NEWS

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ibis.iSDM 0.1.7

New features

• Implementation of small ensemble of models for linear engines (add_control_esm()) #141
• Raise informative error if bias layer has negative values. #148
• Update engine_xgboost() to work with latest development build and remove [pdp] as dependency #149
• Improvement of document grammar and readability. Few more vignette examples based on latest development.
• :bug: Fixing of engine_inlabru() to work with latest version #150 #145
• :bug: Fixes to add_control_bias() to have it working again.
• :bug: Refactor code to avoid importing namespaces #95

Minor improvements and bug fixes

ibis.iSDM 0.1.6

New features

• Support for [data.frame] as predictors in add_predictors() #136
• Convenience function to allow [data.frame] and [SpatRaster] to be supplied directly via project() #136
• Small helper function to summarize values in a zone [predictor_summarize_zones()].
• New scenario projection constraint option in [add_constraint_adaptability()] for (thermal) limitation of a variable #137

Minor improvements and bug fixes

• Fix kissmig to work with version 2.0 #140
• IIASA internal functionalities such as preparation of GLOBIOM data have been transferred to BNRTools
• Small bug fixed related to manual provision of scenario thresholds.
• predictor_filter() now also accepts [SpatRaster] objects as inputs.
• Small fix so that bounding box extent is correctly printed #138
• Small :bug: fixes to engine_gdb in dev branch.

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 :bug: fix related to misaligned thresholds and negative exponential kernels.
• :fire: :bug: fix for scenario projections that use different grain sizes than for inference.

ibis.iSDM 0.1.4

New features

• Support for carnying over latent spatial effects (add_latent_spatial()) to scenario() projections.
• Convenience functions to remove limits and controls rm_limits()/rm_control() #121
• :fire: Enable stars and multi-temporal SpatRaster zones for scenario() and distribution() #121

Minor improvements and bug fixes

• :bug: fix for support of factor x continuous variable interaction #131
• Renamed add_control_extrapolation to add_limits_extrapolation().
• :bug: fix to engine_gdb also to support non-linear smooth functions (again).
• Small fix to support deprecated field_occurrence field in validate for convenience.
• :bug: fix that prevented BART models to be saved/loaded from disk #127.
• :bug: fixes related to factor handling for all engines.
• :bug: fixes related to is_comparable_raster and add_predictors/add_predictors_range #130
• :bug: 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
• :fire: hot fixes for scenario scaling and normalization issue #113
• :bug: 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

• Minor corrective fixes and additions to add_offset().
• Switch to engine_glm() in many of the unittests for better coverage.
• Several bug fixes and improvements in thin_observations()
• global, probs, and centers argument for better control of thin_observations()
• Harmonization of parameters for spartial() and addressing #80

ibis.iSDM 0.1.0

New features

• Added a small convenience wrapper to add model outputs to another model add_predictors_model()
• Started adding mechanistic SDM vignette #67
• Wrapper for steps implemented via simulate_population_steps() #68

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

• Small fix to ensemble() so that ensembles of future scenarios use correct standardization.
• Small fix to threshold() now returning threshold values correctly.
• Bug fix and error catching to distribution() and ensemble_partial(),ensemble_spartial()
• Further checks added to check() #45
• Small fix to alignRasters().
• Small fix to harmonize field_column throughout.
• Improved error messages and handling of formula's.

ibis.iSDM 0.0.8

New features

• Implemented min size constraint (add_constraint_minsize()) #56
• Added a function for estimating partial effects of ensembles ensemble_spartial().

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...