Use case and analysis repository of the spectre package.
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.
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├── 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.RprojThis analysis is packaged into an R-package. To use thr analysis either just click 
# 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