Requires sdtemple/pblas as well.
remotes::install_github("sdtemple/pblas")
remotes::install_github("sdtemple/peirrs")
library(peirrs)
library(pblas)
This package has no dependencies on other packages. You likely can use any version of R 3+ or R 4+.
I developed the package with versions:
- R 4.1+
Estimate infection and removal rates with partially observed removal and infection times. The following functions are the ones you would likely use, in order of relevance:
- Real data analysis
peirr_tau()peirr_bayes()peirr_pbla_infection_rate()peirr_bootstrap()
- Simulation experiments
simulator()
All functions have docstrings. As a result, you can get help for instance with:
help(peirr_tau)
?peirr_tau
There are also functions with the suffixes *_multitype() and *_spatial() for estimators with multiple classes and spatial kernels, respectively.
The peirr_bootstrap() function does not provide confidence intervals but rather bootstrap samples. You can perform bias correction or interval estimation according to Wikipedia.
Some of the scripts for my analyses are under scripts/. These may provide examples of how to run the functions.
The function tau_moment() calculates the complicated equations derived in our paper. It is not meant for users but invoked in the estimator functions.
