tiny release to CRAN

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: aqp
-Version: 2.01
+Version: 2.0.1
 Title: Algorithms for Quantitative Pedology
 Authors@R: c(person(given="Dylan", family="Beaudette", role = c("aut", "cre"), email = "[email protected]"), person(given="Pierre", family="Roudier", email="[email protected]", role = c("aut", "ctb")), person(given="Andrew", family="Brown", email="[email protected]", role = c("aut", "ctb")))
 Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]

NEWS.md

@@ -1,4 +1,4 @@
-# aqp 2.01 (2023-09-03)
+# aqp 2.0.1 (2023-09-03)
  * new function `flagOverlappingHz()` for identifying horizons with perfect overlap
  * `fillHzGaps()`, `dice()`, `slab()`, and several other functions now safely handle horizons with perfect overlap (#296)
 

misc/sandbox/SOC-stock-examples.R

@@ -1,4 +1,4 @@
-# library(aqp)
+library(aqp)
 library(soilDB)
 library(lattice)
 library(tactile)
@@ -19,7 +19,7 @@ table(x$taxonname)
 
 
 # ignoring rock fragments for now
-# SOC stock by horizon = thick (cm) * Db 1/3 bar (g/cm^3) * (soil fraction) * conversion factor (10)
+# SOC stock by horizon = thick (cm) * Db 1/3 bar (g/cm^3) * (soil fraction) * SOC (%) * conversion factor (10)
 x$thick <- x$hzn_bot - x$hzn_top
 x$soc_kg_sq.m <- x$thick * x$db_13b * (x$estimated_oc / 100) * 10
 
@@ -31,8 +31,9 @@ z <- subset(x, soc.complete.pct > 0.9)
 
 table(z$taxonname)
 
-par(mar = c(0, 0, 3, 0))
+par(mar = c(0, 0, 3, 2))
 plotSPC(z, color = 'soc_kg_sq.m', width = 0.35, label = 'taxonname', name.style = 'center-center')
+
 groupedProfilePlot(z, groups = 'taxonname', color = 'soc_kg_sq.m', width = 0.35, name.style = 'center-center', group.name.offset = -10, max.depth = 150)
 
 groupedProfilePlot(z, groups = 'taxonname', color = 'moist_soil_color', width = 0.35, name.style = 'center-center', group.name.offset = -10, max.depth = 150)
@@ -55,7 +56,10 @@ x$SOC_stock <- profileApply(x, function(i) {
   sum(i$soc_kg_sq.m, na.rm = TRUE)
 })
 
-par(mar = c(0, 0, 3, 1))
+par(mar = c(0, 0, 3, 2))
+
+groupedProfilePlot(x, groups = 'taxonname', color = 'moist_soil_color', width = 0.35, name.style = 'center-center', group.name.offset = -15, max.depth = 200, cex.names = 0.8)
+
 groupedProfilePlot(x, groups = 'taxonname', color = 'soc_kg_sq.m', width = 0.35, name.style = 'center-center', group.name.offset = -15, max.depth = 200, cex.names = 0.8)
 
 
@@ -74,10 +78,10 @@ z$SOC_stock <- profileApply(z, function(i) {
   sum(i$soc_kg_sq.m, na.rm = TRUE)
 })
 
-par(mar = c(0, 0, 3, 1))
+par(mar = c(0, 0, 3, 2))
 groupedProfilePlot(z, groups = 'taxonname', color = 'soc_kg_sq.m', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.8, print.id = FALSE)
 
-par(mar = c(0, 0, 3, 1))
+par(mar = c(0, 0, 3, 2))
 groupedProfilePlot(z, groups = 'taxonname', color = 'moist_soil_color', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.66, print.id = FALSE)
 
 d <- site(z)
@@ -89,7 +93,7 @@ tapply(d$SOC_stock, d$taxonname, quantile)
 
 a <- alignTransect(z$SOC_stock, x.min = 1, x.max = length(z), fix = TRUE, thresh = 0.4, method = 'E', q = 2)
 
-par(mar = c(2, 0, 3, 1))
+par(mar = c(2, 0, 3, 2))
 plotSPC(z, width = 0.25, name.style = 'center-center', 
         cex.names = 0.75, label = 'taxonname', color = 'moist_soil_color',
         relative.pos = a$relative.pos, plot.order = a$order)
@@ -102,8 +106,8 @@ z$cumulative.soc_kg_sq.m <- profileApply(z, function(i) {
 })
 
 
-par(mar = c(2.5, 0, 3, 1))
-groupedProfilePlot(z, groups = 'taxonname', color = 'cumulative.soc_kg_sq.m', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', cex.depth.axis = 1, axis.line.offset = -4)
+par(mar = c(3, 0, 3, 2), xpd = NA)
+groupedProfilePlot(z, groups = 'taxonname', color = 'cumulative.soc_kg_sq.m', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', depth.axis = list(cex = 1, line = -3))
 
 .lsp <- get('last_spc_plot', envir = aqp.env)
 
@@ -113,8 +117,8 @@ text(x = 1:length(z), y = 105, labels = .lab, cex = 0.85)
 mtext('SOC Stock (kg / m^2)', side = 1, line = 0.75, font = 2, cex = 0.85)
 
 
-par(mar = c(2.5, 0, 0, 1))
-groupedProfilePlot(z, groups = 'taxonname', color = 'moist_soil_color', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', cex.depth.axis = 1, axis.line.offset = -4)
+par(mar = c(2.5, 0, 0, 2), xpd = NA)
+groupedProfilePlot(z, groups = 'taxonname', color = 'moist_soil_color', width = 0.35, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', depth.axis = list(cex = 1, line = -3))
 
 .lsp <- get('last_spc_plot', envir = aqp.env)
 .lab <- round(z$SOC_stock)[.lsp$plot.order]
@@ -123,8 +127,8 @@ text(x = 1:length(z), y = 105, labels = .lab, cex = 0.85)
 mtext('SOC Stock (kg / m^2)', side = 1, line = 0.75, font = 2, cex = 0.85)
 
 
-par(mar = c(2.5, 0, 0, 1))
-groupedProfilePlot(z, groups = 'taxonname', name = NA, color = 'moist_soil_color', width = 0.4, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', cex.depth.axis = 1, axis.line.offset = -4, break.style = 'arrow', arrow.offset = -2, group.line.lty = 1, group.line.lwd = 1)
+par(mar = c(2.5, 0, 0, 1), xpd = NA)
+groupedProfilePlot(z, groups = 'taxonname', name = NA, color = 'moist_soil_color', width = 0.4, name.style = 'center-center', group.name.offset = -5, cex.names = 0.75, print.id = FALSE, col.label = 'Cumulative SOC Stock (kg C / m^2)', depth.axis = list(cex = 1, line = -3), break.style = 'arrow', arrow.offset = -2, group.line.lty = 1, group.line.lwd = 1)
 
 .lsp <- get('last_spc_plot', envir = aqp.env)
 .lab <- round(z$SOC_stock)[.lsp$plot.order]
@@ -137,14 +141,19 @@ mtext('SOC Stock (kg / m^2)', side = 1, line = 0.75, font = 2, cex = 0.85)
 
 agg <- slab(z, fm = taxonname ~ cumulative.soc_kg_sq.m)
 
+tps <- tactile.theme(
+  superpose.line = list(col = 'royalblue', lwd = 3)
+)
+
 xyplot(top ~ p.q50 | taxonname, data=agg, ylab='Depth',
-       xlab='median bounded by 25th and 75th percentiles',
+       xlab='Cumulative Soil Organic Carbon Stock (kg / m^2)\nmedian bounded by 5th and 95th percentiles',
        lower=agg$p.q5, upper=agg$p.q95, ylim=c(110,-5),
        panel=panel.depth_function,
        prepanel=prepanel.depth_function,
-       cf=agg$contributing_fraction,
-       alpha=0.5,
-       layout=c(3,1), scales=list(x=list(alternating=1))
+       sync.colors = TRUE,
+       alpha=0.25,
+       layout=c(3,1), scales=list(x=list(relation = 'free', alternating = 1)),
+       par.settings = tps
 )
 
 

misc/sandbox/SPC-bracket-interval-via-transparency.R

@@ -0,0 +1,51 @@
+library(aqp)
+
+# example data from three official series descriptions
+data("osd")
+
+
+
+# https://msalganik.wordpress.com/2017/01/21/making-sense-of-the-rlnorm-function-in-r/comment-page-1/
+# make rlnorm simpler to parameterize
+# m: arithmetic mean
+# s: standard deviation
+rlnorm.helper <- function(n, m, s) {
+  location <- log(m^2 / sqrt(s^2 + m^2))
+  shape <- sqrt(log(1 + (s^2 / m^2)))
+  rlnorm(n, location, shape)
+}
+
+d <- lapply(profile_id(osd), function(i) {
+  s <- data.frame(id = i, top = rlnorm.helper(50, m = 50, s = 15))
+  s$bottom <- 0
+
+  for(i in seq_along(s$bottom)) {
+    s$bottom[i] <- s$top[i] + rlnorm.helper(1, m = 25, s = 15)
+  }
+
+  return(s)
+})
+
+d <- do.call('rbind', d)
+
+
+# tighter margins
+par(mar = c(0, 0, 0, 0))
+
+
+# adjust default style
+plotSPC(
+  osd, 
+  name.style = 'center-center', 
+  cex.names = 1,
+  width = 0.33,
+  cex.id = 0.9,
+  hz.distinctness.offset = 'hzd', 
+  max.depth = 175, 
+  depth.axis = FALSE, 
+  hz.depths = TRUE
+)
+
+addBracket(d, offset = -0.38, tick.length = 0, lwd = 12, col = rgb(red=0, green=0, blue=1, alpha=0.03))
+
+