README.md

In JimMcL/trajr: Animal Trajectory Analysis

trajr

Trajectory Analysis in R

An R package for analysing animal trajectories, which represent the movements of animals through space and time. It provides functions to easily calculate various quantitative measures of trajectories such as speed and straightness or tortuosity. It also provides a range of other trajectory operations such as resampling to fixed step lengths (rediscretization), determining turning angles and step lengths, and so on. While mainly focussed on 2-dimensional trajectories, trajr does have some functionality for analysing 3-dimensional trajectories. If you use trajr in your research, please cite McLean, D. J., & Skowron Volponi, M. A. (2018). trajr: An R package for characterisation of animal trajectories. Ethology, 124(6), 440-448. https://doi.org/10.1111/eth.12739.

trajr does not provide functionality to create trajectories; it operates on existing trajectories that are sequences of (x, y, time) coordinates. It does, however, provide some functionality to generate random or constrained trajectories for simulations or for testing of analyses.

Refer to NEWS.md for a list of changes in each version. The article trajr: An R package for characterisation of animal trajectories described trajr version 1.0.0. Please refer to NEWS.md for a brief summary of what has changed since the article was written.

Installation

$ install.packages("trajr")

Or to install the latest development version directly from Github:

$ install.packages("devtools")
$ devtools::install_github("JimMcL/trajr")

Or else, to install from Github and get the user documentation (vignette):

$ install.packages("devtools")
$ devtools::install_github("JimMcL/trajr", build_vignettes = TRUE)

Unfortunately, installing vignettes can be time-consuming.

Using trajr

The best way to start is to read our paper and the package vignette. After installation from CRAN (or from github including vignettes), the vignette can be accessed by running browseVignettes(package = "trajr"). The vignette for the CRAN version is available on CRAN at https://cran.r-project.org/web/packages/trajr/vignettes/trajr-vignette.html.

A vignette demonstrating trajectory simulation is available online at https://cran.r-project.org/web/packages/trajr/vignettes/simulations.html.

Environment

``` ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.2 (2022-10-31 ucrt) os Windows 10 x64 (build 22631) system x86_64, mingw32 ui RStudio language (EN) collate English_Australia.utf8 ctype English_Australia.utf8 tz Australia/Sydney date 2023-11-28 rstudio 2023.09.1+494 Desert Sunflower (desktop) pandoc 2.9.2.1 @ C:\Users\87054612\AppData\Local\Pandoc\pandoc.exe

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0) callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2) cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.2) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.2) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.2) digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.2) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.3) glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.2) htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.2) httpuv 1.6.8 2023-01-12 [1] CRAN (R 4.2.2) later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0) lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) MASS 7.3-58.1 2022-08-03 [2] CRAN (R 4.2.2) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) mime 0.12 2021-09-28 [1] CRAN (R 4.2.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.2) pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2) pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.2) profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.1) promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0) ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.2) purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.2) R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.2) remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0) rlang 1.1.0 2023-03-14 [1] CRAN (R 4.2.3) rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.2) signal 0.7-7 2021-05-25 [1] CRAN (R 4.2.0) stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.2) stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.2) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.2) usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.2) vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.2) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.2) ```

JimMcL/trajr documentation built on Jan. 31, 2024, 12:57 a.m.