Merge pull request #126 from iiasa/dev

Dev to master for 0.1.3 version bump

.github/workflows/R-CMD-check.yaml

@@ -67,6 +67,7 @@ jobs:
             any::glmnetUtils,
             any::pdp,
             stan-dev/cmdstanr,
+            ElliotDovers/scampr,
             any::igraph,
             any::lwgeom,
             any::ncmeta,

.github/workflows/pkgdown.yaml

@@ -32,6 +32,9 @@ jobs:
           sudo apt-get -y install \
           libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev
 
+      - name: Install inla
+        run: Rscript -e 'install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"),dep=TRUE)'
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

CITATION.cff

@@ -1,5 +1,5 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.5.0
+# CITATION file created with {cffr} R package, v1.0.0
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
 
@@ -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: 0.1.2
+version: 0.1.3
 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
@@ -196,29 +196,31 @@ references:
   - family-names: Dunnington
     given-names: Dewey
     orcid: https://orcid.org/0000-0002-9415-4582
+  - family-names: Brand
+    given-names: Teun
+    name-particle: van den
+    orcid: https://orcid.org/0000-0002-9335-7468
   year: '2024'
 - type: software
   title: graphics
   abstract: 'R: A Language and Environment for Statistical Computing'
   notes: Imports
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
   notes: Imports
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: Matrix
   abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
@@ -255,11 +257,10 @@ references:
   notes: Imports
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: posterior
   abstract: 'posterior: Tools for Working with Posterior Distributions'
@@ -312,11 +313,10 @@ references:
   notes: Imports
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: terra
   abstract: 'terra: Spatial Data Analysis'
@@ -366,22 +366,20 @@ references:
   notes: Imports
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
 - type: software
   title: 'R: A Language and Environment for Statistical Computing'
   notes: Depends
   url: https://www.R-project.org/
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 4.1.0'
 - type: software
   title: abind
@@ -670,7 +668,7 @@ references:
   title: ncmeta
   abstract: 'ncmeta: Straightforward ''NetCDF'' Metadata'
   notes: Suggests
-  url: https://github.com/hypertidy/ncmeta
+  url: https://hypertidy.github.io/ncmeta/
   repository: https://CRAN.R-project.org/package=ncmeta
   authors:
   - family-names: Sumner
@@ -745,6 +743,22 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2024'
+- type: software
+  title: lubridate
+  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
+  notes: Suggests
+  url: https://lubridate.tidyverse.org
+  repository: https://CRAN.R-project.org/package=lubridate
+  authors:
+  - family-names: Spinu
+    given-names: Vitalie
+    email: [email protected]
+  - family-names: Grolemund
+    given-names: Garrett
+  - family-names: Wickham
+    given-names: Hadley
+  year: '2024'
+  version: '>= 1.9.0'
 - type: software
   title: rstan
   abstract: 'rstan: R Interface to Stan'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",
@@ -76,6 +76,7 @@ Suggests:
     progress,
     pdp,
     rmarkdown,
+    lubridate (>= 1.9.0),
     rstan (>= 2.21.0),
     rstantools (>= 2.1.1),
     testthat (>= 3.0.0),
@@ -123,6 +124,7 @@ Collate:
     'utils-inla.R'
     'engine_inla.R'
     'engine_inlabru.R'
+    'engine_scampr.R'
     'engine_stan.R'
     'engine_xgboost.R'
     'ensemble.R'
@@ -145,6 +147,7 @@ Collate:
     'priors.R'
     'project.R'
     'pseudoabsence.R'
+    'render_html.R'
     'scenario.R'
     'similarity.R'
     'simulate_population_steps.R'
@@ -165,3 +168,5 @@ Collate:
     'validate.R'
     'write_output.R'
     'zzz.R'
+Remotes:
+  ElliotDovers/scampr

NAMESPACE

@@ -63,6 +63,7 @@ export(add_constraint_boundary)
 export(add_constraint_connectivity)
 export(add_constraint_dispersal)
 export(add_constraint_minsize)
+export(add_constraint_threshold)
 export(add_control_bias)
 export(add_control_extrapolation)
 export(add_latent_spatial)
@@ -82,6 +83,7 @@ export(alignRasters)
 export(as.Id)
 export(bivplot)
 export(check)
+export(combine_formulas)
 export(distribution)
 export(emptyraster)
 export(engine_bart)
@@ -91,6 +93,7 @@ export(engine_glm)
 export(engine_glmnet)
 export(engine_inla)
 export(engine_inlabru)
+export(engine_scampr)
 export(engine_stan)
 export(engine_xgboost)
 export(ensemble)
@@ -129,6 +132,7 @@ export(predictor_transform)
 export(priors)
 export(project.BiodiversityScenario)
 export(pseudoabs_settings)
+export(render_html)
 export(rm_biodiversity)
 export(rm_latent)
 export(rm_offset)

NEWS.md

@@ -1,4 +1,22 @@
-# ibis.iSDM 0.1.2 (current dev branch)
+# ibis.iSDM 0.1.3 (current dev branch)
+
+#### 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

R/add_biodiversity.R

@@ -13,7 +13,7 @@ NULL
 #' @param formula A [`character`] or [`formula`] object to be passed. Default is
 #' to use all covariates (if specified).
 #' @param family A [`character`] stating the family to be used (Default: \code{'Poisson'}).
-#' @param link A [`character`] to overwrite the default link function (Default: code{NULL}).
+#' @param link A [`character`] to overwrite the default link function (Default: \code{NULL}).
 #' @param weight A [`numeric`] value acting as a multiplier with regards to any
 #' weights used in the modelling. Larger weights indicate higher weighting
 #' relative to any other datasets. By default set to \code{1} if only one
@@ -130,7 +130,7 @@ methods::setMethod(
 
     # Create a new biodiversity dataset
     bd <- BiodiversityDataset$new(
-      name = ifelse(is.null(name), "Species: ",name),
+      name = ifelse(is.null(name), substring(id[[1]], 1, 8), name),
       id = id,
       equation = formula,
       family = family,
@@ -232,6 +232,11 @@ methods::setMethod(
                             is.numeric(weight) && all(weight > 0),
                             is.logical(docheck)
     )
+    # Raise a warning if there NA data
+    assertthat::assert_that(!anyNA(poipa[[field_occurrence]]) || !is.null(poipa[[field_occurrence]]),
+                            msg = "NA observations or NULL occurrence field?")
+
+    # Check for that presence and absence are there.
     assertthat::assert_that(length(unique(poipa[[field_occurrence]])) == 2,
                             msg = "Presence-Absence requires at exactly 2 unique values.")
 
@@ -268,7 +273,7 @@ methods::setMethod(
 
     # Define the biodiversity object
     bd <- BiodiversityDataset$new(
-      name = ifelse(is.null(name), "Species: ",name),
+      name = ifelse(is.null(name), substring(id[[1]], 1, 8), name),
       id = id,
       equation = formula,
       family = family,
@@ -460,7 +465,7 @@ methods::setMethod(
 
       # Define the biodiversity object
       bd <- BiodiversityDataset$new(
-        name = ifelse(is.null(name), "Species: ",name),
+        name = ifelse(is.null(name), substring(id[[1]], 1, 8), name),
         id = id,
         equation = formula,
         family = family,
@@ -681,7 +686,7 @@ methods::setMethod(
 
       # Define the biodiversity object
       bd <- BiodiversityDataset$new(
-        name = ifelse(is.null(name), "Species: ",name),
+        name = ifelse(is.null(name), substring(id[[1]], 1, 8), name),
         id = id,
         equation = formula,
         family = family,