Merge pull request #132 from iiasa/dev

Version bump

CITATION.cff

@@ -1,14 +1,14 @@
-# -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v1.0.0
+# --------------------------------------------
+# CITATION file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# -----------------------------------------------------------
+# --------------------------------------------
 
 cff-version: 1.2.0
 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: 0.1.3
+version: 0.1.4
 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
@@ -153,7 +153,7 @@ references:
   title: geodist
   abstract: 'geodist: Fast, Dependency-Free Geodesic Distance Calculations'
   notes: Imports
-  url: https://github.com/hypertidy/geodist
+  url: https://hypertidy.github.io/geodist/
   repository: https://CRAN.R-project.org/package=geodist
   authors:
   - family-names: Padgham
@@ -566,7 +566,20 @@ references:
     given-names: Fabian E.
     email: [email protected]
   year: '2024'
-  version: '>= 2.6.0'
+  version: '>= 2.10.0'
+- type: software
+  title: fmesher
+  abstract: 'fmesher: Triangle Meshes and Related Geometry Tools'
+  notes: Suggests
+  url: https://inlabru-org.github.io/fmesher/
+  repository: https://CRAN.R-project.org/package=fmesher
+  authors:
+  - family-names: Lindgren
+    given-names: Finn
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-5833-2011
+  year: '2024'
+  version: '>= 0.1.7'
 - type: software
   title: igraph
   abstract: 'igraph: Network Analysis and Visualization'
@@ -867,3 +880,4 @@ references:
     given-names: Jiaming
     email: [email protected]
   year: '2024'
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",
@@ -66,7 +66,8 @@ Suggests:
     glmnetUtils,
     gnlm,
     geosphere,
-    inlabru (>= 2.6.0),
+    inlabru (>= 2.10.0),
+    fmesher (>= 0.1.7),
     igraph,
     knitr,
     mboost,
@@ -83,7 +84,7 @@ Suggests:
     xgboost
 URL: https://iiasa.github.io/ibis.iSDM/
 BugReports: https://github.com/iiasa/ibis.iSDM/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
 Biarch: true
@@ -98,8 +99,8 @@ Collate:
     'add_constraint.R'
     'add_constraint_MigClim.R'
     'add_control_bias.R'
-    'add_control_extrapolation.R'
     'add_latent.R'
+    'add_limits_extrapolation.R'
     'class-log.R'
     'add_log.R'
     'add_offset.R'

NAMESPACE

@@ -65,8 +65,8 @@ export(add_constraint_dispersal)
 export(add_constraint_minsize)
 export(add_constraint_threshold)
 export(add_control_bias)
-export(add_control_extrapolation)
 export(add_latent_spatial)
+export(add_limits_extrapolation)
 export(add_log)
 export(add_offset)
 export(add_offset_bias)
@@ -134,7 +134,9 @@ export(project.BiodiversityScenario)
 export(pseudoabs_settings)
 export(render_html)
 export(rm_biodiversity)
+export(rm_control)
 export(rm_latent)
+export(rm_limits)
 export(rm_offset)
 export(rm_predictors)
 export(rm_priors)

NEWS.md

@@ -1,4 +1,21 @@
-# ibis.iSDM 0.1.3 (current dev branch)
+# ibis.iSDM 0.1.4 (current dev branch)
+
+#### 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`.

R/add_control_bias.R

@@ -159,3 +159,47 @@ methods::setMethod(
     return(y)
   }
 )
+
+#' Remove control from an existing distribution object
+#'
+#' @description This function allows to remove set control obtions from an existing [distribution]
+#' object.
+#'
+#' @param x [distribution] (i.e. [`BiodiversityDistribution-class`]) object.
+#'
+#' @family control
+#' @seealso [add_control_bias()]
+#'
+#' @examples
+#' \dontrun{
+#'  x <- distribution(background) |>
+#'    add_predictors(covariates) |>
+#'    add_control_bias(method = "proximity")
+#'  x <- x |> rm_control()
+#'  x
+#' }
+#'
+#' @name rm_control
+NULL
+
+#' @rdname rm_control
+#' @export
+methods::setGeneric(
+  "rm_control",
+  signature = methods::signature("x"),
+  function(x) standardGeneric("rm_control"))
+
+#' @rdname rm_control
+methods::setMethod(
+  "rm_control",
+  methods::signature(x = "BiodiversityDistribution"),
+  function(x) {
+    assertthat::assert_that(inherits(x, "BiodiversityDistribution") )
+    # Make a deep copy
+    y <- x$clone(deep = TRUE)
+
+    y <- y$rm_control()
+    # Return x without control
+    return(y)
+  }
+)

R/add_latent.R

@@ -84,7 +84,7 @@ methods::setMethod(
   methods::signature(x = "BiodiversityDistribution"),
   function(x, method = 'spde', priors = NULL, separate_spde = FALSE, ...) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),
-                            is.character(method) && !missing(method),
+                            is.character(method),
                             is.null(priors) || inherits(priors, 'PriorList'),
                             is.logical(separate_spde)
                             )
@@ -110,6 +110,49 @@ methods::setMethod(
   }
 )
 
+#### Latent for scenarios ####
+#' Add latent spatial effect to the model equation
+#' @param layer A [`SpatRaster`] layer describing alternative latent effects to be used instead
+#' if \code{"reuse_latent"} is set to \code{FALSE}.
+#' @param reuse_latent A [`logical`] flag on whether any latent effects found
+#' in the fitted model should be reused (Default \code{TRUE}).
+#' @rdname add_latent_spatial
+methods::setMethod(
+  "add_latent_spatial",
+  methods::signature(x = "BiodiversityScenario"),
+    function(x, layer = NULL, reuse_latent = TRUE, ...) {
+      assertthat::assert_that(
+        inherits(x, "BiodiversityScenario"),
+        is.Raster(layer) || is.null(layer),
+        is.logical(reuse_latent)
+      )
+
+      # Check existing model if latent factors are set there
+      if(reuse_latent){
+        # Try and see if model has been defined?
+        fit <- x$get_model()
+        if(!is.Waiver(fit)){
+          # Latent-factors specified?
+          check <- fit$has_latent()
+          assertthat::assert_that(
+            check,
+            msg = "Latent factors are to be reused, but could not be found in fitted model?"
+          )
+        }
+      }
+
+      # Build latent object
+      lat <- list("layer" = layer, "reuse_latent" = reuse_latent)
+
+      # Make a clone copy of the object
+      y <- x$clone(deep = TRUE)
+
+      # Add to data to the BiodiversityDistribution object
+      y$set_latent(lat)
+    }
+)
+
+
 #' Function to remove a latent effect
 #'
 #' @description This is just a wrapper function for removing specified offsets
@@ -156,3 +199,23 @@ methods::setMethod(
     y$rm_latent()
   }
 )
+
+#' @rdname rm_latent
+methods::setMethod(
+  "rm_latent",
+  methods::signature(x = "BiodiversityScenario"),
+  function(x) {
+    assertthat::assert_that(inherits(x, "BiodiversityScenario") )
+    # If no offset can be found, just return proto object
+    if(is.Waiver(x$latentfactors)){ return(x) }
+
+    # Messenger
+    if(getOption('ibis.setupmessages', default = TRUE)) myLog('[Setup]','yellow','Removing latent effects.')
+
+    # Make a clone copy of the object
+    y <- x$clone(deep = TRUE)
+
+    # Now remove the offset
+    y$rm_latent()
+  }
+)