panel.depth_function: Lattice Panel Function for Soil Profiles

In aqp: Algorithms for Quantitative Pedology

Lattice Panel Function for Soil Profiles

Description

Panel function for plotting grouped soil property data, along with upper and lower estimates of uncertainty.

This function can be used to replace panel.superpose when plotting depth function data. When requested, contributing fraction data are printed using colors the same color as corresponding depth function lines unless a single color value is given via cf.col.

This function is not able to apply transformations (typically log = 10) applied in the scales argument to xyplot to upper/lower bounds. These will have to be manually applied. See examples.

Usage

panel.depth_function(
  x,
  y,
  id,
  upper = NA,
  lower = NA,
  subscripts = NULL,
  groups = NULL,
  sync.colors = FALSE,
  cf = NA,
  cf.col = NA,
  cf.interval = 20,
  ...
)

prepanel.depth_function(
  x,
  y,
  upper = NA,
  lower = NA,
  subscripts,
  groups = NULL,
  ...
)

Arguments

x	x values (generated by calling lattice function)
y	y values (generated by calling lattice function)
id	vector of id labels, same length as x and y–only required when plotting segments (see Details section)
upper	vector of upper confidence envelope values
lower	vector of lower confidence envelope values
subscripts	paneling indices (generated by calling lattice function)
groups	grouping data (generated by calling lattice function)
sync.colors	optionally sync the fill color within the region bounded by (lower–upper) with the line colors
cf	optionally annotate contributing fraction data at regular depth intervals see slab
cf.col	optional color for contributing fraction values, typically used to override the line color
cf.interval	number of depth units to space printed contributing fraction values
...	further arguments to lower-level lattice plotting functions, see below

Author(s)

D.E. Beaudette

See Also

sp1, slice, slab

Examples

library(lattice)
data(sp1)

# 1. plotting mechanism for step-functions derived from soil profile data
xyplot(
  cbind(top, bottom) ~ prop,
  data = sp1,
  id = sp1$id,
  panel = panel.depth_function,
  ylim = c(250, -10),
  scales = list(y = list(tick.number = 10)),
  xlab = 'Property',
  ylab = 'Depth (cm)',
  main = 'panel.depth_function() demo'
)

# 1.1 include groups argument to leverage lattice styling framework
sp1$group <- factor(sp1$group, labels = c('Group 1', 'Group2'))

xyplot(
  cbind(top, bottom) ~ prop,
  groups = group,
  data = sp1,
  id = sp1$id,
  panel = panel.depth_function,
  ylim = c(250, -10),
  scales = list(y = list(tick.number = 10)),
  xlab = 'Property',
  ylab = 'Depth (cm)',
  main = 'panel.depth_function() demo',
  auto.key = list(
    columns = 2,
    points = FALSE,
    lines = TRUE
  ),
  par.settings = list(superpose.line = list(col = c(
    'Orange', 'RoyalBlue'
  )))
)


# more complex examples, using step functions with grouped data
# better looking figures with less customization via tactile package
if(requireNamespace('tactile')) {
  
  library(data.table)
  library(lattice)
  library(tactile)
  
  # example data
  data(sp6)
  
  # a single profile
  x <- sp6[1:5, ]
  
  # wide -> long format
  x.long <- data.table::melt(
    data.table::data.table(x), 
    id.vars = c('id', 'top', 'bottom'), 
    measure.vars = c('sand', 'silt', 'clay')
  )
  
  # (optional) convert back to data.frame
  x.long <- as.data.frame(x.long)
  
  # three variables sharing a common axis
  # factor levels set by melt()
  xyplot(
    cbind(top, bottom) ~ value | id,
    groups = variable,
    data = x.long,
    id = x.long$id,
    ylim = c(200, -5), xlim = c(10, 60),
    scales = list(alternating = 1, y = list(tick.number = 10)),
    par.settings = tactile.theme(superpose.line = list(lwd = 2)),
    xlab = 'Sand, Silt, Clay (%)',
    ylab = 'Depth (cm)',
    panel = panel.depth_function,
    auto.key = list(columns = 3, lines = TRUE, points = FALSE),
    asp = 1.5
  )
  
  
  # all profiles
  x <- sp6
  
  # wide -> long format
  x.long <- data.table::melt(
    data.table::data.table(x), 
    id.vars = c('id', 'top', 'bottom'), 
    measure.vars = c('sand', 'silt', 'clay')
  )
  
  # (optional) convert back to data.frame
  x.long <- as.data.frame(x.long)
  
  # three variables sharing a common axis
  # factor levels set by melt()
  xyplot(
    cbind(top, bottom) ~ value | id,
    groups = variable,
    data = x.long,
    id = x.long$id,
    ylim = c(200, -5), xlim = c(0, 70),
    scales = list(alternating = 1, y = list(tick.number = 10)),
    par.settings = tactile.theme(superpose.line = list(lwd = 2)),
    xlab = 'Sand, Silt, Clay (%)',
    ylab = 'Depth (cm)',
    panel = panel.depth_function,
    auto.key = list(columns = 3, lines = TRUE, points = FALSE),
    as.table = TRUE
  )
  
  xyplot(
    cbind(top, bottom) ~ value,
    groups = variable,
    data = x.long,
    id = x.long$id,
    ylim = c(200, -5), xlim = c(0, 70),
    scales = list(alternating = 1, y = list(tick.number = 10)),
    par.settings = tactile.theme(superpose.line = list(lwd = 2)),
    xlab = 'Sand, Silt, Clay (%)',
    ylab = 'Depth (cm)',
    panel = panel.depth_function,
    auto.key = list(columns = 3, lines = TRUE, points = FALSE),
    as.table = TRUE
  )
  
  xyplot(
    cbind(top, bottom) ~ value | variable,
    groups = variable,
    data = x.long,
    id = x.long$id,
    ylim = c(200, -5), xlim = c(0, 70),
    scales = list(alternating = 1, y = list(tick.number = 10)),
    par.settings = tactile.theme(superpose.line = list(lwd = 2)),
    xlab = 'Sand, Silt, Clay (%)',
    ylab = 'Depth (cm)',
    panel = panel.depth_function,
    auto.key = list(columns = 3, lines = TRUE, points = FALSE),
    as.table = TRUE
  )
  
  
  xyplot(
    cbind(top, bottom) ~ value | variable,
    data = x.long,
    id = x.long$id,
    ylim = c(200, -5), xlim = c(0, 70),
    scales = list(alternating = 1, y = list(tick.number = 10)),
    par.settings = tactile.theme(superpose.line = list(lwd = 2)),
    xlab = 'Sand, Silt, Clay (%)',
    ylab = 'Depth (cm)',
    panel = panel.depth_function,
    auto.key = list(columns = 3, lines = TRUE, points = FALSE),
    as.table = TRUE
  )
  
  
}

aqp documentation built on Oct. 19, 2024, 5:06 p.m.