adding files

collections/qgis_rscripts/rscripts/Distance.rsx

@@ -1,16 +1,22 @@
 ##Basic statistics=group
-##Layer1=vector
-##Layer2=vector
-##Field=Field Layer1
-##output= output vector
-library(geosphere)
-library(rgeos)
-line<-gLineMerge(Layer2, byid=FALSE, id = NULL)
-x<-coordinates(Layer1)
-X<-dist2Line(x, line, distfun=distHaversine)
-matrix<-as.matrix(X[,2:3])
-X<-cbind(X, as.data.frame(Layer1[[Field]]))
-result<-SpatialPointsDataFrame(matrix, as.data.frame(X, row.names=NULL))
-proj4string(Layer1)->crs
-proj4string(result)<-crs
-output<-result
+##Input_Point_Layer=vector
+##Line_Layer=vector
+##ID_Field=Field Input_Point_Layer
+##Nearest=output vector
+library(geosphere)
+library(rgeos)
+
+# Remove the z and m dimensions
+PointsXY=st_zm(Input_Point_Layer)
+LinesXY=st_zm(Line_Layer)
+# Change format
+SpatPointsXY=as(PointsXY, "Spatial")
+SpatLinesXY=as(LinesXY, "Spatial")
+
+line=gLineMerge(SpatLinesXY, byid=FALSE, id = NULL)
+x=coordinates(SpatPointsXY)
+X=dist2Line(x, line, distfun=distHaversine)
+matrix=as.matrix(X[,2:3])
+X=cbind(X, as.data.frame(SpatPointsXY[[ID_Field]]))
+result=SpatialPointsDataFrame(matrix, as.data.frame(X, row.names=NULL))
+Nearest=st_set_crs(st_as_sf(result),st_crs(Input_Point_Layer))

collections/qgis_rscripts/rscripts/Distance.rsx.help

@@ -1 +1 @@
-{"Layer2": "a line", "ALG_DESC": "This script calculates the distance between two geometries: a line and points.", "ALG_CREATOR": "JEANDENANS L.", "Layer1": "a set of data (points)", "Field": "identification of points", "ALG_HELP_CREATOR": "JEANDENANS L.", "output": "a shapfile with points and the distance."}
+{"Line_Layer": "A line layer", "ALG_DESC": "This script calculates the distance from points in a point layer to the nearest line in a line layer. Coordinates have to be in the latitude / longitude ranges.", "ALG_CREATOR": "QGIS community", "Input_Point_Layer": "a set of points (lat/lon)", "Field": "ID field for the points", "ALG_HELP_CREATOR": "QGIS community", "Nearest": "A point layer (the nearest point on the line for each input point) with the distance."}

collections/qgis_rscripts/rscripts/G_function.rsx

@@ -4,5 +4,6 @@
 ##showplots
 library("maptools")
 library("spatstat")
-ppp=as(as(Layer, "SpatialPoints"),"ppp")
+#ppp=as(as(Layer, "SpatialPoints"),"ppp")
+ppp=as(as(Layer, "Spatial"),"ppp")
 plot(envelope(ppp, Gest, nsim=Nsim))

collections/qgis_rscripts/rscripts/Kernel_density_estimation.rsx

@@ -2,7 +2,7 @@
 ##Layer1=vector
 ##Layer2=vector
 ##methode=number 1
-##Output= output raster
+##Output=output raster
 library(rgdal)
 library(surveillance)
 library(maptools)
@@ -103,8 +103,18 @@ ZNA = f0$estimate,
 H = fhat$H,
 W = fhat$W)
 }
-points<-coordinates(Layer1)
-polygon<-Layer2
+
+#points<-coordinates(Layer1)
+spatpoints = as(Layer1, "Spatial")
+points<-coordinates(spatpoints)
+>print("---points-----------------------------------------------------")
+>str(points)
+
+#polygon<-Layer2
+polygon<-as(Layer2, "Spatial")
+>print("---polygon-----------------------------------------------------")
+>str(polygon)
+
 if(methode==0){
 estimate <- sKDE(U = points, polygon = polygon,
 optimal=TRUE, parallel = FALSE)
@@ -135,6 +145,7 @@ coordinates(Grille)=c("X","Y")
 gridded(Grille)<-TRUE
 library(raster)
 result<-raster(Grille,layer=1, values=TRUE)
-proj4string(Layer1)->crs
+#proj4string(Layer1)->crs
+proj4string(spatpoints)->crs
 proj4string(result)<-crs
 Output=result

collections/qgis_rscripts/rscripts/Minimum_convex_polygon.rsx

@@ -1,7 +1,12 @@
 ##Home Range Analysis=group
 ##Layer=vector
-##Percentage=number 10
+##Percentage=number 90
 ##Field=Field Layer
 ##Home_ranges=Output vector
 library(adehabitatHR)
-Home_ranges<-mcp(Layer[,Field],percent=Percentage)
+
+SpatialLayer = as(Layer, "Spatial")
+HR<-mcp(SpatialLayer[,Field],percent=Percentage)
+Home_ranges<-st_as_sf(HR)
+
+

collections/qgis_rscripts/rscripts/Monte-Carlo_spatial_randomness.rsx

@@ -1,12 +1,14 @@
 ##Point pattern analysis=group
 ##Layer=vector point
 ##Simulations=number 100
-##Optional_plot_name=string
+##Plot_name=string 'K function'
 ##showplots
 library(spatstat)
 library(maptools)
-sp <- as(Layer, "SpatialPoints")
+
+sp <- as(Layer, "Spatial")
 sp <- as(sp, "ppp")
+
 e <- envelope(sp, Kest, nsim = Simulations)
->e
-plot(e, main = Optional_plot_name)
+plot(e, main = Plot_name)
+

collections/qgis_rscripts/rscripts/Quadrat_analysis.rsx

@@ -3,7 +3,8 @@
 ##showplots
 library("maptools")
 library("spatstat")
-ppp=as(as(Layer, "SpatialPoints"),"ppp")
+#ppp=as(as(Layer, "SpatialPoints"),"ppp")
+ppp=as(as(Layer, "Spatial"),"ppp")
 qc=quadratcount(ppp)
 plot(Layer)
 plot(qc, add=TRUE)

collections/qgis_rscripts/rscripts/Random_sampling_grid.rsx

@@ -1,6 +1,10 @@
 ##Point pattern analysis=group
-##Layer=vector
+##Layer=vector polygon
 ##Size=number 10
 ##Output= output vector
-pts=spsample(Layer,Size,type="random")
-Output=SpatialPointsDataFrame(pts, as.data.frame(pts))
+spatpoly = as(Layer, "Spatial")
+
+pts=spsample(spatpoly,Size,type="random")
+spdf=SpatialPointsDataFrame(pts, as.data.frame(pts))
+
+Output=st_as_sf(spdf)

collections/qgis_rscripts/rscripts/Regular_sampling_grid.rsx

@@ -1,6 +1,10 @@
 ##Point pattern analysis=group
-##Layer=vector
+##Layer=vector polygon
 ##Size=number 10
 ##Output= output vector
-pts=spsample(Layer,Size,type="regular")
-Output=SpatialPointsDataFrame(pts, as.data.frame(pts))
+spatpoly = as(Layer, "Spatial")
+
+pts=spsample(spatpoly,Size,type="regular")
+spdf=SpatialPointsDataFrame(pts, as.data.frame(pts))
+
+Output=st_as_sf(spdf)

collections/qgis_rscripts/rscripts/Ripley_-_Rasson_spatial_domain.rsx

@@ -3,10 +3,12 @@
 ##Output=output vector
 library("spatstat")
 library("maptools")
-proj4string(Layer)->crs
-spatpoints = as(Layer,"SpatialPoints")
+
+crs=st_crs(Layer)
+spatpoints = as(Layer, "Spatial")
+
 ripras=ripras(as(spatpoints,"ppp"))
 polyg=as(ripras,"SpatialPolygons")
-Output1= SpatialPolygonsDataFrame(polyg, data.frame(1))
-proj4string(Output1)<-crs
-Output<-Output1
+SPDF=SpatialPolygonsDataFrame(polyg, data.frame(1))
+
+Output=st_set_crs(st_as_sf(SPDF), crs)

collections/qgis_rscripts/rscripts/Tobler.rsx

@@ -1,29 +1,43 @@
 ##Basic statistics=group
-##Layer=raster
-##x_depart= number 0.1
-##y_depart= number 0.1
-##x_arrivee= number 0.1
-##y_arrivee= number 1
+##DEM_Layer=raster
+# ##Start=point
+##x_start=number 10.0
+##y_start=number 60.0
+# ##Destination=point
+##x_destination=number 11.0
+##y_destination=number 59.0
 ##Output= output vector
 library(gdistance)
 library(rgdal)
-datas<-raster(Layer)
+
+dem=raster(DEM_Layer)
 
 heightDiff <-function(x)(x[2] - x[1])
-hd <- transition(datas,heightDiff,8)#packages gdistance
+hd <- transition(dem,heightDiff,8)#packages gdistance
 slope <- geoCorrection(hd, scl=FALSE)#packages gdistance
-adj <- adjacent(x = datas, cells = 1:ncell(datas),pairs=TRUE ,directions=8) #packages raster
+adj <- adjacent(x=dem, cells=1:ncell(dem), pairs=TRUE, directions=8) #packages raster
 speed <- slope
 speed[adj] <- exp(-3.5 * abs(slope[adj])+0.05)
 speed<-geoCorrection(speed) #packages gdistance
+>print("--speed------------------------------------------------------")
+>str(speed)
 
-Ax=x_depart
-Ay=y_depart
-Bx=x_arrivee
-By=y_arrivee
+Ax=x_start
+Ay=y_start
+Bx=x_destination
+By=y_destination
 
 c1<-c(Ax, Ay)
+#c1=Start
+>print("--c1------------------------------------------------------")
+>str(c1)
+
 c2<-c(Bx, By)
+#c2 = Destination
+>print("---c2-----------------------------------------------")
+>str(c2)
 
 sPath1 <-shortestPath(speed, c1, c2,output="SpatialLines")
-Output=SpatialLinesDataFrame(sPath1, data=as.data.frame(c(1:length(sPath1))), match.ID = F)
+sldf=SpatialLinesDataFrame(sPath1, data=as.data.frame(c(1:length(sPath1))), match.ID = F)
+Output=st_as_sf(sldf)
+

collections/qgis_rscripts2/rscripts/Distance.rsx

@@ -0,0 +1,16 @@
+##Basic statistics=group
+##Layer1=vector
+##Layer2=vector
+##Field=Field Layer1
+##output= output vector
+library(geosphere)
+library(rgeos)
+line<-gLineMerge(Layer2, byid=FALSE, id = NULL)
+x<-coordinates(Layer1)
+X<-dist2Line(x, line, distfun=distHaversine)
+matrix<-as.matrix(X[,2:3])
+X<-cbind(X, as.data.frame(Layer1[[Field]]))
+result<-SpatialPointsDataFrame(matrix, as.data.frame(X, row.names=NULL))
+proj4string(Layer1)->crs
+proj4string(result)<-crs
+output<-result

collections/qgis_rscripts2/rscripts/Distance.rsx.help

@@ -0,0 +1 @@
+{"Layer2": "a line", "ALG_DESC": "This script calculates the distance between two geometries: a line and points.", "ALG_CREATOR": "JEANDENANS L.", "Layer1": "a set of data (points)", "Field": "identification of points", "ALG_HELP_CREATOR": "JEANDENANS L.", "output": "a shapfile with points and the distance."}

collections/qgis-rscripts2/rscripts/G_function.rsx → collections/qgis_rscripts2/rscripts/G_function.rsx

@@ -2,9 +2,7 @@
 ##Layer=vector point
 ##Nsim=number 10
 ##showplots
-
 library("maptools")
 library("spatstat")
-
-ppp=as(as(Layer, "Spatial"),"ppp")
+ppp=as(as(Layer, "SpatialPoints"),"ppp")
 plot(envelope(ppp, Gest, nsim=Nsim))