satisfying r-devel checks

R/colorQuantiles.R

@@ -20,9 +20,9 @@
 #'
 #' @description Estimate central tendency and spread of soil color using marginal quantiles and L1 median of CIELAB coordinates.
 #' 
-#' @details Colors are converted from sRGB to CIELAB (D65 illuminant), marginal quantiles of L,A,B coordinates are estimated, and L1 median {L,A,B} is estimates. The closest Munsell chips (via Munsell/CIELAB lookup table provided by \code{munsell}) and R colors are determined by locating chips closest to the marginal quantiles and L1 median.
+#' @details Colors are converted from sRGB to CIELAB (D65 illuminant), marginal quantiles of (L,A,B) coordinates are estimated, and L1 median (L,A,B) is estimates. The closest Munsell chips (via Munsell/CIELAB lookup table provided by `munsell`) and R colors are determined by locating chips closest to the marginal quantiles and L1 median.
 #' 
-#' The results can be conveniently inspected using \code{plotColorQuantiles}.
+#' The results can be conveniently inspected using [plotColorQuantiles()].
 #' 
 #' @author D.E. Beaudette
 #' 

R/generalize.hz.R

@@ -170,9 +170,9 @@ setMethod("generalizeHz", signature(x = "SoilProfileCollection"), function(x, ne
 #' @description Convert a cross-tabulation: {original, genhz} to adjacency matrix.
 #' 
 #' @param tab table, cross-tabulation of original and generalized horizon labels e.g. `table(original, genhz)`
-#'
+#' @return adjacency matrix
+#' @author D.E. Beaudette
 #' @export
-#' @rdname hzTransitionProbabilities
 genhzTableToAdjMat <- function(tab) {
   tab <- as.matrix(tab)
   # extract unique set of names

R/hzTransitionProbabilities.R

@@ -1,4 +1,4 @@
-# generate transition probability matrix from horizon designations
+
 #' @title Horizon Transition Probabilities
 #'
 #' @description Functions for creating and working with horizon (sequence) transition
@@ -9,7 +9,7 @@
 #'   * [horizon designation TP](http://ncss-tech.github.io/AQP/aqp/hz-transition-probabilities.html)
 #'   * [soil color TP](http://ncss-tech.github.io/AQP/aqp/series-color-TP-graph.html)
 #'
-#' @aliases hzTransitionProbabilities genhzTableToAdjMat mostLikelyHzSequence
+#' @aliases hzTransitionProbabilities mostLikelyHzSequence
 #' 
 #' @param x a `SoilProfileCollection` object.
 #' 

R/mostLikelyHzSequence.R

@@ -46,6 +46,7 @@ mostLikelyHzSequence <- function(mc, t0, maxIterations = 10) {
     if(i > maxIterations)
       break
   }
+
   return(s)
 }