NEWS.md

In cjcampbell/isocat: Isotope Origin Clustering and Assignment Tools

isocat 2.0.0.9000

Updates to rely on terra and sf for long-term package stability

• isotopeAssignmentModel now relies on terra instead of raster. Depreciated the parallel processing capability within this function
• schoenersD now expects inputs of SpatRasters, will automatically convert raster-class objects.
• New function schoenersDsimmatrix generates a similarity matrix comprising Schoener's D values for all layers in a SpatRaster. Function simmatrixMaker retained as a legacy/depreciated function that still uses rasterStacks as input.

TODO -- make schoenersDsimmatrix that runs in parallel

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.

cjcampbell/isocat documentation built on June 13, 2024, 9:26 p.m.