SpaDES.tools 2.0.7

bug fixes

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

SpaDES.tools 2.0.6

Enhancements

• minor documentation updates

Dependency changes

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

Bug fixes

• none

SpaDES.tools 2.0.5

Enhancements

• randomPolygons() works with sf objects;
• 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 in reproducible::Filenames() (#91)

SpaDES.tools 2.0.4

Enhancements

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

Dependency changes

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

Bug fixes

• none

SpaDES.tools 2.0.0

Enhancements

• wholesale transition to terra from raster and sp. Some functionality is available for sf, 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 reproducible supports 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 parallel raster operations;
• added tools to Suggests for file.ext()

Bugfixes

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

SpaDES.tools 1.0.2

Dependency changes

• none

Enhancements

• terra compatibility added
• neutralLandscapeMap expanded to use more NLMR functions

Bug Fixes

• suppress additional spurious warnings

SpaDES.tools 1.0.1

Enhancements

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

SpaDES.tools 1.0.0

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 via gaussMap(); 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 using splitRaster())

Bug Fixes

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

SpaDES.tools 0.3.10

Dependency changes

• drop support for R 3.6 (#65)

Enhancements

• none

Bug Fixes

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

SpaDES.tools 0.3.9

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)

SpaDES.tools 0.3.8

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 an mclapply 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)

SpaDES.tools 0.3.6

Dependency changes

• none

Bug Fixes

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

Enhancements

• none

SpaDES.tools 0.3.5

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 for allowOverlap = TRUE
• New values for returnIndices arg in spread, allowing for numeric. New option, 2 allows for the fastest return possible, only pixelIndices

SpaDES.tools 0.3.4

Dependency changes

• none

Bugfixes

• fix issues with failing tests on CRAN

Enhancements

• none

SpaDES.tools 0.3.3

Dependency changes

• Requires R >= 3.5
• Added animation since it is used in the spread3 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

SpaDES.tools 0.3.2

Dependency changes

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

Bugfixes

• minor bug fixes

Enhancements

• spread2 now takes a numeric for allowOverlap, 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

SpaDES.tools 0.3.1

Dependency changes

• RandomFields moved to Suggests to prevent clashes with data.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 newer raster package versions (@rhijmans)

SpaDES.tools 0.3.0

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

SpaDES.tools 0.2.0

New features

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

Deprecated functions

• fastCrop(): raster::crop is faster than velox::crop under many tests.
• fastMask(): moved to the reproducible package.

Bug Fixes

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

Dependency changes

• dplyr and mgcv added to Suggests because they are used in tests.

SpaDES.tools 0.1.1

• add more detailed information to package Description, per CRAN.
• add randomPolygon function for single random polygon.
• speed improvements with spread2 when asymmetry used.
• minor bug fixes.

SpaDES.tools 0.1.0

• 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.