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RRgeo provides functions for modeling the geographic
distribution of extremely rare species and determining the area of their
origin and the history of their past contacts. The package encompasses
ENphylo, a recently developed Species Distribution Model (SDM)
which couples Environmental Niche Factor Analysis (ENFA) and
phylogenetic imputation. ENphylo first calculates the
marginality and specialization values for all species with abundant
occurrence record. For rare species, these values are estimated through
phylogenetic imputation. Marginality and specialization are converted
into habitat suitability values allowing for spatially explicit model
predictions (Mondanaro et al. 2023). In this vignette, we demonstrate
how to format and process occurrence data to run ENphylo by
using 15 Late Pleistocene mammal species as a case study. We also
introduce an R function for downloading and manipulating the mammal
occurrences and the paleoclimatic/vegetational data published in the
EutherianCop database (Mondanaro et al. 2025). EutherianCop includes a
comprehensive global dataset of mammal occurrences and past
climatic/vegetational conditions covering the last 130 ka (Mondanaro et
al. 2025). For a full list of references please run:
## ENphylo method
##
## Mondanaro, A., Di Febbraro, M., Castiglione, S., Melchionna, M.,
## Serio, C., Girardi, G., Blefiore, A.M., & Raia, P. (2023). ENphylo: A
## new method to model the distribution of extremely rare species.
## Methods in Ecology and Evolution, 14: 911-922.
## doi:10.1111/2041-210X.14066
##
## ENphylo application on extremely rare species
##
## Mondanaro, A., Di Febbraro, M., Castiglione, S., Belfiore, A. M.,
## Girardi, G., Melchionna, M., Serio, C., Esposito, A., & Raia, P.
## (2024). Modelling reveals the effect of climate and land use change
## on Madagascar’s chameleons fauna. Communications Biology, 7: 889.
## doi:10.1038/s42003-024-06597-5
##
## EutherianCoP Database
##
## Mondanaro, A., Girardi, G., Castiglione, S., Timmermann, A., Zeller,
## E., Venugopal, T., Serio, C., Melchionna, M., Esposito, A., Di
## Febbraro, M., & Raia, P. (2025). EutherianCoP. An integrated biotic
## and climate database for conservation paleobiology based on eutherian
## mammals. Scientific Data, 12: 6. doi:10.1038/s41597-024-04181-4
##
## RRphylogeography method
##
## Mondanaro, A., Castiglione, S., Di Febbraro, M., Timmermann, A.,
## Girardi, G., Melchionna, M., Serio, C., Belfiore, A.M., & Raia, P.
## (2025). RRphylogeography: A new method to find the area of origin of
## species and the history of past contacts between species. Methods in
## Ecology and Evolution, 16: 546-557. doi: 10.1111/2041-210X.14478
##
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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