docs: Add documentation, new functions, and dependency/CI updates

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

@@ -31,13 +31,13 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -48,7 +48,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -76,7 +76,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -29,6 +29,7 @@ Imports:
     RColorBrewer,
     wgaim
 Suggests: 
+    ASExtras4,
     lubridate,
     maptools,
     ncdf4,
@@ -40,5 +41,5 @@ Enhances: asreml
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3
 SystemRequirements: asreml-R 4.x

NAMESPACE

@@ -8,6 +8,7 @@ export(coord_distance)
 export(extract)
 export(extract_time_series)
 export(fast)
+export(fastIC)
 export(fineMap)
 export(fixedRegress)
 export(herit.asreml)
@@ -19,6 +20,7 @@ export(outlier.rem)
 export(pad.data)
 export(phenClones)
 export(phenfixClones)
+export(prune)
 export(randomRegress)
 export(reinstall_packages)
 export(sunrise_time)
@@ -29,6 +31,7 @@ export(theme_design_heat)
 export(theme_scatter)
 export(transfer_packages)
 export(update_asreml)
+export(wald.test)
 import(wgaim)
 importFrom(crayon,blue)
 importFrom(crayon,green)

R/BiometryTools.R

@@ -1,10 +1,6 @@
-#' BiometryTools: A package containing some useful functions for linear mixed model analysis
+#' BiometryTools: A package containing useful functions for linear mixed model analysis
 #'
 #' The BiometryTools package provides ...
 #'
-#' @section Foo functions:
-#' The foo functions ...
-#'
-#' @docType package
-#' @name BiometryTools
-NULL
+#' @keywords internal
+"_PACKAGE"