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 @@