Version bump, partial 🔥 fix to gdb and parameters

iiasa · Jun 8, 2024 · 3b8f8fb · 3b8f8fb
1 parent c60a791
commit 3b8f8fb
Show file tree

Hide file tree

Showing 7 changed files with 75 additions and 27 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,14 @@
-# ibis.iSDM 0.1.3 (current dev branch)
+# ibis.iSDM 0.1.4 (current dev branch)
+
+#### New features
+
+#### Minor improvements and bug fixes
+* :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.
+
+# ibis.iSDM 0.1.3
 
 #### New features
 * Add functions that creates HTML file base on `DistributionModel`.
@@ -15,8 +25,6 @@
 * 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.
-* :bug: fix that prevented `BART` models to be saved/loaded from disk #127.
-* :bug: fixes related to `factor` handling for all engines.
 
 # ibis.iSDM 0.1.2
 

diff --git a/R/engine_gdb.R b/R/engine_gdb.R
@@ -631,20 +631,22 @@ engine_gdb <- function(x,
                                                       newdata = dummy_temp, which = v,
                                                       type = type, aggregate = 'sum'))
 
-        # Check duplicates. If bbs is present and non-linear, use bbs estimate
-        # MH: As far as I see it the pp will always only store the result of the
-        # current variable due to which = v, so we can just grab the first column
-        out[[v]] <- data.frame(variable = v, partial_effect = dummy_temp[, v], mean = pp[, 1])
-
-        # if(!self$settings$data$only_linear){
-        #   # Combine with
-        #   out[[v]] <- data.frame(variable = v, partial_effect = dummy_temp[, v],
-        #                          mean = pp[,grep(paste0("bbs\\(", v,"\\)"), colnames(pp))])
-        # } else {
-        #   # Combine with
-        #   out[[v]] <- data.frame(variable = v, partial_effect = dummy_temp[, v],
-        #                          mean = pp[,grep(v, colnames(pp))])
-        # }
+        # If bbs is present and non-linear, use bbs estimate. If model is fitted
+        # to non-linear then always the linear (bols, fitted by default) and smooth (bbs)
+        # is stored in bbs. In most cases the linear effect is stable and regularized out
+        # though.
+        # Propose to always take non-linear when found in settings
+        if(!settings$get("only_linear")){
+          # Combine with
+          out[[v]] <- data.frame(variable = v, partial_effect = dummy_temp[, v],
+                                 mean = pp[, 2] #pp[,grep(paste0("bbs\\(", v,"\\)"), colnames(pp))]
+                                 )
+        } else {
+          # Combine with
+          out[[v]] <- data.frame(variable = v, partial_effect = dummy_temp[, v],
+                                 mean = pp[, 1] #pp[,grep(v, colnames(pp))]
+                                 )
+        }
       }
 
       # bind to one data.frame
@@ -656,7 +658,8 @@ engine_gdb <- function(x,
           ggplot2::theme_classic() +
           ggplot2::geom_line(ggplot2::aes(y = mean)) +
           ggplot2::facet_wrap(. ~ variable, scales = "free") +
-          ggplot2::labs(x = "Variable", y = "Partial effect")
+          ggplot2::labs(x = "Variable",
+                        y = paste0("Partial effect (",ifelse(settings$get("only_linear"),"linear","smooth"),")"))
         print(g)
       }
       return(out)

diff --git a/R/validate.R b/R/validate.R
@@ -14,6 +14,8 @@
 #' @param point A [`sf`] object with type `POINT` or `MULTIPOINT`.
 #' @param point_column A [`character`] vector with the name of the column containing
 #' the independent observations. (Default: \code{'observed'}).
+#' @param field_occurrence (Deprectated) A [`character`] field pointing to the name
+#' of the independent observations. Identical to \code{"point_column"}
 #' @param ... Other parameters that are passed on. Currently unused.
 #'
 #' @details The \code{'validate'} function calculates different validation
@@ -79,14 +81,14 @@ NULL
 methods::setGeneric("validate",
                     signature = methods::signature("mod"),
                     function(mod, method = 'continuous', layer = "mean",
-                             point = NULL, point_column = 'observed', ...) standardGeneric("validate"))
+                             point = NULL, point_column = 'observed', field_occurrence = NULL, ...) standardGeneric("validate"))
 
 #' @rdname validate
 methods::setMethod(
   "validate",
   methods::signature(mod = "ANY"),
   function(mod, method = 'continuous', layer = "mean",
-           point = NULL, point_column = 'observed', ...){
+           point = NULL, point_column = 'observed', field_occurrence = NULL,...){
     assertthat::assert_that(
       inherits(mod, "DistributionModel"),
       inherits(point, 'sf') || is.null(point),
@@ -98,6 +100,11 @@ methods::setMethod(
     assertthat::assert_that( "prediction" %in% mod$show_rasters(),msg = "No prediction of the fitted model found!" )
     # Check that independent data is provided and if so that the used column is there
     if(!is.null(point)){
+      # Use field occurrence if point column is not found or set
+      if(!utils::hasName(point, point_column) && !is.null(field_occurrence)){
+        point_column <- field_occurrence
+      }
+
       assertthat::assert_that(is.character(point_column),
                               utils::hasName(point, point_column),
                               anyNA(point[[point_column]])==FALSE
@@ -250,7 +257,8 @@ methods::setMethod(
 methods::setMethod(
   "validate",
   methods::signature(mod = "SpatRaster"),
-  function(mod, method = 'continuous', layer = NULL, point = NULL, point_column = 'observed', ...){
+  function(mod, method = 'continuous', layer = NULL, point = NULL,
+           point_column = 'observed', field_occurrence = NULL, ...){
     assertthat::assert_that(
       is.Raster(mod),
       inherits(point, 'sf'),
@@ -259,6 +267,14 @@ methods::setMethod(
     )
     method <- match.arg(method, c("discrete", "continuous"),several.ok = FALSE)
 
+    # Use field occurrence if point column is not found or set
+    # Fallback arguement
+    if(!is.null(point)){
+      if(!utils::hasName(point, point_column) && !is.null(field_occurrence)){
+        point_column <- field_occurrence
+      }
+    }
+
     # If mode truncate was used, also switch to continuous data
     if(method == "discrete"){
       # Get parameter if there

diff --git a/README.Rmd b/README.Rmd
@@ -61,6 +61,7 @@ Jung, Martin. 2023. “An Integrated Species Distribution Modelling Framework fo
 
 ## Contributors
 
+
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
@@ -82,6 +83,12 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 </a><br>
 <a href="https://github.com/iiasa/ibis.iSDM/commits?author=mhesselbarth">mhesselbarth</a>
 </td>
+<td align="center">
+<a href="https://github.com/jeffreyhanson">
+<img src="https://avatars.githubusercontent.com/u/3610005?v=4" width="100px;" alt=""/>
+</a><br>
+<a href="https://github.com/iiasa/ibis.iSDM/commits?author=jeffreyhanson">jeffreyhanson</a>
+</td>
 </tr>
 
 </table>
@@ -90,3 +97,4 @@ All contributions to this project are gratefully acknowledged using the [`allcon
 <!-- prettier-ignore-end -->
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
+
diff --git a/README.md b/README.md
@@ -68,17 +68,15 @@ Systems Analysis (IIASA), Austria.
 
 ## Contributors
 
+
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 
-All contributions to this project are gratefully acknowledged using the
-[`allcontributors`
-package](https://github.com/ropenscilabs/allcontributors) following the
-[all-contributors](https://allcontributors.org) specification.
-Contributions of any kind are welcome!
+All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropenscilabs/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
 
 <table>
+
 <tr>
 <td align="center">
 <a href="https://github.com/Martin-Jung">
@@ -92,8 +90,17 @@ Contributions of any kind are welcome!
 </a><br>
 <a href="https://github.com/iiasa/ibis.iSDM/commits?author=mhesselbarth">mhesselbarth</a>
 </td>
+<td align="center">
+<a href="https://github.com/jeffreyhanson">
+<img src="https://avatars.githubusercontent.com/u/3610005?v=4" width="100px;" alt=""/>
+</a><br>
+<a href="https://github.com/iiasa/ibis.iSDM/commits?author=jeffreyhanson">jeffreyhanson</a>
+</td>
 </tr>
+
 </table>
+
 <!-- markdownlint-enable -->
 <!-- prettier-ignore-end -->
 <!-- ALL-CONTRIBUTORS-LIST:END -->
+
diff --git a/man/validate.Rd b/man/validate.Rd