Merge branch 'HannaMeyer:master' into master

HannaMeyer · Mar 13, 2024 · 15b2884 · 15b2884
2 parents ae1e3f2 + 7572bc6
commit 15b2884
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@ vignettes/CAST-intro_files
 ^docs$
 ^pkgdown$
 ^\.github$
+data-raw/
diff --git a/CAST.Rproj b/CAST.Rproj
@@ -18,5 +18,6 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --resave-data
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,6 +40,11 @@ Suggests:
     MASS,
     twosamples,
     RColorBrewer,
+    geodata,
+    tmap,
+    PCAmixdata, 
+    gower, 
+    clustMixType,
     testthat (>= 3.0.0)
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -42,6 +42,7 @@ importFrom(graphics,segments)
 importFrom(stats,complete.cases)
 importFrom(stats,dist)
 importFrom(stats,lm)
+importFrom(stats,median)
 importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
 importFrom(stats,predict)

diff --git a/NEWS.md b/NEWS.md
@@ -3,9 +3,12 @@
   * option of spatial error profiles (errorProfiles with variable="geodist")
   * normalize_DI for a more intuitive interpretation
   * geodist allows calculating temporal distances
+  * ffs now can be run in parallel (Linux only)
 * modifications:
   * function DItoErrormetric renamed to errorProfiles and allows for other dissimilarity measures
   * Improvement and homogenization of plotting methods for nndm, knndm and geodist objects
+  * aoa and trainDI `weight` now allows list input
+  * vignette on Introduction to CAST updated
 * deprecated:
   *plot_geodist (replaced by plot.geodist)
   *plot_ffs (replaced by plot.ffs)

diff --git a/R/CAST-package.R b/R/CAST-package.R
@@ -23,7 +23,7 @@
 #' }
 #'
 #' @import caret
-#' @importFrom stats sd dist na.omit lm predict quantile na.exclude complete.cases
+#' @importFrom stats sd dist na.omit lm predict quantile na.exclude complete.cases median
 #' @importFrom utils combn txtProgressBar setTxtProgressBar
 #' @importFrom grDevices rainbow
 #' @importFrom graphics axis plot segments

diff --git a/R/cookfarm.R b/R/cookfarm.R
@@ -0,0 +1,22 @@
+#' Cookfarm soil logger data
+#'
+#' spatio-temporal data of soil properties and associated predictors for the Cookfarm in South Africa
+#' @format
+#' A sf data.frame with 128545 rows and 17 columns:
+#' \describe{
+#'   \item{SOURCEID}{sPlotOpen Metadata}
+#'   \item{VW}{Response Variable - Soil Moisture}
+#'   \item{altitude}{Measurement depth of VW}
+#'   \item{Date, cdata}{Measurement Date, Cumulative Date}
+#'   \item{Easting, Northing}{Location Coordinates (EPSG:26911)}
+#'   \item{DEM, TWI, NDRE.M, NDRE.Sd, Precip_wrcc, MaxT_wrcc, MinT_wrcc, Precip_cum}{Predictor Variables}
+#' }
+#'
+#' @references \itemize{
+#' \item{Gash et al. 2015 - Spatio-temporal interpolation of soil water, temperature, and electrical conductivity in 3D + T: The Cook Agronomy Farm data set \doi{https://doi.org/10.1016/j.spasta.2015.04.001}}
+#' \item{Meyer et al. 2018 - Improving performance of spatio-temporal machine learning models using forward feature selection and target-oriented validation \doi{https://doi.org/10.1016/j.envsoft.2017.12.001}}
+#' }
+#' @usage data(cookfarm)
+#'
+"cookfarm"
+