From dad4b7003eed5c6c6773da5bc53f5b34359dd19a Mon Sep 17 00:00:00 2001
From: Beaudette <dylan.beaudette@usda.gov>
Date: Wed, 16 Oct 2024 13:56:25 -0700
Subject: [PATCH] minor updates

---
 R/addVolumeFraction.R                       |  6 +++---
 man/addVolumeFraction.Rd                    |  3 +++
 misc/sandbox/morphologic-grid/2024-reboot.R | 12 +++++++++---
 3 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/R/addVolumeFraction.R b/R/addVolumeFraction.R
index 39e5e29f..8820d0fb 100644
--- a/R/addVolumeFraction.R
+++ b/R/addVolumeFraction.R
@@ -51,6 +51,8 @@
 #' @title Symbolize Volume Fraction within a Soil Profile Collection Plot
 #' 
 #' @description Symbolize volume fraction on an existing soil profile collection plot.
+#' 
+#' @note It may be necessary to adjust both `res`, `cex.min`, and `cex.max` for optimal legibility.
 #'
 #' @param x a `SoilProfileCollection` object
 #' @param colname character vector of length 1, naming the column containing volume fraction data (horizon-level attribute). Values should be within 0-100 percent.
@@ -68,9 +70,7 @@
 #'
 #' @export
 #' 
-
-
-## TODO: symbol size must be controlled by `res`
+#' 
 addVolumeFraction <- function(x, colname, res = 10, cex.min = 0.1, cex.max = 0.5, pch = 1, col = 'black') {
   
   # color should be either:
diff --git a/man/addVolumeFraction.Rd b/man/addVolumeFraction.Rd
index 5169230b..a3aa79c3 100644
--- a/man/addVolumeFraction.Rd
+++ b/man/addVolumeFraction.Rd
@@ -35,6 +35,9 @@ Symbolize volume fraction on an existing soil profile collection plot.
 \details{
 This function can only be called after plotting a \code{SoilProfileCollection} object. Details associated with a call to \code{plotSPC()} are automatically accounted for within this function: e.g. \code{plot.order}, \code{width}, etc..
 }
+\note{
+It may be necessary to adjust both \code{res}, \code{cex.min}, and \code{cex.max} for optimal legibility.
+}
 \seealso{
 \code{\link[=plotSPC]{plotSPC()}}
 }
diff --git a/misc/sandbox/morphologic-grid/2024-reboot.R b/misc/sandbox/morphologic-grid/2024-reboot.R
index 71fe4a59..63478021 100644
--- a/misc/sandbox/morphologic-grid/2024-reboot.R
+++ b/misc/sandbox/morphologic-grid/2024-reboot.R
@@ -179,8 +179,13 @@ library(aqp)
 # plot: graphical sanity check on results
 initHzDepthFunctions <- function(hz, plot = TRUE) {
   
+  # number of horizons
+  n <- nrow(hz)
+  
+  # plot colors
+  
   # generate a depth function for each horizon template
-  p <- lapply(seq_along(1:nrow(hz)), function(i) {
+  p <- lapply(1:n, function(i) {
     zapsmall(
       # work at depth interval mid points
       dnorm(z.i + (dz / 2), mean = hz$m[i], sd = hz$sd[i])
@@ -202,7 +207,8 @@ initHzDepthFunctions <- function(hz, plot = TRUE) {
       x = z.i, 
       y = pp, 
       type = 'b', 
-      pch = 1, 
+      pch = 1,
+      lwd = 1.5,
       cex = 0.5,
       xlab = 'Depth (cm)',
       ylab = 'Pr(H | depth)',
@@ -330,7 +336,7 @@ p <- initHzDepthFunctions(hz)
 
 
 ## simulation
-n.profiles <- 8
+n.profiles <- 10
 pIDs <- sprintf("p%02d", 1:n.profiles)
 
 s <- lapply(1:n.profiles, function(i) {