README.md

In KevinSee/PITcleanr: Cleans up PIT tag capture histories

PITcleanr

Description

PITcleanr is an R package for preparing PIT tag data for further analysis. The package can help import complete tag histories from PTAGIS, 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 package for estimating abundance of returning anadromous adult fish moving upstream. PITcleanr was designed to prepare the raw PIT tag observations from PTAGIS 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.

Installation Instructions

The PITcleanr package can be installed as an R package from GitHub by using Hadley Wickham’s devtools package:

# install and load remotes, if necessary
install.packages("devtools")
remotes::install_github("KevinSee/PITcleanr", 
                         build_vignettes = TRUE)

devtools may require a working development environment. Further details around the installation of devtools can be found here.

• For Windows, that will involve the downloading and installation of Rtools. The latest version of Rtools can be found here.
• For Mac OS, that may involve installing Xcode from teh Mac App Store.
• For Linux, that may involve installing a compiler and various development libraries, depending on the specific version of Linux.

To install the latest development version of PITcleanr:

remotes::install_github("KevinSee/PITcleanr@develop")

Alternatively, the PITcleanr compendium can be downloaded as a zip file from from this URL: https://github.com/KevinSee/PITcleanr/archive/master.zip Once extracted, the functions can be sourced individually, or a user can build the R package locally.

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:

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

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. 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.

KevinSee/PITcleanr documentation built on Feb. 27, 2024, 11:03 p.m.