# Introduction to RRgeo

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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:

    citation("RRgeo")

    ## 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)'.