https://github.com/g-rppl/movetrack
Model flight paths from radio-telemetry data using a hidden Markov model.
https://github.com/g-rppl/movetrack
hmm motus movement-ecology movement-modeling r random-walk stan telemetry
Last synced: 8 months ago
JSON representation
Model flight paths from radio-telemetry data using a hidden Markov model.
- Host: GitHub
- URL: https://github.com/g-rppl/movetrack
- Owner: g-rppl
- License: other
- Created: 2023-11-29T10:42:21.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2025-01-23T15:02:03.000Z (9 months ago)
- Last Synced: 2025-01-23T16:20:05.830Z (9 months ago)
- Topics: hmm, motus, movement-ecology, movement-modeling, r, random-walk, stan, telemetry
- Language: R
- Homepage: https://g-rppl.github.io/movetrack/
- Size: 9.75 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
# movetrack
[](https://github.com/g-rppl/movetrack/actions)
[](https://app.codecov.io/gh/g-rppl/movetrack)
[](https://g-rppl.r-universe.dev/movetrack)
[](https://github.com/g-rppl/movetrack/blob/main/LICENSE)
`movetrack` is an `R` package that provides simple functionality to estimate individual flight tracks from radio-telemetry data such as [Motus](https://motus.org/) using a hidden Markov model written in [Stan](https://mc-stan.org/).
## Installation
You can install `movetrack` from the R Universe with
```r
install.packages("movetrack", repos = c("https://g-rppl.r-universe.dev", getOption("repos")))
```
To instead install the latest development version of the package from GitHub use
```r
devtools::install_github("g-rppl/movetrack@dev")
```
During the initial installation, make sure that the C++ toolchain required for `CmdStan` is set up properly. You can find more information [here](https://mc-stan.org/cmdstanr/articles/cmdstanr.html).
```r
library(cmdstanr)
check_cmdstan_toolchain(fix = TRUE)
```
If not, go to and follow the instructions for your platform. Once your toolchain is configured correctly `CmdStan` can be installed:
```r
install_cmdstan(cores = 2)
```
## Details
This package provides two main functions: `locate()` and `track()`. The first function calculates location estimates based on antenna bearing and signal strength. The second function estimates individual flight paths based on the estimated locations using a hidden Markov model written in [Stan](https://mc-stan.org/).
## Getting started
You can find a quickstart example in the vignette [movetrack_example](https://g-rppl.github.io/movetrack/articles/movetrack_example.html).
## References
Auger‐Méthé, M., Newman, K., Cole, D., Empacher, F., Gryba, R., King, A. A., ... & Thomas, L. (2021). A guide to state–space modeling of ecological time series. *Ecological Monographs*, 91(4), e01470. doi: [10.1002/ecm.1470](https://doi.org/10.1002/ecm.1470)
Baldwin, J. W., Leap, K., Finn, J. T., & Smetzer, J. R. (2018). Bayesian state-space models reveal unobserved off-shore nocturnal migration from Motus data. *Ecological Modelling*, 386, 38-46. doi: [10.1016/j.ecolmodel.2018.08.006](https://doi.org/10.1016/j.ecolmodel.2018.08.006)
Jonsen, I. D., Flemming, J. M., & Myers, R. A. (2005). Robust state–space modeling of animal movement data. *Ecology*, 86(11), 2874-2880. doi: [10.1890/04-1852](https://doi.org/10.1890/04-1852)