updated rgl-code and proj4-code

vignettes/spcosa.Rmd

@@ -8,56 +8,15 @@ output:
     toc_depth: 4
 vignette: >
     %\VignetteIndexEntry{Introduction to the **spcosa**-package}
-    %\VignetteEngine{knitr::rmarkdown}
     %\VignetteEncoding{UTF-8}
+    %\VignetteEngine{knitr::rmarkdown}
 ---
 
 
 ```{r, echo=FALSE}
-
-# suggested package (see 1.1.3.1 of writing R extensions)
 if (requireNamespace("rgl", quietly = TRUE)) {
-
-  # source: setup.R in rgl-package (by Duncan Murdoch)
-  options(rgl.useNULL=TRUE)
-  
-  hook_webgl <- local({
-    commonParts <- TRUE
-    function (before, options, envir) 
-    {
-      if (before || rgl::rgl.cur() == 0 || !requireNamespace("knitr")) 
-        return()
-      out_type <- knitr::opts_knit$get("out.format")
-      if (!length(intersect(out_type, c("markdown", "html"))))       
-        stop("hook_webgl is for HTML only.  Use knitr::hook_rgl instead.")
-      
-      name <- tempfile("webgl", tmpdir = ".", fileext = ".html")
-      on.exit(unlink(name))
-      dpi <- 96 # was options$dpi
-      rgl::par3d(windowRect = dpi * c(0, 0, options$fig.width, 
-                                            options$fig.height))
-      Sys.sleep(0.1)
-      prefix = gsub("[^[:alnum:]]", "_", options$label)
-      prefix = sub("^([^[:alpha:]])", "_\\1", prefix)
-      rgl::writeWebGL(dir = dirname(name), 
-                      filename = name, 
-                      snapshot = !rgl::rgl.useNULL(),
-                      template = NULL, 
-                      prefix = prefix, 
-                      commonParts = commonParts)
-      if (!isTRUE(options$rgl.keepopen) && rgl::rgl.cur())
-        rgl::rgl.close()
-      commonParts <<- FALSE
-      res <- readLines(name)
-      res <- res[!grepl("^\\s*$", res)]
-      paste(gsub("^\\s+", "", res), collapse = "\n")
-    }
-  })
-  
-  knitr::knit_hooks$set(rgl = hook_webgl)
-
-}  
-
+  knitr::knit_hooks$set(webgl = rgl::hook_webgl)
+}
 knitr::opts_chunk$set(comment = NA)
 set.seed(314)
 ```
@@ -240,7 +199,7 @@ As an example, we will use the **gstat** package for predicting clay contents by
 #coordinates(sp_data) <- ~ x * y
 sp_data <- SpatialPointsDataFrame(coords = sampling_points, data = my_data)
 ```
-Next, the sample variogram for clay has to be estimated, and needs to be fitted by a permissable model:
+Next, the sample variogram for clay has to be estimated, and needs to be fitted by a permissible model:
 ```{r, fig.width=7, fig.height=5, out.width=400}
 sample_variogram <- variogram(clay ~ 1, sp_data)
 variogram_model <- fit.variogram(sample_variogram, 
@@ -510,7 +469,7 @@ grd <- expand.grid(
 gridded(grd) <-  ~ longitude * latitude
 
 grd_crs <- grd
-proj4string(grd_crs) <- CRS("+proj=longlat +ellps=WGS84")
+proj4string(grd_crs) <- CRS("EPSG:4326")
 
 ```
 Note that `grd` is identical to `grd_crs`, except that `grd_crs` has projection attributes. If no projection attributes are available, the algorithms in the **spcosa**-package use squared Euclidean distances in the _k_-means algorithms. However, if projection attributes have been set, the coordinates will be transformed to lat/long format (latitude/longitude) and squared great circle distances will be used instead.
@@ -530,7 +489,7 @@ Note that `grd` seems to have more compact strata near the geographic poles than
 
 
 
-```{r, echo=FALSE}
+```{r, echo=FALSE, eval=requireNamespace("rgl", quietly = TRUE)}
 # internal function for converting LatLong to XYZ format (r: radius of the earth in km)
 .latLongToXYZ <-
 function(x, r = 6378.1) {
@@ -580,8 +539,7 @@ function(x) {
 }
 ```
 
-
-```{r, rgl=TRUE, eval=requireNamespace("rgl", quietly = TRUE), echo=FALSE, results='hide', fig.width=7, fig.height=4}
+```{r, eval=requireNamespace("rgl", quietly = TRUE), echo=FALSE, results='hide', fig.width=7, fig.height=4, webgl=TRUE}
 rgl::open3d(userMatrix = rbind(
     c( 0.73, -0.63, 0.25, 0),
     c( 0.37,  0.69, 0.63, 0),