Package: prodlim 2025.03.03

prodlim: Product-Limit Estimation for Censored Event History Analysis

Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.

Authors:Thomas A. Gerds

# Install 'prodlim' in R:

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

Bug tracker:https://github.com/tagteam/prodlim/issues

On CRAN:prodlim-2024.06.25(2024-06-24)

12.18 score 7 stars 462 packages 1000 scripts 129k downloads 27 mentions 52 exports 45 dependencies

Last updated 4 days agofrom:d1a0ed131c. Checks:12 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 04 2025
R-4.5-win-x86_64	OK	Mar 04 2025
R-4.5-mac-x86_64	OK	Mar 04 2025
R-4.5-mac-aarch64	OK	Mar 04 2025
R-4.5-linux-x86_64	OK	Mar 04 2025
R-4.4-win-x86_64	OK	Mar 04 2025
R-4.4-mac-x86_64	OK	Mar 04 2025
R-4.4-mac-aarch64	OK	Mar 04 2025
R-4.4-linux-x86_64	OK	Mar 04 2025
R-4.3-win-x86_64	OK	Mar 04 2025
R-4.3-mac-x86_64	OK	Mar 04 2025
R-4.3-mac-aarch64	OK	Mar 04 2025

Exports:[.Hist as_tibble.prodlim as.data.frame.prodlim as.data.table.prodlim atRisk backGround checkCauses confInt crModel dimColor EventHistory.frame followup getEvent getStates ggprodlim head.Hist Hist is.na.Hist jackknife jackknife.competing.risks jackknife.survival leaveOneOut leaveOneOut.competing.risks leaveOneOut.survival lines.prodlim List2Matrix markTime meanNeighbors model.design neighborhood parseSpecialNames PercentAxis plot.Hist plot.prodlim plotCompetingRiskModel plotIllnessDeathModel predictSurvIndividual prodlim quantile.prodlim redist row.match SimCompRisk SimSurv sindex SmartControl stopTime str.Hist strip.terms subset.Hist summary.prodlim survModel tail.Hist

Dependencies:cli codetools colorspace data.table diagram digest fansi farver future future.apply ggplot2 globals glue gtable isoband KernSmooth labeling lattice lava lifecycle listenv magrittr MASS Matrix mgcv munsell nlme numDeriv parallelly pillar pkgconfig progressr R6 RColorBrewer Rcpp rlang scales shape SQUAREM survival tibble utf8 vctrs viridisLite withr

Citation

To cite package ‘prodlim’ in publications use:

Gerds TA (2025). prodlim: Product-Limit Estimation for Censored Event History Analysis. R package version 2025.03.03, https://github.com/tagteam/prodlim.

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.

Corresponding BibTeX entry:

  @Manual{,
    title = {prodlim: Product-Limit Estimation for Censored Event
      History Analysis},
    author = {Thomas A. Gerds},
    year = {2025},
    note = {R package version 2025.03.03},
    url = {https://github.com/tagteam/prodlim},
  }

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset an event history object	[.Hist
Turn prodlim objects into a 'tibble'	as_tibble.prodlim
Turn prodlim objects into a data.frame	as.data.frame.prodlim
Turn prodlim objects into a 'data.table'	as.data.table.prodlim
Drawing numbers of subjects at-risk of experiencing an event below Kaplan-Meier and Aalen-Johansen plots.	atRisk
Background and grid color control.	backGround
Check availability of a cause in competing risk settings	checkCauses
Add point-wise confidence limits to the graphs of Kaplan-Meier and Aalen-Johansen estimates.	confInt
Competing risks model for simulation	crModel
Dim a given color to a specified density	dimColor
Event history frame	EventHistory.frame
Estimation of the median potential followup time.	followup
Extract a column from an event history object.	getEvent
States of a multi-state model	getStates
ggplot2::ggplot support for Kaplan-Meier and Aalen-Johansen estimators	ggprodlim
Check the head of an event history object	head.Hist
Create an event history object	Hist
Check for missing values in event history object	is.na.Hist
Compute jackknife pseudo values.	jackknife jackknife.competing.risks jackknife.survival
Compute jackknife pseudo values.	leaveOneOut leaveOneOut.competing.risks leaveOneOut.survival
Reduce list to a matrix or data.frame with names as new columns	List2Matrix
Marking product-limit plots at the censored times.	markTime
Helper function to obtain running means for prodlim objects.	meanNeighbors
Extract a design matrix and specials from a model.frame	model.design
Nearest neighborhoods for kernel smoothing	neighborhood
Parse special terms	parseSpecialNames
Percentage-labeled axis.	PercentAxis
Box-arrow diagrams for multi-state models.	plot.Hist
Plotting event probabilities over time	lines.prodlim plot.prodlim
Plotting a competing-risk-model.	plotCompetingRiskModel
Plotting an illness-death-model.	plotIllnessDeathModel
Predicting event probabilities from product limit estimates	predict.prodlim predictAbsrisk predictCuminc predictSurv
Predict individual survival probabilities	predictSurvIndividual
Print objects in the prodlim library	print.Hist print.neighborhood print.prodlim
product limit method	prodlim
Quantiles for Kaplan-Meier and Aalen-Johansen estimates.	quantile.prodlim
Calculation of Efron's re-distribution to the right algorithm to obtain the Kaplan-Meier estimate.	redist
Identifying rows in a matrix or data.frame	row.match
Simulate competing risks data	SimCompRisk
Simulate survival data	SimSurv
Index for evaluation of step functions.	sindex
Function to facilitate the control of arguments passed to subroutines.	SmartControl
Stop the time of an event history object	stopTime
Check the structure of an event history object	str.Hist
Strip special functions from terms	strip.terms
Subset an event history object	subset.Hist
Summary of event histories	summary.Hist
Summary method for prodlim objects.	summary.prodlim
Survival model for simulation	survModel
Check the tail of an event history object	tail.Hist