NEWS.md

In Waller-SUSAN/envi: Environmental Interpolation using Spatial Kernel Density Estimation

envi (development version)

envi v1.0.0

• Fixed bug in lrren() to properly extract predicted RR values for cross validation after update using terra::extract()
• Fixed NOTE in CRAN checks to provide package anchors for Rd \link{} targets not in the package itself and the base packages within 'envi-package.Rd', 'lrren.Rd', and 'perlrren.Rd'
• Fixed NOTE in Windows check to remove detritus files after testing
• Renamed 'package.R' to 'envi-package.R' after Roxygen (>=7.3.0) update
• Updated CITATION with peer-review publication

envi v0.1.19

• Fixed 'Moved Permanently' content by replacing the old URL with the new URL

envi v0.1.18

• Fixed bug in calculation of False Discovery Rate in internal pval_correct() function
• Fixed test for plot_perturb() function that was presenting a warning by specifying cref0
• Argument plot_cols correctly renamed cols in div_plot() and seq_plot() functions

envi v0.1.17

• Fixed broken link in CITATION

envi v0.1.16

• Migrated R-spatial dependencies
• Replaced raster, rgeos, and sp packages in Imports with terra and sf because of imminent package retirements
• Removed maptools from Suggests (replaced with new internal function as.im.SpatRaster())
• Thank you, Roger Bivand, for the notice. Relates to ndi Issue #3
• Note: raster is a dependency of RStoolbox (at present) which is used in the vignette
• Updated test, examples, vignette, and documentation throughout
• Added GitHub R-CMD-check
• Updated citation style for CITATION file

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
• Added maptools and RStoolbox to Suggests (used in the package vignette)
• Added CITATION file
• Fixed typos in documentation throughout

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
• 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.
• spatstat.geom and spatstat.random are now Imports
• spatstat.data is now Suggests.
• See the GitHub merge pull request.
• 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

envi v0.1.10

• Addressed ERROR on R-devel CRAN environments by setting parallelly.makeNodePSOCK.setup_strategy = sequential for all CRAN tests as suggested by the maintainer for the future and parallelly packages who is actively working on a solution. See the GitHub issue.

envi v0.1.9

• Removed LazyData: true from 'DESCRIPTION' file because the package has no data accessed via a data() command and has no data/ directory (in response to CRAN NOTE: 'LazyData' is specified without a 'data' directory)
• Following advice from future package maintainer, now spatial_power() and jitter_power() functions reset future strategy when exiting
• Addressed ERROR in MacOS environments on rhub by setting the parallelly.makeNodePSOCK.setup_strategy = sequential for MacOS environments running tcltk until parallelly (>=1.26.1-9002) is on CRAN. This workaround was suggested by the parallelly maintainer. See the GitHub issue.

envi v0.1.8

• Updated spatstat package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). Now spatstat.geom, spatstat.core, spatstat.linnet, and spatstat (>= 2.0-0) are in Depends
• Replaced parallel and doParallel packages in Imports with doFuture, doRNG, and future packages to allow for parallel processing in lrren() and perlrren() functions to work across all CRAN environments
• Removed utils package from Imports because the progress bar in lrren() and perlrren() functions is now produced with a helper function in utils.R that imports the iterators package
• Set default for n_core argument in lrren() and perlrren() to be n_core = 2 to match documentation
• Fixed bug in pval_correct() when p_correct = "FDR" that will return the minimum p-value instead of NULL if no p-value is less than the p-critical value
• Updated cref0 and cref1 arguments in plot_predict() and plot_perturb() functions for PROJ6. Now calls sp::CRS() function within the raster::projectRaster() function and reformats the default argument values
• Updated testthat checks for parallelization in lrren() and perlrren() functions and testthat checks for PROJ6 updates in plot_predict() and plot_perturb() functions

envi v0.1.7

• Updated spatstat package to new subsetted packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). spatstat.geom and spatstat.core packages replace spatstat package in Imports
• Added p_correct argument to lrren() and perlrren() which calls a new, internal function pval_correct() that calculates three types of corrections for multiple testing (FDR, Sidak, Bonferroni)
• Removed a cv output for pval surface in lrren() that is not used in plot_cv()

envi v0.1.6

• Updated URLs in envi-package.Rd

envi v0.1.5

• Updated URLs in envi-package.Rd
• Updated year in DESCRIPTION

envi v0.1.4

• Fixed testthat preparation for plot_cv(), plot_obs(), and plot_predict() to remove "Warning message: In graphics::par(op): calling par(new=TRUE) with no plot"
• Removed parallel tests in testthat for lrren() and perlrren() as there is a known error with makePSOCKcluster() in R version > 4.0.0 (created error only in r-patched-solaris-x86 and r-release-macos-x86_64).

Waller-SUSAN/envi documentation built on Nov. 8, 2024, 12:35 a.m.