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https://github.com/edwardlavender/patter-demo

R code supporting Lavender et al. (in prep). patter: particle algorithms for animal tracking in R and Julia.
https://github.com/edwardlavender/patter-demo

animal-tracking julia package particle-filter particle-smoother patter patter-jl r simulation two-filter-smoother

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R code supporting Lavender et al. (in prep). patter: particle algorithms for animal tracking in R and Julia.

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README 

        
---

title: A simple demonstration of the `patter` package

author: Edward Lavender*

output: github_document

---



^\*^This repository is maintained by Edward Lavender ([email protected]).



[![Project Status: Active -- The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)



# Introduction



This repository contains methods, written in [R](https://www.r-project.org/) and organised as an [RStudio](https://www.rstudio.com/) [Project](https://r4ds.had.co.nz/workflow-projects.html), for Lavender et al. (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.



# Description



## Dependencies



The 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`).



## Directories



The 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:



1.  **`renv/`** implements local dependency management.



2.  **`data/`** contains data:



    -   `spatial/` contains spatial datasets (sourced from [`patter-flapper`](https://github.com/edwardlavender/patter-flapper));

    -   `data.table/`, `filter/`, `smoother/`, `sim/` and `ud/` contain script outputs;

    -   `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):

        -   `dependencies.rds` is a list of dependencies;

        -   `session-info.rds` is a record of information about the `R` Session;

        -   `tree.rds` is a record of the project directory tree (as generated by `dv::use_template_tree()` in `dev/01-dev.R`, see below); 



4.  **`R/`** contains scripts for data preparation, simulation and analysis:



    -   `preparation.R` prepares spatial dataset(s);

    -   `workflow.R` simulates and analyses animal tracking datasets;

    -   `figs.R` produces manuscript figures;



5. **`src/`** contains helper (`R`) functions.



6. **`Julia/`** contains a `Julia` project.



    -   This is set up by `patter`;



7.  **`dev/`** contains project-management scripts.



    -   `01-dev.R` and `02-clone.R` are standard [`dv`](https://github.com/edwardlavender/dv) scripts:

        -   `01-dev.R` records project set up and development;

        -   `02-clone.R` is used to clone the project (see 'Instructions');



8.  **`fig/`** contains figures.



9.  **`doc/`** contains supporting documents.



Note that the `data/` (except `data/inst/`), `fig/` and `doc` directories are not provided in the online version of this repository.



# Instructions



Follow the steps described below to clone the project and reproduce the workflow.



1.  **Clone the project** via GitHub. Follow the instructions in `dev/02-clone.R` to install packages and directories:



    -   **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).

    -   **Directories.** Rebuild the project directory tree, via `dv::use_template_proj()` and `dv::use_template_tree()`.



2.  **Source (raw) data** via the links provided (or the authors).



3.  **Implement workflow** via `R` scripts. 



# Citation



Lavender et al. (in prep). `patter`: particle algorithms for animal tracking in `R` and `Julia.`



# Code of conduct



Please 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.



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