trias-project/occurrence-cube-paper

📄 Script, data and figures for methodological paper about occurrence cubes

aoo-paper

Code, data and figures for onepager describing the methodology of making occurrence cubes.

Repo structure

The repository structure is based on Cookiecutter Data Science. Files and directories indicated with GENERATED should not be edited manually.

├── README.md            : Description of this repository
├── LICENSE              : Repository license
├── aoo-paper.Rproj : RStudio project file
├── .gitignore           : Files and directories to be ignored by git
│
├── data
│   ├── raw              : Occurrence data as downloaded from GBIF GENERATED
│   └── processed        : occurrence data cube and taxonomic compendium GENERATED
│   └── external
        ├── utm1_bel     : EEA reference grid at 1km scale GENERATED
└── src
    ├── make_cube_reynoutria.R     : Script to generate occurrence cube
    ├── add_uncertainty_1000m.R    : Script to show occurrences with default uncertainty of 1000m
    ├── table_taxa_in_occurrences.R : Script to generate data.frame with all taxa in occurrence cube
    ├── code_occurrence-as-circles-and-random-pts-on-grid.R   : Script to show the method of assigning an occurrence to a grid cell
    ├── project_cube_to_2d.R      : Script to generate the subfigures (B) (C) and (D) about the projection of the cube on the 2d planes

Contributors

List of contributors

License

MIT License for the code and documentation in this repository.

occurrence-cube-paper's Issues

notes about draft study

From @qgroom 's trias-project/indicators#40 (comment) related to _grid_size_effect.Rmd:

• Remove the line in downscaling graphs. The line is misleading.
• Show only the mean of simple ensemble methods.
• Show three maps with the grids of Belgium: 1x1km, 10x10km and 100x100km.

The 4th note is related to bias correction and is out of the scope of this methodological paper.

Also adding common species in the paper (trias-project/indicators#39) will be tackled here.