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graphPAF (version 1.0.0)

Estimating and Displaying Population Attributable Fractions

Description

Estimation and display of various types of population attributable fraction and impact fractions. As well as the usual calculations of attributable fractions and impact fractions, functions are provided for continuous exposures, for pathway specific population attributable fractions, and for joint, average and sequential population attributable fractions. See O'Connell and Ferguson (2022) , Ferguson et al. (2020) , Ferguson et al. (2019) , Ferguson et al. (2019) , as well the accompanying package vignette, for an overview of methods implemented.

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Version

Install

install.packages('graphPAF')

Monthly Downloads

262

Version

1.0.0

License

MIT + file LICENSE

Issues

4

Pull Requests

0

Stars

3

Forks

2

Maintainer

John Ferguson

Last Published

September 22nd, 2022

Functions in graphPAF (1.0.0)

data_clean

Clean a dataset to make modeling fitting more efficient
impact_fraction

General calculations of impact fractions
plot.PAF_q

Plot of impact fractions against over risk-quantile interventions for several risk factors
PAF_calc_continuous

Calculation of attributable fraction with a continuous risk factor
plot.SAF_summary

Produce plots of sequential and average PAF
joint_paf

Calculation of joint paf taking into account risk factor sequencing
automatic_fit

Automatic fitting models for Bayesian network.
Hordaland_data

Simulated case control dataset for 5000 cases (individuals with chronic cough) and 5000 controls
average_paf

Calculation of average and sequential paf taking into account risk factor sequencing
PAF_calc_discrete

Calculation of attributable fraction using a categorized risk factor
predict_df_continuous

Create a data frame for predictions (when risk factor is continuous).
print.SAF_summary

Print out SAF_summary object
ps_paf

Estimate Pathway specific population attributable fractions
print.PAF_q

Print out PAF_q for differing risk factors
seq_paf

Calculation of Sequential paf taking into account risk factor sequencing
plot_continuous

Plot hazard ratios, odds ratios or risk ratios comparing differing values of a continuous risk factor to a reference
risk_quantiles

Return the vector of risk quantiles for a continuous risk factor.
plot.rf.data.frame

Create a fan_plot of a rf.data.frame object
predict_df_discrete

Create a data frame for predictions (when risk factor is discrete).
rf_summary

Create a summary data frame for risk factors
stroke_reduced

Simulated case control dataset for 6856 stroke cases and 6856 stroke controls