In ncss-tech/soilReports: R Markdown Reports and Convenience Functions for Soil Survey
Inputs {.sidebar data-width=300}
INPUT
# LOAD PACKAGES (used in config.R, shiny.Rmd and report.Rmd)
source("packages.R")
# ABSTRACT APPLICATION LOGIC
source('util.R')
# REPORT SETTINGS / USER DATA
source('config.R')
knitr::opts_chunk$set(
echo = FALSE,
message = FALSE,
warning = FALSE,
fig.align = 'center',
fig.retina = 2,
dev = 'png',
antialias = 'cleartype'
)
if (!exists("loaded")) {
loaded <<- FALSE
}
res <- loadReportData()
# global variables pedons and pedons_sf shared between chunks
pedons <<- res$pedons
pedons_sf <<- res$pedons_sf
inputPanel({
textInput("s.mu",
label = sprintf("Pattern [%s]:", musym.col),
value = ".*")
})
inputPanel({
textInput("report_name",
label = "Report name:",
value = paste0("ReportName_", Sys.Date()))
})
inputPanel({
textInput("pedon_pattern",
label = "Pattern [taxonname]:",
value = ".*")
})
inputPanel({
textInput("phase_pattern",
label = "Pattern [localphase]:",
value = ".*")
})
inputPanel({
selectInput(
"taxon_kind",
label = "Select [taxonkind]: ",
choices = c(".*", "family", "series",
"taxadjunct",
"taxon above family")
)
})
inputPanel({
textInput("upid_pattern",
label = "Pattern [upedonid]:",
value = ".*")
})
# renderUI( {
# inputPanel( {
# textInput("pedon_list",
# label="Comma-delimited list of pedons (in lieu of above):",
# value="")
# })
# })
#
if (loaded & !is.null(isolate(input))) {
renderUI(inputPanel({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
selectInput(
"modal_pedon",
label = "Select modal pedon (peiid:upedonid): ",
choices = paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")
)
# TODO: Is it possible to copedon rv
}))
}
inputPanel(
selectInput(
"thematic_field",
label = "Select horizon data to plot: ",
choices = c(
"clay",
"sand",
"phfield",
"total_frags_pct",
"moist_soil_color",
"dry_soil_color"
),
selected = "clay"
)
)
actionButton("refresh_tabular", "Refresh Tabular")
actionButton("export_report", "Export Report")
observeEvent(input$refresh_tabular, {
res <- loadReportData()
# global variables pedons and pedons_sf shared between chunks
pedons <<- res$pedons
pedons_sf <<- res$pedons_sf
})
observeEvent(
input$export_report,
{
# create output folder if needed
if (!dir.exists("output"))
dir.create("output")
# build report environment with user-selected filter settings
my.env <- new.env()
sys.source('config.R', my.env)
sys.source('util.R', my.env)
res <- loadReportData()
GHL(res$pedons) <- "genhz"
my.env$input <- isolate(input)
my.env$inputreportname <- input$reportname
my.env$peds <- getPedonsByPattern(
input = input,
s.pedons = res$pedons,
musym = input$s.mu,
compname = input$pedon_pattern,
upid = input$upid_pattern,
pedon_list = input$pedon_list,
taxon_kind = input$taxon_kind,
phasename = input$phase_pattern
)
my.env$peds$genhz <- factor(my.env$peds$genhz,
levels = aqp::guessGenHzLevels(res$pedons)$levels)
my.env$s <- summarize.component(my.env$peds)
# render in constructed environment
rmarkdown::render(
input = 'report.Rmd',
envir = my.env,
output_file = paste0("output/report_", input$report_name, ".html")
)
})
Column {.tabset}
Grouped profile plot
if (loaded)
renderPlot({
if (!is.null(isolate(input)) & length(pedons)) {
#print(isolate(input))
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
peds$taxonname <- factor(peds$taxonname)
# fix for single-group sets
gno <- c(-6, -10)
if (length(levels(peds$taxonname)) == 1)
gno <- -8
aqp::groupedProfilePlot(
peds,
groups = 'taxonname',
label = 'pedon_id',
print.id = TRUE,
id.style = 'side',
cex.id = 1.2,
cex.names = 1,
depth.axis = list(cex = 1.25, line = -3.0),
y.offset = 7,
group.name.cex = 1,
group.name.offset = gno,
color = input$thematic_field,
width = 0.1,
shrink = T,
shrink.cutoff = 3
)
options = list(width = "100%", height = 700)
}
}
})
Map view
if (loaded)
renderLeaflet({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
pedon_locations <- as(peds, 'sf')
if (length(peds) &
inherits(pedon_locations, 'sf') &
nrow(pedon_locations) > 0) {
# access leaflet map slot directly for renderLeaflet()
# TODO: subset columns
slot(mapview::mapview(pedon_locations), 'map')
## alternative: terra leaflet plot
# terra::plet(terra::vect(pedon_locations))
}
}
)
Slab-wise Profile plot
Blue line shows the median slab value for the selected set of pedons, with the 5th to 95th percentile envelope shown in gray. Thick red line shows the values from selected modal pedon. Slabs with less than 1% of pedon data contributing have been omitted for clarity.
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & length(input$thematic_field)) {
if (!input$thematic_field %in% c("moist_soil_color", "dry_soil_color")) {
s <- aqp::slab(peds, fm = as.formula(sprintf(" ~ %s", input$thematic_field)))
# max depth is <1% contributing fraction
max.idx <- which(s$contributing_fraction <= 0.01)
if (!length(max.idx))
max.idx <- nrow(s)
s.sub <- s[1:max.idx[1], ]
s.sub <- s.sub[complete.cases(s.sub), ]
a <- xyplot(
top ~ p.q50,
data = s.sub,
ylab = 'Depth',
xlab = paste0(
input$thematic_field,
'\nmedian bounded by 5th and 95th percentiles'
),
lower = s$p.q5,
upper = s$p.q95,
ylim = c(max(s.sub$bottom, na.rm = TRUE), -5),
panel = aqp::panel.depth_function,
prepanel = aqp::prepanel.depth_function,
cf = s$contributing_fraction,
layout = c(1, 1),
scales = list(x = list(alternating = 1))
)
b <- aqp::slab(peds[1, ], fm = as.formula(paste0(" ~ ", input$thematic_field)))
if (length(input$modal_pedon) &
!is.na(input$modal_pedon)) {
modalped <-
horizons(peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep =
":")), ])
#TODO: select modal pedon from RV copedon
modalped$middepth <-
modalped$hzdept + (modalped$hzdepb - modalped$hzdept) / 2
foo <- 1:(length(modalped$middepth) * 3)
modalpedplot <- data.frame(foo)
modalpedplot$y <- 1:length(foo)
modalpedplot$y[which((foo %% 3) == 1)] <- modalped$hzdept
modalpedplot$y[which((foo %% 3) == 2)] <- modalped$middepth
modalpedplot$y[which((foo %% 3) == 0)] <- modalped$hzdepb
modalpedplot$x <- rep(modalped[[input$thematic_field]], each = 3)
b <- xyplot(
y ~ x,
data = modalpedplot,
type = "l",
col = "RED",
lwd = 3,
ylim = c(250, -5),
layout = c(1, 1),
scales = list(x = list(alternating = 1)),
par.settings = list(superpose.line = list(lwd = 3))
)
(a + as.layer(b))
} else {
a
}
} else {
print("Color quantiles by depth coming soon")
}
}
})
Generalized GPP
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
peds$genhz <-
factor(peds$genhz, levels = guessGenHzLevels(peds)$levels)
if (length(peds)) {
# this plot function gets mad if hzname is a factor...
# but taxonname must be a factor
peds$genhzraw <- as.character(peds$genhz)
peds$taxonname <- factor(peds$taxonname)
# fix for single-group sets
gno <- c(-6, -10)
if (length(levels(peds$taxonname)) == 1)
gno <- -8
groupedProfilePlot(
peds,
name = 'genhzraw',
groups = 'taxonname',
label = 'pedon_id',
print.id = TRUE,
id.style = 'side',
cex.id = 1.2,
cex.names = 1,
depth.axis = list(cex = 1.25, line = -3.0),
y.offset = 7,
group.name.cex = 1,
group.name.offset = gno,
color = input$thematic_field,
width = 0.1,
shrink = T,
shrink.cutoff = 3
)
options = list(width = "100%", height = 700)
}
})
Generalized Hz Probability
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
peds$genhz <- factor(peds$genhz,
levels = guessGenHzLevels(peds)$levels)
if (length(peds)) {
s <- suppressWarnings(summarize.component(peds))
return(s$ml.hz.plot)
}
})
Depth Class
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
depthz <- profileApply(peds, estimateSoilDepth, p = "Cr|Cd|R|qm")
return({
plot(density(depthz, na.rm = TRUE),
main = "Density plot of depth to Cr, Cd, R, or *qm horizon",
xlab = "Depth, centimeters")
abline(v = c(25, 50, 100, 150))
})
}
})
Depth Table
if (loaded)
renderDataTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
dc <- aqp::getSoilDepthClass(peds, p = "Cr|Cd|R|qm")$depth.class
dc <- factor(
as.character(dc),
levels = c("very.shallow", "shallow",
"mod.deep", "deep", "very.deep"),
labels = c(
"very shallow",
"shallow",
"moderately deep",
"deep",
"very deep"
)
)
dct <- as.data.frame(base::table(dc))
names(dct) <- c("Depth Class", "# of Profiles")
DT::datatable(dct, options = list(bPaginate = FALSE))
}
}, striped = TRUE, rownames = FALSE)
Geomorphology
Hillslope position (2D)
if (loaded)
renderTable({
if (!length(input) | !length(pedons))
return(data.frame())
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
return(categorical.prop.table(peds$hillslopeprof))
}
}, striped = T)
if (loaded)
renderUI({
sourcemu <- input$s.mu
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$hillslopeprof))
}
})
Geomorphic position - Hills (3D)
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & any(!is.na(peds$geomposhill))) {
categorical.prop.table(peds$geomposhill)
} else {
print("No Hill 3D Geomorph")
}
}, striped = TRUE)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$geomposhill))
}
})
Geomorphic position - Mountains (3D)
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & any(!is.na(peds$geomposmntn))) {
categorical.prop.table(peds$geomposmntn)
} else {
print("No Mountain 3D Geomorph")
}
}, striped = TRUE)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$geomposmntn))
}
})
Geomorphic position - Flats (3D)
if (loaded)
renderTable( {
peds <- getPedonsByPattern(input, pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern)
if(length(peds) & any(!is.na(peds$geomposflats))) {
categorical.prop.table(peds$geomposflats)
} else {
print("No Flats 3D Geomorph")
}
}, striped=TRUE)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$geomposmntn))
}
})
Geomorphons
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & ("gis_geomorphons" %in% siteNames(peds))) {
return(categorical.prop.table(peds$gis_geomorphons))
} else {
print("Could not find attribute `gis_geomorphons` in `pedon` object.")
}
}, striped = TRUE)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ]
if ("gis_geomorphons" %in% siteNames(modal)) {
print(paste0("Modal pedon value: ", modal$gis_geomorphons))
} else {
print("Could not find attribute `gis_geomorphons` in selected modal pedon")
}
}
})
Drainage class
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & any(!is.na(peds$drainagecl))) {
return(categorical.prop.table(peds$drainagecl))
}
}, striped = TRUE)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$drainagecl))
}
})
Surface Shape (DOWN/ACROSS)
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
# make combined curvature classes
down <- factor(
as.character(peds$shapedown),
labels = c("V", "L", "C"),
levels = c("convex", "linear", "concave")
)
acro <- factor(
as.character(peds$shapeacross),
labels = c("V", "L", "C"),
levels = c("convex", "linear", "concave")
)
shape <- factor(paste(as.character(down),
as.character(acro),
sep = "/"))
shape[grepl(shape, pattern = "NA")] <- NA
shape <- factor(shape)
return(categorical.prop.table(shape))
}
}, striped = TRUE
)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ",
modal$shapedown,
modal$shapeacross))
}
})
Aspect
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
# cannot make aspect plot with 3 or less profiles
if (length(peds) & length(peds) > 2)
aspect.plot(
peds$aspect_field,
q = p.low.rv.high,
plot.title = input$pedon_pattern,
pch = 21,
bg = 'RoyalBlue',
col = 'black',
cex = 0.75,
arrow.col = c('darkgrey', 'blue', 'darkgrey')
)
else
return(-1)
}
)
if (loaded)
renderUI({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$aspect_field))
}
})
Ecology
Ecological site
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
df <- categorical.prop.table(peds$ecositeid)
df
}, striped = TRUE)
renderUI({
sourcemu <-
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
print(paste0("Modal pedon value: ", modal$ecositeid))
}
})
Plant list
TODO: Print vegplot data
Horizon
Field-described versus Generalized Horizonation
if (loaded)
renderDataTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
m <- as.matrix(table(peds$hzname, peds$genhz))
colz <- colnames(m)
rowz <- rownames(m)
x <- length(colz)
y <- length(rowz)
buf <- data.frame(field.hz = rowz)
for (i in 1:x) {
buf <- cbind(buf, data.frame(m[, i]))
}
colnames(buf) <- c("Field HZ", colz)
rownames(buf) <- NULL
DT::datatable(buf, options = list(pageLength = 10))
}
}
)
Horizon Relation
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels)
if (length(peds)) {
# convert contingency table -> adj. matrix
m <- genhzTableToAdjMat(table(peds$genhz, peds$hzname))
if (nrow(m))
plotSoilRelationGraph(
m,
graph.mode = 'directed',
edge.arrow.size = 0.5,
vertex.label.family = 'sans'
)
}
})
Modal
#### Modal pedon (field horizonation : generalized horizonation)
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) &
length(input$modal_pedon) & !is.na(input$modal_pedon)) {
modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid,
site(peds)$pedon_id,
sep = ":")), ]
modal$hzagg <- paste0(modal$hzname, ":", modal$genhz)
if (length(modal))
aqp::groupedProfilePlot(
modal,
name = 'hzagg',
groups = "taxonname",
label = 'pedon_id',
print.id = TRUE,
id.style = 'side',
cex.id = 1.2,
cex.names = 1,
depth.axis = list(cex = 1.25, line = -3.0),
y.offset = 7,
group.name.cex = 1,
group.name.offset = -6,
color = input$thematic_field,
width = 0.1,
shrink = T,
shrink.cutoff = 3
)
options = list(width = "100%", height = 700)
}
})
Texture
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
s <- suppressWarnings(summarize.component(peds))
s$tt
}
})
Texture Triangle
if(loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
x <- na.omit(data.frame(
genhz = peds$genhz,
SAND = peds$sand,
SILT = peds$silt,
CLAY = peds$clay
))
if (nrow(x)) {
x <- x[rowSums(x[, 2:4]) == 100, ]
aqp::textureTriangleSummary(x[, 2:4],
pch = ".",
range.col = 'darkgreen')
# x$genhz <- factor(x$genhz)
# # try to set up table structure
# res <- lapply(split(x, x$genhz), function(hz) {
# if(nrow(hz) >= 3) {
# aqp::textureTriangleSummary(hz[,2:4],
# pch=".",
# range.col='darkgreen',
# main=sprintf("Textures (%s)",
# unique(hz$genhz)))
# }
# })
# do.call('rbind', res)
}
}
})
Color
if(loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
peds$genhz <-
factor(peds$genhz, levels = aqp::guessGenHzLevels(peds)$levels)
if (length(peds)) {
aggregateColorPlot(
aggregateColor(peds, groups = 'genhz',
col = 'soil_color'),
label.font = 2,
label.cex = 0.95,
print.n.hz = TRUE
)
}
}
)
Morphology
Numeric attributes summarized by: min, 5th-50th-95th percentiles, max and aggregated by generalized horizon label (NASIS phorizon "Component Layer ID"").
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels)
if (length(peds)) {
s <- suppressWarnings(summarize.component(peds))
return(s$rt)
}
})
Surface Fragments
if (loaded)
renderTable({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
s <- suppressWarnings(summarize.component(peds))
return(s$sf)
}
})
Diagnostics
if (loaded)
renderTable({
peds <- getPedonsByPattern(input, pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern)
if(length(peds)) {
s <- summarize.component(peds)
s$dt
}
})
Diagnostics plot
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds) & nrow(diagnostic_hz(peds))) {
#return(diagnostic_hz(peds))
v.possible <- c(
"anthropic epipedon",
"abrupt textural change",
"andic soil properties",
"cambic horizon",
"calcic horizon",
"durinodes",
"petrocalcic horizon",
"fragipan",
"gypsic horizon",
"gilgai",
"glossic horizon",
"aquic conditions",
"histic epipedon",
"sombric horizon",
"petrogypsic horizon",
"placic horizon",
"kandic horizon",
"lithic contact",
"secondary carbonates",
"mollic epipedon",
"melanic epipedon",
"natric horizon",
"ochric epipedon",
"plaggen epipedon",
"petroferric contact",
"permafrost",
"plinthite",
"albic horizon",
"agric horizon",
"spodic horizon",
"slickensides",
"argillic horizon",
"umbric epipedon",
"sulfuric horizon",
"paralithic contact",
"oxic horizon",
"salic horizon",
"duripan",
"sulfidic materials",
"interfingering of albic materials",
"fibric soil materials",
"hemic soil materials",
"sapric soil materials",
"humilluvic material",
"limnic materials",
"coprogenous earth",
"diatomaceous earth",
"marl",
"albic materials",
"mottles with chroma 2 or less",
"lamellae",
"ortstein",
"fragic soil properties",
"densic contact",
"densic materials",
"paralithic materials",
"anhydrous conditions",
"cryoturbation",
"gelic materials",
"glacic layer",
"folistic epipedon",
"redox concentrations",
"redox depletions with chroma 2 or less",
"reduced matrix",
"endosaturation",
"episaturation",
"anthric saturation",
"lithologic discontinuity",
"strongly contrasting particle size class",
"gypsum accumulations",
"salt accumulations",
"volcanic glass",
"n value > 0.7",
"spodic materials",
"artifacts",
"fibers",
"free carbonates",
"resistant minerals",
"weatherable minerals",
"anhydritic horizon",
"human-altered material",
"human-transported material",
"manufactured layer",
"manufactured layer contact"
)
v.use <- gsub(v.possible, pattern = "\\s{1}", replacement = ".")
v <- v.use[v.use %in% siteNames(peds)]
h <- site(peds)
lapply(as.list(v), function(vv) {
h[is.na(h[, vv]), vv] <- FALSE
})
sharpshootR::diagnosticPropertyPlot(peds, v = v, k = 2)
} else {
print("No pedons matching criteria or diagnostic features populated.")
}
})
Mapunit Summary
if (loaded)
renderPlot({
peds <- getPedonsByPattern(
input,
pedons,
input$s.mu,
input$pedon_pattern,
input$upid_pattern,
input$pedon_list,
input$taxon_kind,
input$phase_pattern
)
if (length(peds)) {
s <- suppressWarnings(summarize.component(peds))
print(s$pmg)
}
})
ncss-tech/soilReports documentation built on April 25, 2024, 1:03 a.m.
R Package Documentation
Browse R Packages
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Inputs {.sidebar data-width=300}
INPUT
# LOAD PACKAGES (used in config.R, shiny.Rmd and report.Rmd) source("packages.R") # ABSTRACT APPLICATION LOGIC source('util.R') # REPORT SETTINGS / USER DATA source('config.R')
knitr::opts_chunk$set( echo = FALSE, message = FALSE, warning = FALSE, fig.align = 'center', fig.retina = 2, dev = 'png', antialias = 'cleartype' ) if (!exists("loaded")) { loaded <<- FALSE } res <- loadReportData() # global variables pedons and pedons_sf shared between chunks pedons <<- res$pedons pedons_sf <<- res$pedons_sf
inputPanel({ textInput("s.mu", label = sprintf("Pattern [%s]:", musym.col), value = ".*") }) inputPanel({ textInput("report_name", label = "Report name:", value = paste0("ReportName_", Sys.Date())) }) inputPanel({ textInput("pedon_pattern", label = "Pattern [taxonname]:", value = ".*") }) inputPanel({ textInput("phase_pattern", label = "Pattern [localphase]:", value = ".*") }) inputPanel({ selectInput( "taxon_kind", label = "Select [taxonkind]: ", choices = c(".*", "family", "series", "taxadjunct", "taxon above family") ) }) inputPanel({ textInput("upid_pattern", label = "Pattern [upedonid]:", value = ".*") }) # renderUI( { # inputPanel( { # textInput("pedon_list", # label="Comma-delimited list of pedons (in lieu of above):", # value="") # }) # }) # if (loaded & !is.null(isolate(input))) { renderUI(inputPanel({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) selectInput( "modal_pedon", label = "Select modal pedon (peiid:upedonid): ", choices = paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":") ) # TODO: Is it possible to copedon rv })) } inputPanel( selectInput( "thematic_field", label = "Select horizon data to plot: ", choices = c( "clay", "sand", "phfield", "total_frags_pct", "moist_soil_color", "dry_soil_color" ), selected = "clay" ) ) actionButton("refresh_tabular", "Refresh Tabular") actionButton("export_report", "Export Report") observeEvent(input$refresh_tabular, { res <- loadReportData() # global variables pedons and pedons_sf shared between chunks pedons <<- res$pedons pedons_sf <<- res$pedons_sf }) observeEvent( input$export_report, { # create output folder if needed if (!dir.exists("output")) dir.create("output") # build report environment with user-selected filter settings my.env <- new.env() sys.source('config.R', my.env) sys.source('util.R', my.env) res <- loadReportData() GHL(res$pedons) <- "genhz" my.env$input <- isolate(input) my.env$inputreportname <- input$reportname my.env$peds <- getPedonsByPattern( input = input, s.pedons = res$pedons, musym = input$s.mu, compname = input$pedon_pattern, upid = input$upid_pattern, pedon_list = input$pedon_list, taxon_kind = input$taxon_kind, phasename = input$phase_pattern ) my.env$peds$genhz <- factor(my.env$peds$genhz, levels = aqp::guessGenHzLevels(res$pedons)$levels) my.env$s <- summarize.component(my.env$peds) # render in constructed environment rmarkdown::render( input = 'report.Rmd', envir = my.env, output_file = paste0("output/report_", input$report_name, ".html") ) })
Column {.tabset}
Grouped profile plot
if (loaded) renderPlot({ if (!is.null(isolate(input)) & length(pedons)) { #print(isolate(input)) peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { peds$taxonname <- factor(peds$taxonname) # fix for single-group sets gno <- c(-6, -10) if (length(levels(peds$taxonname)) == 1) gno <- -8 aqp::groupedProfilePlot( peds, groups = 'taxonname', label = 'pedon_id', print.id = TRUE, id.style = 'side', cex.id = 1.2, cex.names = 1, depth.axis = list(cex = 1.25, line = -3.0), y.offset = 7, group.name.cex = 1, group.name.offset = gno, color = input$thematic_field, width = 0.1, shrink = T, shrink.cutoff = 3 ) options = list(width = "100%", height = 700) } } })
Map view
if (loaded) renderLeaflet({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) pedon_locations <- as(peds, 'sf') if (length(peds) & inherits(pedon_locations, 'sf') & nrow(pedon_locations) > 0) { # access leaflet map slot directly for renderLeaflet() # TODO: subset columns slot(mapview::mapview(pedon_locations), 'map') ## alternative: terra leaflet plot # terra::plet(terra::vect(pedon_locations)) } } )
Slab-wise Profile plot
Blue line shows the median slab value for the selected set of pedons, with the 5th to 95th percentile envelope shown in gray. Thick red line shows the values from selected modal pedon. Slabs with less than 1% of pedon data contributing have been omitted for clarity.
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$thematic_field)) { if (!input$thematic_field %in% c("moist_soil_color", "dry_soil_color")) { s <- aqp::slab(peds, fm = as.formula(sprintf(" ~ %s", input$thematic_field))) # max depth is <1% contributing fraction max.idx <- which(s$contributing_fraction <= 0.01) if (!length(max.idx)) max.idx <- nrow(s) s.sub <- s[1:max.idx[1], ] s.sub <- s.sub[complete.cases(s.sub), ] a <- xyplot( top ~ p.q50, data = s.sub, ylab = 'Depth', xlab = paste0( input$thematic_field, '\nmedian bounded by 5th and 95th percentiles' ), lower = s$p.q5, upper = s$p.q95, ylim = c(max(s.sub$bottom, na.rm = TRUE), -5), panel = aqp::panel.depth_function, prepanel = aqp::prepanel.depth_function, cf = s$contributing_fraction, layout = c(1, 1), scales = list(x = list(alternating = 1)) ) b <- aqp::slab(peds[1, ], fm = as.formula(paste0(" ~ ", input$thematic_field))) if (length(input$modal_pedon) & !is.na(input$modal_pedon)) { modalped <- horizons(peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ]) #TODO: select modal pedon from RV copedon modalped$middepth <- modalped$hzdept + (modalped$hzdepb - modalped$hzdept) / 2 foo <- 1:(length(modalped$middepth) * 3) modalpedplot <- data.frame(foo) modalpedplot$y <- 1:length(foo) modalpedplot$y[which((foo %% 3) == 1)] <- modalped$hzdept modalpedplot$y[which((foo %% 3) == 2)] <- modalped$middepth modalpedplot$y[which((foo %% 3) == 0)] <- modalped$hzdepb modalpedplot$x <- rep(modalped[[input$thematic_field]], each = 3) b <- xyplot( y ~ x, data = modalpedplot, type = "l", col = "RED", lwd = 3, ylim = c(250, -5), layout = c(1, 1), scales = list(x = list(alternating = 1)), par.settings = list(superpose.line = list(lwd = 3)) ) (a + as.layer(b)) } else { a } } else { print("Color quantiles by depth coming soon") } } })
Generalized GPP
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels) if (length(peds)) { # this plot function gets mad if hzname is a factor... # but taxonname must be a factor peds$genhzraw <- as.character(peds$genhz) peds$taxonname <- factor(peds$taxonname) # fix for single-group sets gno <- c(-6, -10) if (length(levels(peds$taxonname)) == 1) gno <- -8 groupedProfilePlot( peds, name = 'genhzraw', groups = 'taxonname', label = 'pedon_id', print.id = TRUE, id.style = 'side', cex.id = 1.2, cex.names = 1, depth.axis = list(cex = 1.25, line = -3.0), y.offset = 7, group.name.cex = 1, group.name.offset = gno, color = input$thematic_field, width = 0.1, shrink = T, shrink.cutoff = 3 ) options = list(width = "100%", height = 700) } })
Generalized Hz Probability
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels) if (length(peds)) { s <- suppressWarnings(summarize.component(peds)) return(s$ml.hz.plot) } })
Depth Class
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { depthz <- profileApply(peds, estimateSoilDepth, p = "Cr|Cd|R|qm") return({ plot(density(depthz, na.rm = TRUE), main = "Density plot of depth to Cr, Cd, R, or *qm horizon", xlab = "Depth, centimeters") abline(v = c(25, 50, 100, 150)) }) } })
Depth Table
if (loaded) renderDataTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { dc <- aqp::getSoilDepthClass(peds, p = "Cr|Cd|R|qm")$depth.class dc <- factor( as.character(dc), levels = c("very.shallow", "shallow", "mod.deep", "deep", "very.deep"), labels = c( "very shallow", "shallow", "moderately deep", "deep", "very deep" ) ) dct <- as.data.frame(base::table(dc)) names(dct) <- c("Depth Class", "# of Profiles") DT::datatable(dct, options = list(bPaginate = FALSE)) } }, striped = TRUE, rownames = FALSE)
Geomorphology
Hillslope position (2D)
if (loaded) renderTable({ if (!length(input) | !length(pedons)) return(data.frame()) peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { return(categorical.prop.table(peds$hillslopeprof)) } }, striped = T) if (loaded) renderUI({ sourcemu <- input$s.mu peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$hillslopeprof)) } })
Geomorphic position - Hills (3D)
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & any(!is.na(peds$geomposhill))) { categorical.prop.table(peds$geomposhill) } else { print("No Hill 3D Geomorph") } }, striped = TRUE) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$geomposhill)) } })
Geomorphic position - Mountains (3D)
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & any(!is.na(peds$geomposmntn))) { categorical.prop.table(peds$geomposmntn) } else { print("No Mountain 3D Geomorph") } }, striped = TRUE) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$geomposmntn)) } })
Geomorphic position - Flats (3D)
if (loaded) renderTable( { peds <- getPedonsByPattern(input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern) if(length(peds) & any(!is.na(peds$geomposflats))) { categorical.prop.table(peds$geomposflats) } else { print("No Flats 3D Geomorph") } }, striped=TRUE) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$geomposmntn)) } })
Geomorphons
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & ("gis_geomorphons" %in% siteNames(peds))) { return(categorical.prop.table(peds$gis_geomorphons)) } else { print("Could not find attribute `gis_geomorphons` in `pedon` object.") } }, striped = TRUE) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] if ("gis_geomorphons" %in% siteNames(modal)) { print(paste0("Modal pedon value: ", modal$gis_geomorphons)) } else { print("Could not find attribute `gis_geomorphons` in selected modal pedon") } } })
Drainage class
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & any(!is.na(peds$drainagecl))) { return(categorical.prop.table(peds$drainagecl)) } }, striped = TRUE) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$drainagecl)) } })
Surface Shape (DOWN/ACROSS)
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { # make combined curvature classes down <- factor( as.character(peds$shapedown), labels = c("V", "L", "C"), levels = c("convex", "linear", "concave") ) acro <- factor( as.character(peds$shapeacross), labels = c("V", "L", "C"), levels = c("convex", "linear", "concave") ) shape <- factor(paste(as.character(down), as.character(acro), sep = "/")) shape[grepl(shape, pattern = "NA")] <- NA shape <- factor(shape) return(categorical.prop.table(shape)) } }, striped = TRUE ) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$shapedown, modal$shapeacross)) } })
Aspect
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) # cannot make aspect plot with 3 or less profiles if (length(peds) & length(peds) > 2) aspect.plot( peds$aspect_field, q = p.low.rv.high, plot.title = input$pedon_pattern, pch = 21, bg = 'RoyalBlue', col = 'black', cex = 0.75, arrow.col = c('darkgrey', 'blue', 'darkgrey') ) else return(-1) } ) if (loaded) renderUI({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$aspect_field)) } })
Ecology
Ecological site
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) df <- categorical.prop.table(peds$ecositeid) df }, striped = TRUE) renderUI({ sourcemu <- peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] print(paste0("Modal pedon value: ", modal$ecositeid)) } })
Plant list
TODO: Print vegplot data
Horizon
Field-described versus Generalized Horizonation
if (loaded) renderDataTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { m <- as.matrix(table(peds$hzname, peds$genhz)) colz <- colnames(m) rowz <- rownames(m) x <- length(colz) y <- length(rowz) buf <- data.frame(field.hz = rowz) for (i in 1:x) { buf <- cbind(buf, data.frame(m[, i])) } colnames(buf) <- c("Field HZ", colz) rownames(buf) <- NULL DT::datatable(buf, options = list(pageLength = 10)) } } )
Horizon Relation
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels) if (length(peds)) { # convert contingency table -> adj. matrix m <- genhzTableToAdjMat(table(peds$genhz, peds$hzname)) if (nrow(m)) plotSoilRelationGraph( m, graph.mode = 'directed', edge.arrow.size = 0.5, vertex.label.family = 'sans' ) } })
Modal
#### Modal pedon (field horizonation : generalized horizonation) if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & length(input$modal_pedon) & !is.na(input$modal_pedon)) { modal <- peds[which(input$modal_pedon == paste(site(peds)$peiid, site(peds)$pedon_id, sep = ":")), ] modal$hzagg <- paste0(modal$hzname, ":", modal$genhz) if (length(modal)) aqp::groupedProfilePlot( modal, name = 'hzagg', groups = "taxonname", label = 'pedon_id', print.id = TRUE, id.style = 'side', cex.id = 1.2, cex.names = 1, depth.axis = list(cex = 1.25, line = -3.0), y.offset = 7, group.name.cex = 1, group.name.offset = -6, color = input$thematic_field, width = 0.1, shrink = T, shrink.cutoff = 3 ) options = list(width = "100%", height = 700) } })
Texture
renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { s <- suppressWarnings(summarize.component(peds)) s$tt } })
Texture Triangle
if(loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { x <- na.omit(data.frame( genhz = peds$genhz, SAND = peds$sand, SILT = peds$silt, CLAY = peds$clay )) if (nrow(x)) { x <- x[rowSums(x[, 2:4]) == 100, ] aqp::textureTriangleSummary(x[, 2:4], pch = ".", range.col = 'darkgreen') # x$genhz <- factor(x$genhz) # # try to set up table structure # res <- lapply(split(x, x$genhz), function(hz) { # if(nrow(hz) >= 3) { # aqp::textureTriangleSummary(hz[,2:4], # pch=".", # range.col='darkgreen', # main=sprintf("Textures (%s)", # unique(hz$genhz))) # } # }) # do.call('rbind', res) } } })
Color
if(loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) peds$genhz <- factor(peds$genhz, levels = aqp::guessGenHzLevels(peds)$levels) if (length(peds)) { aggregateColorPlot( aggregateColor(peds, groups = 'genhz', col = 'soil_color'), label.font = 2, label.cex = 0.95, print.n.hz = TRUE ) } } )
Morphology
Numeric attributes summarized by: min, 5th-50th-95th percentiles, max and aggregated by generalized horizon label (NASIS phorizon "Component Layer ID"").
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) peds$genhz <- factor(peds$genhz, levels = guessGenHzLevels(peds)$levels) if (length(peds)) { s <- suppressWarnings(summarize.component(peds)) return(s$rt) } })
Surface Fragments
if (loaded) renderTable({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { s <- suppressWarnings(summarize.component(peds)) return(s$sf) } })
Diagnostics
if (loaded) renderTable({ peds <- getPedonsByPattern(input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern) if(length(peds)) { s <- summarize.component(peds) s$dt } })
Diagnostics plot
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds) & nrow(diagnostic_hz(peds))) { #return(diagnostic_hz(peds)) v.possible <- c( "anthropic epipedon", "abrupt textural change", "andic soil properties", "cambic horizon", "calcic horizon", "durinodes", "petrocalcic horizon", "fragipan", "gypsic horizon", "gilgai", "glossic horizon", "aquic conditions", "histic epipedon", "sombric horizon", "petrogypsic horizon", "placic horizon", "kandic horizon", "lithic contact", "secondary carbonates", "mollic epipedon", "melanic epipedon", "natric horizon", "ochric epipedon", "plaggen epipedon", "petroferric contact", "permafrost", "plinthite", "albic horizon", "agric horizon", "spodic horizon", "slickensides", "argillic horizon", "umbric epipedon", "sulfuric horizon", "paralithic contact", "oxic horizon", "salic horizon", "duripan", "sulfidic materials", "interfingering of albic materials", "fibric soil materials", "hemic soil materials", "sapric soil materials", "humilluvic material", "limnic materials", "coprogenous earth", "diatomaceous earth", "marl", "albic materials", "mottles with chroma 2 or less", "lamellae", "ortstein", "fragic soil properties", "densic contact", "densic materials", "paralithic materials", "anhydrous conditions", "cryoturbation", "gelic materials", "glacic layer", "folistic epipedon", "redox concentrations", "redox depletions with chroma 2 or less", "reduced matrix", "endosaturation", "episaturation", "anthric saturation", "lithologic discontinuity", "strongly contrasting particle size class", "gypsum accumulations", "salt accumulations", "volcanic glass", "n value > 0.7", "spodic materials", "artifacts", "fibers", "free carbonates", "resistant minerals", "weatherable minerals", "anhydritic horizon", "human-altered material", "human-transported material", "manufactured layer", "manufactured layer contact" ) v.use <- gsub(v.possible, pattern = "\\s{1}", replacement = ".") v <- v.use[v.use %in% siteNames(peds)] h <- site(peds) lapply(as.list(v), function(vv) { h[is.na(h[, vv]), vv] <- FALSE }) sharpshootR::diagnosticPropertyPlot(peds, v = v, k = 2) } else { print("No pedons matching criteria or diagnostic features populated.") } })
Mapunit Summary
if (loaded) renderPlot({ peds <- getPedonsByPattern( input, pedons, input$s.mu, input$pedon_pattern, input$upid_pattern, input$pedon_list, input$taxon_kind, input$phase_pattern ) if (length(peds)) { s <- suppressWarnings(summarize.component(peds)) print(s$pmg) } })
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