casebase: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression

Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) <doi:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <doi:10.1111/sjos.12125>, and Saarela (2015) <doi:10.1007/s10985-015-9352-x>.

Version:	0.10.6
Depends:	R (≥ 3.5.0)
Imports:	data.table, ggplot2 (≥ 3.4.0), methods, mgcv, stats, survival, VGAM
Suggests:	colorspace, covr, dplyr, eha, glmnet, knitr, lubridate, progress, rmarkdown, splines, testthat (≥ 3.0.0), visreg
Published:	2024-08-17
DOI:	10.32614/CRAN.package.casebase
Author:	Sahir Bhatnagar [aut, cre] (https://sahirbhatnagar.com/), Maxime Turgeon [aut] (https://www.maxturgeon.ca/), Jesse Islam [aut] (https://www.jesseislam.com/), Olli Saarela [aut] (https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/), James Hanley [aut] (https://jhanley.biostat.mcgill.ca/)
Maintainer:	Sahir Bhatnagar <sahir.bhatnagar at gmail.com>
BugReports:	https://github.com/sahirbhatnagar/casebase/issues
License:	MIT + file LICENSE
URL:	https://sahirbhatnagar.com/casebase/
NeedsCompilation:	no
Citation:	casebase citation info
Materials:	README NEWS
In views:	Survival
CRAN checks:	casebase results

Documentation:

Reference manual:	casebase.pdf
Vignettes:	Competing risk analysis (source, R code) Customizing Population Time Plots (source, R code) Plot Cumulative Incidence and Survival Curves (source, R code) Plot Hazards and Hazard Ratios (source, R code) Population Time Plots (source, R code) Introduction to casebase sampling (source, R code) Time-Varying Covariates (source, R code)

Downloads:

Package source:	casebase_0.10.6.tar.gz
Windows binaries:	r-devel: casebase_0.10.6.zip, r-release: casebase_0.10.6.zip, r-oldrel: casebase_0.10.6.zip
macOS binaries:	r-release (arm64): casebase_0.10.6.tgz, r-oldrel (arm64): casebase_0.10.6.tgz, r-release (x86_64): casebase_0.10.6.tgz, r-oldrel (x86_64): casebase_0.10.6.tgz
Old sources:	casebase archive

Reverse dependencies:

Reverse suggests:

riskRegression

Linking:

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