v4.2-4-9 fixed predict for RF with do.classif = FALSE

biomodhub · Aug 21, 2023 · ad3976c · ad3976c
1 parent 22cf431
commit ad3976c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: biomod2
 Type: Package
 Title: Ensemble Platform for Species Distribution Modeling
-Version: 4.2-4-8
+Version: 4.2-4-9
 Date: 2023-06-15
 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut")
                     , email = "[email protected]"),

diff --git a/R/biomod2_classes_4.R b/R/biomod2_classes_4.R
@@ -1048,16 +1048,22 @@ setClass('RF_biomod2_model',
 
 setMethod('predict2', signature(object = 'RF_biomod2_model', newdata = "SpatRaster"),
           function(object, newdata, ...) {
-            predfun <- function(object, newdata, mod.name){
-              # new predict command used with terra
-              subset(predict(newdata, model = get_formal_model(object),
-                             type = 'prob',
-                             wopt = list(names = rep(mod.name,2))), 
-                     2)   
-              # old predict function used with raster
-              # predict(newdata, model = get_formal_model(object), type = 'prob', index = 2)            
-
-
+            if (object@model_options$do.classif == TRUE) {
+              predfun <- function(object, newdata, mod.name){
+                # new predict command used with terra
+                subset(predict(newdata, model = get_formal_model(object),
+                               type = 'prob',
+                               wopt = list(names = rep(mod.name,2))), 
+                       2)   
+                # old predict function used with raster
+                # predict(newdata, model = get_formal_model(object), type = 'prob', index = 2)
+              }
+            } else { #regression case
+              predfun <- function(object, newdata, mod.name){
+                predict(newdata, model = get_formal_model(object),
+                        type = 'response',
+                        wopt = list(names = rep(mod.name,2))) 
+              }
             }
             # redirect to predict2.biomod2_model.SpatRaster
             callNextMethod(object, newdata, predfun = predfun, ...)
@@ -1068,8 +1074,14 @@ setMethod('predict2', signature(object = 'RF_biomod2_model', newdata = "SpatRast
 ##' @rdname predict2.bm
 setMethod('predict2', signature(object = 'RF_biomod2_model', newdata = "data.frame"),
           function(object, newdata, ...) {
-            predfun <- function(object, newdata, not_na_rows){
-              as.numeric(predict(get_formal_model(object), as.data.frame(newdata[not_na_rows, , drop = FALSE]), type = 'prob')[, '1'])        
+            if (object@model_options$do.classif == TRUE) {
+              predfun <- function(object, newdata, not_na_rows) {
+                as.numeric(predict(get_formal_model(object), as.data.frame(newdata[not_na_rows, , drop = FALSE]), type = 'prob')[, '1'])        
+              }
+            } else { # regression case
+              predfun <- function(object, newdata, not_na_rows) {
+                as.numeric(predict(get_formal_model(object), as.data.frame(newdata[not_na_rows, , drop = FALSE]), type = 'response'))        
+              }
             }
 
             # redirect to predict2.biomod2_model.data.frame

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diff --git a/docs/reference/BIOMOD.ensemble.models.out.html b/docs/reference/BIOMOD.ensemble.models.out.html
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diff --git a/docs/reference/BIOMOD_ConvertOldRun-deprecated.html b/docs/reference/BIOMOD_ConvertOldRun-deprecated.html
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diff --git a/docs/reference/BIOMOD_FormatingData.html b/docs/reference/BIOMOD_FormatingData.html