Merge branch 'master' into suggest-sp

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

@@ -34,10 +34,9 @@ jobs:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+      
     steps:
-      - uses: actions/checkout@v4
-
+      - uses: actions/checkout@v4        
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
@@ -52,15 +51,8 @@ jobs:
           brew install --cask xquartz
           
       - uses: r-lib/actions/setup-r-dependencies@v2
-        if: matrix.config.r == '3.6'
         with:
-          extra-packages: any::rcmdcheck, soiltexture=?ignore-before-r=4.3.0, markovchain=?ignore-before-r=4.0.0, Hmisc=?ignore
-          needs: check
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        if: matrix.config.r != '3.6'
-        with:
-          extra-packages: any::rcmdcheck, markovchain=?ignore-before-r=4.0.0
+          extra-packages: any::rcmdcheck, soiltexture=?ignore-before-r=4.3.0, markovchain=?ignore-before-r=4.0.0, Hmisc=?ignore, knitr=?ignore-before-r=4.0.0, rmarkdown=?ignore-before-r=4.0.0, testthat=?ignore-before-r=4.0.0,
           needs: check
 
       - name: Install soilDB from r-universe (R-devel only)
@@ -70,6 +62,14 @@ jobs:
         shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
+        if: matrix.config.r != '3.6'
+        with:
+          upload-snapshots: true
+
+      - uses: r-lib/actions/check-r-package@v2
+        if: matrix.config.r == '3.6'
         with:
+          args: 'c("--no-manual", "--as-cran", "--ignore-vignettes", "--no-tests")'
+          build_args: 'c("--no-manual", "--no-build-vignettes")'
           upload-snapshots: true
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: aqp
-Version: 2.0.3
+Version: 2.0.4
 Title: Algorithms for Quantitative Pedology
 Authors@R: c(person(given="Dylan", family="Beaudette", role = c("aut", "cre"), email = "[email protected]"), person(given="Pierre", family="Roudier", email="[email protected]", role = c("aut", "ctb")), person(given="Andrew", family="Brown", email="[email protected]", role = c("aut", "ctb")))
 Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
@@ -15,6 +15,6 @@ URL: https://github.com/ncss-tech/aqp, https://ncss-tech.github.io/AQP/
 BugReports: https://github.com/ncss-tech/aqp/issues
 Language: en-US
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

NAMESPACE

@@ -3,7 +3,6 @@
 export(HzDepthLogicSubset)
 export(L1_profiles)
 export(NCSP)
-export(PSCS_levels)
 export(ReactionClassLevels)
 export(SANN_1D)
 export(SoilProfileCollection)
@@ -102,6 +101,7 @@ export(hz_lag)
 export(hz_segment)
 export(hz_to_taxpartsize)
 export(invertLabelColor)
+export(lookup_taxpartsize)
 export(lunique)
 export(maxDepthOf)
 export(minDepthOf)
@@ -175,6 +175,7 @@ exportMethods("horizons<-")
 exportMethods("hzID<-")
 exportMethods("hzdesgnname<-")
 exportMethods("hzidname<-")
+exportMethods("hzmetaname<-")
 exportMethods("hztexclname<-")
 exportMethods("initSpatial<-")
 exportMethods("metadata<-")
@@ -207,6 +208,7 @@ exportMethods(hzID)
 exportMethods(hzMetadata)
 exportMethods(hzdesgnname)
 exportMethods(hzidname)
+exportMethods(hzmetaname)
 exportMethods(hztexclname)
 exportMethods(idname)
 exportMethods(isEmpty)

NEWS.md

@@ -1,3 +1,10 @@
+# aqp 2.0.4 (2024-10-04)
+ * CRAN release
+ * ragged bottom lines in `plotSPC()` now adjusted as function of number of profiles and device width
+ * additional metadata from `plotSPC()` saved to `last_spc_plot` in `aqp.env`
+ * added Munsell values of 8.5 and 9.5 to Munsell LUT and (interpolated) reference spectra (#318)
+ * `munsell2rgb()` now safely selects the closest Munsell value and chroma to those available in the package LUT 
+
 # aqp 2.0.3 (2024-04-18)
  * CRAN release
  * `simulateColor()` gains new method `mvnorm` for simulating plausible colors

R/SoilProfileCollection-metadata.R

@@ -293,3 +293,74 @@ setReplaceMethod("GHL",
                      allowednames = "horizon"
                    )
                  })
+
+setGeneric("hzmetaname", function(object, attr, required = FALSE)
+  standardGeneric("hzmetaname"))
+
+#' @title Get or Set Horizon Metadata Column Name
+#' @name hzmetaname
+#' @aliases hzmetaname hzmetaname,SoilProfileCollection-method hzmetaname<- hzmetaname,SoilProfileCollection-method
+#' @details Store the column name containing a specific type of horizon data in the metadata slot of the SoilProfileCollection.
+#' @description `hzmetaname()`: Get column name containing horizon data of interest 
+#' @param object a SoilProfileCollection
+#' @param attr character. Base name for attribute to be stored in metadata. This is prefixed with `"aqp_hz"` for horizon-level metadata for column attributes. e.g. `attr="clay"` results in metadata value retrieved from `"aqp_hzclay"`.
+#' @param required logical, is this attribute required? If it is, set to `TRUE` to trigger error on invalid result
+#' @docType methods
+#' @rdname hzmetaname
+#' @export
+setMethod("hzmetaname", signature(object = "SoilProfileCollection"),
+          function(object, attr, required = FALSE) {
+            .require.metadata.aqp(object,
+                                  attr = paste0("aqp_hz", attr),
+                                  attrlabel = paste0("Horizon metadata (", attr, ") column"),
+                                  message = "\nSee ??hzmetaname",
+                                  required = required)
+          })
+
+setGeneric('hzmetaname<-', function(object, attr, required = FALSE, value)
+  standardGeneric('hzmetaname<-'))
+
+#' @description `hzmetaname<-`: Set horizon designation column name
+#' @param object A _SoilProfileCollection_
+#' @param attr _character_. Base name for attribute to be stored in metadata. This is prefixed with `"aqp_hz"` for horizon-level metadata for column attributes. e.g. `attr="clay"` results in metadata value retrieved from `"aqp_hzclay"`.
+#' @param value _character_. Name of horizon-level column containing  data corresponding to `attr`.
+#' @param required _logical_. Is this attribute required? If it is, set to `TRUE` to trigger error on invalid `value`.
+#' @docType methods
+#' @seealso [guessHzAttrName()]
+#' @rdname hzmetaname
+#' @export
+#' @examples
+#'
+#' data(sp1)
+#'
+#' # promote to SPC
+#' depths(sp1) <- id ~ top + bottom
+#'
+#' # set important metadata columns
+#' hzdesgnname(sp1) <- "name"
+#' hztexclname(sp1) <- "texture"
+#' 
+#' # set custom horizon property (clay content) column
+#' hzmetaname(sp1, "clay") <- "prop"
+#' 
+#' # inspect metadata list
+#' metadata(sp1)
+#'
+#' # get horizon clay content column
+#' hzmetaname(sp1, "clay")
+#' 
+#' # uses hzdesgname(), hztexclname(), hzmetaname(attr="clay") in function definition
+#' estimatePSCS(sp1)
+setReplaceMethod("hzmetaname",
+                 signature(object = "SoilProfileCollection"),
+                 function(object, attr, required = FALSE, value) {
+                   .set.metadata.aqp(
+                     object = object,
+                     value = value,
+                     required =  required,
+                     attr = paste0("aqp_hz", attr),
+                     attrlabel = paste0("Horizon metadata (", attr, ") column"),
+                     message = "\nSee ??hzmetaname",
+                     allowednames = "horizon"
+                   )
+                 })