manual issues on win devel check

R/bootstrapSoilTexture.R

@@ -7,24 +7,22 @@
 #' 
 #' @author D.E. Beaudette
 #' 
-#' @param ssc a \code{data.frame} object with 3 columns: `sand`, `silt`, `clay` and at least three rows of data within the range of 0-100 (percent). NA are automatically removed, but care should be taken to ensure that the sand/silt/clay values add to 100 percent. Simulations are based on these examples.
+#' @param ssc a `data.frame` object with 3 columns: 'sand', 'silt', 'clay' and at least three rows of data within the range of 0-100 (percent). NA are automatically removed, but care should be taken to ensure that the sand/silt/clay values add to 100 percent. Simulations are based on these examples.
 #' 
-#' @param method type of simulation: `dirichlet` or `normal`. See details.
+#' @param method type of simulation: 'dirichlet' or 'normal'. See details.
 #' 
 #' @param n number of simulated compositions. See details.
 #' 
-#' @return a \code{list} containing:
+#' @return a `list` containing:
 #' 
-#' \itemize{
-#'  \item{\code{samples}} - {\code{data.frame} of simulated sand, silt, clay values}
-#'  \item{\code{mean}} - {compositional mean}
-#'  \item{\code{var}} - {compositional variance-covariance matrix}
-#'  \item{\code{D.alpha}} - {(fitted) alpha parameters of the Dirichlet distribution, \code{NULL} when \code{method = 'normal'}}
-#' }
+#'  * `samples` - `data.frame` of simulated sand, silt, clay values
+#'  * `mean` - compositional mean
+#'  * `var` - compositional variance-covariance matrix
+#'  * `D.alpha` - (fitted) alpha parameters of the Dirichlet distribution, `NULL` when `method = 'normal'`
 #' 
 #' @details Simulations from the multivariate normal distribution will more closely track the marginal distributions of sand, silt, and clay--possibly a better fit for "squished" compositions (TODO elaborate). However, these simulations can result in extreme (unlikely) estimates. 
 #' 
-#' Simulations from the Dirichlet distribution will usually be a better fit (fewer extreme estimates) but require a fairly large number of records in \code{ssc} (\code{n >= 30}?) for a reliable fit.
+#' Simulations from the Dirichlet distribution will usually be a better fit (fewer extreme estimates) but require a fairly large number of records in `ssc` (`n >= 30`?) for a reliable fit.
 #' 
 #' Additional examples will be added to [this tutorial](http://ncss-tech.github.io/AQP/aqp/soiltexture-vizualization-ideas.html).
 #' 

R/colorQuantiles.R

@@ -28,10 +28,8 @@
 #' 
 #' @return A List containing the following elements:
 #' 
-#' \itemize{
-#' \item{marginal: }{\code{data.frame} containing marginal quantiles in CIELAB (D65), closest Munsell chips, and dE00}
-#' \item{L1: }{L1 median CIELAB (D65) values, closest Munsell chip, and dE00}
-#' }
+#'   * `marginal`: `data.frame` containing marginal quantiles in CIELAB (D65), closest Munsell chips, and dE00
+#'   * `L1`: L1 median CIELAB (D65) values, closest Munsell chip, and dE00
 #' 
 #' @export
 #'

R/hzTransitionProbabilities.R

@@ -1,33 +1,38 @@
 # generate transition probability matrix from horizon designations
-#' Horizon Transition Probabilities
+#' @title Horizon Transition Probabilities
 #'
-#' Functions for creating and working with horizon (sequence) transition
+#' @description Functions for creating and working with horizon (sequence) transition
 #' probability matrices.
 #'
-#' See the following tutorials for some ideas: \describe{ \item{horizon
-#' designation
-#' TP}{\url{http://ncss-tech.github.io/AQP/aqp/hz-transition-probabilities.html}}
-#' \item{soil color
-#' TP}{\url{http://ncss-tech.github.io/AQP/aqp/series-color-TP-graph.html}} }
+#' See the following tutorials for some ideas: 
+#' 
+#'   * [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
-#' @param x A \code{SoilProfileCollection} object.
-#' @param name A horizon level attribute in \code{x} that names horizons.
+#' 
+#' @param x a `SoilProfileCollection` object.
+#' 
+#' @param name A horizon level attribute in `x` that names horizons.
+#' 
 #' @param loopTerminalStates should terminal states loop back to themselves?
+#' 
 #' This is useful when the transition probability matrix will be used to
-#' initialize a \code{markovchain} object. See examples below.
-#' @return The function \code{hzTransitionProbabilities} returns a square
-#' matrix of transition probabilities. See examples.
+#' initialize a `markovchain` object. See examples below.
+#' 
+#' @return A square matrix of transition probabilities. See examples.
 #'
-#' The function \code{genhzTableToAdjMat} returns a square adjacency matrix.
+#' The function [genhzTableToAdjMat()] returns a square adjacency matrix.
 #' See examples.
 #'
-#' The function \code{mostLikelyHzSequence} returns the most likely sequence of
-#' horizons, given a \code{markovchain} object initialized from horizon
-#' transition probabilities and an initial state, \code{t0}. See examples.
+#' The function [mostLikelyHzSequence()] returns the most likely sequence of
+#' horizons, given a `markovchain` object initialized from horizon
+#' transition probabilities and an initial state, `t0`. See examples.
+#' 
 #' @note These functions are still experimental and subject to change.
+#' 
 #' @author D.E. Beaudette
-#' @seealso \code{\link{generalize.hz}}
+#' @seealso [generalize.hz()]
 #' @keywords manip
 #' @export
 #' @examples

R/mixMunsell.R

@@ -148,15 +148,11 @@
 #' Marcus, R.T. (1998). The Measurement of Color. In K. Nassau (Ed.), Color for Science, Art, and Technology (pp. 32-96). North-Holland.
 #' 
 #' 
+#'  * [inspiration / calculations based on the work of Scott Burns](https://arxiv.org/ftp/arxiv/papers/1710/1710.06364.pdf)
 #'
-#' \itemize{
-#'    \item{inspiration / calculations based on the work of Scott Burns: }{\url{https://arxiv.org/ftp/arxiv/papers/1710/1710.06364.pdf}}
+#'  * [related discussion on Stack Overflow](https://stackoverflow.com/questions/10254022/implementing-kubelka-munk-like-krita-to-mix-colours-color-like-paint/29967630#29967630)
 #'
-#'    \item{related discussion on Stack Overflow: }{\url{https://stackoverflow.com/questions/10254022/implementing-kubelka-munk-like-krita-to-mix-colours-color-like-paint/29967630#29967630}}
-#'
-#'    \item{spectral library source: }{\url{https://www.munsellcolourscienceforpainters.com/MunsellResources/SpectralReflectancesOf2007MunsellBookOfColorGlossy.txt}}
-#'
-#' }
+#'  * [spectral library source](https://www.munsellcolourscienceforpainters.com/MunsellResources/SpectralReflectancesOf2007MunsellBookOfColorGlossy.txt)
 #'
 #'
 #' @details