Package: AF 0.1.5

Elisabeth Dahlqwist

AF: Model-Based Estimation of Confounder-Adjusted Attributable Fractions

Estimates the attributable fraction in different sampling designs adjusted for measured confounders using logistic regression (cross-sectional and case-control designs), conditional logistic regression (matched case-control design), Cox proportional hazard regression (cohort design with time-to- event outcome), gamma-frailty model with a Weibull baseline hazard and instrumental variables analysis. An exploration of the AF with a genetic exposure can be found in the package 'AFheritability' Dahlqwist E et al. (2019) <doi:10.1007/s00439-019-02006-8>.

Authors:Elisabeth Dahlqwist and Arvid Sjolander

AF_0.1.5.tar.gz
AF_0.1.5.tar.gz(r-4.5-noble)AF_0.1.5.tar.gz(r-4.4-noble)
AF_0.1.5.tgz(r-4.4-emscripten)AF_0.1.5.tgz(r-4.3-emscripten)
AF.pdf |AF.html✨
AF/json (API)

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

Peer review:

Datasets:
  • clslowbwt - Birthweight data clustered on the mother.
  • rott2 - Cohort study on breast cancer patients from the Netherlands.
  • singapore - Case-control study on oesophageal cancer in Chinese Singapore men.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.40 score 25 scripts 478 downloads 106 mentions 8 exports 12 dependencies

Last updated 6 years agofrom:05fa5acf22. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-linuxOKOct 28 2024

Exports:AF.ccAF.chAF.csAFclogitAFcoxphAFglmAFivglmAFparfrailty

Dependencies:ahazdata.tabledrgeeivtoolslatticeMatrixnleqslvnumDerivRcppRcppArmadillostdRegsurvival

Readme and manuals

Help Manual

Help pageTopics
Attributable fraction for mached and non-matched case-control sampling designs. NOTE! Deprecated function. Use 'AFglm' (for unmatched case-control studies) or 'AFclogit' (for matched case-control studies).AF.cc
Attributable fraction function for cohort sampling designs with time-to-event outcomes. NOTE! Deprecated function. Use 'AFcoxph'.AF.ch
Attributable fraction for cross-sectional sampling designs. NOTE! Deprecated function. Use 'AFglm'.AF.cs
Attributable fraction estimation based on a conditional logistic regression model as a 'clogit' object (commonly used for matched case-control sampling designs).AFclogit
Attributable fraction function based on a Cox Proportional Hazard regression model as a 'coxph' object (commonly used for cohort sampling designs with time-to-event outcomes).AFcoxph
Attributable fraction estimation based on a logistic regression model from a 'glm' object (commonly used for cross-sectional or case-control sampling designs).AFglm
Attributable fraction function based on Instrumental Variables (IV) regression as an 'ivglm' object in the 'ivtools' package.AFivglm
Attributable fraction function based on a Weibull gamma-frailty model as a 'parfrailty' object (commonly used for cohort sampling family designs with time-to-event outcomes).AFparfrailty
Birthweight data clustered on the mother.clslowbwt
Plot function for objects of class "'AF'" from the function 'AFcoxph' or 'AFparfrailty'.plot.AF
Cohort study on breast cancer patients from the Netherlands.rott2
Case-control study on oesophageal cancer in Chinese Singapore men.singapore
Summary function for objects of class "'AF'".summary.AF