NEWS (original) (raw)

• cleanup test files left behind indistanceFromEachPoint;

Dependency changes

• drop support for R 4.2;

Enhancements

• improved spread for use with SpatRasters(#93);
• improved speed of .pointDistance (#97);
• fix a failing test when using testthat > 3.2.3(#98);
• documentation improvements;

Bug fixes

• fixed issue with rasterizeReduced();
• updates to deal with changes to RNG in dqrng (#96;@rstub). if backwards compatibility is needed, setdqrng::dqRNGkind("Xoroshiro128+") before runningspread to ensure numerical reproducibility with previous versions;

Enhancements

• minor documentation updates

Dependency changes

• drop support for R 4.1 due to changes in dependency packages

Bug fixes

• none

Enhancements

• randomPolygons() works with sfobjects;
• use numeric vector in crw to accommodate downstream dependency changes;

Dependency changes

• requires reproducible (>= 2.0.9)

Bug fixes

• fixed splitRaster() tests that broke due to changes inreproducible::Filenames() (#91)

Enhancements

• improved documentation
• address new features of quickPlot
• minor modifications to crw to allow downstream packages that use matrix classes instead of sf orSpatVector classes for “agents”
• address timing issue on CRAN machines

Dependency changes

• removed Suggests dependencies CircStats,dplyr, purrr, DBI,RColorBrewer, googledrive,snow

Bug fixes

• none

Enhancements

• wholesale transition to terra from rasterand sp. Some functionality is available forsf, but this will not be complete.
• splitRaster() uses ".tif" as the default raster file type
• most example plotting uses terra::plot directly, but in a few cases, quickPlot::Plot is used as it is much better (e.g., spread2(plot.it = TRUE))

Dependency changes

• drop support for R 4.0 (dependency package reproduciblesupports R >= 4.1);
• now has only 7 Imports and Depends, which becomes 15 recursive dependencies (down from 40)
• add terra to Imports
• removed dependencies magrittr, rgeos,rlang, Require, graphics
• added to Suggests: withr
• moved to Suggests: quickPlot, fastmatch,raster, sp, sf,CircStats
• added snow to Suggests as it’s used for parallelraster operations;
• added tools to Suggests forfile.ext()

Bugfixes

• all open issues dealt with
• fixes related to migration to terra
• other minor bug fixes

Dependency changes

• none

Enhancements

• terra compatibility added
• neutralLandscapeMap expanded to use moreNLMR functions

Bug Fixes

• suppress additional spurious warnings

Enhancements

• a new function, neutralLandscapeMap, replaces the defunct gaussMap in creating a neutral landscape map using the midpoint displacement algorithm available inNLMR::nlm_mpd.

This is a major SpaDES.tools update causing breaking changes due to multiple CRAN packages no longer available as of R version 4.2 released April 2022.

Dependency changes

• Removed dependencies ffbase and ff and deprecated use of lowMemory argument in spread(ffbase was removed from CRAN April 2022).
• Removed dependency RandomFields which is no longer maintained. We had to drop support for random landscape generation viagaussMap(); but see the NLMR package for tools to create random neutral landscapes.

Enhancements

• mergeRaster() can deal with rasters with different origins extents (i.e., that were not produced usingsplitRaster())

Bug Fixes

• spread2 was unable to use maxSize whenstart was the output of a previous spread2call to which maxSize had not been supplied. This has now been fixed.

Dependency changes

• drop support for R 3.6 (#65)

Enhancements

• none

Bug Fixes

• fix error in spread2() causing failures on R-devel

Dependency changes

• Require moved to Suggests, because it’s only used in examples.

Enhancements

• none

Bug Fixes

• fixed misc CRAN check issues with Suggested packages
• fixed bug in splitRaster() (#62; @anbm-dk)

Dependency changes

• Dropped support for R 3.5 due to changes in dependency packages. R versions 3.6 and higher are supported.

Enhancements

• distanceFromEachPoint: cl argument can now accept a numeric scalar indicating how many cores to use with anmclapply internally
• distanceFromEachPoint: minor speed improvements
• spread3 has new arguments (sdDist,dispersalKernel)
• improved speed for spread under most conditions, especially larger events, possibly up to 2x.
• splitRaster() can now specify file extension, instead of defaulting to .grd
• several under the hood improvements for stability, speed

Bug Fixes

• distanceFromEachPoint bugfixes under some cases (some values of toCells, angles would cause errors)

Dependency changes

• none

Bug Fixes

• spread with allowOverlap = TRUE would give wrong results. Fixed.
• update a test to deal with forthcoming rasterchanges.

Enhancements

• none

We have identified a non-trivial bug in spread when using allowOverlap = TRUE. Until we can patch this bug, using this argument value will generate an error. We are currently working on a fix, which may take some time.

Dependency changes

• removed orphaned package bit; its reverse dependencies,ff and ffbase, moved to Suggests

Bugfixes

• none

Enhancements

• spread sped up forallowOverlap = TRUE
• New values for returnIndices arg inspread, allowing for numeric. New option,2 allows for the fastest return possible, onlypixelIndices

Dependency changes

• none

Bugfixes

• fix issues with failing tests on CRAN

Enhancements

• none

Dependency changes

• Requires R >= 3.5
• Added animation since it is used in thespread3 example.
• Added backports for R-oldrel support
• Removed profvis and microbenchmark from Suggests: all benchmarking is removed from automated tests

Bugfixes

• minor Bug Fixes

Enhancements

• spread2 speed enhancements

Dependency changes

• Added animation, fasterize, andsf to suggests (used in examples)

Bugfixes

• minor bug fixes

Enhancements

• spread2 now takes a numeric forallowOverlap, to allow for 1 more scenario of overlapping, namely, allow between event overlapping, and within event overlapping only if the overlap occurs in the same iteration, otherwise, do not allow overlap within event.
• new function spread3 for simulating e.g., insect spread
• pointDistance is now exported

Dependency changes

• RandomFields moved to Suggests to prevent clashes withdata.table multithreading

Enhancements

• randomPolygon now has area argument, instead of hectares (deprecated), and it now succeeds for more cases.
• mergeRaster now accepts a function passed by the user when mosaic is triggered (#55, @tati-micheletti)
• initiateAgents example fixed to work with newerraster package versions (@rhijmans)

New features

• splitRaster defaults to in-memory rasters when no file path specified (#47, @ianmseddy).

Removed features

• Previously deprecated functions removed to fix CRAN check WARNINGs. These are now located in the reproducible package.
• compiler package no longer used; is automatic in R >= 3.5

New features

• new arguments added to gaussMap (#20, @ianmseddy).
• move fastMask to reproducible package

Deprecated functions

• fastCrop(): raster::crop is faster thanvelox::crop under many tests.
• fastMask(): moved to the reproduciblepackage.

Bug Fixes

• minor bug fixes (spread2)
• minor test fixes.

Dependency changes

• dplyr and mgcv added to Suggests because they are used in tests.
• add more detailed information to package Description, per CRAN.
• add randomPolygon function for single random polygon.
• speed improvements with spread2 whenasymmetry used.
• minor bug fixes.
• A new package, which takes all auxiliary modelling functions out of the SpaDES package:
  • see ?SpaDES.tools::SpaDES.tools for an overview of included functionality.