grainscape - v1.0.0

grainscape 1.0.0

Dependency changes

• Migrated from raster/sp to terra/sf for all spatial operations:
  • terra and sf added to Imports;
  • raster and sp dependencies removed entirely.
• Vignette diagrams are now generated from code with DiagrammeRsvg and rsvg (added to
  Suggests); webshot2 is no longer needed for the vignettes and was removed from Suggests.

Breaking changes

• MPG(), patchFilter(), and ggGS() no longer accept RasterLayer inputs;
  pass SpatRaster objects (from terra) instead;
• corridor(), distance(), and point() no longer accept SpatialPoints inputs;
  pass a two-column matrix or sf object instead;
• Slot types in mpg, goc, grain, and corridor S4 classes have changed from
  RasterLayer/SpatialPoints/SpatialLines/SpatialLinesDataFrame to SpatRaster/sf;
• The long-deprecated gs-prefixed functions (gsMPG(), gsGOC(), gsGOCCorridor(),
  gsGOCDistance(), gsGOCPoint(), gsGOCVisualize(), gsGraphDataFrame(), gsMPGstitch())
  are now defunct and error with a pointer to their replacement (deprecated since 0.4.0; #10);

New features

• New exported plotting helpers plotResistance() and plotWithResistance(): draw a
  resistance surface with a consistent colour scheme (and a discrete-value legend), and
  place it as an equally-sized reference panel beside a network plot for visual comparison.
  Both are demonstrated in the vignette's introductory figures (plotWithResistance() uses
  cowplot).

Bugfixes

• Fixed incorrect least-cost paths in MPG (#72);
• Fixed a regression in the #72 work where legitimate, non-redundant MPG links were dropped on
  high-variance resistance surfaces: the indirect-path search could treat an unset cell id
  (the internal -99 sentinel) as a pivot patch, fabricating a bogus two-hop route that
  suppressed a valid direct link. Such malformed links are now rejected and non-patch pivots
  are ignored (#72);
• Fixed patches being left isolated in the MPG: a patch cell that was never added as an
  active cell during spreading (e.g. a single-cell patch) kept the internal -99 id, so it
  was an unresolved link endpoint and all of its links were silently dropped. Every cell's id
  is now seeded from the voronoi map at initialization, so such patches are linked correctly
  (#72);
• Fixed an infinite loop (hang) in MPG(): a resistance surface whose first cell is NA left
  the C++ engine's internal cost range as NaN, so every patch cell was assigned a NaN
  resistance and never "settled", spinning forever. The engine now derives the cost range while
  skipping NA cells, and fully initializes its spreading-state struct, hardening it against
  this class of hang (#72);
• Fixed a Voronoi tessellation bias on high-variance resistance surfaces: patch (source) cells
  now begin spreading at the uniform minimum cost rather than the resistance of the cell they
  happen to overlap. Previously a patch sitting on a high-resistance cell spread late and lost
  territory to its neighbours, distorting the tessellation (and, in the extreme, leaving a
  patch with a single-cell region and no links). The fix changes only the tessellation: link
  weights are accumulated from the entered cells' resistances (independent of the source cell),
  so on the package's test surfaces the MPG and its weights are unchanged, and still match
  independent least-cost paths exactly (#72);
• Fixed graphdf returning a transposed (single-column) data frame for MPGs with only one link;
• patchFilter() no longer errors on R < 4.6 (with recent terra): it masked small patches via
  out[out %in% rmpatch] <- NA, which relies on %in% dispatching for a SpatRaster and fails
  with "'match' requires vector arguments" under older R; it now uses terra::subst() (#76);
• point() (and distance(), which calls it) now emit the "coords correspond to NA cells" warning once per call instead of once per coordinate-threshold combination (#50);
• The corridor plot() method now uses the linewidth aesthetic (rather than the deprecated
  size aesthetic) for its link segments, silencing a ggplot2 (>= 3.4.0) deprecation warning;

Vignette

• The "Calculating the minimum planar graph" vignette now generates its UML class diagrams, the
  algorithm flow chart, and the Engine call graphs directly from Graphviz/DiagrammeR
  specifications (rendered to vector PDFs with DiagrammeRsvg and rsvg) rather than embedding
  static images, so they stay in sync with the C++ engine; its technical reference was also
  updated for the #72 least-cost-path changes (the settled_map, createLinks(), and the
  parentResistance field) (#75);
• Corrected the thresholded-MPG figure (Figure 6), which plotted links above the dispersal
  threshold instead of the retained links below it (so the cheap, low-resistance links
  between neighbouring patches were hidden);
• Made the Euclidean-vs-resistance path-distance table robust by matching rows on the node
  pair (rather than column-binding two independently sorted tables), and the "patch 7
  neighbours" table now filters explicitly for patch 7. The minimum-planar-graph figure above
  that table now labels exactly node 7 and its linked neighbours, derived from the graph rather
  than a hard-coded list of patch ids.

Biosphere - Conservation and Restoration - TeX
Published by achubaty about 2 months ago

grainscape - v0.5.0

grainscape 0.5.0

Dependency changes

• Require R 4.2 or higher (for native pipe and placeholder)
• Add DiagrammeR, dplyr, webshot2 and withr to Suggests for use with vignettes and tests

Bugfixes

• Fixed documentation issues and 'memory not mapped' segfault errors on R-devel (#73)
• Improved handling of user-added attributes in exported objects (#71)
• Fixed partial match warnings
• Use replacements for deprecated igraph functions

New features & enhancements

• Use native R pipe throughout instead of magrittr pipe
• Improved documentation

Biosphere - Conservation and Restoration - TeX
Published by achubaty over 1 year ago

grainscape - v0.4.4

Known issues: https://github.com/achubaty/grainscape/issues

version 0.4.4

Dependency changes

• Removed retiring spatial packages rgdal and rgeos (#68)
• Use sf for writing shapefiles.

Bugfixes

• Improved plotting of lattice MPGs (#51)
• Removed unused eucPerimWeight from documentation (#56)
• Improved error messaging for undefined thresholds in GOC() (#57)

New features & enhancements

• None

Biosphere - Conservation and Restoration - TeX
Published by achubaty over 3 years ago

grainscape - v0.4.3

Known issues: https://github.com/achubaty/grainscape/issues

version 0.4.3

Dependency changes

• none

Bugfixes

• none

New features & enhancements

• added MEE paper citation and updated package DESCRIPTION & README.

Biosphere - Conservation and Restoration - TeX
Published by achubaty almost 6 years ago

grainscape - v0.4.2

Known issues: https://github.com/achubaty/grainscape/issues

version 0.4.2

Dependency changes

• removed unused dependency hunspell from Suggests

Bugfixes

• reduced package tarball size

New features & enhancements

• none

Biosphere - Conservation and Restoration - TeX
Published by achubaty over 6 years ago

grainscape - v0.4.0

version 0.4.0

Dependency changes

• Requires R >= 3.5
• remove rgeos dependency and deprecate use of sp argument to many functions (#38)

Bugfixes

• numerous bug fixes

New features & enhancements

• reimplement an algorithm to calculate the minimum planar graph using C++;
  no longer relies on SELES binary and is now cross-platform.
• use updated igraph functions internally
• updated vignette / tutorial (#5)
• renamed functions to remove gs and gsGOC prefixes; old names have been deprecated and will be removed in a future release (#10)
• MPG() can now handle large rasters
• use S4 classes and methods (#3, #19)
• improved plotting using ggplot2 by default (#22, #47)
• new functions export() (#39) and patchFilter() (#40)
• fix typos (#58, @jsta)

Removed features

• removed gsMPGstitch() as it was unreliable

Biosphere - Conservation and Restoration - TeX
Published by achubaty about 7 years ago