movetrack

movetrack is an R package that provides simple functionality to estimate individual flight tracks from radio-telemetry data such as Motus using a hidden Markov model written in Stan.

Installation

You can install movetrack from the R Universe with

install.packages("movetrack",
  repos = c("https://g-rppl.r-universe.dev", getOption("repos"))
)

To instead install the latest development version of the package from Codeberg use

devtools::install_git("https://codeberg.org/g-rppl/movetrack.git", ref = "dev")

During the initial installation, make sure that the C++ toolchain required for CmdStan is set up properly. You can find more information here.

library(cmdstanr)
check_cmdstan_toolchain(fix = TRUE)

If not, go to https://mc-stan.org/docs/cmdstan-guide/cmdstan-installation.html#cpp-toolchain and follow the instructions for your platform. Once your toolchain is configured correctly, CmdStan can be installed:

install_cmdstan(cores = 2)

Details

Automated radio-telemetry provides a scalable, lightweight tracking solution for mobile animals, but existing localisation methods rely solely on receiver locations or offer only small-scale, site-specific estimates, limiting their ability to reconstruct full flight paths. movetrack estimates full flight paths by combining coarse geometric position estimates---based on antenna bearing and signal strength---with an hidden Markov model that accounts for measurement error, temporal gaps, and movement dynamics. This two-step process is implemented in the main function track():

1. It first calculates point estimates based on antenna bearing and signal strength as described in Baldwin et al. (2018) (see vignette("raw_positions")).
2. The results are then passed to Stan and individual flights paths are estimated using a hidden Markov model (see vignette("hmm")).

You can find a quickstart example here: vignette("movetrack").

Citing movetrack and related software

When using movetrack, please cite the following publication:

Rüppel, G., Karwinkel, T., Brust, V., Schmaljohann, H. (2026). movetrack: An R package to model flight paths from radio-telemetry networks. Methods in Ecology and Evolution, 17(4), 1069--1081. doi: 10.1111/2041-210x.70273

As movetrack is a high-level interface to Stan, please additionally cite Stan (see https://mc-stan.org/users/citations).

A note about human.json

Instead of using pkgdown's default of adding LLM-readable files to the documentation, movetrack adopts the human.json protocol.

human.json is a lightweight protocol for humans to assert authorship of their site content and vouch for the humanity of others.

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

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

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