envi (development version)

envi v1.0.1

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 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

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

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

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’

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

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

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

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

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.

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.

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

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()

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).