Merge pull request #76 from iiasa/dev

Merging latest dev branch to main.

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

@@ -46,7 +46,7 @@ jobs:
         run: |
           if [ "$RUNNER_OS" == "Linux" ]; then
             sudo apt-get -y install \
-            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev
+            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev libglu1-mesa-dev
           elif [ "$RUNNER_OS" == "macOS" ]; then
             brew install --cask xquartz
             brew install pkg-config
@@ -68,6 +68,8 @@ jobs:
             any::pdp,
             stan-dev/cmdstanr,
             any::igraph,
+            any::lwgeom,
+            any::ncmeta,
             any::xgboost,
             any::dbarts,
             any::mboost,

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: 0.0.8
+version: 0.0.9
 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: 0.0.5
+  version: 0.0.9
 - type: software
   title: assertthat
   abstract: 'assertthat: Easy Pre and Post Assertions'
@@ -217,6 +217,17 @@ 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: Matrix
   abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
@@ -235,17 +246,6 @@ references:
     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: parallel
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -306,6 +306,18 @@ references:
     orcid: https://orcid.org/0000-0001-5872-2872
   year: '2023'
   version: '>= 1.7-10'
+- type: software
+  title: lwgeom
+  abstract: 'lwgeom: Bindings to Selected ''liblwgeom'' Functions for Simple Features'
+  notes: Imports
+  url: https://github.com/r-spatial/lwgeom/
+  repository: https://CRAN.R-project.org/package=lwgeom
+  authors:
+  - family-names: Pebesma
+    given-names: Edzer
+    email: edzer.pebesma@uni-muenster.de
+    orcid: https://orcid.org/0000-0001-8049-7069
+  year: '2023'
 - type: software
   title: sf
   abstract: 'sf: Simple Features for R'
@@ -714,6 +726,9 @@ references:
   - family-names: Goodrich
     given-names: Ben
     email: benjamin.goodrich@columbia.edu
+  - family-names: Johnson
+    given-names: Andrew
+    email: andrew.johnson@arjohnsonau.com
   - family-names: Weber
     given-names: Sebastian
     email: sdw.post@waebers.de

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.0.8
+Version: 0.0.9
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",
@@ -19,6 +19,7 @@ Description: Integrated framework of modelling the distribution of species and e
 Language: en-GB
 License: CC BY 4.0
 Encoding: UTF-8
+Additional_repositories: https://inla.r-inla-download.org/R/testing
 Imports: 
     assertthat (>= 0.2.0),
     doFuture (>= 0.12.2),
@@ -30,12 +31,13 @@ Imports:
     graphics,
     methods,
     ncdf4,
-    Matrix,
     ncmeta,
+    Matrix,
     parallel,
     posterior,
     proto (>= 1.0.0),
     terra (>= 1.7-10),
+    lwgeom,
     sf (>= 1.0),
     stars (>= 0.5),
     stats,
@@ -122,6 +124,7 @@ Collate:
     'get_data.R'
     'ibis.iSDM-package.R'
     'limiting.R'
+    'mask.R'
     'misc.R'
     'partial.R'
     'plot.R'

NAMESPACE

@@ -3,6 +3,10 @@
 S3method(as.Id,character)
 S3method(coef,DistributionModel)
 S3method(effects,DistributionModel)
+S3method(mask,BiodiversityDatasetCollection)
+S3method(mask,BiodiversityScenario)
+S3method(mask,DistributionModel)
+S3method(mask,PredictorDataset)
 S3method(partial,DistributionModel)
 S3method(plot,BiodiversityDatasetCollection)
 S3method(plot,BiodiversityScenario)
@@ -211,4 +215,10 @@ importFrom(graphics,par)
 importFrom(methods,as)
 importFrom(stats,complete.cases)
 importFrom(stats,effects)
+importFrom(stats,mad)
 importFrom(stats,residuals)
+importFrom(stats,sd)
+importFrom(stats,terms.formula)
+importFrom(stats,update.formula)
+importFrom(terra,mask)
+importFrom(utils,install.packages)

NEWS.md

@@ -1,15 +1,29 @@
-# ibis.iSDM 0.0.8 (current dev branch)
+# ibis.iSDM 0.0.9 (current dev branch)
+#### 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 hamornizations to `ensemble_partial()`, `partial()` and `spartial()`. 
-* Small fix to `threshold()` now returning threshold values correctly. 
+* 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

R/add_biodiversity.R

@@ -71,7 +71,7 @@ NULL
 methods::setGeneric(
   "add_biodiversity_poipo",
   signature = methods::signature("x", "poipo"),
-  function(x, poipo, name = NULL, field_occurrence = "Observed", formula = NULL, family = "poisson", link = NULL,
+  function(x, poipo, name = NULL, field_occurrence = "observed", formula = NULL, family = "poisson", link = NULL,
            weight = 1, separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ...) {standardGeneric("add_biodiversity_poipo") })
 
 #' @name add_biodiversity_poipo
@@ -81,7 +81,7 @@ methods::setGeneric(
 methods::setMethod(
   "add_biodiversity_poipo",
   methods::signature(x = "BiodiversityDistribution", poipo = "sf"),
-  function(x, poipo, name = NULL, field_occurrence = "Observed", formula = NULL, family = "poisson", link = NULL,
+  function(x, poipo, name = NULL, field_occurrence = "observed", formula = NULL, family = "poisson", link = NULL,
            weight = 1, separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ...) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),
                             inherits(poipo, "Spatial") || inherits(poipo, "sf") || inherits(poipo, "data.frame") || inherits(poipo, "tibble"),
@@ -171,7 +171,7 @@ methods::setMethod(
 #' @param name The name of the biodiversity dataset used as internal identifier.
 #' @param field_occurrence A [`numeric`] or [`character`] location of
 #'   biodiversity point records indicating presence/absence. By default set to
-#'   \code{"Observed"} and an error will be thrown if a [`numeric`] column with
+#'   \code{"observed"} and an error will be thrown if a [`numeric`] column with
 #'   that name does not exist.
 #' @param formula A [`character`] or [`formula`] object to be passed. Default
 #'   (\code{NULL}) is to use all covariates (if specified).
@@ -214,7 +214,7 @@ NULL
 methods::setGeneric(
   "add_biodiversity_poipa",
   signature = methods::signature("x", "poipa"),
-  function(x, poipa, name = NULL, field_occurrence = "Observed", formula = NULL, family = "binomial", link = NULL,
+  function(x, poipa, name = NULL, field_occurrence = "observed", formula = NULL, family = "binomial", link = NULL,
            weight = 1, separate_intercept = TRUE, docheck = TRUE, ...) standardGeneric("add_biodiversity_poipa"))
 
 #' @name add_biodiversity_poipa
@@ -224,7 +224,7 @@ methods::setGeneric(
 methods::setMethod(
   "add_biodiversity_poipa",
   methods::signature(x = "BiodiversityDistribution", poipa = "sf"),
-  function(x, poipa, name = NULL, field_occurrence = "Observed", formula = NULL, family = "binomial", link = NULL,
+  function(x, poipa, name = NULL, field_occurrence = "observed", formula = NULL, family = "binomial", link = NULL,
            weight = 1, separate_intercept = TRUE, docheck = TRUE, ... ) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),
                             inherits(poipa, "Spatial") || inherits(poipa, "sf") || inherits(poipa, "data.frame") || inherits(poipa, "tibble"),
@@ -362,7 +362,7 @@ NULL
 methods::setGeneric(
   "add_biodiversity_polpo",
   signature = methods::signature("x", "polpo"),
-  function(x, polpo, name = NULL, field_occurrence = "Observed", formula = NULL, family = "poisson", link = NULL,
+  function(x, polpo, name = NULL, field_occurrence = "observed", formula = NULL, family = "poisson", link = NULL,
            weight = 1, simulate = FALSE, simulate_points = 100, simulate_bias = NULL, simulate_strategy = "random",
            separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ...) standardGeneric("add_biodiversity_polpo"))
 
@@ -373,7 +373,7 @@ methods::setGeneric(
 methods::setMethod(
   "add_biodiversity_polpo",
   methods::signature(x = "BiodiversityDistribution", polpo = "sf"),
-  function(x, polpo, name = NULL, field_occurrence = "Observed", formula = NULL,family = "poisson", link = NULL,
+  function(x, polpo, name = NULL, field_occurrence = "observed", formula = NULL,family = "poisson", link = NULL,
            weight = 1, simulate = FALSE, simulate_points = 100, simulate_bias = NULL, simulate_strategy = "random",
            separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ... ) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),
@@ -559,7 +559,7 @@ NULL
 methods::setGeneric(
   "add_biodiversity_polpa",
   signature = methods::signature("x", "polpa"),
-  function(x, polpa, name = NULL, field_occurrence = "Observed", formula = NULL, family = "binomial", link = NULL,
+  function(x, polpa, name = NULL, field_occurrence = "observed", formula = NULL, family = "binomial", link = NULL,
            weight = 1, simulate = FALSE, simulate_points = 100, simulate_bias = NULL, simulate_strategy = "random",
            separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ...) standardGeneric("add_biodiversity_polpa"))
 
@@ -570,7 +570,7 @@ methods::setGeneric(
 methods::setMethod(
   "add_biodiversity_polpa",
   methods::signature(x = "BiodiversityDistribution", polpa = "sf"),
-  function(x, polpa, name = NULL, field_occurrence = "Observed", formula = NULL, family = "binomial", link = NULL,
+  function(x, polpa, name = NULL, field_occurrence = "observed", formula = NULL, family = "binomial", link = NULL,
            weight = 1, simulate = FALSE, simulate_points = 100, simulate_bias = NULL, simulate_strategy = "random",
            separate_intercept = TRUE, docheck = TRUE, pseudoabsence_settings = NULL, ... ) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),

R/add_offset.R

@@ -397,7 +397,7 @@ methods::setGeneric(
   signature = methods::signature("x", "layer"),
   function(x, layer, distance_max = Inf, family = "poisson", presence_prop = 0.9,
            distance_clip = FALSE, distance_function = "negexp",
-           field_occurrence = "Observed", fraction = NULL,
+           field_occurrence = "observed", fraction = NULL,
            point = FALSE, add = TRUE) standardGeneric("add_offset_range"))
 
 #' Function for when raster is directly supplied (precomputed)
@@ -467,7 +467,7 @@ methods::setMethod(
   methods::signature(x = "BiodiversityDistribution", layer = "sf"),
   function(x, layer, distance_max = Inf, family = "poisson", presence_prop = 0.9,
            distance_clip = FALSE, distance_function = "negexp",
-           field_occurrence = "Observed", fraction = NULL, point = FALSE, add = TRUE ) {
+           field_occurrence = "observed", fraction = NULL, point = FALSE, add = TRUE ) {
     assertthat::assert_that(inherits(x, "BiodiversityDistribution"),
                             inherits(layer, 'sf'),
                             is.null(distance_max) || is.numeric(distance_max) || is.infinite(distance_max),
@@ -480,7 +480,7 @@ methods::setMethod(
                             is.character(field_occurrence),
                             is.logical(add)
     )
-    # distance_max = Inf; family = "poisson"; presence_prop = 0.9; distance_clip = FALSE; distance_function = "negexp"; field_occurrence = "Observed"; fraction = NULL; add = TRUE
+    # distance_max = Inf; family = "poisson"; presence_prop = 0.9; distance_clip = FALSE; distance_function = "negexp"; field_occurrence = "observed"; fraction = NULL; add = TRUE
     # Match the type if set
     family <- match.arg(family, c("poisson", "binomial"), several.ok = FALSE)
 

R/bdproto-biodiversitydataset.R

@@ -84,6 +84,22 @@ BiodiversityDatasetCollection <- bdproto(
     # Return coordinates
     if(utils::hasName(o,'geom')) sf::st_coordinates(o) else o[,c('x','y')]
   },
+  # Masking function
+  mask = function(self, mask, inverse = FALSE){
+    # Check whether prediction has been created
+    biob <- self$data
+    if(!is.Waiver(biob)){
+      # If mask is SpatRaster, convert to polygons
+      if(!inherits(mask, 'sf')){
+        mask <- terra::as.polygons(mask) |> sf::st_as_sf()
+      }
+      # Now for each element in biob, mask
+      for(id in names(biob)){
+        biob[[id]]$mask(mask, inverse = inverse)
+      }
+      invisible()
+    }
+  },
   # Remove a specific biodiversity dataset by id
   rm_data = function(self, id) {
     assertthat::assert_that(is.Id(id) || is.character(id),
@@ -300,5 +316,25 @@ BiodiversityDataset <- bdproto(
   # Collect info statistics
   get_observations = function(self) {
     nrow(self$data)
-  }
+  },
+  # Masking function
+  mask = function(self, mask, inverse = FALSE){
+    # Check whether prediction has been created
+    biob <- self$data
+    if(!is.Waiver(biob)){
+      # If mask is SpatRaster, convert to polygons
+      if(!inherits(mask, 'sf')){
+        mask <- terra::as.polygons(mask) |> sf::st_as_sf()
+      }
+      # Now for each element in biob, mask
+      biob <-
+        suppressMessages(
+          suppressWarnings(
+            sf::st_crop(guess_sf(biob), mask)
+          )
+        )
+      self$data <- biob
+      invisible()
+    }
+  },
 )

R/bdproto-biodiversitydistribution.R

@@ -348,6 +348,7 @@ BiodiversityDistribution <- bdproto(
   plot = function(self){
     message("No generic plotting implemented!")
   },
+  # Summary function
   summary = function(self){
     message("No generic summary function implemented! Try print.")
   }