fix #27 actieve haarden (WIP) + replace sp,rgdal,rgeos functions

.gitignore

@@ -50,3 +50,6 @@ alienSpecies/man/
 
 # Large data files
 alienSpecies/inst/extdata/full_timeseries.csv
+
+# Tmp files for #27
+/verspaVelutina/

alienSpecies/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: alienSpecies
 Type: Package
 Title: Portal for alien and invasive species indicators
-Version: 0.0.3
+Version: 0.0.4
 Date: 2023-02-01
 Author: Machteld Varewyck
 Maintainer: Machteld Varewyck <machteld.varewyck@openanalytics.eu>
@@ -16,14 +16,12 @@ Imports:
     INBOtheme (<= 0.5.9),
     jsonlite,
     leaflet,
+    leaflet.extras,
     plotly,
     rgbif,
-	rgdal,
-	rgeos,
-    shiny,
+	shiny,
 	shinycssloaders,
 	sf,
-	sp,
 	tidyverse,
 	trias (>= 2.0.3),
 	webshot

alienSpecies/NAMESPACE

@@ -31,6 +31,9 @@ export(loadTabularData)
 export(mapCube)
 export(mapCubeServer)
 export(mapCubeUI)
+export(mapHeat)
+export(mapHeatServer)
+export(mapHeatUI)
 export(mapOccurrence)
 export(mapRegions)
 export(mapRegionsServer)
@@ -92,11 +95,15 @@ importFrom(htmltools,div)
 importFrom(htmlwidgets,saveWidget)
 importFrom(jsonlite,toJSON)
 importFrom(leaflet,`%>%`)
+importFrom(leaflet,addCircleMarkers)
+importFrom(leaflet,addLegend)
 importFrom(leaflet,addMarkers)
+importFrom(leaflet,addScaleBar)
 importFrom(leaflet,addTiles)
 importFrom(leaflet,leaflet)
 importFrom(leaflet,leafletOutput)
 importFrom(leaflet,markerClusterOptions)
+importFrom(leaflet.extras,addHeatmap)
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
 importFrom(plotly,plotlyOutput)
@@ -106,17 +113,14 @@ importFrom(rgbif,occ_download_get)
 importFrom(rgbif,occ_download_import)
 importFrom(rgbif,occ_download_wait)
 importFrom(rgbif,pred)
-importFrom(rgdal,readOGR)
-importFrom(rgeos,gUnaryUnion)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_drop_geometry)
 importFrom(sf,st_read)
 importFrom(sf,st_transform)
+importFrom(sf,st_union)
 importFrom(shiny,runApp)
 importFrom(shiny,singleton)
 importFrom(shinycssloaders,withSpinner)
-importFrom(sp,CRS)
-importFrom(sp,spTransform)
 importFrom(stats,aggregate)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)

alienSpecies/R/data_createOccupancy.R

@@ -8,8 +8,6 @@
 #' @return TRUE if creation succeeded
 #' 
 #' @author mvarewyck
-#' @importFrom rgdal readOGR
-#' @importFrom sp spTransform CRS
 #' @importFrom sf st_read
 #' @importFrom data.table as.data.table
 #' @export
@@ -21,16 +19,15 @@ createOccupancyCube <- function(dataDir = "~/git/alien-species-portal/data/trend
 
   # geojson: https://zenodo.org/record/3835756#.Yoc5oLxBw5m
   data_t0 <- lapply(seq(2016, 2020, by = 2), function(iYear) {
-      dataYear <- rgdal::readOGR(dsn = file.path(dataDir, paste0("ias_belgium_t0_", iYear, ".geojson")), verbose = TRUE)
-      dataYear <- sp::spTransform(dataYear, sp::CRS("+proj=longlat +datum=WGS84"))
+      dataYear <- sf::st_read(file.path(dataDir, paste0("ias_belgium_t0_", iYear, ".geojson")), quiet = TRUE)
       # inconsistent colnames over the years
-      colnames(dataYear@data) <- c("cellcode", "reference", "data_partn", "accepted", "species", "notes")
+      colnames(dataYear) <- c("cellcode", "reference", "data_partn", "accepted", "species", "notes")
       dataYear$year <- iYear
       dataYear
     })
   # sp::plot(data_t0[[1]])
 
-  data_t0_all <- do.call(rbind, data_t0)@data
+  data_t0_all <- do.call(rbind, data_t0)
   data_t0_all$source <- "t0"
   # table(data_t0_all)
 

alienSpecies/R/data_load.R

@@ -5,8 +5,6 @@
 #' @return list with sf objects
 #' 
 #' @author mvarewyck
-#' @importFrom rgdal readOGR
-#' @importFrom sp spTransform
 #' @importFrom sf st_read
 #' @export
 readShapeData <- function(extension = c(".gpkg", ".shp", ".geojson"),
@@ -29,8 +27,7 @@ readShapeData <- function(extension = c(".gpkg", ".shp", ".geojson"),
 
     toReturn <- lapply(shapeFiles, function(iFile) {
 
-        spatialData <- readOGR(dsn = file.path(dataDir, iFile), verbose = FALSE)
-        sp::spTransform(spatialData, CRS("+proj=longlat +datum=WGS84"))
+        sf::st_read(file.path(dataDir, iFile), layer = gsub(extension, "", iFile), quiet = TRUE)
 
       })