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#
# Copyright 2025, PBL Netherlands Environmental Assessment Agency
# See the copyright notice at the end of this file.
#
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## BioScore_model_settings.R
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## File type : R script, secondary file for model settings
## Purpose   : Store model settings for various scenarios and runs
## 
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## Description of the variables
##
## taxo_group:  either "plants" or "butterflies". which taxonomic group is run
## CPU:         : number of CPU's to use during the run
## SaveIntRes:  logical. save intermediate biomod2-results. default is FALSE. 
## min_observations: minimum number of observation for the SDMs to be fitted
## Name: name of the person who runs the script
## DropHabitats_plots: list of characters referring to habitat types which should be removed from the plots. e.g.inland waters, fresh water, marine water and man-made
## MinYear:     first year of the period for which you want to select the plots
## VIFthreshold: maximum VIF-value, in order to decrease correlation between variables
## PerformanceMetric: Metric used to weigh the range maps per algorithm into an ensemble map. Either "ROC" (=AUC) or " TSS" 
## modeltesting: Do you want to run the model for testing purposes only? Setting this to TRUE will only project SDMs for Northern Italy.
## ProjectScenarios: names of scenarios to be run. Scenario names should be identical to the names in Input/Variables/OverviewVariables.csv, but can be a selection of scenarios in this table.
## MIVCalc: Metric to describe if you want to calculate and save MIVs and response curves or not
## AllMetricsSave : metric if you want to save the all metric file or not
## Removeoriginal: metric if you want to remove the original metric files or not 

taxo_group <- "Vascular plant"
CPU <- 23
SaveIntRes <- FALSE
min_obs_per_var <- 5
Name <- "Name of user"
DropHabitats_plots <- c("^C","MA","Q5","^V")
Drophabitat_species <- c("^C","MA","Q5","^V")
MinYear <- 1990
VIFthreshold <- 10
PerformanceMetric <- "TSS"
modeltesting <- TRUE
ProjectScenarios <- c("current","ssp126")
MIVCalc <- TRUE
AllMetricsSave <-TRUE
Removeoriginal <- TRUE





# ====================================================================
#
# Copyright 2025, PBL Netherlands Environmental Assessment Agency
# 
# This source code of the BioScore model is owned by PBL Netherlands Environmental Assessment Agency. 
# It is not permitted to copy, redistribute, remix, transform, and build upon the material without written approval of PBL. 
# Permission for commercial purposes will not be granted. 
# This code is published to improve the transparency of the models used by PBL, 
# but without any warranty for fitness for any other purpose. 
# After approval of PBL to use the code, PBL will not provide any support.
#
# 
# ====================================================================

