From 4164cd7918d6bb078602308ce5a4ee028f9d8e1b Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Thu, 13 Jun 2024 15:00:31 +0200 Subject: [PATCH] Correct checks and documentation for evaluation metrics (remove HK and HSS) --- R/BIOMOD_EnsembleForecasting.R | 12 +++---- R/BIOMOD_EnsembleModeling.R | 36 +++++++++---------- R/BIOMOD_LoadModels.R | 6 ++-- R/BIOMOD_Modeling.R | 12 +++---- R/BIOMOD_Projection.R | 12 +++---- R/biomod2_classes_3.R | 24 ++++++------- R/bm_PlotEvalMean.R | 6 ++-- R/bm_RunModelsLoop.R | 12 +++---- .../reference/BIOMOD_EnsembleForecasting.html | 12 +++---- docs/reference/BIOMOD_EnsembleModeling.html | 30 ++++++++-------- docs/reference/BIOMOD_LoadModels.html | 6 ++-- docs/reference/BIOMOD_Modeling.html | 6 ++-- docs/reference/BIOMOD_Projection.html | 12 +++---- docs/reference/bm_PlotEvalMean.html | 6 ++-- docs/reference/bm_RunModelsLoop.html | 6 ++-- docs/reference/getters.out.html | 24 ++++++------- docs/reference/index.html | 22 ++++++------ man/BIOMOD_EnsembleForecasting.Rd | 12 +++---- man/BIOMOD_EnsembleModeling.Rd | 30 ++++++++-------- man/BIOMOD_LoadModels.Rd | 6 ++-- man/BIOMOD_Modeling.Rd | 6 ++-- man/BIOMOD_Projection.Rd | 12 +++---- man/bm_PlotEvalMean.Rd | 6 ++-- man/bm_RunModelsLoop.Rd | 6 ++-- man/getters.out.Rd | 24 ++++++------- 25 files changed, 170 insertions(+), 176 deletions(-) diff --git a/R/BIOMOD_EnsembleForecasting.R b/R/BIOMOD_EnsembleForecasting.R index f95e9841..44b0541d 100644 --- a/R/BIOMOD_EnsembleForecasting.R +++ b/R/BIOMOD_EnsembleForecasting.R @@ -38,16 +38,16 @@ ##' A \code{vector} containing evaluation metric names to be used to transform prediction values ##' into binary values based on models evaluation scores obtained with the ##' \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -##' those of \code{modeling.output}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' those of \code{modeling.output}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +##' \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +##' \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' @param metric.filter (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing evaluation metric names to be used to transform prediction values ##' into filtered values based on models evaluation scores obtained with the ##' \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -##' those of \code{modeling.output}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' those of \code{modeling.output}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +##' \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +##' \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' ##' @param compress (\emph{optional, default} \code{TRUE}) \cr ##' A \code{logical} or a \code{character} value defining whether and how objects should be diff --git a/R/BIOMOD_EnsembleModeling.R b/R/BIOMOD_EnsembleModeling.R index 4cf969a3..b82a581f 100644 --- a/R/BIOMOD_EnsembleModeling.R +++ b/R/BIOMOD_EnsembleModeling.R @@ -26,27 +26,25 @@ ##' \code{metric.select.thresh} to exclude single models based on their evaluation scores ##' (for ensemble methods like probability weighted mean or committee averaging). Must be among ##' \code{all} (same evaluation metrics than those of \code{bm.mod}), \code{user.defined} -##' (and defined through \code{metric.select.table}) or \code{ROC}, \code{TSS}, \code{KAPPA}, -##' \code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, -##' \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' (and defined through \code{metric.select.table}) or \code{POD}, \code{FAR}, \code{POFD}, +##' \code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, +##' \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' @param metric.select.thresh (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} of \code{numeric} values corresponding to the minimum scores (one for each ##' \code{metric.select}) below which single models will be excluded from the ensemble model ##' building -##' @param metric.select.table (\emph{optional, default} \code{NULL}) \cr If -##' \code{metric.select = 'user.defined'}, a \code{data.frame} containing -##' evaluation scores calculated for each single models and that will be -##' compared to \code{metric.select.thresh} values to exclude some of them -##' from the ensemble model building, with \code{metric.select} rownames, and -##' \code{models.chosen} colnames -##' @param metric.select.dataset (\emph{optional, default} \code{'validation'} -##' \emph{if possible}). A character determining which dataset should be used -##' to filter and/or weigh the ensemble models should be among 'evaluation', -##' 'validation' or 'calibration'. +##' @param metric.select.table (\emph{optional, default} \code{NULL}) \cr If +##' \code{metric.select = 'user.defined'}, a \code{data.frame} containing evaluation scores +##' calculated for each single models and that will be compared to \code{metric.select.thresh} +##' values to exclude some of them from the ensemble model building, with \code{metric.select} +##' rownames, and \code{models.chosen} colnames +##' @param metric.select.dataset (\emph{optional, default} \code{'validation'} +##' \emph{if possible}). A character determining which dataset should be used to filter and/or +##' weigh the ensemble models should be among 'evaluation', 'validation' or 'calibration'. ##' @param metric.eval a \code{vector} containing evaluation metric names to be used, must -##' be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -##' \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -##' \code{ORSS} +##' be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +##' \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +##' \code{BOYCE}, \code{MPA} ##' @param var.import (\emph{optional, default} \code{NULL}) \cr ##' An \code{integer} corresponding to the number of permutations to be done for each variable to ##' estimate variable importance @@ -961,9 +959,9 @@ BIOMOD_EnsembleModeling <- function(bm.mod, ## 7. Check metric.eval ----------------------------------------------------- metric.eval <- unique(metric.eval) - avail.eval.meth.list <- c('TSS', 'KAPPA', 'ACCURACY', 'BIAS', 'POD', 'FAR', 'POFD' - , 'SR', 'CSI', 'ETS', 'HK', 'HSS', 'OR', 'ORSS', 'ROC' - , 'BOYCE', 'MPA') + avail.eval.meth.list <- c('POD', 'FAR', 'POFD', 'SR', 'ACCURACY', 'BIAS' + , 'ROC', 'TSS', 'KAPPA', 'OR', 'ORSS', 'CSI' + , 'ETS', 'BOYCE', 'MPA') .fun_testIfIn(TRUE, "metric.eval", metric.eval, avail.eval.meth.list) ## 8. Check selected EM algo ------------------------------------------------ diff --git a/R/BIOMOD_LoadModels.R b/R/BIOMOD_LoadModels.R index 4022abf2..3f8e5a30 100644 --- a/R/BIOMOD_LoadModels.R +++ b/R/BIOMOD_LoadModels.R @@ -40,9 +40,9 @@ ##' \code{MAXENT}, \code{MAXNET}, \code{RF}, \code{SRE}, \code{XGBOOST}, \code{mergedAlgo} ##' @param filtered.by (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing evaluation metric selected to filter single models to build the -##' ensemble models, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' ensemble models, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +##' \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, +##' \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' ##' ##' @return diff --git a/R/BIOMOD_Modeling.R b/R/BIOMOD_Modeling.R index c08cfd5a..e6da4b13 100644 --- a/R/BIOMOD_Modeling.R +++ b/R/BIOMOD_Modeling.R @@ -79,9 +79,9 @@ ##' A \code{numeric} between \code{0} and \code{1} corresponding to the species prevalence to ##' build '\emph{weighted response weights}' (see Details) ##' @param metric.eval a \code{vector} containing evaluation metric names to be used, must -##' be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -##' \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -##' \code{ORSS}, \code{BOYCE}, \code{MPA} +##' be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +##' \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +##' \code{BOYCE}, \code{MPA} ##' @param var.import (\emph{optional, default} \code{NULL}) \cr ##' An \code{integer} corresponding to the number of permutations to be done for each variable to ##' estimate variable importance @@ -744,9 +744,9 @@ BIOMOD_Modeling <- function(bm.format, ## 7. Check metric.eval arguments ------------------------------------------- metric.eval <- unique(metric.eval) - avail.eval.meth.list <- c('TSS', 'KAPPA', 'ACCURACY', 'BIAS', 'POD', 'FAR', 'POFD' - , 'SR', 'CSI', 'ETS', 'HK', 'HSS', 'OR', 'ORSS', 'ROC' - , 'BOYCE', 'MPA') + avail.eval.meth.list <- c('POD', 'FAR', 'POFD', 'SR', 'ACCURACY', 'BIAS' + , 'ROC', 'TSS', 'KAPPA', 'OR', 'ORSS', 'CSI' + , 'ETS', 'BOYCE', 'MPA') .fun_testIfIn(TRUE, "metric.eval", metric.eval, avail.eval.meth.list) diff --git a/R/BIOMOD_Projection.R b/R/BIOMOD_Projection.R index a7c3ab14..f1dec594 100644 --- a/R/BIOMOD_Projection.R +++ b/R/BIOMOD_Projection.R @@ -33,16 +33,16 @@ ##' A \code{vector} containing evaluation metric names to be used to transform prediction values ##' into binary values based on models evaluation scores obtained with the ##' \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -##' those of \code{bm.mod}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' those of \code{bm.mod}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +##' \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +##' \code{ETS}, \code{BOYCE}, \code{MPA} ##' @param metric.filter (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing evaluation metric names to be used to transform prediction values ##' into filtered values based on models evaluation scores obtained with the ##' \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -##' those of \code{bm.mod}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' those of \code{bm.mod}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +##' \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +##' \code{ETS}, \code{BOYCE}, \code{MPA} ##' ##' @param compress (\emph{optional, default} \code{TRUE}) \cr ##' A \code{logical} or a \code{character} value defining whether and how objects should be diff --git a/R/biomod2_classes_3.R b/R/biomod2_classes_3.R index 99ecd67b..82b58931 100644 --- a/R/biomod2_classes_3.R +++ b/R/biomod2_classes_3.R @@ -69,27 +69,27 @@ ##' \code{MAXENT}, \code{MAXNET}, \code{RF}, \code{SRE}, \code{XGBOOST}, \code{mergedAlgo} ##' @param filtered.by (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing evaluation metric selected to filter single models to build the -##' ensemble models, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -##' \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -##' \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' ensemble models, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +##' \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +##' \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' ##' @param metric.eval (\emph{optional, default} \code{NULL}) \cr -##' A \code{vector} containing evaluation metric to be kept, must be among \code{ROC}, -##' \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, -##' \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' A \code{vector} containing evaluation metric to be kept, must be among \code{POD}, +##' \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, +##' \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' @param expl.var (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing explanatory variables to be kept, that can be obtained with the ##' \code{\link{get_formal_data}(obj, subinfo = 'expl.var.names')} function ##' ##' @param metric.binary (\emph{optional, default} \code{NULL}) \cr ##' A \code{vector} containing evaluation metric selected to transform predictions into binary -##' values, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, -##' \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, -##' \code{HSS}, \code{OR}, \code{ORSS} +##' values, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +##' \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +##' \code{ETS}, \code{BOYCE}, \code{MPA} ##' @param metric.filter (\emph{optional, default} \code{NULL}) \cr -##' A \code{vector} containing evaluation metric to filter predictions, must be among \code{ROC}, -##' \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, -##' \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS} +##' A \code{vector} containing evaluation metric to filter predictions, must be among \code{POD}, +##' \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, +##' \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA} ##' ##' @param model.as.col (\emph{optional, default} \code{FALSE}) \cr ##' A \code{boolean} given to \code{\link{get_predictions}}. If \code{TRUE} diff --git a/R/bm_PlotEvalMean.R b/R/bm_PlotEvalMean.R index 5098ec2d..9877f80a 100644 --- a/R/bm_PlotEvalMean.R +++ b/R/bm_PlotEvalMean.R @@ -16,9 +16,9 @@ ##' object that can be obtained with the \code{\link{BIOMOD_Modeling}} or ##' \code{\link{BIOMOD_EnsembleModeling}} functions ##' @param metric.eval a \code{vector} containing evaluation metric names to be used, must -##' be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -##' \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -##' \code{ORSS} +##' be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +##' \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +##' \code{BOYCE}, \code{MPA} ##' @param dataset a \code{character} corresponding to the dataset upon which evaluation metrics ##' have been calculated and that is to be represented, must be among \code{calibration}, ##' \code{validation}, \code{evaluation} diff --git a/R/bm_RunModelsLoop.R b/R/bm_RunModelsLoop.R index f0e6d64b..81132010 100644 --- a/R/bm_RunModelsLoop.R +++ b/R/bm_RunModelsLoop.R @@ -29,9 +29,9 @@ ##' @param bm.options a \code{\link{BIOMOD.models.options}} object returned by the ##' \code{\link{bm_ModelingOptions}} function ##' @param metric.eval a \code{vector} containing evaluation metric names to be used, must -##' be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -##' \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -##' \code{ORSS} +##' be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +##' \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +##' \code{BOYCE}, \code{MPA} ##' @param var.import (\emph{optional, default} \code{NULL}) \cr ##' An \code{integer} corresponding to the number of permutations to be done for each variable to ##' estimate variable importance @@ -655,9 +655,9 @@ bm_RunModel <- function(model, run.name, dir.name = '.' ## 4. Check models.eval.meth arguments -------------------------------------- metric.eval <- unique(metric.eval) - avail.eval.meth.list <- c('TSS', 'KAPPA', 'ACCURACY', 'BIAS', 'POD', 'FAR', 'POFD' - , 'SR', 'CSI', 'ETS', 'HK', 'HSS', 'OR', 'ORSS', 'ROC' - , 'BOYCE', 'MPA') + avail.eval.meth.list <- c('POD', 'FAR', 'POFD', 'SR', 'ACCURACY', 'BIAS' + , 'ROC', 'TSS', 'KAPPA', 'OR', 'ORSS', 'CSI' + , 'ETS', 'BOYCE', 'MPA') # .fun_testIfIn(TRUE, "metric.eval", metric.eval, avail.eval.meth.list) if (sum(!(metric.eval %in% avail.eval.meth.list)) > 0) { tmp = which(metric.eval %in% avail.eval.meth.list) diff --git a/docs/reference/BIOMOD_EnsembleForecasting.html b/docs/reference/BIOMOD_EnsembleForecasting.html index 2a86f366..897229f0 100644 --- a/docs/reference/BIOMOD_EnsembleForecasting.html +++ b/docs/reference/BIOMOD_EnsembleForecasting.html @@ -180,9 +180,9 @@

Arguments

A vector containing evaluation metric names to be used to transform prediction values into binary values based on models evaluation scores obtained with the BIOMOD_Modeling function. Must be among all (same evaluation metrics than -those of modeling.output) or ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+those of modeling.output) or POD, FAR, POFD, SR, +ACCURACY, BIAS, ROC, TSS, KAPPA, OR, ORSS, +CSI, ETS, BOYCE, MPA

metric.filter
@@ -190,9 +190,9 @@

Arguments

A vector containing evaluation metric names to be used to transform prediction values into filtered values based on models evaluation scores obtained with the BIOMOD_Modeling function. Must be among all (same evaluation metrics than -those of modeling.output) or ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+those of modeling.output) or POD, FAR, POFD, SR, +ACCURACY, BIAS, ROC, TSS, KAPPA, OR, ORSS, +CSI, ETS, BOYCE, MPA

compress
diff --git a/docs/reference/BIOMOD_EnsembleModeling.html b/docs/reference/BIOMOD_EnsembleModeling.html index 65e0713e..8296f0e2 100644 --- a/docs/reference/BIOMOD_EnsembleModeling.html +++ b/docs/reference/BIOMOD_EnsembleModeling.html @@ -177,9 +177,9 @@

Arguments

metric.select.thresh to exclude single models based on their evaluation scores (for ensemble methods like probability weighted mean or committee averaging). Must be among all (same evaluation metrics than those of bm.mod), user.defined -(and defined through metric.select.table) or ROC, TSS, KAPPA, -ACCURACY, BIAS, POD, FAR, POFD, SR, CSI, -ETS, HK, HSS, OR, ORSS

+(and defined through metric.select.table) or POD, FAR, POFD, +SR, ACCURACY, BIAS, ROC, TSS, KAPPA, OR, +ORSS, CSI, ETS, BOYCE, MPA

metric.select.thresh
@@ -190,26 +190,24 @@

Arguments

metric.select.table
-

(optional, default NULL)
If -metric.select = 'user.defined', a data.frame containing -evaluation scores calculated for each single models and that will be -compared to metric.select.thresh values to exclude some of them -from the ensemble model building, with metric.select rownames, and -models.chosen colnames

+

(optional, default NULL)
If +metric.select = 'user.defined', a data.frame containing evaluation scores +calculated for each single models and that will be compared to metric.select.thresh +values to exclude some of them from the ensemble model building, with metric.select +rownames, and models.chosen colnames

metric.select.dataset
-

(optional, default 'validation' -if possible). A character determining which dataset should be used -to filter and/or weigh the ensemble models should be among 'evaluation', -'validation' or 'calibration'.

+

(optional, default 'validation' +if possible). A character determining which dataset should be used to filter and/or +weigh the ensemble models should be among 'evaluation', 'validation' or 'calibration'.

metric.eval

a vector containing evaluation metric names to be used, must -be among ROC, TSS, KAPPA, ACCURACY, BIAS, POD, -FAR, POFD, SR, CSI, ETS, HK, HSS, OR, -ORSS

+be among POD, FAR, POFD, SR, ACCURACY, BIAS, +ROC, TSS, KAPPA, OR, ORSS, CSI, ETS, +BOYCE, MPA

var.import
diff --git a/docs/reference/BIOMOD_LoadModels.html b/docs/reference/BIOMOD_LoadModels.html index 905979c9..d95012ae 100644 --- a/docs/reference/BIOMOD_LoadModels.html +++ b/docs/reference/BIOMOD_LoadModels.html @@ -183,9 +183,9 @@

Arguments

filtered.by

(optional, default NULL)
A vector containing evaluation metric selected to filter single models to build the -ensemble models, must be among ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+ensemble models, must be among POD, FAR, POFD, SR, +ACCURACY, BIAS, ROC, TSS, KAPPA, OR, +ORSS, CSI, ETS, BOYCE, MPA

diff --git a/docs/reference/BIOMOD_Modeling.html b/docs/reference/BIOMOD_Modeling.html index b297ecd6..f291b37e 100644 --- a/docs/reference/BIOMOD_Modeling.html +++ b/docs/reference/BIOMOD_Modeling.html @@ -298,9 +298,9 @@

Arguments

metric.eval

a vector containing evaluation metric names to be used, must -be among ROC, TSS, KAPPA, ACCURACY, BIAS, POD, -FAR, POFD, SR, CSI, ETS, HK, HSS, OR, -ORSS, BOYCE, MPA

+be among POD, FAR, POFD, SR, ACCURACY, BIAS, +ROC, TSS, KAPPA, OR, ORSS, CSI, ETS, +BOYCE, MPA

var.import
diff --git a/docs/reference/BIOMOD_Projection.html b/docs/reference/BIOMOD_Projection.html index 775b6dc7..628aa5bd 100644 --- a/docs/reference/BIOMOD_Projection.html +++ b/docs/reference/BIOMOD_Projection.html @@ -172,9 +172,9 @@

Arguments

A vector containing evaluation metric names to be used to transform prediction values into binary values based on models evaluation scores obtained with the BIOMOD_Modeling function. Must be among all (same evaluation metrics than -those of bm.mod) or ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+those of bm.mod) or POD, FAR, POFD, SR, ACCURACY, +BIAS, ROC, TSS, KAPPA, OR, ORSS, CSI, +ETS, BOYCE, MPA

metric.filter
@@ -182,9 +182,9 @@

Arguments

A vector containing evaluation metric names to be used to transform prediction values into filtered values based on models evaluation scores obtained with the BIOMOD_Modeling function. Must be among all (same evaluation metrics than -those of bm.mod) or ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+those of bm.mod) or POD, FAR, POFD, SR, ACCURACY, +BIAS, ROC, TSS, KAPPA, OR, ORSS, CSI, +ETS, BOYCE, MPA

compress
diff --git a/docs/reference/bm_PlotEvalMean.html b/docs/reference/bm_PlotEvalMean.html index be799f5d..0d7a6595 100644 --- a/docs/reference/bm_PlotEvalMean.html +++ b/docs/reference/bm_PlotEvalMean.html @@ -142,9 +142,9 @@

Arguments

metric.eval

a vector containing evaluation metric names to be used, must -be among ROC, TSS, KAPPA, ACCURACY, BIAS, POD, -FAR, POFD, SR, CSI, ETS, HK, HSS, OR, -ORSS

+be among POD, FAR, POFD, SR, ACCURACY, BIAS, +ROC, TSS, KAPPA, OR, ORSS, CSI, ETS, +BOYCE, MPA

dataset
diff --git a/docs/reference/bm_RunModelsLoop.html b/docs/reference/bm_RunModelsLoop.html index a2971936..661a613a 100644 --- a/docs/reference/bm_RunModelsLoop.html +++ b/docs/reference/bm_RunModelsLoop.html @@ -191,9 +191,9 @@

Arguments

metric.eval

a vector containing evaluation metric names to be used, must -be among ROC, TSS, KAPPA, ACCURACY, BIAS, POD, -FAR, POFD, SR, CSI, ETS, HK, HSS, OR, -ORSS

+be among POD, FAR, POFD, SR, ACCURACY, BIAS, +ROC, TSS, KAPPA, OR, ORSS, CSI, ETS, +BOYCE, MPA

var.import
diff --git a/docs/reference/getters.out.html b/docs/reference/getters.out.html index 0641821b..93eb0ef0 100644 --- a/docs/reference/getters.out.html +++ b/docs/reference/getters.out.html @@ -317,9 +317,9 @@

Arguments

metric.eval

(optional, default NULL)
-A vector containing evaluation metric to be kept, must be among ROC, -TSS, KAPPA, ACCURACY, BIAS, POD, FAR, -POFD, SR, CSI, ETS, HK, HSS, OR, ORSS

+A vector containing evaluation metric to be kept, must be among POD, +FAR, POFD, SR, ACCURACY, BIAS, ROC, TSS, +KAPPA, OR, ORSS, CSI, ETS, BOYCE, MPA

expl.var
@@ -350,24 +350,24 @@

Arguments

filtered.by

(optional, default NULL)
A vector containing evaluation metric selected to filter single models to build the -ensemble models, must be among ROC, TSS, KAPPA, ACCURACY, -BIAS, POD, FAR, POFD, SR, CSI, ETS, -HK, HSS, OR, ORSS

+ensemble models, must be among POD, FAR, POFD, SR, +ACCURACY, BIAS, ROC, TSS, KAPPA, OR, ORSS, +CSI, ETS, BOYCE, MPA

metric.binary

(optional, default NULL)
A vector containing evaluation metric selected to transform predictions into binary -values, must be among ROC, TSS, KAPPA, ACCURACY, BIAS, -POD, FAR, POFD, SR, CSI, ETS, HK, -HSS, OR, ORSS

+values, must be among POD, FAR, POFD, SR, ACCURACY, +BIAS, ROC, TSS, KAPPA, OR, ORSS, CSI, +ETS, BOYCE, MPA

metric.filter

(optional, default NULL)
-A vector containing evaluation metric to filter predictions, must be among ROC, -TSS, KAPPA, ACCURACY, BIAS, POD, FAR, -POFD, SR, CSI, ETS, HK, HSS, OR, ORSS

+A vector containing evaluation metric to filter predictions, must be among POD, +FAR, POFD, SR, ACCURACY, BIAS, ROC, TSS, +KAPPA, OR, ORSS, CSI, ETS, BOYCE, MPA

...
diff --git a/docs/reference/index.html b/docs/reference/index.html index 433cf8d2..0f9a04c8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -232,27 +232,27 @@

Objects

plot(<BIOMOD.formated.data>,<missing>)

-

plot method for BIOMOD.formated.data object class

+

plot method for BIOMOD.formated.data object class

summary(<BIOMOD.formated.data>)

-

summary method for BIOMOD.formated.data object class

+

summary method for BIOMOD.formated.data object class

BIOMOD.options.default(<character>,<character>)

-

bm_ModelingOptions output object class

+

bm_ModelingOptions output object class

BIOMOD.options.dataset(<character>) show(<BIOMOD.options.dataset>) print(<BIOMOD.options.dataset>)

-

bm_ModelingOptions output object class

+

bm_ModelingOptions output object class

show(<BIOMOD.models.options>) print(<BIOMOD.models.options>)

-

bm_ModelingOptions output object class

+

bm_ModelingOptions output object class

BIOMOD.stored.data BIOMOD.stored.data-class BIOMOD.stored.data.frame-class BIOMOD.stored.SpatRaster-class BIOMOD.stored.files-class BIOMOD.stored.formated.data-class BIOMOD.stored.options-class BIOMOD.stored.models.out-class

-

BIOMOD_Modeling and BIOMOD_EnsembleModeling output object class

+

BIOMOD_Modeling and BIOMOD_EnsembleModeling output object class

show(<biomod2_model>)

@@ -280,23 +280,23 @@

Getters

load_stored_object()

-

Functions to load BIOMOD.stored.data objects

+

Functions to load BIOMOD.stored.data objects

get_formal_model(<biomod2_model>) get_scaling_model(<biomod2_model>)

-

Functions to extract informations from biomod2_model objects

+

Functions to extract informations from biomod2_model objects

get_species_data(<BIOMOD.formated.data>) get_species_data(<BIOMOD.formated.data.PA>) get_eval_data(<BIOMOD.formated.data>) get_options(<BIOMOD.models.out>) get_calib_lines(<BIOMOD.models.out>) get_formal_data(<BIOMOD.models.out>) get_predictions(<BIOMOD.models.out>) get_built_models(<BIOMOD.models.out>) get_evaluations(<BIOMOD.models.out>) get_variables_importance(<BIOMOD.models.out>) get_projected_models(<BIOMOD.projection.out>) free(<BIOMOD.projection.out>) get_predictions(<BIOMOD.projection.out>) get_formal_data(<BIOMOD.ensemble.models.out>) get_built_models(<BIOMOD.ensemble.models.out>) get_kept_models(<BIOMOD.ensemble.models.out>) get_predictions(<BIOMOD.ensemble.models.out>) get_evaluations(<BIOMOD.ensemble.models.out>) get_variables_importance(<BIOMOD.ensemble.models.out>)

-

Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects

+

Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects

predict(<biomod2_model>)

-

Functions to get predictions from biomod2_model objects

+

Functions to get predictions from biomod2_model objects

predict.em

-

Functions to get predictions from biomod2_ensemble_model objects

+

Functions to get predictions from biomod2_ensemble_model objects

Data

diff --git a/man/BIOMOD_EnsembleForecasting.Rd b/man/BIOMOD_EnsembleForecasting.Rd index 92f97867..e85dc142 100644 --- a/man/BIOMOD_EnsembleForecasting.Rd +++ b/man/BIOMOD_EnsembleForecasting.Rd @@ -53,17 +53,17 @@ be used to project the ensemble species distribution model(s)} A \code{vector} containing evaluation metric names to be used to transform prediction values into binary values based on models evaluation scores obtained with the \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -those of \code{modeling.output}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +those of \code{modeling.output}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +\code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +\code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{metric.filter}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing evaluation metric names to be used to transform prediction values into filtered values based on models evaluation scores obtained with the \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -those of \code{modeling.output}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +those of \code{modeling.output}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +\code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +\code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{compress}{(\emph{optional, default} \code{TRUE}) \cr A \code{logical} or a \code{character} value defining whether and how objects should be diff --git a/man/BIOMOD_EnsembleModeling.Rd b/man/BIOMOD_EnsembleModeling.Rd index 16eb7a04..9816c445 100644 --- a/man/BIOMOD_EnsembleModeling.Rd +++ b/man/BIOMOD_EnsembleModeling.Rd @@ -50,31 +50,29 @@ must be among \code{'EMmean'}, \code{'EMmedian'}, \code{'EMcv'}, \code{'EMci'}, \code{metric.select.thresh} to exclude single models based on their evaluation scores (for ensemble methods like probability weighted mean or committee averaging). Must be among \code{all} (same evaluation metrics than those of \code{bm.mod}), \code{user.defined} -(and defined through \code{metric.select.table}) or \code{ROC}, \code{TSS}, \code{KAPPA}, -\code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, -\code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +(and defined through \code{metric.select.table}) or \code{POD}, \code{FAR}, \code{POFD}, +\code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, +\code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{metric.select.thresh}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} of \code{numeric} values corresponding to the minimum scores (one for each \code{metric.select}) below which single models will be excluded from the ensemble model building} -\item{metric.select.table}{(\emph{optional, default} \code{NULL}) \cr If -\code{metric.select = 'user.defined'}, a \code{data.frame} containing -evaluation scores calculated for each single models and that will be -compared to \code{metric.select.thresh} values to exclude some of them -from the ensemble model building, with \code{metric.select} rownames, and -\code{models.chosen} colnames} +\item{metric.select.table}{(\emph{optional, default} \code{NULL}) \cr If +\code{metric.select = 'user.defined'}, a \code{data.frame} containing evaluation scores +calculated for each single models and that will be compared to \code{metric.select.thresh} +values to exclude some of them from the ensemble model building, with \code{metric.select} +rownames, and \code{models.chosen} colnames} -\item{metric.select.dataset}{(\emph{optional, default} \code{'validation'} -\emph{if possible}). A character determining which dataset should be used -to filter and/or weigh the ensemble models should be among 'evaluation', -'validation' or 'calibration'.} +\item{metric.select.dataset}{(\emph{optional, default} \code{'validation'} +\emph{if possible}). A character determining which dataset should be used to filter and/or +weigh the ensemble models should be among 'evaluation', 'validation' or 'calibration'.} \item{metric.eval}{a \code{vector} containing evaluation metric names to be used, must -be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -\code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -\code{ORSS}} +be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +\code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +\code{BOYCE}, \code{MPA}} \item{var.import}{(\emph{optional, default} \code{NULL}) \cr An \code{integer} corresponding to the number of permutations to be done for each variable to diff --git a/man/BIOMOD_LoadModels.Rd b/man/BIOMOD_LoadModels.Rd index 3c20a1b7..5f20f190 100644 --- a/man/BIOMOD_LoadModels.Rd +++ b/man/BIOMOD_LoadModels.Rd @@ -54,9 +54,9 @@ A \code{character} containing merged algorithm to be loaded, must be among \item{filtered.by}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing evaluation metric selected to filter single models to build the -ensemble models, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +ensemble models, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +\code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, +\code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} } \value{ A \code{vector} containing the names of the loaded models. diff --git a/man/BIOMOD_Modeling.Rd b/man/BIOMOD_Modeling.Rd index 2d510f80..d1e4676b 100644 --- a/man/BIOMOD_Modeling.Rd +++ b/man/BIOMOD_Modeling.Rd @@ -131,9 +131,9 @@ A \code{numeric} between \code{0} and \code{1} corresponding to the species prev build '\emph{weighted response weights}' (see Details)} \item{metric.eval}{a \code{vector} containing evaluation metric names to be used, must -be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -\code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -\code{ORSS}, \code{BOYCE}, \code{MPA}} +be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +\code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +\code{BOYCE}, \code{MPA}} \item{var.import}{(\emph{optional, default} \code{NULL}) \cr An \code{integer} corresponding to the number of permutations to be done for each variable to diff --git a/man/BIOMOD_Projection.Rd b/man/BIOMOD_Projection.Rd index f8fbf273..d4509c76 100644 --- a/man/BIOMOD_Projection.Rd +++ b/man/BIOMOD_Projection.Rd @@ -47,17 +47,17 @@ used to project the species distribution model(s)} A \code{vector} containing evaluation metric names to be used to transform prediction values into binary values based on models evaluation scores obtained with the \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -those of \code{bm.mod}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +those of \code{bm.mod}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +\code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +\code{ETS}, \code{BOYCE}, \code{MPA}} \item{metric.filter}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing evaluation metric names to be used to transform prediction values into filtered values based on models evaluation scores obtained with the \code{\link{BIOMOD_Modeling}} function. Must be among \code{all} (same evaluation metrics than -those of \code{bm.mod}) or \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +those of \code{bm.mod}) or \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +\code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +\code{ETS}, \code{BOYCE}, \code{MPA}} \item{compress}{(\emph{optional, default} \code{TRUE}) \cr A \code{logical} or a \code{character} value defining whether and how objects should be diff --git a/man/bm_PlotEvalMean.Rd b/man/bm_PlotEvalMean.Rd index cef6fb7e..57ece607 100644 --- a/man/bm_PlotEvalMean.Rd +++ b/man/bm_PlotEvalMean.Rd @@ -19,9 +19,9 @@ object that can be obtained with the \code{\link{BIOMOD_Modeling}} or \code{\link{BIOMOD_EnsembleModeling}} functions} \item{metric.eval}{a \code{vector} containing evaluation metric names to be used, must -be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -\code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -\code{ORSS}} +be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +\code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +\code{BOYCE}, \code{MPA}} \item{dataset}{a \code{character} corresponding to the dataset upon which evaluation metrics have been calculated and that is to be represented, must be among \code{calibration}, diff --git a/man/bm_RunModelsLoop.Rd b/man/bm_RunModelsLoop.Rd index 023b1922..de43aa1c 100644 --- a/man/bm_RunModelsLoop.Rd +++ b/man/bm_RunModelsLoop.Rd @@ -65,9 +65,9 @@ are to be used, must be among \code{colnames(bm.format@PA.table)}} \code{\link{bm_ModelingOptions}} function} \item{metric.eval}{a \code{vector} containing evaluation metric names to be used, must -be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, -\code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, -\code{ORSS}} +be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, +\code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, +\code{BOYCE}, \code{MPA}} \item{var.import}{(\emph{optional, default} \code{NULL}) \cr An \code{integer} corresponding to the number of permutations to be done for each variable to diff --git a/man/getters.out.Rd b/man/getters.out.Rd index 4b9c63c5..ee9f0589 100644 --- a/man/getters.out.Rd +++ b/man/getters.out.Rd @@ -197,9 +197,9 @@ as a long \code{data.frame} with many additional informations readily available.} \item{metric.eval}{(\emph{optional, default} \code{NULL}) \cr -A \code{vector} containing evaluation metric to be kept, must be among \code{ROC}, -\code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, -\code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +A \code{vector} containing evaluation metric to be kept, must be among \code{POD}, +\code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, +\code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{expl.var}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing explanatory variables to be kept, that can be obtained with the @@ -220,20 +220,20 @@ A \code{vector} containing merged pseudo-absence set to be loaded, must be among \item{filtered.by}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing evaluation metric selected to filter single models to build the -ensemble models, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, -\code{BIAS}, \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, -\code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +ensemble models, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, +\code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, +\code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{metric.binary}{(\emph{optional, default} \code{NULL}) \cr A \code{vector} containing evaluation metric selected to transform predictions into binary -values, must be among \code{ROC}, \code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, -\code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, -\code{HSS}, \code{OR}, \code{ORSS}} +values, must be among \code{POD}, \code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, +\code{BIAS}, \code{ROC}, \code{TSS}, \code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, +\code{ETS}, \code{BOYCE}, \code{MPA}} \item{metric.filter}{(\emph{optional, default} \code{NULL}) \cr -A \code{vector} containing evaluation metric to filter predictions, must be among \code{ROC}, -\code{TSS}, \code{KAPPA}, \code{ACCURACY}, \code{BIAS}, \code{POD}, \code{FAR}, -\code{POFD}, \code{SR}, \code{CSI}, \code{ETS}, \code{HK}, \code{HSS}, \code{OR}, \code{ORSS}} +A \code{vector} containing evaluation metric to filter predictions, must be among \code{POD}, +\code{FAR}, \code{POFD}, \code{SR}, \code{ACCURACY}, \code{BIAS}, \code{ROC}, \code{TSS}, +\code{KAPPA}, \code{OR}, \code{ORSS}, \code{CSI}, \code{ETS}, \code{BOYCE}, \code{MPA}} \item{\ldots}{(\emph{optional, one or several of the following arguments depending on the selected function})}