diff --git a/R/colorQuantiles.R b/R/colorQuantiles.R
index d99a6f40d..0bcd3f4f8 100644
--- a/R/colorQuantiles.R
+++ b/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
 #' 
diff --git a/R/generalize.hz.R b/R/generalize.hz.R
index f79f43b02..8570f1370 100644
--- a/R/generalize.hz.R
+++ b/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
diff --git a/R/hzTransitionProbabilities.R b/R/hzTransitionProbabilities.R
index 121541d31..cdd5f7bd2 100644
--- a/R/hzTransitionProbabilities.R
+++ b/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.
 #' 
diff --git a/R/mostLikelyHzSequence.R b/R/mostLikelyHzSequence.R
index 29f9b9288..48bd06d38 100644
--- a/R/mostLikelyHzSequence.R
+++ b/R/mostLikelyHzSequence.R
@@ -46,6 +46,7 @@ mostLikelyHzSequence <- function(mc, t0, maxIterations = 10) {
     if(i > maxIterations)
       break
   }
+  
   return(s)
 }
 
diff --git a/man/colorQuantiles.Rd b/man/colorQuantiles.Rd
index 84b770728..67755c451 100644
--- a/man/colorQuantiles.Rd
+++ b/man/colorQuantiles.Rd
@@ -22,9 +22,9 @@ A List containing the following elements:
 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.
+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.
 
-The results can be conveniently inspected using \code{plotColorQuantiles}.
+The results can be conveniently inspected using \code{\link[=plotColorQuantiles]{plotColorQuantiles()}}.
 }
 \examples{
 
diff --git a/man/genhzTableToAdjMat.Rd b/man/genhzTableToAdjMat.Rd
new file mode 100644
index 000000000..30010556c
--- /dev/null
+++ b/man/genhzTableToAdjMat.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/generalize.hz.R
+\name{genhzTableToAdjMat}
+\alias{genhzTableToAdjMat}
+\title{Convert cross-tabulation to adjacency matrix.}
+\usage{
+genhzTableToAdjMat(tab)
+}
+\arguments{
+\item{tab}{table, cross-tabulation of original and generalized horizon labels e.g. \code{table(original, genhz)}}
+}
+\value{
+adjacency matrix
+}
+\description{
+Convert a cross-tabulation: {original, genhz} to adjacency matrix.
+}
+\author{
+D.E. Beaudette
+}
diff --git a/man/hzTransitionProbabilities.Rd b/man/hzTransitionProbabilities.Rd
index e2a0baec9..4e8680172 100644
--- a/man/hzTransitionProbabilities.Rd
+++ b/man/hzTransitionProbabilities.Rd
@@ -1,14 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generalize.hz.R, R/hzTransitionProbabilities.R,
+% Please edit documentation in R/hzTransitionProbabilities.R,
 %   R/mostLikelyHzSequence.R
-\name{genhzTableToAdjMat}
-\alias{genhzTableToAdjMat}
+\name{hzTransitionProbabilities}
 \alias{hzTransitionProbabilities}
 \alias{mostLikelyHzSequence}
-\title{Convert cross-tabulation to adjacency matrix.}
+\title{Horizon Transition Probabilities}
 \usage{
-genhzTableToAdjMat(tab)
-
 hzTransitionProbabilities(
   x,
   name = GHL(x, required = TRUE),
@@ -18,8 +15,6 @@ hzTransitionProbabilities(
 mostLikelyHzSequence(mc, t0, maxIterations = 10)
 }
 \arguments{
-\item{tab}{table, cross-tabulation of original and generalized horizon labels e.g. \code{table(original, genhz)}}
-
 \item{x}{a \code{SoilProfileCollection} object.}
 
 \item{name}{A horizon level attribute in \code{x} that names horizons.}
@@ -46,8 +41,6 @@ horizons, given a \code{markovchain} object initialized from horizon
 transition probabilities and an initial state, \code{t0}. See examples.
 }
 \description{
-Convert a cross-tabulation: {original, genhz} to adjacency matrix.
-
 Functions for creating and working with horizon (sequence) transition
 probability matrices.