Prepare for CRAN v0.1.15 release

* Uwe Ligges suggested (2022-08-26) that some parallel cluster is not cleanly closed in the tests * Added `future::plan(future::multisession)` in tests to remove the files in temp directory * Added links to `sparr` package in 'package.R'
lance-waller-lab · Aug 30, 2022 · f305c1a · f305c1a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: envi
 Type: Package
 Title: Environmental Interpolation using Spatial Kernel Density Estimation
-Version: 0.1.14
-Date: 2022-08-25
+Version: 0.1.15
+Date: 2022-08-30
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # envi (development version)
 
+# envi v0.1.15
+* Uwe Ligges suggested (2022-08-26) that some parallel cluster is not cleanly closed in the tests
+* Added `future::plan(future::multisession)` in tests to remove the files in temp directory
+* Added links to `sparr` package in 'package.R'
+
 # envi v0.1.14
 * Updated package URL and BugReports to renamed GitHub account "lance-waller-lab" (previously "Waller-SUSAN")
 * Replaced `methods::is()` with `inherits()` and `methods` is no longer Imports

diff --git a/R/package.R b/R/package.R
@@ -2,7 +2,7 @@
 #'
 #' Estimates an ecological niche model using occurrence data, covariates, and kernel density-based estimation methods.
 #'
-#' @details For a single species with presence and absence data, the 'envi' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) \doi{10.1002/sim.7577}. Details about kernel density estimation can be found in J. F. Bithell (1990) \doi{10.1002/sim.4780090616}. More information about relative risk functions using kernel density estimation (KDE) can be found in J. F. Bithell (1991) \doi{10.1002/sim.4780101112}.
+#' @details For a single species with presence and absence data, the 'envi' package uses the spatial relative risk function estimated using the \code{\link{sparr}} package. Details about the \code{\link{sparr}} package methods can be found in the tutorial: Davies et al. (2018) \doi{10.1002/sim.7577}. Details about kernel density estimation can be found in J. F. Bithell (1990) \doi{10.1002/sim.4780090616}. More information about relative risk functions using kernel density estimation (KDE) can be found in J. F. Bithell (1991) \doi{10.1002/sim.4780101112}.
 #' 
 #' This package provides a function to estimate the ecological niche for a single species with presence and absence data. The 'envi' package also provides some sensitivity and visualization tools for the estimated ecological niche, its predicted spatial distribution, and prediction diagnostics. Various options for the correction of multiple testing are available. 
 #' 

diff --git a/R/utils.R b/R/utils.R
@@ -31,4 +31,4 @@ progBar <- function(kk, N, per = 1) {
             appendLF = FALSE)
     if (kk == N) cat("\r")
   }
-}
+}
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ envi: Environmental Interpolation using Spatial Kernel Density Estimation <img s
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5347826.svg)](https://doi.org/10.5281/zenodo.5347826)
 <!-- badges: end -->
 
-**Date repository last updated**: August 25, 2022
+**Date repository last updated**: August 30, 2022
 
 <h2 id="overview">
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,17 +1,16 @@
-## This is the fourteenth resubmission
+## This is the fifteenth resubmission
 
 * Updates since previous submission:
-  * Updated package URL and BugReports to renamed GitHub account "lance-waller-lab" (previously "Waller-SUSAN")
-  * Replaced `methods::is()` with `inherits()` and `methods` is no longer Imports
-  * Added `maptools` and `RStoolbox` to Suggests (used in the package vignette)
-  * Added CITATION file
-  * Fixed typos in documentation throughout
+  * Uwe Ligges suggested (2022-08-26) that some parallel cluster is not cleanly closed in the tests
+  * Added `future::plan(future::multisession)` in tests to remove the files in temp directory
+  * Added links to `sparr` package in 'package.R'
 
-* Documentation for "man/envi-package", man/pval_correct.Rd", and DESCRIPTION references the following DOIs, which throws a NOTE but are valid URLs:
+* Documentation for "envi-package.Rd", "pval_correct.Rd", DESCRIPTION, and vignette 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>
+  * <https://doi.org/10.1111/j.1475-4991.2008.00309.x>
 
 ## Test environments
 * local OS X install, R 4.2.1

diff --git a/inst/CITATION b/inst/CITATION
@@ -5,15 +5,15 @@ citEntry(entry = "manual",
   author        = personList(as.person("Ian D. Buller")),
   publisher     = "The Comprehensive R Archive Network",
   year          = "2022",
-  number        = "0.1.14",
+  number        = "0.1.15",
   doi           = "10.5281/zenodo.5347826",
   url           = "https://cran.r-project.org/package=envi",
 
   textVersion = 
   paste("Ian D. Buller (2022).",
         "envi: Environmental Interpolation using Spatial Kernel Density Estimation.",
         "The Comprehensive R Archive Network.",
-        "v0.1.14.",
+        "v0.1.15.",
         "DOI:10.5281/zenodo.5347826",
         "Accessed by: https://cran.r-project.org/package=envi")
 )
diff --git a/man/envi-package.Rd b/man/envi-package.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -7,3 +7,4 @@ library(envi)
 options(parallelly.makeNodePSOCK.setup_strategy = "sequential")
 
 test_check("envi")
+future::plan(future::sequential)
-Original file line number
+Diff line change
@@ Expand Up / @@ -31,4 +31,4 @@ progBar <- function(kk, N, per = 1) { @@
                 appendLF = FALSE)
         if (kk == N) cat("\r")
       }
-    }
+    }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,3 +7,4 @@ library(envi)
		options(parallelly.makeNodePSOCK.setup_strategy = "sequential")

		test_check("envi")
		future::plan(future::sequential)