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https://github.com/pratikunterwegs/atlas-best-practices

Source code for a paper on pre-processing high frequency animal tracking data.
https://github.com/pratikunterwegs/atlas-best-practices

animal-movement movement-ecology pre-processing r-package

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Source code for a paper on pre-processing high frequency animal tracking data.

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# Source Code and Supplementary Material for: _A Guide to Pre-processing High-throughput Animal Tracking Data_



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This is source code for a manuscript that sets out a pipeline for pre-processing data from ATLAS systems, but which can be applied to any high-throughput tracking data.



## [Readable, Online Version of Worked-out Examples](https://pratikunterwegs.github.io/atlas-best-practices/validating-the-residence-patch-method-with-calibration-data.html)



The worked out examples mentioned in the manuscript and provided in the supplementary material as a PDF, can also be found hosted on Github Pages in its online version, here: [Online Version of Worked-out Examples](https://pratikunterwegs.github.io/atlas-best-practices/validating-the-residence-patch-method-with-calibration-data.html).



## Source Code for Figures and Analyses



Most of the source code may be found in the folder `scripts`, with numbers indicating the order in which it is to be run.

This source code (for figures 7 and 8) is partially generated from the `.Rmd` files in the directory `supplement` using `knitr::purl`.

See the `render_books.sh` file for details of the conversion from `.Rmd` to `.R`.



### renv/



Settings to store and restore the R packages to the versions used in this project.



### scripts/



- 01_background.R: Simulating data using the `R` package `smoove` for the section _Pipeline Overview, Getting `atlastools`, and Simulating Data_.

Simulated data is saved into the `data` folder as `data_sim.csv` (uniform correlated velocity model data), and `data_for_patch.csv` (three rotational/advection correlated velocity model datasets). 

No seed was set for `data_sim.csv`, but `data_for_res_patch.csv` was generated using a set seed.



- 02_filtering_data.R: Source code for figures that support the sections _Spatio-Temporal Filtering_ and _Filtering to Reduce Location Errors_.

Also adds error to the UCVM dataset (`data_sim.csv`) using functions defined in `R/helper_functions.R`.

Makes Figures 2 -- 3.

Writes cleaned data to `data/data_no_reflections.csv`.



- 03_smoothing_tracks.R: Code to make Figures 4 -- 5 in the section _Smoothing and Thinning Data_.



- 04_residence_patch.R: Code to make Figure 6 in the section _Creating System-Specific Pre-processing Tools_.



- 05_calibration_data.R: Code for Figure 7 in the main text subsection _A Real-World Test of User-Built Pre-Processing Tools_. 

Shows a fully worked out example of pre-processing ATLAS data, as well as the linear model validating the residence patch method.

Also used in Supplementary Material 01 (`docs/ms_atlas_preproc_supplementary_material_DATE.pdf`) section _Validating the Residence Patch Method with Calibration Data_.



- 06_bat_data.R: Shows a fully worked out example of pre-processing ATLAS tracking data from fruit bats in the Hula Valley, Israel, which forms the main text section _Worked out Example on Animal Tracking Data_.

Also used in Supplementary Material 01 (`docs/ms_atlas_preproc_supplementary_material_DATE.pdf`) section _Processing Egyptian Fruit Bat Tracks_.



- 0x_get_srtm_hula.py`: Python code to retrieve Shuttle Radio Topography Mission 30m resolution data for the Hula Valley, Israel.

This is used solely as a background for Figure 8 in the main text.



- helper_functions.R: Script with helpful functions to simulate errors in data.



## Main Text



The main text is also copied from a local source into the `docs/` as a PDF.



## Supplementary Material



Supplementary Material 01 is rendered into the `docs/` folder as `docs/ms_atlas_preproc_supplementary_material_DATE.pdf`, where `DATE` is the date of rendering.

The rendering code using the `R` package `bookdown` is run from the shell script `render_books.sh`.



This material is placed in the `supplement/` folder.



### supplement/



- `figures/` The supplementary material figures.



- `latex/` and `*.yml` Formatting options for the supplementary material output.



- `.Rmd` files to create the supplementary material.



- `render_books.sh`: A shell script with helper commands to generate the Supplementary Material and the source code as `R` scripts from the `Rmd` files.



- `references.bib`: References for the main text and Supplementary Material 01.



The `xx_references.Rmd` file ensures a _References_ section in Supplementary Material 01.



---



Supplementary Material 02 is the PDF manual for the `R` package `atlastools`, which is rendered from the installed version of `atlastools` using `devtools::build_manual`.

The rendered output is `atlastools_VERSION.pdf`.

Versioning is not implemented in the naming.

This command is also run from the shell script `render_books.sh`.



## Auxiliary Files



- `atlas_best_practices.qgz`: A QGIS 3 project file to generate Figure 8 in the main text.



- `.git*`: Files for git repository organisation. The submodule `atlas-manuscript` contains the `TEX` source of the main text and is private.



## Data 



The `data/` folder contains the following main datasets.



### Simulated Movement Data



1. `data_sim.csv`: Data simulated from `R/_01_background.R`. An UCVM track simulated using `smoove`.



2. `data_for_res_patch.csv`: Data simulated from `R/_01_background.R`. Three RACVM tracks simulated using `smoove`.



### Empirical Movement Data



1. `atlas1060_allTrials_annotated.csv`: A hand held calibration ATLAS track collected in August 2020 in the Dutch Wadden Sea.

Used to make Figure 7 in the main text subsection _Validating the Residence Patch Method_, and in Supplementary Material 01 (`docs/ms_atlas_preproc_supplementary_material_DATE.pdf`), section _Validating the Residence Patch Method with Calibration Data_.



2. `Three_example_bats.sql`: Tracks from three Egyptian fruit bats (_Rousettus aegyptiacus_)from the Hula Valley, Israel.

Used to make Figure 8 in the main text section _Worked out Example on Animal Tracking Data_, and for the Supplementary Material 01 (`docs/ms_atlas_preproc_supplementary_material_DATE.pdf`) section _Processing Egyptian Fruit Bat Tracks_.



3. `bat_data.csv`: The above data saved as a `csv` file.



### Empirical Spatial Data



1. `griend_polygon/`: A shapefile with the polygon outline of the Dutch Wadden Sea island of Griend, where the calibration data was collected.



2. `hula_valley/`: A shapefile of the extent of the study site of the Hula Valley, Israel.



3. `griend_hut.gpkg`: The location of the field station on Griend.



4. `Roosts.csv`: The locations of bat roosts in the Hula Valley.



5. `trees_update_clusters_Aug2020.csv`: The locations of fruit trees in the Hula Valley, Israel.



6. `srtm_30.tif`: A digital elevation model (DEM) of the Hula Valley, Israel.



### Processed Data



All other data are processed forms of the simulated or empirical movement data and not described further.



## Figures



The figures folder contains the main text, as well as supplementary material figures.