From d858afd15fbd7f00f39519bb591394ec847ae14e Mon Sep 17 00:00:00 2001
From: sylvainschmitt <sylvain.schmitt@agroparistech.fr>
Date: Fri, 14 Jun 2019 13:25:55 +0200
Subject: [PATCH] SSDM 0.2.5.9001 #36 and #49 fixed

---
 NEWS.md          |  5 +++++
 R/PA.select.R    |  4 ++--
 R/project.R      | 14 +-------------
 cran-comments.md |  4 +---
 4 files changed, 9 insertions(+), 18 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 85944b4..330e2e0 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,11 @@
 NEWS
 ================
 
+SSDM 0.2.5.9001
+===============
+
+- #36 and #49 fixed
+
 SSDM 0.2.5.9000
 ===============
 
diff --git a/R/PA.select.R b/R/PA.select.R
index cee14e1..0252fad 100755
--- a/R/PA.select.R
+++ b/R/PA.select.R
@@ -15,8 +15,8 @@ setMethod('PA.select', "Algorithm.SDM", function(obj, Env, PA = NULL, verbose =
   }
 
   # Mask defining
-  if (PA$strat == '2nd') {
-    if(verbose) {cat('   second far selection \n')}
+  if (PA$strat == 'disk') {
+    if(verbose) {cat('   disk selection \n')}
     circles = list()
     for (i in seq_len(length(obj@data$X))) {
       x = obj@data$X[i]
diff --git a/R/project.R b/R/project.R
index 457766a..e310040 100755
--- a/R/project.R
+++ b/R/project.R
@@ -14,20 +14,8 @@ setMethod("project", "Algorithm.SDM", function(obj, Env, ...) {
   factors[sapply(factors, is.null)] <- NULL
   names(factors) <- unlist(sapply(seq_len(length(Env@layers)), function(i)
     if(Env[[i]]@data@isfactor) names(Env[[i]])))
+  if(length(factors)==0) factors <- NULL
   proj = suppressWarnings(raster::predict(Env, model, factors = factors))
-  # proj = suppressWarnings(raster::predict(Env, model, fun = function(model,
-  #                                                                    x) {
-  #   x = as.data.frame(x)
-  #   for (i in seq_len(length(Env@layers))) {
-  #     if (Env[[i]]@data@isfactor) {
-  #       x[, i] = as.factor(x[, i])
-  #       x[, i] = droplevels(x[, i])
-  #       levels(x[, i]) = Env[[i]]@data@attributes[[1]]$ID
-  #     }
-  #   }
-  #   return(predict(model, x))
-  # }))
-  # Rescaling projection
   proj = reclassify(proj, c(-Inf, 0, 0))
   if(all(obj@data$Presence %in% c(0,1))) # MEMs should not be rescaled
     if(proj@data@max > 0) proj = proj / proj@data@max
diff --git a/cran-comments.md b/cran-comments.md
index 98dd42c..7845aaa 100755
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -13,6 +13,4 @@ There were no NOTEs, ERRORs or WARNINGs.
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* Fixed dependency compatibility with raster 2.9-5
-* Changed maintainter mail adress (permanent adress)
-* Removed rgdal from vignette builder as asked by mail
+* Fixed a major bug from version 0.2.4 due to dependency compatibility with raster 2.9-5