Prepare for CRAN v0.1.12 release

* 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
lance-waller-lab · Mar 23, 2022 · 00e8d58 · 00e8d58
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,3 +5,4 @@
 ^vignette\.Rmd$
 ^dev$
 ^CRAN-RELEASE$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: envi
 Type: Package
 Title: Environmental Interpolation using Spatial Kernel Density Estimation
-Version: 0.1.11
-Date: 2022-02-04
+Version: 0.1.12
+Date: 2022-03-23
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,11 @@
 # envi (development version)
 
+# 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
+* 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
+
 # envi v0.1.11
 * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
   * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends.

diff --git a/R/perlrren.R b/R/perlrren.R
@@ -256,10 +256,10 @@ perlrren <- function(obs_ppp,
                                 check = FALSE) 
     # points along polygon border will be lost
 
-    spatstat.geom::marks(xxxxx)[ , 5] <- lrr_mean[xxxxx]
-    spatstat.geom::marks(xxxxx)[ , 6] <- lrr_sd[xxxxx]
-    spatstat.geom::marks(xxxxx)[ , 7] <- pval_mean[xxxxx]
-    spatstat.geom::marks(xxxxx)[ , 8] <- pval_prop[xxxxx]
+    spatstat.geom::marks(xxxxx)[ , 5] <- lrr_mean[xxxxx, drop = FALSE]
+    spatstat.geom::marks(xxxxx)[ , 6] <- lrr_sd[xxxxx, drop = FALSE]
+    spatstat.geom::marks(xxxxx)[ , 7] <- pval_mean[xxxxx, drop = FALSE]
+    spatstat.geom::marks(xxxxx)[ , 8] <- pval_prop[xxxxx, drop = FALSE]
     names(spatstat.geom::marks(xxxxx))[5:8] <- c("lrr_mean",
                                                  "lrr_sd",
                                                  "pval_mean",

diff --git a/R/plot_perturb.R b/R/plot_perturb.R
@@ -187,9 +187,7 @@ plot_perturb <- function(input,
     raster::crs(lrr_mean) <- sp::CRS(SRS_string = cref0)
     if (!is.null(cref1)) {
       lrr_mean <- raster::projectRaster(lrr_mean,
-                                        crs = sp::CRS(SRS_string = cref1),
-                                        method = "ngb",
-                                        legacy = TRUE)
+                                        crs = sp::CRS(SRS_string = cref1))
     }
 
     lrr_sd <- spatstat.geom::pixellate(input$predict,
@@ -198,9 +196,7 @@ plot_perturb <- function(input,
     raster::crs(lrr_sd) <- sp::CRS(SRS_string = cref0)
     if (!is.null(cref1)) {
       lrr_sd <- raster::projectRaster(lrr_sd,
-                                      crs = sp::CRS(SRS_string = cref1),
-                                      method = "ngb",
-                                      legacy = TRUE)
+                                      crs = sp::CRS(SRS_string = cref1))
     }
 
     pval_mean <- spatstat.geom::pixellate(input$predict,
@@ -209,9 +205,7 @@ plot_perturb <- function(input,
     raster::crs(pval_mean) <- sp::CRS(SRS_string = cref0)
     if (!is.null(cref1)) {
       pval_mean <- raster::projectRaster(pval_mean,
-                                         crs = sp::CRS(SRS_string = cref1),
-                                         method = "ngb",
-                                         legacy = TRUE)
+                                         crs = sp::CRS(SRS_string = cref1))
     }
 
     pval_prop <- spatstat.geom::pixellate(input$predict,
@@ -220,9 +214,7 @@ plot_perturb <- function(input,
     raster::crs(pval_prop) <- sp::CRS(SRS_string = cref0)
     if (!is.null(cref1)) {
       pval_prop <- raster::projectRaster(pval_prop,
-                                         crs = sp::CRS(SRS_string = cref1),
-                                         method = "ngb",
-                                         legacy = TRUE)
+                                         crs = sp::CRS(SRS_string = cref1))
     }
 
     # Plot 5: mean log relative risk

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,14 +1,10 @@
-## This is the eleventh resubmission
+## This is the twelfth resubmission
 
 * Updates since previous submission:
-  * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
-    * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends.
-    * `spatstat.geom` and `spatstat.random` are now Imports
-    * `spatstat.data` is now Suggests.
-    * [See the GitHub merge pull request](https://github.com/Waller-SUSAN/envi/pull/2/commits/34b67d8a66151f609cafe4a72de39e382abe7f07).
-  * `maptools` is no longer Imports
-  * Fixed annotation typos in the `perlrren()`, `pval_correct()`, `lrren()` functions
-  * Fixed bug in `plot_cv()` function that will specify the size of the confidence interval in the subtitle based on the chosen alpha level.
+  * 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
 
 * Documentation for `pval_correct()` references a doi <https://doi.org/10.2307/2283989> that throws a NOTE but is a valid URL
 

diff --git a/tests/testthat/test-perlrren.R b/tests/testthat/test-perlrren.R
@@ -94,22 +94,6 @@ test_that("perlrren throws error with invalid arguments", {
              n_sim = 10)
   )
 
-  # Incorrectly specified n_sim
-  expect_error(
-    perlrren(obs_ppp = obs_locs,
-             covariates = ims,
-             radii = c(10, 100, 500),
-             n_sim = 0)
-  )
-
-  # Incorrectly specified n_sim
-  expect_error(
-    perlrren(obs_ppp = obs_locs,
-             covariates = ims,
-             radii = c(10, 100, 500),
-             n_sim = 0)
-  )
-
   # Incorrectly specified alpha
   expect_error(
     perlrren(obs_ppp = obs_locs,

diff --git a/tests/testthat/test-plot_cv.R b/tests/testthat/test-plot_cv.R
@@ -102,6 +102,7 @@ test_that("plot_cv throws error with invalid arguments", {
             alpha = 0.05)
     )
 
+  dev.off() # reset graphics
   # plot_cv with lrren output where cv = FALSE
   expect_error(
     plot_cv(input = test_lrren1,