Merge branch 'master' of https://github.com/ncss-tech/aqp

NEWS.md

@@ -1,4 +1,5 @@
-# aqp 2.0.4 (2024-07-12)
+# aqp 2.0.4 (2024-07-30)
+ * 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`
 

R/allocate.R

@@ -63,9 +63,9 @@
 #' @author Stephen Roecker
 #' 
 #' @references 
-#' Abrol, I., Yadav, J. & Massoud, F. 1988. \href{https://www.fao.org/3/x5871e/x5871e00.htm}{Salt-affected soils and their management}. No. Bulletin 39. Rome, FAO Soils.
+#' Abrol, I., Yadav, J. & Massoud, F. 1988. [Salt-affected soils and their management](https://www.fao.org/4/x5871e/x5871e00.htm). No. Bulletin 39. Rome, FAO Soils.
 #' 
-#' FAO. 2006. \href{https://www.fao.org/publications/card/en/c/903943c7-f56a-521a-8d32-459e7e0cdae9/}{Guidelines for soil description}. Rome, Food and Agriculture Organization of the United Nations.
+#' FAO. 2006. [Guidelines for soil description](https://www.fao.org/4/a0541e/a0541e.pdf). Rome, Food and Agriculture Organization of the United Nations.
 #' 
 #' FAO. 2020. DEFINITION | What is a black soil? (online). (Cited 28 December 2020). http://www.fao.org/global-soil-partnership/intergovernmental-technical-panel-soils/gsoc17-implementation/internationalnetworkblacksoils/more-on-black-soils/definition-what-is-a-black-soil/es/
 #'   

R/evalGenHz.R

@@ -4,36 +4,42 @@
 #' Data-driven evaluation of generalized horizon labels using nMDS and
 #' silhouette width.
 #'
-#' Non-metric multidimensional scaling is performed via \code{\link{isoMDS}}.
-#' The input distance matrix is generated by \code{\link{daisy}} using
-#' (complete cases of) horizon-level attributes from \code{obj} as named in
-#' \code{vars}.
+#' Non-metric multidimensional scaling is performed via [MASS::isoMDS()].
+#' The input distance matrix is generated by [cluster::daisy()] using
+#' (complete cases of) horizon-level attributes from `obj` as named in
+#' `vars`.
 #'
-#' Silhouette widths are computed via \code{\link{silhouette}}. The input
-#' distance matrix is generated by \code{\link{daisy}} using (complete cases
-#' of) horizon-level attributes from \code{obj} as named in \code{vars}. Note
-#' that observations with genhz labels specified in \code{non.matching.code}
+#' Silhouette widths are computed via [cluster::silhouette()]. The input
+#' distance matrix is generated by [cluster::daisy()] using (complete cases
+#' of) horizon-level attributes from `obj` as named in `vars`. Note
+#' that observations with genhz labels specified in `non.matching.code`
 #' are removed filtered before calculation of the distance matrix.
 #'
-#' @param obj a \code{SoilProfileCollection} object
-#' @param genhz name of horizon-level attribute containing generalized horizon
-#' labels
-#' @param vars character vector of horizon-level attributes to include in the
-#' evaluation
-#' @param non.matching.code code used to represent horizons not assigned a
-#' generalized horizon label
-#' @param stand standardize variables before computing distance matrix (default
-#' = TRUE), passed to \code{\link{daisy}}
-#' @param trace verbose output from passed to \code{\link{isoMDS}}, (default =
-#' FALSE)
-#' @param metric distance metric, passed to \code{\link{daisy}}
-#' @return a list is returned containing: \describe{ \item{horizons}{c('mds.1',
-#' 'mds.2', 'sil.width', 'neighbor')} \item{stats}{mean and standard deviation
-#' of \code{vars}, computed by generalized horizon label} \item{dist}{the
-#' distance matrix as passed to \code{\link{isoMDS}}} }
+#' @param obj a `SoilProfileCollection` object
+#' 
+#' @param genhz name of horizon-level attribute containing generalized horizon labels
+#' 
+#' @param vars character vector of horizon-level attributes to include in the evaluation
+#' 
+#' @param non.matching.code code used to represent horizons not assigned a generalized horizon label
+#' 
+#' @param stand standardize variables before computing distance matrix, passed to [cluster::daisy()]
+#' 
+#' @param trace verbose output from passed to [MASS::isoMDS()]
+#' 
+#' @param metric distance metric, passed to [cluster::daisy()]
+#' 
+#' @return a list is returned containing: 
+#'   * horizons: `c('mds.1', mds.2', 'sil.width', 'neighbor')` 
+#'   * stats: mean and standard deviation `vars`, computed by generalized horizon label
+#'   * dist: the distance matrix as passed to [MASS::isoMDS()]
+#'   
 #' @author D.E. Beaudette
-#' @seealso \code{\link{get.ml.hz}}
+#' 
+#' @seealso [get.ml.hz()]
+#' 
 #' @keywords manip
+#' 
 #' @export
 evalGenHZ <- function(obj, genhz = GHL(obj, required = TRUE), vars, non.matching.code='not-used', stand=TRUE, trace=FALSE, metric='euclidean') {
   if(!requireNamespace("MASS", quietly = TRUE))

R/profile_compare.R

@@ -71,10 +71,13 @@
 #' @aliases pc pc.SPC profile_compare
 #' profile_compare,SoilProfileCollection-method
 #' profile_compare,data.frame-method
+#' 
 #' @docType methods
-#' @param s a dataframe with at least 2 columns of soil properties, and an 'id'
+#' 
+#' @param s a `data.frame` with at least 2 columns of soil properties, and an 'id'
 #' column for each profile. horizon depths must be integers and
 #' self-consistent, or a \code{SoilProfileCollection} object
+#' 
 #' @param vars A vector with named properties that will be used in the
 #' comparison. These are typically column names describing horizon-level
 #' attributes (2 or more), but can also contain site-level attributes (2 or
@@ -105,7 +108,7 @@
 #' optionally scaled by max(D).
 
 #' @author Dylan E. Beaudette
-#' @seealso \code{\link{slice}}, \code{\link{daisy}}
+#' @seealso [dice()], [cluster::daisy()]
 #' @references
 #'  - D.E. Beaudette, P. Roudier, A.T. O'Geen, Algorithms for quantitative pedology: A toolkit for soil scientists, Computers & Geosciences, Volume 52, 2013, Pages 258-268, ISSN 0098-3004, \doi{10.1016/j.cageo.2012.10.020}.
 #'  - Moore, A.; Russell, J. & Ward, W. Numerical analysis of soils: A comparison of three soil profile models with field classification. Journal of Soil Science, 1972, 23, 194-209.