eucop_data_preparation {RRgeo} | R Documentation |
Import and preprocess mammal occurrence data
Description
The function is meant to automatically import and preprocess
fossil mammal occurrences and paleoclimatic/vegetational data available in
EutherianCop dataset (Mondanaro et al., 2025). It also provides two distinct
approaches, both implemented within a user-defined study area, for sampling
a specified number of pseudoabsences or alternatively defining the
background points. This flexibility enables users to assemble a list of
sf
objects that can be easily used to train ENFA, ENphylo or any
other SDM algorithms of their choice.
Usage
eucop_data_preparation(input.dir,species_name,variables="all",which.vars=NULL,
calibration=FALSE,add.modern.occs=FALSE,
combine.ages=NULL,remove.duplicates=TRUE, bk_points=NULL,output.dir)
Arguments
input.dir |
the file path wherein EutherianCop mammal occurrences and paleoclimatic data are to be stored. |
species_name |
character. The name of the single (or multiple) species
used by |
variables |
character. The name of paleoclimatic simulations to be used. The viable options are "climveg", "bio", or "all". |
which.vars |
character vector indicating the name of the variables to be downloaded. The list of accepted names can be found [here](https://www.nature.com/articles/s41597-024-04181-4/tables/1). |
calibration |
logical. If |
add.modern.occs |
logical. If |
combine.ages |
one of |
remove.duplicates |
logical. If |
bk_points |
a list including parameters to add background/pseudoabsence (i.e. absence) points (following the procedure described in Mondanaro et al. 2024). The list includes:
If provided as an empty |
output.dir |
the file path wherein |
Details
The variables argument allows the selection of climatic and environmental variables ("climveg"), bioclimatic variables ("bio"), or both sets of variables.
Through the bk_strategy
argument,
eucop_data_preparation
offers two different approaches to generate
absence points. The definition of the study area is the same for both
methods. Under bk_strategy = "background"
, the bk_n
argument
defines the maximum number of background points sampled from the study area
within each time bin. Under bk_strategy = "pseudoabsence"
, the
bk_n
argument represents the maximum number of pseudoabsence points
across all time bins. This flexibility allows users to accommodate the
different requirements for training the traditional envelope models (i.e.
ENFA, ENphylo) and the common correlative or machine learning models (i.e.
generalized linear model, MaxEnt, Random Forest).
Additionally, if bk_points
is not NULL
, the ages of
presences and pseudoabsences or background points are forced to 1 kyr
resolution according to the temporal resolution of the
paleoclimatic/vegetational or bioclimatic data.
Value
eucop_data_preparation
does not store any results in the global
environment. Instead, a list of GeoPackage files, one per selected species,
is saved in the directory specified by output.dir
. The names of these
files depend on the combination of arguments chosen by users: they include
the suffix "cal/uncal" and "combined/multi" depending on whether calibration
(calibration
) and age aggregation (combine.ages
) steps are
performed. In any case, output files include information about ages, a
column called "OBS" including species occurrence data in binary format,
spatial geometry, and all the data information derived from EutherianCop
dataset.
Author(s)
Alessandro Mondanaro, Silvia Castiglione, Pasquale Raia
References
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.
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.
See Also
eucop_data_preparation
vignette
Examples
newwd<-tempdir()
# newwd<-"YOUR_DIRECTORY"
eucop_data_preparation(input.dir=newwd, species_name="Ursus ingressus",
variables="bio",which.vars = "bio1", calibration=FALSE, combine.ages="mean",
bk_points=NULL,output.dir=newwd)