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02-aggregate-soil-data.R
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02-aggregate-soil-data.R
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## TODO:
## * soil parameter files for each map unit key (dominant component)
## * weighted avg. soil properties to contact / rest. feature
## * use ROSETTA for Ksat and water retention curve points
library(aqp)
library(soilDB)
library(lattice)
library(tactile)
library(reshape2)
library(terra)
source('local-functions.R')
## combined mu/component data, as SPC
x <- readRDS('data/combined-tab-data-SPC.rds')
## TODO: move this to 01-prepare-soil-data.R
## mukey grids for area calculation
s.grid <- rast('grids/ssurgo_utm.tif')
r.grid <- rast('grids/rss_utm.tif')
# area by cell value (mukey)
s.area <- expanse(s.grid, byValue = TRUE)
r.area <- expanse(r.grid, byValue = TRUE)
# combine and clean-up
mu.area <- make.groups(ssurgo = s.area, rss = r.area)
mu.area$layer <- NULL
row.names(mu.area) <- NULL
names(mu.area) <- c('mukey', 'mu.area', 'which')
# check: ok
head(mu.area)
tapply(mu.area$mu.area, mu.area$which, sum)
# save a copy for later
saveRDS(mu.area, file = 'data/mu-area.rds')
# join with SPC
site(x) <- mu.area[, c('mukey', 'mu.area')]
# create a component pct & area weight
site(x)$co.wt <- x$mu.area * (x$comppct_r / 100)
## develop ROSETTA estimates
# https://ncss-tech.github.io/AQP/soilDB/ROSETTA-API.html
.v <-c('sandtotal_r', 'silttotal_r', 'claytotal_r', 'dbthirdbar_r', 'wthirdbar_r', 'wfifteenbar_r')
.r <- horizons(x)[, c('hzID', .v)]
R <- ROSETTA(.r, vars = .v, v = '3')
# check: ok
# head(R)
# splice-into horizons
horizons(x) <- R[, c('hzID', 'theta_r', 'theta_s', 'alpha', 'npar', 'ksat')]
## investigate mukind by source
xtabs(~ source + mukind, data = unique(site(x)[, c('mukey', 'source', 'mukind')]))
## restrictive features
r <- diagnostic_hz(x)
# kind
(.tab <- xtabs( ~ reskind + which, data = r))
round(prop.table(.tab, margin = 2), 2)
## a very SIMPLE selection of 1 component / map unit
## based on most frequent component name ~ sum(component percent)
s <- site(x)
ss <- split(s, s$mukey)
z <- lapply(ss, dominantComponent)
dominant.cokey.lut <- do.call('rbind', z)
row.names(dominant.cokey.lut) <- NULL
# check number / source
table(dominant.cokey.lut$source)
table(dominant.cokey.lut$source, dominant.cokey.lut$majcompflag)
# ensure no duplicate map unit keys
stopifnot(! any(table(dominant.cokey.lut$mukey) > 1))
# check for missing mukeys
setdiff(unique(x$mukey), dominant.cokey.lut$mukey)
setdiff(dominant.cokey.lut$mukey, unique(x$mukey))
# save
saveRDS(dominant.cokey.lut, file = 'data/dominant-cokey-LUT.rds')
## weighted mean depth to restrictive features
z <- lapply(ss, wtMeanProperty, v = 'depth.to.restriction')
rest.depth.wt.mean <- do.call('rbind', z)
row.names(rest.depth.wt.mean) <- NULL
# save
saveRDS(rest.depth.wt.mean, file = 'data/rest-depth-wtmean-LUT.rds')
## wt. mean soil properties to contact
# convert log10(cm/day) -> cm/day
x$ksat.rosetta <- 10^x$ksat
# convert um/s -> cm/day
x$ksat_r <- x$ksat_r * 8.64
# truncate each profile, depth to restriction
y <- trunc(x, 0, x$depth.to.restriction)
# weights are mu area * component area fraction
a.site <- slab(y, fm = source ~ sandtotal_r + silttotal_r + claytotal_r + dbthirdbar_r + wthirdbar_r + wfifteenbar_r + ksat_r + ksat.rosetta, weights = 'co.wt')
a.site$source <- factor(a.site$source)
levels(a.site$variable) <- c('Sand (%)', 'Silt (%)', 'Clay (%)', 'Db 1/3 bar (g/cm^3)', 'Water Retention 1/3 bar (%)', 'Water Retention 15 bar (%)', 'Ksat [SSURGO] (cm/d)', 'Ksat [ROSETTA] (cm/d)')
# define plotting style
tps <- tactile.theme(superpose.line = list(col = hcl.colors(2, palette = 'roma'), lwd = 2))
## TODO: save this figure for later use
# plot grouped, aggregate data
xyplot(
top ~ p.q50 | variable,
groups = source,
data = a.site,
ylab = 'Depth (cm)',
xlab = 'median bounded by 25th and 75th percentiles',
lower = a.site$p.q25, upper = a.site$p.q75,
ylim = c(205,-5),
panel = panel.depth_function,
prepanel = prepanel.depth_function,
alpha = 0.25,
sync.colors = TRUE,
cf = a.site$contributing_fraction,
par.strip.text = list(cex = 0.8),
strip = strip.custom(bg = grey(0.85)),
layout = c(4,2),
scales=list(x = list(alternating = 1, relation = 'free'), y = list(alternating = 3)),
par.settings = tps,
as.table = TRUE,
auto.key = list(columns = 2, lines = TRUE, points = FALSE)
)
# ^^ note influence of O horizons, which seem to be present in RSS vs. SSURGO
xyplot(top ~ p.q50 | variable, groups = source, data=a.site, ylab='Depth (cm)',
subset = variable %in% c('Ksat [SSURGO] (cm/d)', 'Ksat [ROSETTA] (cm/d)'),
xlab='median bounded by 25th and 75th percentiles',
lower=a.site$p.q25, upper=a.site$p.q75, ylim=c(205,-5),
panel=panel.depth_function, alpha=0.25, sync.colors=TRUE,
prepanel=prepanel.depth_function,
cf=a.site$contributing_fraction,
par.strip.text=list(cex = 1.1),
strip=strip.custom(bg=grey(0.85)),
layout=c(2,1), scales=list(x=list(alternating=1, relation='free'), y=list(alternating=3)),
par.settings = tps,
as.table = TRUE,
auto.key=list(columns=2, lines=TRUE, points=FALSE)
)
##
# truncate each profile, depth to restriction
y <- trunc(x, 0, x$depth.to.restriction)
a.site <- slab(y, fm = mukey ~ sandtotal_r + silttotal_r + claytotal_r + dbthirdbar_r + wthirdbar_r + wfifteenbar_r + ksat_r + ksat, weights = 'comppct_r')
a.site$mukey <- factor(a.site$mukey)
levels(a.site$variable) <- c('Sand (%)', 'Silt (%)', 'Clay (%)', 'Db 1/3 bar (g/cm^3)', 'Water Retention 1/3 bar (%)', 'Water Retention 15 bar (%)', 'Ksat (SSURGO)', 'Ksat (ROSETTA)')
# define plotting style
tps <- tactile.theme(superpose.line = list(col = c('RoyalBlue', 'DarkRed', 'DarkGreen'), lwd = 2))
# plot grouped, aggregate data
xyplot(top ~ p.q50 | variable, data = a.site,
subset = mukey == '545842',
ylab='Depth',
xlab='median bounded by 25th and 75th percentiles',
lower=a.site$p.q25, upper=a.site$p.q75, ylim=c(155,-5),
panel=panel.depth_function, alpha=0.25, sync.colors=TRUE,
prepanel=prepanel.depth_function,
cf=a.site$contributing_fraction,
par.strip.text=list(cex=0.8),
strip=strip.custom(bg=grey(0.85)),
layout=c(4,2), scales=list(x=list(alternating=1, relation='free'), y=list(alternating=3)),
par.settings=tps,
as.table = TRUE,
auto.key=list(columns=2, lines=TRUE, points=FALSE)
)
## TODO: finish wt. mean over depth-to-restrictive features
#
# a <- slab(
# y,
# fm = cokey ~ sandtotal_r + silttotal_r + claytotal_r + dbthirdbar_r + wthirdbar_r + wfifteenbar_r + ksat_r,
# slab.fun = weighted.mean, na.rm = TRUE)
#
#
# # long -> wide format
# a.wtmean <- dcast(a, cokey ~ variable, fun.aggregate = mean, na.rm = TRUE)
# head(a.wtmean)
# hist(a$sandtotal_r)
# save
## aggregate to mukey
par(mar = c(0, 1, 3, 2))
plotSPC(x, color = 'ksat', print.id = FALSE, name = NA, lwd = 0)
plotSPC(y, color = 'claytotal_r', print.id = FALSE, name = NA, lwd = 0)
########################### old stuff, pending integration ##############################
#
#
#
# ## original proportions of depth class / by source
# xtabs(~ source + depth.class, data = site(x))
#
# histogram(~ depth | source, data = site(x), par.settings = tactile.theme())
#
#
# ## classify: shallow (<50cm) | everything else
# x$depth.class <- factor(x$depth.class, ordered = TRUE)
# x$simple.depth.class <- ifelse(x$depth.class <= 'shallow', 'shallow', 'deep')
#
# # mostly > 50cm
# knitr::kable(
# prop.table(xtabs(~ source + depth.class, data = site(x)), margin = 1),
# digits = 2
# )
#
# prop.table(xtabs(~ source + simple.depth.class, data = site(x)), margin = 1)
#
# ## develop dominant condition: simplified soil depth class
# s <- site(x)
# z <- split(s, s$mukey)
# z <- lapply(z, dominantCondition, v = 'depth.to.restriction')
#
# # develop LUT by mukey/cokey
# depth.lut <- do.call('rbind', z)
#
#
# ## most-frequent soil texture class (<2mm) by dominant soil depth condition
# # SPC
# x.sub <- subset(x, cokey %in% unique(depth.lut$cokey))
#
# # check: ok
# par(mar = c(0, 0, 3, 1))
# plotSPC(x.sub[1:30, ], color = 'texture')
#
# plotSPC(x.sub, color = 'texture', name = '', print.id = FALSE, width = 0.35)
#
# ragg::agg_png(filename = 'figures/coweeta-RSS-SSURGO-components-texture.png', width = 1200, height = 500)
#
# par(mar = c(0, 0, 3, 0))
# groupedProfilePlot(x.sub, groups = 'source', color = 'texture', name = '', print.id = FALSE, width = 0.35, depth.axis = list(style = 'compact', line = -6, cex = 0.8), col.label = 'Texture Class (<2mm fraction)', col.legend.cex = 1.5)
#
# dev.off()
#
#
# par(mar = c(0, 0, 3, 0))
# groupedProfilePlot(x.sub, groups = 'source', color = 'texture', name = '', label = 'compname', width = 0.35, depth.axis = list(style = 'compact', line = -6, cex = 0.8), col.label = 'Texture Class (<2mm fraction)', col.legend.cex = 1.5)
#
#
# ##
#
# x$pi <- profileInformationIndex(x, vars = c('awc_r'), method = 'joint', baseline = FALSE, compression = 'gzip')
# tapply(x$pi, x$source, median)
#
# bwplot(source ~ pi, data = site(x))
#
#
# x.u <- unique(x, vars = c('hzdept_r', 'hzdepb_r', 'awc_r', 'compname', 'hzname'))
# table(x.u$source)
#
# par(mar = c(0, 0, 3, 0))
# groupedProfilePlot(x.u, groups = 'source', color = 'awc_r', name = '', label = 'compname', width = 0.35, depth.axis = list(style = 'compact', line = -4, cex = 0.8), col.label = 'AWC', col.legend.cex = 1)
#
#
#
#
# ## TODO: is this reasonable?
# ## derive most frequent soil texture
#
# ## is this reasonable?
# # --> consider 0-50cm
# ## depth-weighted mean SSC (to depth) -> soil texture
#
# # wt. mean sand and clay to depth
# a <- slab(x.sub, cokey ~ sandtotal_r + claytotal_r, slab.structure = c(0, 200), slab.fun = mean, na.rm = TRUE)
#
# w <- dcast(a, cokey ~ variable, value.var = 'value')
# w$texture <- ssc_to_texcl(sand = w$sandtotal_r, clay = w$claytotal_r, simplify = TRUE)
#
# ## check degree of aggregation
# g <- merge(horizons(x.sub)[, c('cokey', 'texture')], w[, c('cokey', 'texture')], by = 'cokey', all.x = TRUE, sort = FALSE)
#
# names(g) <- c('cokey', 'original.texture', 'agg.texture')
#
# g$agg.texture <- factor(g$agg.texture, levels = levels(g$original.texture))
#
#
# # cross-tabulation
# # note that range of soil texture classes is reduced
# g.tab <- table(original = g$original.texture, aggregated = g$agg.texture)
# round(prop.table(g.tab, margin = 1) * 100)
#
#
#
# ## TODO: report on the loss of detail, esp. abrupt textural changes
# # hmm.. a lot of simplification
# plotSPC(x.sub[1:5, ], color = 'texture')
# w[1:5, ]
#
#
# ## final LUT
# final.lut <- merge(depth.lut, w, by = 'cokey', all.x = TRUE, sort = FALSE)
#
# ## create "soil type" codes: interaction between simple depth class * aggregate soil texture class
# final.lut$soil.type <- interaction(final.lut$simple.depth.class, final.lut$texture)
#
# # check
# table(final.lut$source, final.lut$soil.type)
#
#
# # save
# saveRDS(final.lut, file = 'data/soil-depth-texture-classe-lut.rds')
#