replacing sp by sf and spplot by leaflet

sylvainschmitt · Oct 19, 2023 · e03e882 · e03e882
1 parent d8152bd
commit e03e882
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diff --git a/.travis.yml b/.travis.yml
@@ -15,7 +15,6 @@ addons:
       - libudunits2-dev
 
 r_packages:
-  - rgdal
   - covr
   - devtools
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -18,7 +18,7 @@ Description: Allows to map species richness and endemism based on stacked
 License: GPL (>=3) | file LICENSE
 LazyData: TRUE
 Imports:
-    sp (>= 1.2.0),
+    sf (>= 1.0-14),
     raster (>= 2.9-5),
     methods (>= 3.2.2),
     mgcv (>= 1.8.7),
@@ -42,7 +42,8 @@ Imports:
     iterators (>= 1.0.10),
     itertools (>= 0.1-3),
     parallel (>= 3.5.2),
-    snow (>= 0.4-3)
+    snow (>= 0.4-3),
+    leaflet (>= 2.2.0)
 Depends:
     R (>= 3.2.2)
 Collate:
@@ -81,11 +82,10 @@ Suggests:
     testthat,
     knitr,
     rmarkdown,
-    rgdal,
     geobuffer,
     fasterize,
     sdm
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3
 VignetteBuilder: 
     knitr,
     rmarkdown

diff --git a/NAMESPACE b/NAMESPACE
@@ -56,6 +56,13 @@ importFrom(graphics,barplot)
 importFrom(graphics,legend)
 importFrom(iterators,icount)
 importFrom(itertools,isplitVector)
+importFrom(leaflet,addLegend)
+importFrom(leaflet,addRasterImage)
+importFrom(leaflet,addTiles)
+importFrom(leaflet,colorNumeric)
+importFrom(leaflet,leaflet)
+importFrom(leaflet,leafletOutput)
+importFrom(leaflet,renderLeaflet)
 importFrom(mgcv,gam)
 importFrom(mgcv,gam.control)
 importFrom(nnet,nnet)
@@ -96,6 +103,8 @@ importFrom(reshape2,melt)
 importFrom(rpart,rpart)
 importFrom(rpart,rpart.control)
 importFrom(scales,muted)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_buffer)
 importFrom(shiny,actionButton)
 importFrom(shiny,brushOpts)
 importFrom(shiny,checkboxGroupInput)
@@ -138,13 +147,6 @@ importFrom(shinydashboard,sidebarMenuOutput)
 importFrom(shinydashboard,tabBox)
 importFrom(shinydashboard,tabItem)
 importFrom(shinydashboard,tabItems)
-importFrom(sp,Polygon)
-importFrom(sp,Polygons)
-importFrom(sp,SpatialPoints)
-importFrom(sp,SpatialPolygons)
-importFrom(sp,bbox)
-importFrom(sp,coordinates)
-importFrom(sp,spplot)
 importFrom(spThin,thin)
 importFrom(stats,aggregate.data.frame)
 importFrom(stats,cor)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,13 @@
 NEWS
 ================
 
+SSDM 0.2.8.9001
+===============
+
+bug fixes:
+- totally removing rgdal following r-spatial evolution
+- moving from sp to sf following r-spatial evolution
+
 SSDM 0.2.8.9000
 ===============
 new/edited:

diff --git a/R/PA.select.R b/R/PA.select.R
@@ -1,6 +1,6 @@
 #' @include Algorithm.SDM.R
 #' @import methods
-#' @importFrom sp Polygon Polygons SpatialPolygons bbox
+#' @importFrom sf st_as_sf st_buffer
 #' @importFrom raster raster stack extract predict reclassify layerStats calc Which xyFromCell crs
 NULL
 
@@ -17,17 +17,9 @@ setMethod('PA.select', "Algorithm.SDM", function(obj, Env, PA = NULL, verbose =
   # Mask defining
   if (PA$strat == 'disk') {
     if(verbose) {cat('   disk selection \n')}
-    circles = list()
-    for (i in seq_len(length(obj@data$X))) {
-      x = obj@data$X[i]
-      y = obj@data$Y[i]
-      pts = seq(0, 2 * pi, length.out = 100)
-      xy = cbind(x + 2/60 * sin(pts), y + 2/60 * cos(pts))
-      circle = Polygon(xy)
-      circles[i] = circle
-    }
-    sc= SpatialPolygons(list(Polygons(circles, 'Circles')))
-    Mask = mask(Env[[1]], sc)
+    circles <- st_as_sf(obj@data, coords = c("X", "Y"))
+    circles <- st_buffer(circles, 2/60)
+    Mask = mask(Env[[1]], circles)
   }
   if(PA$strat=='geobuffer'){
     if(!is.null(PA$dist)){

diff --git a/R/SDM.R b/R/SDM.R
@@ -1,5 +1,4 @@
 #' @import methods
-#' @importFrom sp Polygon Polygons SpatialPolygons bbox
 #' @importFrom raster raster stack extract predict reclassify layerStats calc
 #' @importFrom mgcv gam gam.control
 #' @importFrom earth earth

diff --git a/R/evaluate.R b/R/evaluate.R
@@ -7,7 +7,6 @@
 #' @importFrom stats aggregate.data.frame cor glm glm.control rbinom runif sd var
 #' @importFrom utils lsf.str read.csv read.csv2 tail write.csv
 #' @importFrom raster reclassify rasterize extract stack
-#' @importFrom sp SpatialPoints coordinates
 NULL
 
 #' Evaluate

diff --git a/R/mapDiversity.R b/R/mapDiversity.R
@@ -1,5 +1,4 @@
 #' @include Ensemble.SDM.R checkargs.R
-#' @importFrom sp Polygon Polygons SpatialPolygons SpatialPoints bbox
 #' @importFrom raster raster stack reclassify mask calc overlay values rasterize rasterToPoints values<- Which setValues
 #' @importFrom stats lm optim
 #' @importFrom poibin dpoibin
@@ -143,7 +142,7 @@ setMethod("mapDiversity", "Stacked.SDM", function(obj, method, rep.B = 1000,
     # helper functions and maximum likelihood function
     logit = function(x) {x=ifelse(x<0.0001,0.0001,ifelse(x>0.9999,.9999,x));   ;log(x/(1 - x))}
     invlogit = function(x) {exp(x)/(1+exp(x))}
-    
+
     nLL.Calabrese <- function(par,sr,probs) {
       bysite <- function(j) {
         logit.probs <- logit(as.numeric(probs[j,]))
@@ -152,16 +151,16 @@ setMethod("mapDiversity", "Stacked.SDM", function(obj, method, rep.B = 1000,
       }
       - sum(sapply(seq_len(length(sr)),bysite)) 	# optim performs minimization, so for maximum likelihood we need to invert
     }
-    
+
   # find the maximum likelihood estimates for adjustment parameters
-    adj.par <- optim(par=c(0,0), fn=nLL.Calabrese, sr=obs.sr, probs=pred.prob) 
+    adj.par <- optim(par=c(0,0), fn=nLL.Calabrese, sr=obs.sr, probs=pred.prob)
   # adjust the predicted probabilities, transform back with invlogit and stack
     corr.sr <- rowSums(apply(pred.prob,2,FUN=function(x){invlogit(logit(x)+adj.par$par[1]*obs.sr+adj.par$par[2])}))
     ### End of code from Damaris Zurell/Justin Calabrese
-    
+
     diversity.map[ind_notNA] <- corr.sr
   }
-  
+
 
   if (method == "PRR.MEM") {
     # Probability ranking with MEM (SESAM, D'Amen et al, 2015)