Package: prodlim 2024.06.24

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

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prodlim.pdf |prodlim.html✨
prodlim/json (API)

# 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:

12.21 score 7 stars 437 packages 956 scripts 154k downloads 27 mentions 40 exports 20 dependencies

Last updated 3 months agofrom:5f2292016f. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 17 2024
R-4.5-win-x86_64	NOTE	Nov 17 2024
R-4.5-linux-x86_64	NOTE	Nov 17 2024
R-4.4-win-x86_64	OK	Nov 17 2024
R-4.4-mac-x86_64	OK	Nov 17 2024
R-4.4-mac-aarch64	OK	Nov 17 2024
R-4.3-win-x86_64	OK	Nov 17 2024
R-4.3-mac-x86_64	OK	Nov 17 2024
R-4.3-mac-aarch64	OK	Nov 17 2024

Exports:atRisk backGround checkCauses confInt crModel dimColor EventHistory.frame getEvent getStates Hist jackknife jackknife.competing.risks jackknife.survival leaveOneOut leaveOneOut.competing.risks leaveOneOut.survival 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 strip.terms summary.prodlim survModel

Dependencies:cli codetools data.table diagram digest future future.apply globals KernSmooth lattice lava listenv Matrix numDeriv parallelly progressr Rcpp shape SQUAREM survival

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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
Extract a column from an event history object.	getEvent
States of a multi-state model	getStates
Create an event history response variable	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
Strip special functions from terms	strip.terms
Summary of event histories	summary.Hist
Summary method for prodlim objects.	summary.prodlim
Survival model for simulation	survModel