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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# <img src="PIRV2.png" width="120" align="right"/> PooledInfRate
PooledInfRate: Estimation from pooled or group testing.
Current version: 1.6
The website for this project is <https://github.com/CDCgov/PooledInfRate>.
PooledInfRate is an [R](www.r-project.org) package that includes functions to estimate proportions from pooled or group testing data. There is also functionality to estimate differences of such proportions. Finally, for entomologists, there is functionality to compute the so-called "Vector Index" used to quantify the level of pathogen in vector species, such as the amount of West Nile virus in a population of vector mosquitoes.
## Installation
You can install PooledInfRate from GitHub:
``` r
# To install from GitHub
# This will build on the fly, so you need *RTools* (available from CRAN)
Sys.setenv(R_QPDF="true") # to build the vignette during the package build
library(devtools) # need to install this if you do not have it
devtools::install_github("https://github.com/CDCgov/PooledInfRate",build_vignettes = TRUE)
```
For those on Microsoft Windows, the binary build for version #.# is available in the file list as PooledInfRate_#.#.zip, and you can download and install that instead of the build-install. The various versions are available for Windows, as stored here.
## Example
A couple of basic examples with contrived data:
```{r example}
library(PooledInfRate)
## basic example code
x <- c(1,0,0,0)
m <- c(50,25,10,5)
pooledBin(x,m)
pool.dat <- data.frame(Pos = c(1,1,0,0), PoolSize = c(100,50,25,10), NumPools = c(5,8,2,3))
pooledBin(Pos ~ PoolSize, data = pool.dat)
pIR(Pos ~ PoolSize + n(NumPools), data = pool.dat) # pIR is just a short name for 'pooledBin'
```
See the package vignette for detailed examples of the methods and user interface, along with references for the methods.
## Public Domain Standard Notice
This repository constitutes a work of the United States Government and is not
subject to domestic copyright protection under 17 USC § 105. This repository is in
the public domain within the United States, and copyright and related rights in
the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
All contributions to this repository will be released under the CC0 dedication. By
submitting a pull request you are agreeing to comply with this waiver of
copyright interest.
## License Standard Notice
The repository utilizes code licensed under the terms of the Apache Software
License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under
the terms of the Apache Software License version 2, or (at your option) any
later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this
program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
## Privacy Standard Notice
This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
[Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
## Contributing Standard Notice
Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)
and submitting a pull request. (If you are new to GitHub, you might start with a
[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
non-exclusive, transferable license to all users under the terms of the
[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
later.
All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
## Records Management Standard Notice
This repository is not a source of government records, but is a copy to increase
collaboration and collaborative potential. All government records will be
published through the [CDC web site](http://www.cdc.gov).
## Disclaimer
This package/application is provided without warranty of any kind.
While every effort has been made to ensure that that routines provide correct and accurate results, all responsibility for the use of the results belongs to the user.