Package: survivalSL 0.96

survivalSL: Super Learner for Survival Prediction from Censored Data

Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.

Authors:Yohann Foucher [aut, cre], Camille Sabathe [aut]

survivalSL_0.96.tar.gz
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survivalSL.pdf |survivalSL.html✨
survivalSL/json (API)

# Install 'survivalSL' in R:

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

Bug tracker:https://github.com/foucher-y/survivalsl/issues

Datasets:

dataDIVAT2 - A Sample from the DIVAT Data Bank.
dataDIVAT3 - A Sample from the DIVAT Data Bank.
dataOFSEP - A Simulated Sample from the OFSEP Cohort.

On CRAN:

27 exports 1.33 score 134 dependencies 229 downloads

Last updated 22 days agofrom:77c0b72870. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 26 2024
R-4.5-win	OK	Aug 26 2024
R-4.5-linux	OK	Aug 26 2024
R-4.4-win	OK	Aug 26 2024
R-4.4-mac	OK	Aug 26 2024
R-4.3-win	OK	Aug 26 2024
R-4.3-mac	OK	Aug 26 2024

Exports:LIB_AFTgamma LIB_AFTggamma LIB_AFTllogis LIB_AFTweibull LIB_COXaic LIB_COXall LIB_COXen LIB_COXlasso LIB_COXridge LIB_PHexponential LIB_PHgompertz LIB_PHspline LIB_PLANN LIB_RSF LIB_SNN metrics plot.libsl roc survivalSL tuneCOXaic tuneCOXen tuneCOXlasso tuneCOXridge tunePHspline tunePLANN tuneRSF tuneSNN

Dependencies:assertthat base64enc bbmle bdsmatrix BH bit bit64 bslib cachem caret class cli clipr clock codetools colorspace cpp11 crayon data.table data.tree date deSolve diagram DiagrammeR digest dplyr e1071 evaluate fansi farver fastGHQuad fastmap flexsurv fontawesome foreach fs future future.apply generics ggplot2 glmnet glmnetUtils globals glue gower gridExtra gtable hardhat hdnom highr hms htmltools htmlwidgets igraph ipred isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix memoise mgcv mime ModelMetrics mstate muhaz munsell mvtnorm ncvreg nlme nnet numDeriv parallelly penalized pillar pkgconfig plyr prettyunits pROC prodlim progress progressr proxy purrr quadprog R6 randomForestSRC rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr recipes reshape2 rlang rmarkdown rpart rstpm2 rstudioapi sass scales shape SQUAREM statmod stringi stringr survival survivalPLANN tibble tidyr tidyselect timechange timeDate tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A Sample from the DIVAT Data Bank.	dataDIVAT2
A Sample from the DIVAT Data Bank.	dataDIVAT3
A Simulated Sample from the OFSEP Cohort.	dataOFSEP
Library of the Super Learner for an Accelerated Failure Time (AFT) Model with a Gamma Distribution	LIB_AFTgamma
Library of the Super Learner for an Accelerated Failure Time (AFT) Model with a Generalized Gamma Distribution	LIB_AFTggamma
Library of the Super Learner for an Accelerated Failure Time (AFT) Model with a Log Logistic Distribution	LIB_AFTllogis
Library of the Super Learner for an Accelerated Failure Time (AFT) Model with a Weibull Distribution	LIB_AFTweibull
Library of the Super Learner for a Cox Model with Selected Covariates	LIB_COXaic
Library of the Super Learner for Cox Regression	LIB_COXall
Library of the Super Learner for Elastic Net Cox Regression	LIB_COXen
Library of the Super Learner for Lasso Cox Regression	LIB_COXlasso
Library of the Super Learner for Ridge Cox Regression	LIB_COXridge
Library of the Super Learner for a Proportional Hazards (PH) Model with an Exponential Distribution	LIB_PHexponential
Library of the Super Learner for an Proportional Hazards (PH) Model with a Gompertz Distribution	LIB_PHgompertz
Library of the Super Learner for an Survival Regression using the Royston/Parmar Spline Model	LIB_PHspline
Library of the Super Learner for Survival Neural Network Based on the PLANN Method	LIB_PLANN
Library of the Super Learner for Survival Random Survival Forest	LIB_RSF
Library of the Super Learner for Survival Neural Network	LIB_SNN
Metrics to Evaluate the Prognostic Capacities	metrics
Calibration Plot for a Cox-like Model	plot.libsl
Plot Method for 'rocrisca' Objects	plot.rocrisca
Calibration Plot for Super Learner	plot.sltime
Prediction from an Flexible Parametric Model	predict.libsl
Prediction from a Super Learner for Censored Outcomes	predict.sltime
S3 Method for Printing an 'libsl' Object	print.libsl
S3 Method for Printing an 'sltime' Object	print.sltime
Time-Dependent ROC Curves With Right Censored Data	roc
Summaries of a Learner	summary.libsl
Summaries of a Super Learner	summary.sltime
Super Learner for Censored Outcomes	survivalSL
Tune a Cox Model with a Forward Selection Based on the AIC	tuneCOXaic
Tune Elastic Net Cox Regression	tuneCOXen
Tune Lasso Cox Regression	tuneCOXlasso
Tune Ridge Cox Regression	tuneCOXridge
Tune a Survival Regression using the Royston/Parmar Spline Model	tunePHspline
Tune a Survival Neural Network Based on the PLANN Method	tunePLANN
Tune a Survival Random Forest	tuneRSF
Tune a 1-Layer Survival Neural Network	tuneSNN