Dev (#58)

* Update CITATION.cff * Update CITATION.cff * Smaller bug fixes and name sanitations * Update CITATION.cff * Prelunch commit. Some smaller fixes to make writing and loading models work * Update CITATION.cff * Pre-party commit. Similarity still not working yet. * Update CITATION.cff * Several updates, most notably improved 5 parameter Richards curve for offset calculations * Re-build README.md * Attempt to fix ci-error in tests * Small fix for tests * another attempt for ci fix * Update to version 0.0.5 (#53) (#54) * Update CITATION.cff * Update CITATION.cff * Smaller bug fixes and name sanitations * Update CITATION.cff * Prelunch commit. Some smaller fixes to make writing and loading models work * Update CITATION.cff * Pre-party commit. Similarity still not working yet. * Update CITATION.cff * Several updates, most notably improved 5 parameter Richards curve for offset calculations * Re-build README.md * Attempt to fix ci-error in tests * Small fix for tests * another attempt for ci fix --------- Co-authored-by: Martin-Jung <Martin-Jung@users.noreply.github.com> * Small bugfix related to ensemble and min/max of terra (#55) * Small bugfix related to ensemble and min/max of terra * Small bugfix related to ensemble and min/max of terra * Update tests for ensemble * Addition of MCP limits to `distribution` * Update CITATION.cff * Bug and documentation fixes * Update CITATION.cff * Started with implementation of check function #45 * Fix Missing link warning * Smaller documentation fixes * Update CITATION.cff * Warning and documentation fixes, adding aliases * Update CITATION.cff * Small hotfix for gh-pages and aliases * Update CITATION.cff * Small fix to validate * Fix two minor issues related to imports * Update CITATION.cff * Removed documentation whitespaces and minor conversion bug fix * Smaller fixes and implementation of #57 * Hotfix (:fire:) that pkgdown does not break * Small scenario addition and documentation fix. * Implementation of limiting function (#37) and minor bug fixes * 🐛 fix 😪 * Update CITATION.cff --------- Co-authored-by: Martin-Jung <Martin-Jung@users.noreply.github.com> Co-authored-by: Maximilian Hesselbarth <mhk.hesselbarth@gmail.com> Co-authored-by: mhesselbarth <mhesselbarth@users.noreply.github.com>
iiasa · Jul 21, 2023 · d7d7f97 · d7d7f97
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "ibis.iSDM" in publications use:'
 type: software
 license: CC-BY-4.0
 title: 'ibis.iSDM: Modelling framework for integrated biodiversity distribution scenarios'
-version: 0.0.5
+version: 0.0.6
 abstract: Integrated framework of modelling the distribution of species and ecosystems
   in a suitability framing. This package allows the estimation of integrated species
   distribution models (iSDM) based on several sources of evidence and provided presence-only
@@ -64,7 +64,7 @@ references:
   - family-names: Hesselbarth
     given-names: Maximilian H.K.
   year: '2023'
-  version: 0.0.4
+  version: 0.0.5
 - type: software
   title: assertthat
   abstract: 'assertthat: Easy Pre and Post Assertions'
@@ -217,17 +217,6 @@ references:
     given-names: David
     email: dpierce@ucsd.edu
   year: '2023'
-- type: software
-  title: ncmeta
-  abstract: 'ncmeta: Straightforward ''NetCDF'' Metadata'
-  notes: Imports
-  url: https://github.com/hypertidy/ncmeta
-  repository: https://CRAN.R-project.org/package=ncmeta
-  authors:
-  - family-names: Sumner
-    given-names: Michael
-    email: mdsumner@gmail.com
-  year: '2023'
 - type: software
   title: parallel
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -239,6 +228,35 @@ references:
   year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+- type: software
+  title: Matrix
+  abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
+  notes: Imports
+  url: https://R-forge.R-project.org/tracker/?atid=294&group_id=61
+  repository: https://CRAN.R-project.org/package=Matrix
+  authors:
+  - family-names: Bates
+    given-names: Douglas
+    orcid: https://orcid.org/0000-0001-8316-9503
+  - family-names: Maechler
+    given-names: Martin
+    email: mmaechler+Matrix@gmail.com
+    orcid: https://orcid.org/0000-0002-8685-9910
+  - family-names: Jagan
+    given-names: Mikael
+    orcid: https://orcid.org/0000-0002-3542-2938
+  year: '2023'
+- type: software
+  title: ncmeta
+  abstract: 'ncmeta: Straightforward ''NetCDF'' Metadata'
+  notes: Imports
+  url: https://github.com/hypertidy/ncmeta
+  repository: https://CRAN.R-project.org/package=ncmeta
+  authors:
+  - family-names: Sumner
+    given-names: Michael
+    email: mdsumner@gmail.com
+  year: '2023'
 - type: software
   title: posterior
   abstract: 'posterior: Tools for Working with Posterior Distributions'
@@ -427,6 +445,7 @@ references:
     given-names: Fabian E.
     email: bachlfab@gmail.com
   year: '2023'
+  version: '>= 2.6.0'
 - type: software
   title: glmnet
   abstract: 'glmnet: Lasso and Elastic-Net Regularized Generalized Linear Models'
@@ -450,6 +469,7 @@ references:
   - family-names: Yang
     given-names: James
   year: '2023'
+  version: '>= 4.1'
 - type: software
   title: glmnetUtils
   abstract: 'glmnetUtils: Utilities for ''Glmnet'''
@@ -693,6 +713,42 @@ references:
     given-names: Andrew
   year: '2023'
   version: '>= 2.1.1'
+- type: software
+  title: gnlm
+  abstract: 'gnlm: Generalized Nonlinear Regression Models'
+  notes: Suggests
+  url: http://www.commanster.eu/rcode.html
+  repository: https://CRAN.R-project.org/package=gnlm
+  authors:
+  - family-names: Swihart
+    given-names: Bruce
+    email: bruce.swihart@gmail.com
+  - family-names: Lindsey
+    given-names: Jim
+    email: jlindsey@gen.unimaas.nl
+  year: '2023'
+- type: software
+  title: geosphere
+  abstract: 'geosphere: Spherical Trigonometry'
+  notes: Suggests
+  url: https://github.com/rspatial/geosphere/issues/
+  repository: https://CRAN.R-project.org/package=geosphere
+  authors:
+  - family-names: Hijmans
+    given-names: Robert J.
+    email: r.hijmans@gmail.com
+  year: '2023'
+- type: software
+  title: cubelyr
+  abstract: 'cubelyr: A Data Cube ''dplyr'' Backend'
+  notes: Suggests
+  url: https://github.com/hadley/cubelyr
+  repository: https://CRAN.R-project.org/package=cubelyr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@rstudio.com
+  year: '2023'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -704,6 +760,7 @@ references:
     given-names: Hadley
     email: hadley@posit.co
   year: '2023'
+  version: '>= 3.0.0'
 - type: software
   title: xgboost
   abstract: 'xgboost: Extreme Gradient Boosting'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",
@@ -30,6 +30,8 @@ Imports:
     graphics,
     methods,
     ncdf4,
+    parallel,
+    Matrix,
     ncmeta,
     parallel,
     posterior,
@@ -63,7 +65,9 @@ Suggests:
     rstan (>= 2.21.0),
     rstantools (>= 2.1.1),
     gnlm,
-    testthat,
+    geosphere,
+    cubelyr,
+    testthat (>= 3.0.0),
     xgboost
 URL: https://iiasa.github.io/ibis.iSDM/
 BugReports: https://github.com/iiasa/ibis.iSDM/issues
@@ -98,6 +102,7 @@ Collate:
     'add_priors.R'
     'bdproto-engine.R'
     'bdproto-settings.R'
+    'check.R'
     'utils-spatial.R'
     'data.R'
     'distribution.R'
@@ -113,6 +118,7 @@ Collate:
     'engine_xgboost.R'
     'ensemble.R'
     'ibis.iSDM-package.R'
+    'limiting.R'
     'misc.R'
     'partial.R'
     'plot.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -83,6 +83,7 @@ export(add_pseudoabsence)
 export(alignRasters)
 export(as.Id)
 export(bivplot)
+export(check)
 export(distribution)
 export(emptyraster)
 export(engine_bart)
@@ -106,11 +107,13 @@ export(is.Raster)
 export(is.Waiver)
 export(is.formula)
 export(is.stars)
+export(limiting)
 export(load_model)
 export(myLog)
 export(new_id)
 export(new_waiver)
 export(partial)
+export(partial_density)
 export(posterior_predict_stanfit)
 export(predictor_derivate)
 export(predictor_filter)
@@ -172,10 +175,12 @@ exportMethods(add_predictor_range)
 exportMethods(add_predictors)
 exportMethods(add_predictors_globiom)
 exportMethods(add_priors)
+exportMethods(check)
 exportMethods(distribution)
 exportMethods(ensemble)
 exportMethods(ensemble_partial)
 exportMethods(get_priors)
+exportMethods(limiting)
 exportMethods(load_model)
 exportMethods(priors)
 exportMethods(project)
@@ -193,7 +198,6 @@ exportMethods(validate)
 exportMethods(write_model)
 exportMethods(write_output)
 exportMethods(write_summary)
-import(posterior)
 import(sf)
 import(terra)
 importFrom(foreach,"%do%")

diff --git a/NEWS.md b/NEWS.md
@@ -1,26 +1,48 @@
+# ibis.iSDM 0.0.6 (current dev branch)
+
+### 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.frames` 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`.
-* Added Boruta for iterative feature selection of predictor variables.
 
 # 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.