Update to version 0.0.5 (#53)

* 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 <[email protected]>
iiasa · Jun 25, 2023 · 4ec59b4 · 4ec59b4
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diff --git a/CITATION.cff b/CITATION.cff
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,144 +1,146 @@
-Package: ibis.iSDM
-Type: Package
-Title: Modelling Framework for Integrated Biodiversity Distribution Scenarios
-Version: 0.0.4
-Authors@R: 
-    c(person(given = "Martin",
-           family = "Jung",
-           role = c("aut", "cre", "cph"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0002-7569-1390")),
-      person(given = "Maximilian H.K.",
-           family = "Hesselbarth",
-           role = c("ctb"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-1125-9918"))
-      )
-Maintainer: Martin Jung <[email protected]>
-Description: 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 and presence-absence datasets. It makes heavy use of point-process models for estimating habitat suitability and allows to include spatial latent effects and priors in the estimation. To do so 'ibis.iSDM' supports a number of engines for Bayesian and more non-parametric machine learning estimation. Further, the 'ibis.iSDM' is specifically customized to support spatial-temporal projections of habitat suitability into the future.
-Language: en-GB
-License: CC BY 4.0
-Encoding: UTF-8
-Imports: 
-    assertthat (>= 0.2.0),
-    doFuture (>= 0.12.2),
-    foreach,
-    future (>= 1.23.0),
-    dplyr,
-    geodist,
-    ggplot2,
-    graphics,
-    methods,
-    ncdf4,
-    parallel,
-    posterior,
-    proto (>= 1.0.0),
-    terra (>= 1.7-10),
-    sf (>= 0.9),
-    stars (>= 0.5),
-    stats,
-    tibble (>= 2.0.0),
-    uuid, 
-    utils
-Depends:
-    R(>= 4.1.0)
-Suggests:
-    abind,
-    BoomSpikeSlab (>= 1.2.4),
-    covr,
-    inlabru,
-    glmnet,
-    glmnetUtils,
-    dbarts (>= 0.9-22),
-    deldir,
-    doParallel,
-    ellipsis,
-    igraph,
-    knitr,
-    mboost,
-    modEvA,
-    ncmeta,
-    progress,
-    rmarkdown,
-    rstan (>= 2.21.0),
-    rstantools (>= 2.1.1),
-    testthat,
-    xgboost
-URL: https://iiasa.github.io/ibis.iSDM/
-BugReports: https://github.com/iiasa/ibis.iSDM/issues
-RoxygenNote: 7.2.3
-Config/testthat/edition: 3
-Roxygen: list(markdown = TRUE)
-Biarch: true
-SystemRequirements: GNU make
-VignetteBuilder: knitr
-Collate: 
-    'utils.R'
-    'bdproto.R'
-    'waiver.R'
-    'bdproto-biodiversitydataset.R'
-    'bdproto-biodiversitydistribution.R'
-    'add_biodiversity.R'
-    'bdproto-biodiversityscenario.R'
-    'add_constraint.R'
-    'add_constraint_MigClim.R'
-    'add_control_bias.R'
-    'add_latent.R'
-    'bdproto-log.R'
-    'add_log.R'
-    'add_offset.R'
-    'bdproto-predictors.R'
-    'add_predictors.R'
-    'add_predictors_globiom.R'
-    'identifier.R'
-    'bdproto-distributionmodel.R'
-    'bdproto-priorlist.R'
-    'bdproto-prior.R'
-    'add_priors.R'
-    'bdproto-engine.R'
-    'bdproto-settings.R'
-    'utils-spatial.R'
-    'data.R'
-    'distribution.R'
-    'effects.R'
-    'engine_bart.R'
-    'engine_breg.R'
-    'engine_gdb.R'
-    'engine_glmnet.R'
-    'utils-inla.R'
-    'engine_inla.R'
-    'engine_inlabru.R'
-    'engine_stan.R'
-    'engine_xgboost.R'
-    'ensemble.R'
-    'ibis.iSDM-package.R'
-    'misc.R'
-    'partial.R'
-    'plot.R'
-    'print.R'
-    'prior_bart.R'
-    'prior_breg.R'
-    'prior_gdb.R'
-    'prior_glmnet.R'
-    'prior_inla.R'
-    'prior_stan.R'
-    'prior_xgb.R'
-    'priors.R'
-    'project.R'
-    'pseudoabsence.R'
-    'scenario.R'
-    'similarity.R'
-    'summary.R'
-    'threshold.R'
-    'train.R'
-    'utils-bart.R'
-    'utils-breg.R'
-    'utils-gdb.R'
-    'utils-glmnet.R'
-    'utils-predictors.R'
-    'utils-scenario.R'
-    'utils-stan.R'
-    'utils-xgboost.R'
-    'validate.R'
-    'write_output.R'
-    'zzz.R'
+Package: ibis.iSDM
+Type: Package
+Title: Modelling framework for integrated biodiversity distribution scenarios
+Version: 0.0.5
+Authors@R: 
+    c(person(given = "Martin",
+           family = "Jung",
+           role = c("aut", "cre", "cph"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-7569-1390")),
+      person(given = "Maximilian H.K.",
+           family = "Hesselbarth",
+           role = c("ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0003-1125-9918"))
+      )
+Maintainer: Martin Jung <[email protected]>
+Description: 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 and presence-absence datasets. It makes heavy use of point-process models for estimating habitat suitability and allows to include spatial latent effects and priors in the estimation. To do so 'ibis.iSDM' supports a number of engines for Bayesian and more non-parametric machine learning estimation. Further, the 'ibis.iSDM' is specifically customized to support spatial-temporal projections of habitat suitability into the future.
+Language: en-GB
+License: CC BY 4.0
+Encoding: UTF-8
+Imports: 
+    assertthat (>= 0.2.0),
+    doFuture (>= 0.12.2),
+    foreach,
+    future (>= 1.23.0),
+    dplyr,
+    geodist,
+    ggplot2,
+    graphics,
+    methods,
+    ncdf4,
+    ncmeta,
+    parallel,
+    posterior,
+    proto (>= 1.0.0),
+    terra (>= 1.7-10),
+    sf (>= 0.9),
+    stars (>= 0.5),
+    stats,
+    tibble (>= 2.0.0),
+    uuid, 
+    utils
+Depends:
+    R(>= 4.1.0)
+Suggests:
+    abind,
+    BoomSpikeSlab (>= 1.2.4),
+    covr,
+    inlabru (>= 2.6.0),
+    glmnet (>= 4.1),
+    glmnetUtils,
+    dbarts (>= 0.9-22),
+    deldir,
+    doParallel,
+    ellipsis,
+    igraph,
+    knitr,
+    mboost,
+    modEvA,
+    progress,
+    rmarkdown,
+    rstan (>= 2.21.0),
+    rstantools (>= 2.1.1),
+    gnlm,
+    testthat,
+    xgboost
+URL: https://iiasa.github.io/ibis.iSDM/
+BugReports: https://github.com/iiasa/ibis.iSDM/issues
+RoxygenNote: 7.2.3
+Config/testthat/edition: 3
+Roxygen: list(markdown = TRUE)
+Biarch: true
+SystemRequirements: GNU make
+VignetteBuilder: knitr
+Collate: 
+    'utils.R'
+    'bdproto.R'
+    'waiver.R'
+    'bdproto-biodiversitydataset.R'
+    'bdproto-biodiversitydistribution.R'
+    'add_biodiversity.R'
+    'bdproto-biodiversityscenario.R'
+    'add_constraint.R'
+    'add_constraint_MigClim.R'
+    'add_control_bias.R'
+    'add_latent.R'
+    'bdproto-log.R'
+    'add_log.R'
+    'add_offset.R'
+    'bdproto-predictors.R'
+    'add_predictors.R'
+    'add_predictors_globiom.R'
+    'identifier.R'
+    'bdproto-distributionmodel.R'
+    'bdproto-priorlist.R'
+    'bdproto-prior.R'
+    'add_priors.R'
+    'bdproto-engine.R'
+    'bdproto-settings.R'
+    'utils-spatial.R'
+    'data.R'
+    'distribution.R'
+    'effects.R'
+    'engine_bart.R'
+    'engine_breg.R'
+    'engine_gdb.R'
+    'engine_glmnet.R'
+    'utils-inla.R'
+    'engine_inla.R'
+    'engine_inlabru.R'
+    'engine_stan.R'
+    'engine_xgboost.R'
+    'ensemble.R'
+    'ibis.iSDM-package.R'
+    'misc.R'
+    'partial.R'
+    'plot.R'
+    'print.R'
+    'prior_bart.R'
+    'prior_breg.R'
+    'prior_gdb.R'
+    'prior_glmnet.R'
+    'prior_inla.R'
+    'prior_stan.R'
+    'prior_xgb.R'
+    'priors.R'
+    'project.R'
+    'pseudoabsence.R'
+    'scenario.R'
+    'similarity.R'
+    'summary.R'
+    'threshold.R'
+    'train.R'
+    'utils-bart.R'
+    'utils-breg.R'
+    'utils-form.R'
+    'utils-gdb.R'
+    'utils-glmnet.R'
+    'utils-predictors.R'
+    'utils-scenario.R'
+    'utils-stan.R'
+    'utils-xgboost.R'
+    'validate.R'
+    'write_output.R'
+    'zzz.R'
diff --git a/NAMESPACE b/NAMESPACE
@@ -124,6 +124,7 @@ export(rm_offset)
 export(rm_predictors)
 export(rm_priors)
 export(run_stan)
+export(sanitize_names)
 export(scenario)
 export(sel_predictors)
 export(similarity)
@@ -197,4 +198,5 @@ import(sf)
 import(terra)
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
+importFrom(methods,as)
 importFrom(stats,effects)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# ibis.iSDM 0.0.5
+
+* Addition of 5 parameter logistic curve offsets with parameter search to `add_offset`.
+* 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
 
 * Smaller bug fixes with regards to writing outputs and adding pseudo-absences.

diff --git a/R/add_constraint.R b/R/add_constraint.R
@@ -15,9 +15,9 @@ NULL
 #' give the number of iteration steps (or within year migration steps).
 #' For adaptability constraints this parameter specifies the extent (in units of standard deviation) to which extrapolations
 #' should be performed.
-#' @param type A [`character`] indicating the type used in the method. See for instance [`kissmig::kissmig`].
+#' @param type A [`character`] indicating the type used in the method. See for instance \code{`kissmig`}.
 #' @param layer A [`SpatRaster`] object that can be used for boundary constraints (Default: \code{NULL}).
-#' @param pext [`numeric`] indicator for [`kissmig`] of the probability a colonized cell becomes uncolonised,
+#' @param pext [`numeric`] indicator for \code{`kissmig`} of the probability a colonized cell becomes uncolonised,
 #' i.e., the species gets locally extinct (Default: \code{0.1}).
 #' @param pcor [`numeric`] probability that corner cells are considered in the 3x3 neighbourhood (Default: \code{0.2}).
 #' @param ... passed on parameters. See also the specific methods for adding constraints.
@@ -30,7 +30,7 @@ NULL
 #' **Dispersal**:
 #' * \code{sdd_fixed} - Applies a fixed uniform dispersal distance per modelling timestep.
 #' * \code{sdd_nexpkernel} - Applies a dispersal distance using a negative exponential kernel from its origin.
-#' * \code{kissmig} - Applies the kissmig stochastic dispersal model. Requires [`kissmig`] package. Applied at each modelling time step.
+#' * \code{kissmig} - Applies the kissmig stochastic dispersal model. Requires \code{`kissmig`} package. Applied at each modelling time step.
 #' * \code{migclim} - Applies the dispersal algorithm MigClim to the modelled objects. Requires [`MigClim`] package.
 #'
 #' A comprehensive overview of the benefits of including dispersal constrains in species distribution models

diff --git a/R/add_constraint_MigClim.R b/R/add_constraint_MigClim.R
@@ -38,7 +38,8 @@ NULL
 #' \dontrun{
 #' # Assumes that a trained 'model' object exists
 #'  mod <- scenario(model) |>
-#'   add_predictors(env = predictors, transform = 'scale', derivates = "none") |>
+#'   add_predictors(env = predictors, transform = 'scale',
+#'                  derivates = "none") |>
 #'   add_constraint_MigClim() |>
 #'   project()
 #' }

diff --git a/R/add_control_bias.R b/R/add_control_bias.R
@@ -28,7 +28,6 @@
 #' to the target value during projection. By default the value is set to the minimum value found in the layer (Default: \code{NULL}).
 #' @param add [`logical`] specifying whether a new offset is to be added. Setting
 #' this parameter to \code{FALSE} replaces the current offsets with the new one (Default: \code{TRUE}).
-#' @param ... Other parameters or arguments (currently not supported).
 #' @references
 #' * Warton, D.I., Renner, I.W. and Ramp, D., 2013. Model-based control of observer bias for the analysis of presence-only data in ecology. PloS one, 8(11), p.e79168.
 #' * Merow, C., Allen, J.M., Aiello-Lammens, M., Silander, J.A., 2016. Improving niche and range estimates with Maxent and point process models by integrating spatially explicit information. Glob. Ecol. Biogeogr. 25, 1022–1036. https://doi.org/10.1111/geb.12453
@@ -75,15 +74,18 @@ methods::setMethod(
     }
 
     # Calculate a default bias value if not already set
-    if(is.null(bias_value)) bias_value <- terra::global(layer, stat = "min", na.rm = TRUE)
+    if(is.null(bias_value)) bias_value <- terra::global(layer, stat = "min", na.rm = TRUE)[,1]
 
     # Check for infinite values
     assertthat::assert_that(
       terra::nlyr(layer) == length(bias_value),
-      all( terra::global(layer, "range", na.rm = TRUE) > 0),
-      msg = "Infinite values found in the layer (maybe log of 0?)."
+      all( terra::global(layer, "max", na.rm = TRUE)[,1] > 0),
+      msg = "Infinite values found in the bias layer (maybe log of 0?)."
     )
 
+    # Sanitize names if specified
+    if(getOption('ibis.cleannames')) names(layer) <- sanitize_names(names(layer))
+
     # Now precede depending on method
     if(method == "partial"){
       if(getOption('ibis.setupmessages')) myLog('[Setup]','green','Adding bias controlled variable...')