Package: biostat3 0.2.2

biostat3: Utility Functions, Datasets and Extended Examples for Survival Analysis

Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".

Authors:Annika Tillander [ctb], Andreas Karlsson [aut], Johan Zetterqvist [ctb], Peter Strom [ctb], Benedicte Delcoigne [ctb], Mark Clements [aut, cre]

biostat3_0.2.2.tar.gz
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biostat3.pdf |biostat3.html✨
biostat3/json (API)

# Install 'biostat3' in R:
install.packages('biostat3', repos = c('https://mclements.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mclements/biostat3/issues

Datasets:
  • brv - Bereavement dataset
  • colon - Colon cancer dataset
  • colon_sample - Sample from the 'colon' dataset used for teaching.
  • diet - Diet data set
  • melanoma - Melanoma cancer dataset
  • popmort - Popmort dataset, with population-based mortality rates

On CRAN:

4.54 score 6 stars 145 scripts 899 downloads 1 mentions 36 exports 4 dependencies

Last updated 8 days agofrom:9a32f65e42. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 24 2025
R-4.5-winWARNINGJan 24 2025
R-4.5-linuxWARNINGJan 24 2025
R-4.4-winWARNINGJan 24 2025
R-4.4-macWARNINGJan 24 2025
R-4.3-winWARNINGJan 24 2025
R-4.3-macWARNINGJan 24 2025

Exports:addIndicatorsas.data.frame.bshazardas.data.frame.coxphHazas.data.frame.coxphHazListas.data.frame.muhazas.data.frame.muhazListcoxphHazeformeform.defaultformat_percggplot.muhazListirrlifetablifetab2lincomlines.coxphHazListlines.lifetab2lines.muhaz2lines.muhazListmuhaz2orplot.coxphHazplot.coxphHazListplot.lifetab2plot.muhaz2plot.muhazListplot.smoothHazpoints.lifetab2poisson.ciprint.coxphHazsmoothHazsummary.muhazListsurvPHplotsurvRateupdateListyear

Dependencies:latticeMASSMatrixsurvival

Readme and manuals

Help Manual

Help pageTopics
Utility Functions, Datasets and Extended Examples for Survival Analysisbiostat3-package biostat3
Utility to add indicators from a data-frame based on a formula.addIndicators
Functions to work with bshazard objects.as.data.frame.bshazard
Bereavement datasetbrv
Colon cancer datasetcolon
Sample from the 'colon' dataset used for teaching.colon_sample
Smoothed hazard estimates for 'coxph'as.data.frame.coxphHaz as.data.frame.coxphHazList coxphHaz lines.coxphHazList plot.coxphHaz plot.coxphHazList print.coxphHaz
Diet data setdiet
Calculate the exponential form for coefficients and their confidence intervals using either profile likelihood-based or Wald-based confidence intervals.eform eform.default irr or
Create cohort life tablelifetab
Formula wrapper for 'lifetab' from the 'KMsurv' package.lifetab2 lines.lifetab2 plot.lifetab2
Linear combination of regression parameters.lincom
Melanoma cancer datasetmelanoma
Formula wrapper for the 'muhaz' function from the 'muhaz' package.as.data.frame.muhaz as.data.frame.muhazList ggplot.muhazList lines.muhaz2 lines.muhazList muhaz2 plot.muhaz2 plot.muhazList summary.muhazList
Exact Poisson confidence intervals.poisson.ci
popmort dataset, with population-based mortality ratespopmort
Simple implementation for kernel density smoothing of the Nelson-Aalen estimator.plot.smoothHaz smoothHaz
Plot to assess non-proportionalitysurvPHplot
Describe ratessurvRate
Utility functions for the 'biostat3' packageformat_perc updateList
Convert a 'Date' vector to a numeric vectoryear