Merge pull request #1537 from ecor/master

Watershed Analysis - Test and Ducumentation with new names

.gitignore

@@ -5,6 +5,8 @@ src/Makevars.ucrt.rej
 proj_conf_test
 .Rproj
 
+proj_conf_test*
+*.Rproj
 *.tar.gz
 *Rcheck/
 *.o

DESCRIPTION

@@ -20,7 +20,7 @@ Authors@R: c(
 	person("Robert J.", "Hijmans", role = c("cre", "aut"),  
 			email = "[email protected]", comment = c(ORCID = "0000-0001-5872-2872")),
     person("Roger", "Bivand",  role = "ctb", comment = c(ORCID = "0000-0003-2392-6140")),
-    person("Cordana", "Emanuele", role="ctb"),
+    person("Emanuele", "Cordano", role="ctb",comment = c(ORCID=  "0000-0002-3508-5898")),
     person("Krzysztof", "Dyba",  role = "ctb", comment = c(ORCID = "0000-0002-8614-3816")),
     person("Edzer", "Pebesma", role = "ctb", comment = c(ORCID = "0000-0001-8049-7069")),
     person("Michael D.", "Sumner", role = "ctb"))

NAMESPACE

@@ -5,7 +5,9 @@ exportMethods("[", "[[", "!", "%in%", activeCat, "activeCat<-", "add<-", addCats
 
 ## EC 20210702 ecor
 exportMethods(watershed, pitfinder, NIDP, flowAccumulation)
-
+## EC 20250606 ecor
+###exportMethods(watershed2,pitfinder2,NIDP2,flowAccu2,flowAccu2_weight)
+## END EC 
 
 S3method(cbind, SpatVector)
 S3method(rbind, SpatVector)
@@ -28,3 +30,4 @@ export(add_box, add_legend, add_grid, focalMat, extractAlong, gdal, getGDALconfi
 
 
 
+

R/generics.R

@@ -1060,15 +1060,16 @@ setMethod("terrain", signature(x="SpatRaster"),
 	function(x, v="slope", neighbors=8, unit="degrees", filename="", ...) {
 
 	  if (v=="flowacc") {
-	       flowAccu2(x,filename=filename,...)
+	       flowAccumulation(x,filename=filename,...)
 
 	  } else {
 		  unit <- match.arg(unit, c("degrees", "radians"))
 		  opt <- spatOptions(filename, ...)
 		  seed <- ifelse("flowdir" %in% v, .seed(), 0)
 		  x@ptr <- x@ptr$terrain(v, neighbors[1], unit=="degrees", seed, opt)
-		  messages(x, "terrain")
+
 	  }
+	  messages(x, "terrain")
 	}
 )
 

inst/tinytest/test_flowacc2.R → inst/tinytest/test_flowAccumulation.R

@@ -27,7 +27,7 @@ flowacc0 <- c(001,001,001,001,001,001,
 
 
 flowdir1 <- terrain(elev,"flowdir")
-flowacc1 <- flowAccu2(flowdir1)
+flowacc1 <- flowAccumulation(flowdir1)
 
 result <- (flowacc1==flowacc0) & (flowdir1==flowdir0)
 

inst/tinytest/test_pitfinder2.R → inst/tinytest/test_pitfinder.R

@@ -30,7 +30,7 @@ flowdir<- terrain(elev,v="flowdir")
 
 ## Pit Detect
 
-pits1 <- pitfinder2(flowdir)
+pits1 <- pitfinder(flowdir)
 
 xypit <- as.data.frame(pits1,xy=TRUE)
 names(xypit) <- c("x","y","pit")

man/NIPD.Rd

@@ -82,8 +82,8 @@ plot(flowdir1)
 plot(flowdir2)
 
 ## 
-nidp1 <- NIDP2((flowdir1))
-nidp2 <- NIDP2((flowdir2))
+nidp1 <- NIDP((flowdir1))
+nidp2 <- NIDP((flowdir2))
 
 t(array(nidp1[],rev(dim(nidp1)[1:2])))
 t(array(nidp2[],rev(dim(nidp2)[1:2])))

man/flowAccumulaion.Rd → man/flowAccumulation.Rd

@@ -12,7 +12,7 @@ Computes flow accumulation or the total contributing area in terms of numbers of
 }
 
 \usage{
-\S4method{flowAccu2}{SpatRaster}(x, weight=NULL, filename="", ...) 
+\S4method{flowAccumulation}{SpatRaster}(x, weight=NULL, filename="", ...) 
 }
 
 \arguments{
@@ -30,7 +30,7 @@ SpatRaster
 The algorithm is an adaptation of the one proposed by Zhou at al, 2019. 
 }
 
-\seealso{\code{\link{terrain}},\code{\link{watershed2}},\code{\link{NIDP2}}}
+\seealso{\code{\link{terrain}},\code{\link{watershed}},\code{\link{NIDP}}}
 
 \author{
 Emanuele Cordano
@@ -53,7 +53,7 @@ for (r in 1:nrow(elev1)) {
 
     x <- (c-5)*dy
     elev1[r,c] <- 5*(x^2+y^2)
-    elev2[r,c] <- 10+5*(abs(x))-0.001*y ### 5*(x^2+y^2)
+    elev2[r,c] <- 10+5*(abs(x))-0.001*y 
   }
 } 
 
@@ -80,10 +80,10 @@ plot(flowdir1)
 plot(flowdir2)
 
 ## 
-flow_acc1 <- flowAccu2((flowdir1))
-flow_acc2 <- flowAccu2((flowdir2))
+flow_acc1 <- flowAccumulation((flowdir1))
+flow_acc2 <- flowAccumulation((flowdir2))
 ## Alternative option 
-## here the argument of "terrain"functions is not elevation but flow directions.
+## here the argument of "terrain" functions is  flow directions instead of elevation.
 
 flow_acc2a <- terrain(flowdir2,"flowacc") 
 t(array(flow_acc1[],rev(dim(flow_acc1)[1:2])))
@@ -95,8 +95,8 @@ plot(flow_acc2)
 weight <- elev1*0+10
 
 
-flow_acc1w <- flowAccu2_weight(flowdir1,weight)
-flow_acc2w <- flowAccu2_weight(flowdir2,weight)
+flow_acc1w <- flowAccumulation(flowdir1,weight)
+flow_acc2w <- flowAccumulation(flowdir2,weight)
 
 t(array(flow_acc1w[],rev(dim(flow_acc1w)[1:2])))
 t(array(flow_acc2w[],rev(dim(flow_acc2w)[1:2])))
@@ -111,8 +111,8 @@ elev <- rast(system.file('ex/elev.tif',package="terra"))
 flowdir <- terrain(elev,"flowdir")
 
 weight <- cellSize(elev,unit="km")
-flowacc_weight <- flowAccu2_weight(flowdir,weight)
-flowacc  <- flowAccu2(flowdir)
+flowacc_weight <- flowAccumulation(flowdir,weight)
+flowacc  <- flowAccumulation(flowdir)
 
 
 }

man/pitfinder.Rd

@@ -16,7 +16,7 @@ find pits (depressions with no outlet )
 }
 
 \arguments{
-  \item{p}{SpatRaster wih flow-direcion. See \code{\link{terrain}}}
+  \item{x}{SpatRaster wih flow-direcion. See \code{\link{terrain}}}
   \item{filename}{character. Output filename}
   \item{...}{additional arguments for writing files as in \code{\link{writeRaster}}}  
 }
@@ -32,7 +32,7 @@ A \code{\link{SpatRaster-class}} (raster) map containing value 1 for the pits  a
 Emanuele Cordano
 }
 
-\seealso{\code{\link{terrain}},\code{\link{watershed2}},\code{\link{flowAccu2}},\code{\link{flowAccu2_weight}},\code{\link{NIDP2}}}
+\seealso{\code{\link{terrain}},\code{\link{watershed}},\code{\link{flowAccumulation}},\code{\link{NIDP}}}
 \examples{
 
 ## Creation of a Digital Elevation Model 
@@ -60,14 +60,14 @@ t(array(flowdir[],rev(dim(flowdir)[1:2])))
 
 ## Pit Detect
 
-pits <- pitfinder2(flowdir)
+pits <- pitfinder(flowdir)
 
 ## Application wth example DEM
 
 elev <- rast(system.file('ex/elev.tif',package="terra"))
 flowdir <- terrain(elev,"flowdir")
 
-pits <- pitfinder2(flowdir)
+pits <- pitfinder(flowdir)
 
 
 

man/watershed.Rd

@@ -16,7 +16,7 @@ delineate the area covered by a catchment from a SpatRaster with flow direction
 }
 
 \arguments{
-  \item{p}{SpatRaster with flow direction. See \code{\link{terrain}}. }
+  \item{x}{SpatRaster with flow direction. See \code{\link{terrain}}. }
   \item{pourpoint}{matrix or SpatVector with the pour point location}
   \item{filename}{character. Output filename}
   \item{...}{additional arguments for writing files as in \code{\link{writeRaster}}}