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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, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
# Please put your title here to include it in the file below.
Title <- "Title of your paper goes here"
```
# PITcleanr <a href='https://github.com/KevinSee/PITcleanr'><img src='man/figures/logo.png' align="right" width="110" /></a>
<!-- badges: start -->
[](https://mybinder.org/v2/gh/KevinSee/PITcleanr/master?urlpath=rstudio)
<!-- badges: end -->
## Description
`PITcleanr` is an R package for preparing PIT tag data for further analysis. The package can help import complete tag histories from [PTAGIS](https://www.ptagis.org/), build a configuration file to help assign each detection to a "node", and compress those detections into a smaller file. It contains functions to determine which detection locations are upstream or downstream of each other, build a parent-child relationship table describing whether detection locations are upstream or downstream in relation to each other, and assign directionality of movement between each detection location. For analyses that focus on one-way directional movement (e.g., straightforward CJS models), `PITcleanr` can help determine which detections fail to meet that one-way movement assumption and should be examined more closely, and which detections can be kept.
It was originally conceived as a companion to the [DABOM](https://github.com/KevinSee/DABOM) package for estimating abundance of returning anadromous adult fish moving upstream. `PITcleanr` was designed to prepare the raw PIT tag observations from [PTAGIS](https://www.ptagis.org/) for use in the `DABOM` package.
***The user can find more information related to installation and use of this package on the [package website](https://kevinsee.github.io/PITcleanr/), https://kevinsee.github.io/PITcleanr.***
## Installation Instructions
```{r child = "vignettes/child_docs/_install-inst.Rmd"}
```
Be sure to use the `build_vignettes = TRUE` argument, as this will build all of the vignettes (i.e., user manuals) that are included with the package. Further instructions on how to use `PITcleanr` can be found in the vignettes, which can be accessed using:
```{r, eval = F}
browseVignettes(package = "PITcleanr")
```
## Authors
PITcleanr is a collaborative project, with the primary contributors being:
* Kevin See (Washington Department of Fish & Wildlife)
* Ryan N. Kinzer (Nez Perce Tribe - Fisheries Resources Management)
* Rick Orme (Nez Perce Tribe - Fisheries Resources Management)
* Mike Ackerman (Nez Perce Tribe - Fisheries Resources Management)
### Licenses
**Text and figures :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)
**Code :** See the [DESCRIPTION](DESCRIPTION) file
**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
### Contributions
We welcome contributions from everyone. Before you get started, please see our [contributor guidelines](CONTRIBUTING.md). Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
## Questions?
Please feel free to post an issue to this repository for requested features, bug fixes, errors in documentation, etc.