diff --git a/DESCRIPTION b/DESCRIPTION index 3ec4f83..acb5382 100644 --- 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 index b88e3ff..b202def 100644 --- 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 index aec3e91..328eff2 100644 --- 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 index 6c77d4d..3b10d06 100644 --- 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") } -} \ No newline at end of file +} diff --git a/README.md b/README.md index abf503b..e78d709 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ envi: Environmental Interpolation using Spatial Kernel Density Estimation -**Date repository last updated**: August 25, 2022 +**Date repository last updated**: August 30, 2022

diff --git a/cran-comments.md b/cran-comments.md index 4602105..a900b1b 100644 --- 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: * * * * + * ## Test environments * local OS X install, R 4.2.1 diff --git a/inst/CITATION b/inst/CITATION index 4d99691..879771f 100755 --- a/inst/CITATION +++ b/inst/CITATION @@ -5,7 +5,7 @@ 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", @@ -13,7 +13,7 @@ citEntry(entry = "manual", 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 index 74fad84..a2cb387 100644 --- a/man/envi-package.Rd +++ b/man/envi-package.Rd @@ -9,7 +9,7 @@ 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}. +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/tests/testthat.R b/tests/testthat.R index e1dd4cc..64ed06e 100644 --- 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)