move example and remove reprojection from diversity_from_plot

DESCRIPTION

 Package: biodivMapR
 Title: biodivMapR: an R package for α- and β-diversity mapping using remotely-sensed images
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(person(given = "Jean-Baptiste", 
 					family = "Feret", 
 					email = "jb.feret@teledetection.fr", 

NEWS.md

-### biodivMapR v1.0.1 (Release date: 2019-09-27)
+# biodivMapR v1.0.2
+## Fixes
 
-Added NEWS.md
-Updated README.md: transfered from gitlab.irstea to github
-changed return() into return(invisible())
-updated vignettes & tutorial with latest outputs and figures from code
+## Changes
+- moved examples to repository root: example files are not installed with package anymore.
+- removed Plots reprojection from `diversity_from_plots`: 
+now, Plots and Raster must be in the same projection. Changed example Plots projection accordingly.
+
+# biodivMapR v1.0.1 (Release date: 2019-09-27)
+
+- Added NEWS.md
+- Updated README.md: transfered from gitlab.irstea to github
+- changed return() into return(invisible())
+- updated vignettes & tutorial with latest outputs and figures from code
 
 # biodivMapR v1.0.0 (Release date: 2019-09-26)
 
 First release in GitHub
-Submission accepted to Methods in Ecology and Evolution
\ No newline at end of file
+Submission accepted to Methods in Ecology and Evolution

R/Lib_Validation_biodivMapR.R

@@ -144,7 +144,7 @@ get_alpha_metrics = function(Distrib){
 #' @importFrom rgdal readOGR
 #' @import tools
 #' @export
-diversity_from_plots = function(Raster, Plots,NbClusters = 50,Name_Plot = FALSE){
+diversity_from_plots = function(Raster, Plots, NbClusters = 50, Name_Plot = FALSE){
   # get hdr from raster
   HDR           = read_ENVI_header(paste(Raster,'.hdr',sep=''))
   nbRepetitions = HDR$bands
@@ -176,12 +176,8 @@ diversity_from_plots = function(Raster, Plots,NbClusters = 50,Name_Plot = FALSE)
       Projection.Plot     = get_projection(File.Vector,'vector')
       Projection.Raster     = get_projection(Raster,'raster')
       # if not, convert vector file
-      if (!Projection.Raster==Projection.Plot){
-        if (!file.exists(File.Vector.reproject)){
-          dir.create(Dir.Vector.reproject, showWarnings = FALSE,recursive = TRUE)
-          reproject_vector(File.Vector,Projection.Raster,File.Vector.reproject)
-        }
-        Plot              = readOGR(Dir.Vector.reproject,Name.Vector[[ip]],verbose = FALSE)
+      if (compareCRS(Projection.Raster, Projection.Plot)){
+        stop('Raster and Plots have different projection. Plots should be reprojected to Raster CRS, see help(')
       }
     } else if (file.exists(paste(File.Vector,'kml','sep'='.'))){
       print('Please convert vector file to shpfile')

inst/extdata/examples/example_script.R → examples/example_script.R

@@ -42,9 +42,9 @@ Input_Image_File  = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset
 # set to FALSE if no mask available
 Input_Mask_File   = FALSE
 
-# relative or absolute path for the Directory where results will be stored
+# Output directory: files created by script will be written there.
 # For each image processed, a subdirectory will be created after its name
-Output_Dir        = 'RESULTS'
+Output_Dir        = '~/biodiv' # fill with your own path
 
 # SPATIAL RESOLUTION
 # resolution of spatial units for alpha and beta diversity maps (in pixels), relative to original image

inst/extdata/VECTOR/Forest_HighDiversity.prj

-GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
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+PROJCS["WGS_1984_UTM_Zone_33N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",15],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]
\ No newline at end of file

inst/extdata/VECTOR/Forest_LowDiversity.prj

-GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
\ No newline at end of file
+PROJCS["WGS_1984_UTM_Zone_33N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",15],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]
\ No newline at end of file

inst/extdata/VECTOR/Forest_MediumDiversity.prj

-GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
\ No newline at end of file
+PROJCS["WGS_1984_UTM_Zone_33N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",15],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]
\ No newline at end of file

inst/extdata/VECTOR/LowVegetation.prj

-GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
\ No newline at end of file
+PROJCS["WGS_1984_UTM_Zone_33N",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",15],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["Meter",1]]
\ No newline at end of file