isocat 1.0.1

Bug fixes

• isotopeAssignmentModel(), schoenersD(), and surfaceSimilarityMatrix() now normalize correctly over isoscapes with masked (NA) cells, passing na.rm = TRUE in their internal sums; previously a single NA cell turned the whole surface NA (and errored in schoenersD()).
• schoenersD() returns a length-1 numeric value rather than a 1x1 data.frame, and coerces legacy Raster* inputs with the correct class check.

isocat 1.0.0

Breaking changes

• isotopeAssignmentModel() now uses terra instead of raster, and its in-function parallel-processing capability is deprecated.
• schoenersD() now expects SpatRaster inputs and automatically converts legacy Raster* objects.

New features

• New surfaceSimilarityMatrix() builds a Schoener’s D similarity matrix across all layers of a SpatRaster. It is vectorized (one value extraction plus base-R pairwise arithmetic), roughly 100x faster than per-pair evaluation. The legacy simmatrixMaker(), which takes a RasterStack, is retained but deprecated.

Bug fixes

• isotopeAssignmentModel() no longer silently discards a supplied SD_indv vector whose first element is 0. The default is now SD_indv = NULL (no individual-level error; isoscape error only), replacing the ambiguous 0 that caused the bug.
• makeMultiMonthIsoscape() now uses terra and corrects two errors in the monthly combination: the precipitation-weighted mean previously divided by the number of months (returning half-magnitude values), and the equal-weight (precip_stack = NULL) path errored. The combined-error surface is unchanged (root-sum-of-square).
• meanAggregateClusterProbability() accepts any cluster labels (integers, letters, factors), not just 1..K; the previous version indexed clusters by position and silently failed for other codings (#5). It also errors clearly when indivIDs do not match the surface layer names, and names each output layer by its cluster.

Minor improvements

• Documentation and test coverage are expanded across all functions.

isocat 0.3.0

New function

• New function makeMultiMonthIsoscape to combine multiple monthly isoscapes and error maps into one of each, for making month-specific isoscape assignments.

Tweaks

• schoenersD function now automatically normalizes surfaces to sum to 1, rather than just advising it in the documentation.
• corrected documentation parameter names in .assignmentMaker

isocat 0.2.6

Publication update

• Publication introducing some of isocat’s functionalities is out.
• Package citation is created, update. See citation("isocat").
• Updated package description with links, typo fixes.

Vignette improvements

• Added some additional text on transfer functions

isocat 0.2.5

Rewrote function isotopeAssignmentModel

• Function now checks for identical projections and resamples secondary models automatically.
• Multiple secondary models can be incorporated as a rasterStack.
• Replaced parallelization package with parallel::mcmapply.
• Removes bug where secondary models not created when running in parallel.

Minor tweaks

• Remove now-unnecessary import of package dplyr.
• Resolved bug in vignette example by adding ‘stringsAsFactors = FALSE’ to example dataframe.
• Removed defunct class test for individual IDs from meanAggregateClusterProbability function.

isocat 0.2.4

Optimize ‘cumsumbelow’ function

• Function deals with NA values more efficiently.
• When imported into makeCumSumSurface, function iterates faster over RasterLayers.
• Removed dependency on purrr::map and pipe operators within function.
• The purrr package removed from suggested packages.

Bug fix for R 4.0.0

• Modified conditional class check within cumsumAtSamplingLocation and clusterSimmatrix functions, in anticipation of change to matrix objects inheriting from class “array” (which broke old class check code).

Vignette updated

• Vignette updated, examples improved, enable stage-skipping with working examples.

Minor tweaks

• Tweaked package title.
• Added ‘additionalModel_name’ argument to isotopeAssignmentModel.
• Added ‘seealso’ and ‘alias’ components to function documentation.
• Fixed typo in examples for makeQuantileSimulationSurface function.
• Clarified function description for schoenersD function.
• Tweaked wording in example for cumsumAtSamplingLocation function.

isocat 0.2.3

Bug fixes

• Updated data file to realistic isoscape standard deviations.
• Fixed dependency / import issues throughout.
• Adjusted file names for cross-platform compatibility.
• Replaced references to superseded snow package with calls to parallel.

Vignette updated

• Vignette updated, TODO’s resolved.

Minor Tweaks

• Expanded DESCRIPTION metadata.
• Resolved spelling errors and improved style throughout package.
• Fixed broken/suspect email and IsoMAP links.
• Corrected donttest wrappers on long analyses.
• Added examples to several functions.
• Switched from ‘installed.packages’ to ‘!requireNamespace’ to check for package loading.

isocat 0.2.2

Vignette Included

• Added vignette with descriptions and example applications of all functions.

New Functions

• New suite of functions for working with cumulative sums: cumsumbelow, makeCumSumSurface, cumsumAtSamplingLocation.
• Added a meanAggregateClusterProbability function to create mean probability-of-origin map based on cluster assignments (for individuals of similar origin).
• Added projectSummarySurface function to show which RasterLayer in a stack has highest value at any given location.

Bug fixes

• Fixed minor issue with running makeQuantileSimulationSurface on object of class RasterLayer.
• Updated clusterSimmatrix function to match pvclust version 2.0-1 with debug of r parameter.
• Replaced buggy projectCluster function with alternative function (projectSummarySurface; see isocat vignette).

isocat 0.2.1

New Functions

• Added a schoenersD function that compares the spatial similarity of two surfaces.
• Added a makeQuantileSimulationSurface function that converts a surface to a quantile-simulation surface.

Minor Tweaks

• Improved code readability within several functions.

isocat 0.2.0

• Added a NEWS.md file to track changes to the package.
• Renamed package from IsoModAT (Isotope Models of Animal Origin Analytical Toolset) to isocat (Isotope Clustering and Assignment Tools).
• Specified CC0 license.

New Functions

• Added a makeQuantileSurface function to converts normalized probability surfaces to quantile surface. Matches makeOddsSurface.
• Added a oddsAtSamplingLocation function that finds odds ratios of origin probability at a set of coordinates within a normalized probability surface. Matches quantileAtSamplingLocation.