NEWS
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...