getENphylo_results: Import ENphylo_modeling results into global environment

In RRgeo: Species Distribution Modelling for Rare Species

Import ENphylo_modeling results into global environment

Description

The function retrieves the ENFA/ENphylo models generated by ENphylo_modeling and arranges them into a named list to be used in ENphylo_prediction function. It also offers the option to choose between retrieving ENFA or ENphylo models and to select the model produced for one or more focal species.

Usage

getENphylo_results(input.dir,mods="all",species_name=NULL,only_evaluations=FALSE)

Arguments

input.dir	the file path wherein the folders "ENphylo_enfa_models" and "ENphylo_imputed_models" generated by ENphylo_modeling are stored.
mods	character. Name of the models to be retrieved. Viable options are: “enfa” (enfa models), “enphylo” (ENphylo models), “all” (default, enfa plus ENphylo models).
species_name	character. The name of the single (or multiple) species for which model results must be imported.
only_evaluations	logical. If TRUE, getENphylo_results returnes model performances only.

Value

A named list of outputs as described in ENphylo_modeling.

Author(s)

Alessandro Mondanaro, Silvia Castiglione, Pasquale Raia

See Also

ENphylo_modeling; getENphylo_results vignette

Examples

library(ape)
library(terra)
library(sf)
library(RRgeo)

newwd<-tempdir()
# newwd<-"YOUR_DIRECTORY"
latesturl<-RRgeo:::get_latest_version("12734585")
curl::curl_download(url = paste0(latesturl,"/files/dat.Rda?download=1"),
                    destfile = file.path(newwd,"dat.Rda"), quiet = FALSE)
load(file.path(newwd,"dat.Rda"))
read.tree(system.file("exdata/Eucopdata_tree.txt", package="RRgeo"))->tree
tree$tip.label<-gsub("_"," ",tree$tip.label)
curl::curl_download(paste0(latesturl,"/files/X35kya.tif?download=1"),
                    destfile = file.path(newwd,"X35kya.tif"), quiet = FALSE)
rast(file.path(newwd,"X35kya.tif"))->map35
project(map35,st_crs(dat[[1]])$proj4string,res = 50000)->map

ENphylo_modeling(input_data=dat[c(1,11)],
                 tree=tree,
                 input_mask=map[[1]],
                 obs_col="OBS",
                 time_col="age",
                 min_occ_enfa=15,
                 boot_test_perc=20,
                 boot_reps=10,
                 swap.args=list(nsim=5,si=0.2,si2=0.2),
                 eval.args=list(eval_metric_for_imputation="AUC",
                                eval_threshold=0.7,
                                output_options="best"),
                 clust=NULL,
                 output.dir=newwd)

getENphylo_results(input.dir =newwd,
                   mods="all",
                   species_name=names(dat)[c(1,11)])->mod

RRgeo documentation built on July 2, 2025, 5:09 p.m.