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Changelog

Source: NEWS.md

ibis.iSDM 0.1.6 (current dev branch)

New features
Minor improvements and bug fixes
  • IIASA internal functionalities such as preparation of GLOBIOM data have been transferred to BNRTools

ibis.iSDM 0.1.5

New features
  • New visualization function nicheplot() to visualize suitability across 2 axes #87.
  • Support for ‘modal’ value calculations in ensemble().
  • Support for ‘superlearner’ in ensemble().
  • Support for ‘kmeans’ derived threshold calculation in threshold() and predictor_derivate().
  • Support for future processing streamlined. See FAQ section for instructions #18.
Minor improvements and bug fixes
  • Now overwriting temporary data by default in predictor_transform() and similar functions.
  • Minor 🐛 fix related to misaligned thresholds and negative exponential kernels.
  • 🔥 🐛 fix for scenario projections that use different grain sizes than for inference.

ibis.iSDM 0.1.4

New features
Minor improvements and bug fixes
  • 🐛 fix for support of factor x continuous variable interaction #131
  • Renamed add_control_extrapolation to add_limits_extrapolation().
  • 🐛 fix to engine_gdb also to support non-linear smooth functions (again).
  • Small fix to support deprecated field_occurrence field in validate for convenience.
  • 🐛 fix that prevented BART models to be saved/loaded from disk #127.
  • 🐛 fixes related to factor handling for all engines.
  • 🐛 fixes related to is_comparable_raster and add_predictors/add_predictors_range #130
  • 🐛 fix related to partial for engine_gdb and priors

ibis.iSDM 0.1.3

New features
  • Add functions that creates HTML file base on DistributionModel.
  • Added new engine engine_scampr() for model-based integration.
  • Allow projection of models using method_integration = "predictor"
Minor improvements and bug fixes
  • Small fixes to ensure boruta filtering works (again)?
  • Small fix to parameter in train() #102 @jeffreyhanson
  • Small helper function for combining 2 different formula objects combine_formulas()
  • Small bug fixes dealing with scenario() projections and limits, plus unit tests #104
  • Bug fixes with adding predictor_derivate() to scenario predictors and added unit tests #106
  • Several fixes related to different engines and priors.
  • Changed default output for netcdf files to multidimensional arrays #109
  • 🔥 hot fixes for scenario scaling and normalization issue #113
  • 🐛 fix so that projection works with different extents than used for inference.

ibis.iSDM 0.1.2

New features
  • Switched object structure to R6 throughout for improved data and memory handling #44
  • Implemented a convenience function ro remove biodiversity datasets (rm_biodiversity()).
Minor improvements and bug fixes
  • Added a logical parameter to ensemble() enabling compositing of thresholds if set #84
  • Support of multi-band rasters in ensemble() for convenience.
  • Fix of bug in threshold() for supplied point data and improved error messages.
  • Cleaner docs and structure
  • Adding wrap_model/unwrap_model functions
  • Added default parameters for all ibis specific options #90
  • Changing behaviour of weights in engine_inlabru() #93

ibis.iSDM 0.1.1

New features
  • Added default engine_glm() for dependency-free inference and projection.
  • Harmonized controls settings and added option to contrain extrapolation add_control_extrapolation()
  • Adding a function for temporal interpolation of predictors #52
Minor improvements and bug fixes

ibis.iSDM 0.1.0

New features
Minor improvements and bug fixes
  • Added R-universe installation option as alternative to github #38
  • Minor bug fixes in scenario() object, and MigClim and Kissmig wrappers.
  • Bug fix related to CRS classes of sp and sf
  • Bug fix related to blas.num.threads
  • Bug fix that crashed write_summary() outputs when no prediction was made.
  • Bug fix related to CRS in engine_inla()
  • Bug fix in engine_stan() related to background layer
  • Class of biodiversity data is identical for PO and PA
  • Bug fix in built_formula_glmnet() and response
  • Bug fix in built_formula_gdb() and response
  • Each model$biodiversity stores only predictors of current ID
  • Bug fix in built_formula_inla() for INLABRU

ibis.iSDM 0.0.9

New features
  • Added new vignette on available functions for data preparation #67
  • Addition of small mask() function that emulates the for terra.
Minor improvements and bug fixes

ibis.iSDM 0.0.8

New features
Minor improvements and bug fixes
  • Added warnings and checks for missing crs in supplied layers #65
  • Smaller bug and code harmonizations to ensemble_partial(), partial() and spartial().
  • Smaller bug fixes to threshold() in scenario() projections.
  • Improved error messages in several functions.
  • Further documentation fixes towards CRAN submission #38
  • Allow to specify location of biodiversity point records in threshold().

ibis.iSDM 0.0.7

New features
  • Added method proximity to add_control_bias() to place lower weights on points closer to another.
  • Added helper functions get_data() and the option to apply threshold() directly on BiodiversityScenarios.
  • Added centroid function to BiodiversityScenarios and DistributionModels #29
Minor improvements and bug fixes
  • Add Error message for background data of different units easier to understand.
  • Added warning message to the threshold creation to use independent data where possible.
  • Fixed min.cv bug in threshold() introduced by #17
  • Fixed add_offset() function now also allowing sf objects as input.
  • Fixed bug with writing outputs in write_output()
  • Fixed a bug so that prediction limits work correctly again (distribution(...,lim = x))

ibis.iSDM 0.0.6

New features
  • partial_density() function implemented #57
  • Re-specification of limits with implementation of minimum convex polygon limits to distribution().
  • Added check() function for assessing assumptions and fits for various objects #45
  • Added minor internal helper functions to duplicate stars objects via st_rep.
  • Implemented local limiting factor function (limiting()) #37
Minor improvements and bug fixes
  • Further smaller documentation fixes towards a CRAN submission #38
  • Bug fix to method buffer in pseudo-absence settings.
  • Minor bug fixes to ensemble() uncertainty calculations.

ibis.iSDM 0.0.5

New features
  • Addition of 5 parameter logistic curve offsets with parameter search to add_offset().
Minor improvements and bug fixes
  • Further smaller documentation fixes towards a CRAN submission #38
  • Bug with with write_model(), now converting terra objects to data.frame between import/export.
  • Smaller bug fixes, for example in similarity(), addition of variable name sanitization to predictors by default.

ibis.iSDM 0.0.4

Minor improvements and bug fixes
  • Smaller bug fixes with regards to writing outputs and adding pseudo-absences.
  • Added short convenience function to convert prediction outputs #48
  • Converted from raster to terra #17
  • Updated and added further unit checks and tests

ibis.iSDM 0.0.3

New features
  • Aded Boruta for iterative feature selection of predictor variables.
Minor improvements and bug fixes
  • Removed Magittr dependency #41
  • Smaller improvements to documentation and removing of CRAN preventing function calls.
  • Made the separation from hyperparameter search functions clearer and added new option to filter highly correlated covariates via train().

ibis.iSDM 0.0.2

Minor improvements and bug fixes
  • Smaller documentation fixes, including to make sure examples and returns are in all exported function documentations.
  • Preparation for cran release #38, including fixing some common issues and checks.
  • Some smaller bug fixes to validate() to make Boyce more robust.
  • Change of the logo. Thanks to @elliwoto
  • Added warning to validate call for users to be aware of non-independent validation.
  • Further fixes on github actions and tests by @mhesselbarth

ibis.iSDM 0.0.1

  • Initial public release version! Finding and fixing further bugs…