataset containing gene expression, annotations and clinical data.
unt7g - Subset of UNT dataset containing gene expression, annotations and clinical data.
upp7g - Subset of UPP dataset containing gene expression, annotations and clinical data.
vdx7g - Subset of VDX dataset containing gene expression, annotations and clinical data.

On BioConductor:survcomp-1.63.0(bioc 3.24)survcomp-1.62.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression differentialexpression visualization cpp

8.63 score 14 packages 508 scripts 117 mentions 37 exports 46 dependencies

Last updated from:650331a141. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	158
linux-devel-arm64	NOTE	164
linux-devel-x86_64	NOTE	231
source / vignettes	OK	198
linux-release-arm64	NOTE	180
linux-release-x86_64	NOTE	248
macos-release-arm64	NOTE	114
macos-release-x86_64	NOTE	336
macos-oldrel-arm64	NOTE	135
macos-oldrel-x86_64	NOTE	225
windows-devel	NOTE	138
windows-release	NOTE	123
windows-oldrel	NOTE	127
wasm-release	OK	122

Exports:balanced.hazard.ratio bhr.comp censor.time cindex.comp cindex.comp.meta combine.est combine.test concordance.index concordanceIndexC cvpl D.index dindex.comp dindex.comp.meta fisherz forestplot.surv get_concordanceIndex_onevariable getsurv2 hazard.ratio hr.comp hr.comp.meta hr.comp2 iauc.comp ibsc.comp km.coxph.plot logpl metaplot.surv mrmr_cIndex mrmr_cIndex_ensemble_remove mrmr.cindex mrmr.cindex.ensemble no.at.risk sbrier.score2proba score2proba td.sens.spec tdrocc test.hetero.est test.hetero.test

Dependencies:bootstrap class cli codetools cpp11 data.table diagram digest farver future future.apply ggplot2 globals glue gtable ipred isoband KernSmooth labeling lattice lava lifecycle listenv MASS Matrix nnet numDeriv parallelly prodlim progressr R6 RColorBrewer Rcpp rlang rmeta rpart S7 scales shape SQUAREM SuppDists survival survivalROC vctrs viridisLite withr

SurvComp: a package for performance assessment and comparison for survival analysis

Introduction | A use case: from expression data to survival analysis | Session Info | Functions within SurvComp

Rendered fromsurvcomp.Rnwusingutils::Sweave

Last update: 2020-01-31
Started: 2014-08-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Performance Assessment and Comparison for Survival Analysis	survcomp-package survcomp
Function to estimate the balanced hazard ratio through Cox regression	balanced.hazard.ratio
Function to statistically compare two balanced hazard ratios	bhr.comp
Sample data containing six datasets for gene expression, annotations and clinical data.	breastCancerData
Function to artificially censor survival data	censor.time
Function to compare two concordance indices	cindex.comp
Function to compare two concordance indices	cindex.comp.meta
Function to combine estimates	combine.est
Function to combine probabilities	combine.test
Function to compute the concordance index for survival or binary class prediction	concordance.index
Concordance index C	concordanceIndexC
Function to compute the CVPL	cvpl
Function to compute the D index	D.index
Function to compare two D indices	dindex.comp
Function to compare two D indices	dindex.comp.meta
Function to compute Fisher z transformation	fisherz
Forest plots enables to display performance estimates of survival models	forestplot.surv
Get concordance index	get_concordanceIndex_onevariable
Function to retrieve the survival probabilities at a specific point in time	getsurv2
Function to estimate the hazard ratio through Cox regression	hazard.ratio
Function to statistically compare two hazard ratios	hr.comp
Function to compare two concordance indices	hr.comp.meta
Function to statistically compare two hazard ratios (alternative interface)	hr.comp2
Function to compare two IAUCs through time-dependent ROC curves	iauc.comp
Function to compare two IBSCs	ibsc.comp
Function to plot several Kaplan-Meier survival curves	km.coxph.plot
Function to compute the log partial likelihood of a Cox model	logpl
Subset of MAINZ dataset containing gene expression, annotations and clinical data.	mainz7g
Meta-analysis plot (forest plot)	metaplot.surv
mRMR cIndex	mrmr_cIndex
mRMR cIndex Ensemble Remove	mrmr_cIndex_ensemble_remove
Function to compute the concordance index for survival or binary class prediction	mrmr.cindex
Function to compute the concordance index for survival or binary class prediction	mrmr.cindex.ensemble
Subset of NKI dataset containing gene expression, annotations and clinical data.	nki7g
Function to compute the number of individuals at risk	no.at.risk
Function to compute the BSCs from a risk score, for all the times of event occurrence	sbrier.score2proba
Function to compute the survival probabilities from a risk score	score2proba
Function to compute sensitivity and specificity for a binary classification of survival data	td.sens.spec
Function to compute time-dependent ROC curves	tdrocc
Function to test the heterogeneity of set of probabilities	test.hetero.est
Function to test the heterogeneity of set of probabilities	test.hetero.test
Subset of the TRANSBIG dataset containing gene expression, annotations and clinical data.	transbig7g
Subset of UNT dataset containing gene expression, annotations and clinical data.	unt7g
Subset of UPP dataset containing gene expression, annotations and clinical data.	upp7g
Subset of VDX dataset containing gene expression, annotations and clinical data.	vdx7g