{"id":15057219,"url":"https://github.com/edwardlavender/patter-demo","last_synced_at":"2026-02-16T08:32:26.916Z","repository":{"id":248903311,"uuid":"807627147","full_name":"edwardlavender/patter-demo","owner":"edwardlavender","description":"R code supporting Lavender et al. (2025). patter: particle algorithms for animal tracking in R and Julia. 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(in prep). `patter`: particle algorithms for animal tracking in `R` and `Julia`. In this project, we simulate animal tracking data and apply particle filtering and smoothing algorithms to reconstruct patterns of space use. The code forms a basic worked example of the `patter` `R` package.\n\n# Description\n\n## Dependencies\n\nThe project was built in [R](https://www.r-project.org/) (version `r paste0(version$major, \".\", version$minor)`) in [RStudio](https://www.rstudio.com/) and implements local dependency management using [`renv`](https://rstudio.github.io/renv/articles/renv.html). This manages the installation of the [`dv`](https://github.com/edwardlavender/dv) package (from [GitHub](https://github.com/)), as well as other packages from the [Comprehensive R Archive Network](https://cran.r-project.org/). The first time the project is opened, [`renv`](https://rstudio.github.io/renv/articles/renv.html) can be used to regenerate the local project library, as described in `renv.lock` (via `.Rprofile` and `renv/activate.R`).\n\n## Directories\n\nThe project follows a standardised structure encouraged by the [`dv`](https://github.com/edwardlavender/dv) package. The high-level structure was generated via `dv::use_template_proj()`. The contents as follows:\n\n1.  **`renv/`** implements local dependency management.\n\n2.  **`data/`** contains data:\n\n    -   `spatial/` contains spatial datasets (sourced from [`patter-flapper`](https://github.com/edwardlavender/patter-flapper));\n    -   `data.table/`, `filter/`, `smoother/`, `sim/` and `ud/` contain script outputs;\n    -   `inst/` contains [RStudio](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html)-management files generated by [`dv`](https://github.com/edwardlavender/dv):\n        -   `dependencies.rds` is a list of dependencies;\n        -   `session-info.rds` is a record of information about the `R` Session;\n        -   `tree.rds` is a record of the project directory tree (as generated by `dv::use_template_tree()` in `dev/01-dev.R`, see below); \u003cbr/\u003e\n\n4.  **`R/`** contains scripts for data preparation, simulation and analysis:\n\n    -   `preparation.R` prepares spatial dataset(s);\n    -   `workflow.R` simulates and analyses animal tracking datasets;\n    -   `figs.R` produces manuscript figures;\n\n5. **`src/`** contains helper (`R`) functions.\n\n6. **`Julia/`** contains a `Julia` project.\n\n    -   This is set up by `patter`;\n\n7.  **`dev/`** contains project-management scripts.\n\n    -   `01-dev.R` and `02-clone.R` are standard [`dv`](https://github.com/edwardlavender/dv) scripts:\n        -   `01-dev.R` records project set up and development;\n        -   `02-clone.R` is used to clone the project (see 'Instructions');\n\n8.  **`fig/`** contains figures.\n\n9.  **`doc/`** contains supporting documents.\n\nNote that the `data/` (except `data/inst/`), `fig/` and `doc` directories are not provided in the online version of this repository.\n\n# Instructions\n\nFollow the steps described below to clone the project and reproduce the workflow.\n\n1.  **Clone the project** via GitHub. Follow the instructions in `dev/02-clone.R` to install packages and directories:\n\n    -   **Packages.** Work through `dev/02-clone.R` to use [`renv`](https://rstudio.github.io/renv/articles/renv.html) to regenerate the local project library. Packages can also be manually reinstalled via `02-clone.R`. If required, `patter` is available [here](https://github.com/edwardlavender/patter).\n    -   **Directories.** Rebuild the project directory tree, via `dv::use_template_proj()` and `dv::use_template_tree()`.\n\n2.  **Source (raw) data** via the links provided (or the authors).\n\n3.  **Implement workflow** via `R` scripts. \n\n# Citation\n\nLavender et al. (2025). `patter`: particle algorithms for animal tracking in `R` and `Julia.` Methods in Ecology and Evolution, 00, 1–8. https://doi.org/10.1111/2041-210X.70029\n\n# Code of conduct\n\nPlease note that this project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n------------------------------------------------------------------------\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedwardlavender%2Fpatter-demo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fedwardlavender%2Fpatter-demo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fedwardlavender%2Fpatter-demo/lists"}