https://github.com/r-spatialecology/spectre_usecase
Use case and analysis repository of the spectre package
https://github.com/r-spatialecology/spectre_usecase
Last synced: 4 months ago
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Use case and analysis repository of the spectre package
- Host: GitHub
- URL: https://github.com/r-spatialecology/spectre_usecase
- Owner: r-spatialecology
- License: gpl-3.0
- Created: 2020-08-31T13:05:19.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-11-17T07:56:07.000Z (over 3 years ago)
- Last Synced: 2025-02-24T07:43:08.722Z (4 months ago)
- Language: R
- Size: 258 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
[](https://mybinder.org/v2/gh/r-spatialecology/spectre_usecase/master?urlpath=rstudio)
# spectre_usecase
Use case and analysis repository of the [`spectre` package](https://github.com/r-spatialecology/spectre).
The main idea of this repository is to accompany the `spectre` R package repository with detailed analyses and additional utility functions that would not fit in the context of the `spectre` package itself. This repository also contains all data and analysis used in the `spectre` manuscript.
## Contents
```bash
./
├── data # all data calculated during the analysis
│ ├── BCI_tree8_MSP.rds
│ ├── Fig4_data
│ ├── virtualspecies_02_advanced_data.rds
│ ├── virtualspecies_04_complete_versionB.rds
│ ├── virtualspecies_benchmark_parallel.rds
│ └── virtualspecies_benchmark.rds
├── DESCRIPTION # meta data about this analysis
├── figures
│ ├── Fig2.png
│ ├── Fig3.png
│ ├── Fig4.png
│ ├── S-Fig1.png
│ └── virtualspecies_complete_versionB
│ ├── mae.png
│ ├── mc.png
│ ├── min_error.png
│ ├── species_richness_map_10.png
│ ├── species_richness_map_20.png
│ └── species_richness_map_30.png
├── LICENSE.md
├── man
│ ├── calculate_mae.Rd
│ ├── calculate_mc.Rd
│ ├── calculate_rce.Rd
│ ├── generate_data_virtualspecies.Rd
│ ├── generate_data_virtualspecies_to_solution.Rd
│ ├── virtualspecies_plot.Rd
│ └── virtualspecies_simfun.Rd
├── NAMESPACE
├── R # all R functions used in the analysis
│ ├── calculate_mae.R
│ ├── calculate_mc.R
│ ├── calculate_rce.R
│ ├── generate_data_virtualspecies.R
│ ├── generate_data_virtualspecies_to_solution.R
│ ├── virtualspecies_plot.R
│ └── virtualspecies_simfun.R
├── raw_data # read-only data used in the analysis
│ ├── BCI_prepare_tree8_data.R
│ └── bci.tree8.rdata
├── README.md # this file
├── Rscripts # all Rscripts used for this analysis
│ ├── Fig2_plot_error.R
│ ├── Fig3_virt_species_scaling_run.R
│ ├── Fig4_BCI_known_sites_plots.R
│ └── Fig4_BCI_known_sites_run.R
└── spectre_usecase.Rproj
```
## Analyses
This analysis is packaged into an R-package. To use thr analysis either just click [](https://mybinder.org/v2/gh/r-spatialecology/spectre_usecase/master?urlpath=rstudio) or
```R
# install.packages("remotes")
# install all dependencies for this analyses:
remotes::install_github("r-spatialecology/spectre_usecase")
library(spectre_usecase)
# run the analyses in the Rscripts folder
```