Merge pull request #20 from jhollist/spatial_updates

Spatial updates

.github/workflows/check-standard.yaml

@@ -0,0 +1,98 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+
+on: [push, pull_request]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: macos-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          
+      - name: "Install spatial libraries on linux"
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev
+
+      - name: "Install spatial libraries on macOS"
+        if: runner.os == 'macOS'
+        run: |
+          # conflicts with gfortran from r-lib/actions when linking gcc
+          # rm '/usr/local/bin/gfortran'
+          brew install pkg-config gdal proj geos sqlite3
+      
+      - name: Install dependencies on windows and mac
+        if: runner.os != 'Linux'
+        run: |
+          remotes::install_deps(dependencies = TRUE, type = "binary")
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install dependencies linux
+        if: runner.os == 'Linux'
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lakemorpho
 Type: Package
 Title: Lake Morphometry Metrics
-Version: 1.2.1.9999
+Version: 1.3.0
 Authors@R: c(
     person(given = "Jeffrey W.", family = "Hollister",
     role = c("aut","cre"),
@@ -32,9 +32,7 @@ Imports:
     methods,
     stats,
     grDevices,
-    rgdal,
     raster,
-    rgeos,
     sp,
     sf,
     geosphere,

NAMESPACE

@@ -21,13 +21,12 @@ import(geosphere)
 import(grDevices)
 import(methods)
 import(raster)
-import(rgdal)
-import(rgeos)
 import(sp)
 importFrom(cluster,ellipsoidhull)
-importFrom(rgeos,gLength)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
+importFrom(sf,st_cast)
+importFrom(sf,st_centroid)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_geometry)
@@ -38,9 +37,6 @@ importFrom(sf,st_sf)
 importFrom(sf,st_sfc)
 importFrom(sf,st_transform)
 importFrom(sf,st_within)
-importFrom(sp,CRS)
-importFrom(sp,SpatialLines)
-importFrom(sp,proj4string)
 importFrom(stats,dist)
 importFrom(stats,lm)
 importFrom(stats,median)

NEWS.md

@@ -1,6 +1,11 @@
-lakemorpho 1.2.1 (2022-04-25)
+lakemorpho 1.99.0 (2023-09-XX)
 ==========================
 
+## Major Changes
+- dropping rgdal and rgeos, switching all vector to sf, coerces sp to sf.
+- removed travis and appveyor
+
+
 ## Bug fixes
 - @aarohall caught a bug with user supplied catchment returning a Null 
 surrounding landscape.

R/calcLakeMetrics.R

@@ -48,7 +48,7 @@
 
 calcLakeMetrics <- function(inLakeMorpho, bearing, pointDens, slope_quant=0.5, 
                             correctFactor = 1, zmax = NULL) {
-    if (class(inLakeMorpho) != "lakeMorpho") {
+    if (!inherits(inLakeMorpho, "lakeMorpho")) {
         return(warning("Input data is not of class 'lakeMorpho'.  Run lakeSurround Topo first."))
     }
     allMet <- list(surfaceArea = lakeSurfaceArea(inLakeMorpho), 

R/lakeFetch.R

@@ -32,7 +32,7 @@
 lakeFetch <- function(inLakeMorpho, bearing, addLine = TRUE) {
 
   inputName <- deparse(substitute(inLakeMorpho))
-  if (class(inLakeMorpho) != "lakeMorpho") {
+  if (!inherits(inLakeMorpho, "lakeMorpho")) {
     stop("Input data is not of class 'lakeMorpho'.  Run lakeSurround Topo or lakeMorphoClass first.")
   }
   result <- NA
@@ -78,7 +78,7 @@ lakeFetch <- function(inLakeMorpho, bearing, addLine = TRUE) {
   # needs centroid, not all coords
   # Slight difference with original which returned the label point which is
   # kinda the centroid...
-  centPts[[1]] <- data.frame(st_coordinates(sf::st_centroid(lakedd)))
+  centPts[[1]] <- data.frame(st_coordinates(sf::st_centroid(sf::st_geometry(lakedd))))
   names(centPts[[1]]) <- c("lon", "lat")
   centPts[[2]] <- destPoint(as.matrix(centPts[[1]]), perpbear1, 100)
   i <- length(centPts)
@@ -113,7 +113,7 @@ lakeFetch <- function(inLakeMorpho, bearing, addLine = TRUE) {
   allLinesSL <- st_sfc(geometry = allLines, crs = st_crs("+proj=longlat +datum=WGS84"))
   # clip out lines that are inside lake
   lakeLinesSL <- sf::st_intersection(allLinesSL, lakedd)
-  lakeLinesSL_proj <- sf::st_transform(lakeLinesSL, st_crs(st_as_sf(inLakeMorpho$lake))$proj4string)
+  lakeLinesSL_proj <- sf::st_transform(lakeLinesSL, st_crs(inLakeMorpho$lake))
 
   # Determine the longest
   lakeLinesSL_proj <- sf::st_as_sf(sf::st_cast(sf::st_cast(lakeLinesSL_proj, "MULTILINESTRING"),"LINESTRING"))
@@ -135,5 +135,5 @@ lakeFetch <- function(inLakeMorpho, bearing, addLine = TRUE) {
     class(inLakeMorpho) <- "lakeMorpho"
     assign(inputName, inLakeMorpho, envir = parent.frame())
   }
-  return(round(result,4))
+  return(round(as.numeric(result),4))
 }

R/lakeMajorAxisLength.R

@@ -18,24 +18,23 @@
 #' internal waves in the bottom boundary layer of ice-covered Lake Mueggelsee,
 #' Germany. Aquatic ecology, 43(3), pp.641-651.
 #' 
-#' @importFrom rgeos gLength
 #' @importFrom cluster ellipsoidhull
 #' @examples
 #' data(lakes)
+#' inputLM <- lakeSurroundTopo(exampleLake, exampleElev)
 #' lakeMajorAxisLength(inputLM)
 
 
 lakeMajorAxisLength <- function(inLakeMorpho, addLine = TRUE) {
 
-  if (class(inLakeMorpho) != "lakeMorpho") {
+  if (!inherits(inLakeMorpho, "lakeMorpho")) {
     stop("Input data is not of class 'lakeMorpho'.  Run lakeSurround Topo or lakeMorphoClass first.")
   }
 
   result <- NA
-  #Change to perhaps deal with noLD
-  lakeShoreLine <- as(inLakeMorpho$lake, "SpatialLines")
-  lakeShorePoints <- as(lakeShoreLine, "SpatialPoints")
-  lakeShoreCoords <- coordinates(lakeShorePoints)
+  lakeShoreLine <- sf::st_cast(inLakeMorpho$lake, "MULTILINESTRING")
+  lakeShorePoints <- sf::st_cast(sf::st_geometry(lakeShoreLine), "MULTIPOINT")
+  lakeShoreCoords <- sf::st_coordinates(lakeShorePoints)[,-3]
 
   # https://stackoverflow.com/questions/18278382/how-to-obtain-the-lengths-of-semi-axes-of-an-ellipse-in-r
   elpshull <- predict(cluster::ellipsoidhull(lakeShoreCoords))
@@ -48,16 +47,15 @@ lakeMajorAxisLength <- function(inLakeMorpho, addLine = TRUE) {
   } else {
     myLine.max <- elpshull[round(dist2center,8) == round(max(dist2center),8),]
   }
+
+  myLine <- st_sfc(sf::st_linestring(myLine.max), crs = sf::st_crs(inLakeMorpho$lake))
 
-  myLine <- sp::SpatialLines(list(Lines(list(Line(myLine.max)), "1")),
-              proj4string = sp::CRS(sp::proj4string(inLakeMorpho$lake)))
-
-  result <- rgeos::gLength(myLine)
 
+  result <- as.numeric(sf::st_length(myLine))
   if (addLine) {
     myName <- deparse(substitute(inLakeMorpho))
     inLakeMorpho$majoraxisLengthLine <- NULL
-    inLakeMorpho <- c(inLakeMorpho, majoraxisLengthLine = myLine)
+    inLakeMorpho$majoraxisLengthLine <- myLine
     class(inLakeMorpho) <- "lakeMorpho"
     assign(myName, inLakeMorpho, envir = parent.frame())
   }

R/lakeMaxDepth.R

@@ -35,7 +35,7 @@
 #' lakeMaxDepth(inputLM)             
 
 lakeMaxDepth <- function(inLakeMorpho, slope_quant = 0.5, correctFactor = 1) {
-    if (class(inLakeMorpho) != "lakeMorpho") {
+    if (!inherits(inLakeMorpho, "lakeMorpho")) {
       stop("Input data is not of class 'lakeMorpho'.  Run lakeSurround Topo or lakeMorphoClass first.")
     }
     if(is.null(inLakeMorpho$elev)){

R/lakeMaxLength.R

@@ -29,19 +29,25 @@
 #'             - Lake Morphometry (2nd ed.). Gainesville: Florida LAKEWATCH,
 #'             Department of Fisheries and Aquatic Sciences.
 #'             \href{http://edis.ifas.ufl.edu/pdffiles/FA/FA08100.pdf}{Link}
-#' @import sp rgeos methods
+#' @import sp methods
 #' @importFrom stats dist
 #' @examples
+#' library(lakemorpho)
 #' data(lakes)
+#' inputLM <- lakeSurroundTopo(exampleLake, exampleElev)  
 #' lakeMaxLength(inputLM,50)
 
 
 lakeMaxLength <- function(inLakeMorpho, pointDens, addLine = TRUE) {
-    if (class(inLakeMorpho) != "lakeMorpho") {
+
+    if (!inherits(inLakeMorpho, "lakeMorpho")) {
         stop("Input data is not of class 'lakeMorpho'.  Run lakeSurround Topo or lakeMorphoClass first.")
     }
     result <- NA
-    lakeShorePoints <- spsample(as(inLakeMorpho$lake, "SpatialLines"), pointDens, "regular")@coords
+    #lakeShorePoints <- spsample(as(inLakeMorpho$lake, "SpatialLines"), pointDens, "regular")@coords
+    lakeShorePoints <- st_coordinates(sf::st_sample(st_cast(inLakeMorpho$lake, 
+                                                            "MULTILINESTRING"), 
+                                                    pointDens, type = "regular"))
     dm <- dist(lakeShorePoints)
     md <- nrow(lakeShorePoints)
     x0 <- lakeShorePoints[which(lower.tri(matrix(1, md, md)) == 1, arr.ind = TRUE)[, 1], ][, 1][order(dm, decreasing = TRUE)]  #[30:md]
@@ -50,24 +56,29 @@ lakeMaxLength <- function(inLakeMorpho, pointDens, addLine = TRUE) {
     y1 <- lakeShorePoints[which(lower.tri(matrix(1, md, md)) == 1, arr.ind = TRUE)[, 2], ][, 2][order(dm, decreasing = TRUE)]  #[30:md]
     xydf <- data.frame(x0, x1, y0, y1)
     xylist <- split(xydf, rownames(xydf))
-    myLines <- SpatialLines(lapply(xylist, function(x) Lines(list(Line(matrix(as.numeric(x), 2, 2))), row.names(x))),
-        proj4string = CRS(proj4string(inLakeMorpho$lake)))
-    myInd <- gContains(inLakeMorpho$lake, myLines, byid = TRUE)
+    #myLines_old <- SpatialLines(lapply(xylist, function(x) Lines(list(Line(matrix(as.numeric(x), 2, 2))), row.names(x))),
+    #    proj4string = CRS(st_crs(inLakeMorpho$lake)$wkt))
+    myLines <- st_sfc(lapply(xylist, 
+                             function(x) st_linestring(matrix(as.numeric(x),2,2))),
+                      crs = sf::st_crs(inLakeMorpho$lake))
+    #myInd_old <- gContains(as(inLakeMorpho$lake, "Spatial"), myLines_old, byid = TRUE)
+
+    myInd <- sf::st_contains(inLakeMorpho$lake, myLines, sparse = FALSE)[1,]
     if (sum(myInd) == 0) {
         return(NA)
     }
     if(capabilities("long.double")){
-      myLine <- myLines[myInd][gLength(myLines[myInd], byid = TRUE) == max(gLength(myLines[myInd], byid = TRUE))]
+      myLine <- myLines[myInd][sf::st_length(myLines[myInd]) == max(sf::st_length(myLines[myInd]))]
     } else {
-      myLine <- myLines[myInd][round(gLength(myLines[myInd], byid = TRUE),8) == round(max(gLength(myLines[myInd], byid = TRUE)),8)]
+      myLine <- myLines[myInd][round(sf::st_length(myLines[myInd]),8) == round(max(sf::st_length(myLines[myInd])),8)]
     }
 
-    result <- gLength(myLine)
-
+    result <- as.numeric(sf::st_length(myLine))
+    
     if (addLine) {
         myName <- deparse(substitute(inLakeMorpho))
         inLakeMorpho$maxLengthLine <- NULL
-        inLakeMorpho <- c(inLakeMorpho, maxLengthLine = myLine)
+        inLakeMorpho$maxLengthLine <- myLine
         class(inLakeMorpho) <- "lakeMorpho"
         assign(myName, inLakeMorpho, envir = parent.frame())
     }