Prepare for CRAN v0.1.13 release

* In the `div_plot()` and `seq_plot()` internal functions, replaced `if (class(input) == "im")` with `if (methods::is(input, "im"))` * Added `methods` package to Imports * Re-added `utils` package to Suggests because "zzz.R" calls the `packageDescription()` function * Moved `spatstat.random` package from Imports to Suggests because the `rpoispp()` function is only used for tests
lance-waller-lab · Mar 24, 2022 · f78b519 · f78b519
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 0.1.12
+Date: 2022-03-23 21:37:00 UTC
+SHA: 00e8d585e836e9e9044f1b14adec291e13c34695
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: envi
 Type: Package
 Title: Environmental Interpolation using Spatial Kernel Density Estimation
-Version: 0.1.12
+Version: 0.1.13
 Date: 2022-03-23
 Authors@R: 
     c(person(given = "Ian D.",
@@ -43,20 +43,22 @@ Imports:
     graphics,
     grDevices,
     iterators,
+    methods,
     pls,
     raster,
     rgeos,
     ROCR,
     sp,
     sparr,
     spatstat.geom,
-    spatstat.random,
     stats
 Suggests: 
     R.rsp,
     spatstat.data,
+    spatstat.random,
     spelling,
-    testthat
+    testthat,
+    utils
 VignetteBuilder: R.rsp
 Language: en-US
 URL: https://github.com/Waller-SUSAN/envi

diff --git a/NAMESPACE b/NAMESPACE
@@ -33,6 +33,7 @@ importFrom(graphics,plot)
 importFrom(graphics,plot.new)
 importFrom(graphics,title)
 importFrom(iterators,icount)
+importFrom(methods,is)
 importFrom(pls,cvsegments)
 importFrom(raster,crs)
 importFrom(raster,cut)
@@ -62,7 +63,6 @@ importFrom(spatstat.geom,ppp)
 importFrom(spatstat.geom,rjitter)
 importFrom(spatstat.geom,setmarks)
 importFrom(spatstat.geom,superimpose)
-importFrom(spatstat.random,rpoispp)
 importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,sd)
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,11 @@
 # envi (development version)
 
+# envi v0.1.13
+* In the `div_plot()` and `seq_plot()` internal functions, replaced `if (class(input) == "im")` with `if (methods::is(input, "im"))`
+* Added `methods` package to Imports
+* Re-added `utils` package to Suggests because "zzz.R" calls the `packageDescription()` function
+* Moved `spatstat.random` package from Imports to Suggests because the `rpoispp()` function is only used for tests
+
 # envi v0.1.12
 * Fixed bug in `perlrren()` function that will now keep the predicted values even if NA
 * Fixed bug in `plot_perturb()` function that will now project rasters using `method = "bilinear"` for continuous values

diff --git a/R/div_plot.R b/R/div_plot.R
@@ -20,6 +20,7 @@
 #' }
 #' 
 #' @importFrom grDevices colorRampPalette
+#' @importFrom methods is
 #' @importFrom raster raster
 #'
 #' @keywords internal
@@ -32,7 +33,7 @@ div_plot <- function(input,
                      digits = 1) {
 
   # Inputs
-  if (class(input) == "im") {
+  if (methods::is(input, "im")) {
     out <- raster::raster(input)
   } else { out <- input }
 

diff --git a/R/lrren.R b/R/lrren.R
@@ -95,8 +95,8 @@
 #' # Presence data
 #'   presence <- spatstat.data::bei
 #'   spatstat.geom::marks(presence) <- data.frame("presence" = rep(1, presence$n),
-#'                                           "lon" = presence$x,
-#'                                           "lat" = presence$y)
+#'                                                "lon" = presence$x,
+#'                                                "lat" = presence$y)
 #'   spatstat.geom::marks(presence)$elev <- elev[presence]
 #'   spatstat.geom::marks(presence)$grad <- grad[presence]
 #' 

diff --git a/R/package.R b/R/package.R
@@ -49,12 +49,12 @@ NULL
 #' @importFrom graphics abline layout legend lines mtext par plot plot.new title
 #' @importFrom grDevices chull colorRampPalette
 #' @importFrom iterators icount
+#' @importFrom methods is
 #' @importFrom pls cvsegments
 #' @importFrom raster crs cut extract image projectRaster raster rasterToPoints reclassify values
 #' @importFrom rgeos gBuffer
 #' @importFrom ROCR performance prediction
 #' @importFrom sp bbox coordinates CRS gridded Polygon Polygons SpatialPolygons
-#' @importFrom stats median na.omit sd
 #' @importFrom spatstat.geom as.solist im.apply marks owin pixellate plot.ppp ppp rjitter setmarks superimpose
-#' @importFrom spatstat.random rpoispp
+#' @importFrom stats median na.omit sd
 NULL
diff --git a/R/perlrren.R b/R/perlrren.R
@@ -77,8 +77,8 @@
 #' # Presence data
 #'   presence <- spatstat.data::bei
 #'   spatstat.geom::marks(presence) <- data.frame("presence" = rep(1, presence$n),
-#'                                               "lon" = presence$x,
-#'                                               "lat" = presence$y)
+#'                                                "lon" = presence$x,
+#'                                                "lat" = presence$y)
 #'                                           
 #' # (Pseudo-)Absence data
 #'   absence <- spatstat.random::rpoispp(0.008, win = ims[[1]])

diff --git a/R/plot_perturb.R b/R/plot_perturb.R
@@ -22,7 +22,6 @@
 #' @importFrom raster crs raster projectRaster
 #' @importFrom sp CRS
 #' @importFrom spatstat.geom pixellate
-#' @importFrom spatstat.random rpoispp
 #' 
 #' @export
 #' 

diff --git a/R/seq_plot.R b/R/seq_plot.R
@@ -18,6 +18,7 @@
 #' }
 #' 
 #' @importFrom grDevices colorRampPalette
+#' @importFrom methods is
 #' 
 #' @keywords internal
 #' 
@@ -27,7 +28,7 @@ seq_plot <- function(input,
                      digits = 1) {
 
   # Inputs
-  if (class(input) == "im") {
+  if (methods::is(input, "im")) {
     out <- raster::raster(input)
   } else { out <- input }
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,12 +1,18 @@
-## This is the twelfth resubmission
+## This is the thirteenth resubmission
 
+* Actions taken regarding feedback from CRAN teams' auto-check service:
+  * In the `div_plot()` and `seq_plot()` internal functions, replaced `if (class(input) == "im")` with `if (methods::is(input, "im"))`
+  * Added `methods` package to Imports
+
 * Updates since previous submission:
-  * Fixed bug in `perlrren()` function that will now keep the predicted values even if NA
-  * Fixed bug in `plot_perturb()` function that will now project rasters using `method = "bilinear"` for continuous values
-  * Streamlined "test-perlrren.R" by removing duplicate tests for "incorrectly specified n_sim"
-  * Fixed bug in "test-plot_cv.R" by resetting the graphics within an error check to clear a warning between tests
+  * Re-added `utils` package to Suggests because "zzz.R" calls the `packageDescription()` function
+  * Moved `spatstat.random` package from Imports to Suggests because the `rpoispp()` function is only used for tests
 
-* Documentation for `pval_correct()` references a doi <https://doi.org/10.2307/2283989> that throws a NOTE but is a valid URL
+* Documentation for "man/envi-packge", man/pval_correct.Rd", and DESCRIPTION references the following DOIs, which throws a NOTE but are valid URLs:
+  * <https://doi.org/10.1002/sim.4780090616>
+  * <https://doi.org/10.1002/sim.4780101112>
+  * <https://doi.org/10.1002/sim.7577>
+  * <https://doi.org/10.1111/j.2517-6161.1995.tb02031.x>
 
 ## Test environments
 * local OS X install, R 4.1.2

diff --git a/man/lrren.Rd b/man/lrren.Rd
diff --git a/man/perlrren.Rd b/man/perlrren.Rd