https://github.com/emilio-berti/sdm_validation
Validate SDMs output using demographic metrics
https://github.com/emilio-berti/sdm_validation
Last synced: 3 months ago
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Validate SDMs output using demographic metrics
- Host: GitHub
- URL: https://github.com/emilio-berti/sdm_validation
- Owner: emilio-berti
- Created: 2020-02-12T11:02:16.000Z (over 5 years ago)
- Default Branch: filter-species
- Last Pushed: 2020-02-14T07:34:24.000Z (over 5 years ago)
- Last Synced: 2025-01-21T04:28:07.758Z (5 months ago)
- Language: R
- Homepage:
- Size: 17.3 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# SDMs validation via COMADRE database
## Code pipeline
1. get_species.R
2. get_occurrences.R
3. clean_occurrences.R
4. grin_records.R (this eats a lot of memory; do not parallelize with < 32 Gb of RAM)
## Occurrence data
We removed from the COMADRE dataset all mammal populations that had: 1) NA values in the MPM; 2) MPMs that were not ergodic, a necessary condition to obtained the asymptotic growth rate $lambda$; 3) population that did not have geo-references locations; and 4) captive or manipulated populations. As we performed the analyses at the species level, we removed sub-species taxonomic classifications. In total, we had 116 populations of 76 species.
We then gathered occurrence locations from several open-access databases (...) using the R package spocc (REF). We then removed spurious data points using R package CoordinateCleaner and thinned the remaining occurence records to have a separation distance of at least 10 km. In total, we identified # species with at least 30 occurrence locations for modelling.
Table: Number of occurrence records (n) per species. Records were obtained from multiple databases using the R package spocc, excluding spurious observations, and the occurrences were then thinned to ensure a minimum distance between point >= 10 km.
|species | n|
|:---------------------------|----:|
|Lycaon pictus | 34|
|Elephas maximus | 40|
|Didelphis aurita | 48|
|Phacochoerus aethiopicus | 75|
|Pan troglodytes | 88|
|Saguinus fuscicollis | 89|
|Papio cynocephalus | 123|
|Acinonyx jubatus | 135|
|Lycalopex culpaeus | 141|
|Eidolon helvum | 146|
|Cebus capucinus | 147|
|Urocitellus armatus | 164|
|Cercopithecus mitis | 173|
|Panthera pardus | 185|
|Chlorocebus aethiops | 194|
|Erythrocebus patas | 224|
|Giraffa camelopardalis | 273|
|Ursus maritimus | 289|
|Urocitellus columbianus | 322|
|Dipodomys spectabilis | 328|
|Alouatta seniculus | 347|
|Connochaetes taurinus | 352|
|Kobus ellipsiprymnus | 362|
|Trichosurus caninus | 378|
|Tamiasciurus douglasii | 547|
|Marmota flaviventris | 662|
|Microtus oeconomus | 782|
|Petaurus australis | 814|
|Ovis canadensis | 890|
|Phascolarctos cinereus | 970|
|Callospermophilus lateralis | 1032|
|Petauroides volans | 1094|
|Puma concolor | 1311|
|Macaca mulatta | 1666|
|Rangifer tarandus | 1743|
|Lontra canadensis | 1819|
|Dasypus novemcinctus | 1943|
|Ursus arctos | 2017|
|Gulo gulo | 2036|
|Sciurus niger | 2150|
|Sigmodon hispidus | 2237|
|Lynx rufus | 2785|
|Ursus americanus | 3012|
|Tamiasciurus hudsonicus | 3044|
|Odocoileus virginianus | 3170|
|Vulpes vulpes | 3195|
|Canis latrans | 4401|
|Alces alces | 4826|
|Procyon lotor | 5092|
|Cervus elaphus | 5582|
|Lutra lutra | 7509|
|Canis lupus | 7892|
|Sus scrofa | 8648|