telemetyr is an R package to ease the burden of processing and interpreting oodles of telemetry observation data. More specifically, telemetyr aims to provide tools to simplify reading, cleaning, reduction, analysis, and visualization of telemetry observational data. The package is initially being developed as part of a radio telemetry project to characterize the distribution, movement, and survival of juvenile Chinook salmon emigrants in the Lemhi and Salmon rivers, Idaho, USA, during winter months. Currently, the package is written specific to radio telemetry data downloaded from NOAA receivers and using the Tracker software; however, the long-term goal is that functions and tools within telemetyr be developed further to accommodate any type of telemetry data (e.g. acoustic, radio, etc.) including from any type of receiver make or model.
At the writing of this README file, the package includes functionality to import, clean, and compress telemetry observations in preparation for analysis. Cleaned observations can then easily be turned into long- or wide-form capture histories which can then be used for data analysis and visualization. Some functions and documentation are also included to help the user run a Cormack-Jolly-Seber model in a Bayesian framework. We also include functions that can be used for perform simple telemetry site "diagnostics" including evaluations of site operation times, site "noise", and the like. Finally, functions are available to summarise and visualize movement, spatially and temporally, along a river network.
The authors hope to continue to develop telemetyr in the long-term and so any feedback on bugs, additional desired functionality, or similar are always appreciated. To report a bug, request features, report errors in documentation, etc. please visit the Issues page for the telemetyr package here and start a "New issue".
telemetyr requires the JAGS software (Just Another Gibbs Sampler). This can be downloaded here:
https://sourceforge.net/projects/mcmc-jags/files/
Please download version >= 4.0.0. You'll need to install JAGS before installing telemetyr.
To install the current working version of this package to your computer, you can use Hadley Wickham's devtools package. To install and load devtools (or any package for that matter) use:
install.packages("devtools")
library(devtools)
Once devtools is successfully installed, use the following to install telemetyr:
devtools::install_github("BiomarkABS/telemetyr", build_vignettes = TRUE)
Be sure to include the build_vignettes = TRUE argument, as this will ensure that vignettes included with the package will be built and made available.
Because the R packages rmarkdown and knitr are used to build this vignette to HTML output, you are required to have these installed to view vignettes available from this package. Both of these packages can be installed and loaded using the directions above for devtools. Vignettes can then be accessed using:
browseVignettes("telemetyr")
Alternatively, vignettes can be viewed in the Help menu using, for example:
vignette("Data_Prep", package = "telemetyr")
telemetyr currently includes the following vignettes:
*Data_Prep: Describes the importing, cleaning, and compression of telemetry observation data including instructions on how to generate capture histories in preparation for data analysis and visualization.
*Diagnostics: A vignette to describe how to perform various study "diagnostics" including evaluations of site/receiver operation times, site noise, tag battery life, and the like.
*CJS: Instructions on how to perform a Bayesian CJS model using wide form capture histories that can be build using the telemetyr package or otherwise.
A quick shout out to the postpack R package available here. The telemetyr package invokes postpack for working with the mcmc.list object resulting from the CJS model performed using JAGS. postpack should be installed with the telemetyr package, but can also be installed using:
devtools::install_github("bstaton1/postpack")
To use devtools you may also have to download and install Rtools. The latest version of Rtools can be found here.
If you are interested in making contributions to telemetyr, consider getting a GitHub account, fork this repository, clone to a local directory, modify, and send me a pull request. The authors can then review any changes and merge.
Please feel free to post an issue to this repository for requested features, bug fixes, errors in documentation, etc.
Text and figures : CC-BY-4.0
Code : See the DESCRIPTION file
Data : CC-0 attribution requested in reuse