inst/scripts/realDataFigures.R
In jayverhoef/fluvgrm: Data in Support of Fluvial Variography
#------------------------------------------------------------------------------
# libraries
#------------------------------------------------------------------------------
library('SSN')
library('fluvgrm')
library('viridis')
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
# SCRIPT
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
# load the SpatialStreamNetwork object
SSN4 <- importSSN(system.file("lsndata/LewWillCol.ssn",
package = "fluvgrm"), o.write = TRUE)
# pull out the data.frame of observed data
DF = getSSNdata.frame(SSN4)
# fit a classical regression model to the observed data
lmout = lm(STREAM_AUG ~ upDist + upDist:upDist + ELEV + ELEV:ELEV,
data = DF)
# compute residuals on the fitted model and add to data.frame
DF[,'resid'] = residuals(lmout)
# put the data.frame back into the SpatialStreamNetwork object
SSN4 = putSSNdata.frame(DF, SSN4)
#------------------------------------------------------------------------------
# plot the SpatialStreamNetwork object and color response variable
#------------------------------------------------------------------------------
plotSSN(SSN4, VariableName = 'resid', pch = 19, cex = 1.2,
addFuncColName = 'afvArea', strCol = 'grey50')
# to create the neighborhood matrix from scratch, use the following command
# Mat = SSNreachNei(SSN4)
# however, it takes a long time, so it is stored as part of the package and
# can be loaded directly
load(system.file("/lsndata/reachnei/neiMatrix-72.Rdata",
package = "fluvgrm"))
# set some of the arguments for the variogram functions
nbrksfc = 12
maxbrksfc = 2.3e+05
nbrksfu = 18
maxbrksfu = 3.5e+05
fcbrks = c(-.001, (1:nbrksfc)/nbrksfc*maxbrksfc)
fubrks = c(-.001, (1:nbrksfu)/nbrksfu*maxbrksfu)
# set the working directory to R's temp directory to save figures
setwd(tempdir())
# to see where this is on your file system
getwd()
# the figures will go away with the temp directory when R quits
#------------------------------------------------------------------------------
# create pdf figure in current working directory
#------------------------------------------------------------------------------
# compute the various variograms
FUSDout = FUSD(SSN4, 'resid', breaks = fubrks)
svgmbar = function(x) {sum(x$np*x$semivar)/sum(x$np)}
FUSDbar = svgmbar(FUSDout[[1]][[1]])
FUDJout = FUDJ(SSN4, 'resid', breaks = fubrks[1:10])
FCSDout = FCSD(SSN4, 'resid', breaks = fcbrks)
FCSD01out = FCSD01(SSN4, 'resid',
breaks = c(0, 600, 1200, 3000, 10000),
ReachNei = Mat)
pdf('FCFUresid.pdf', height = 12, width = 12)
layout(matrix(1:4, nrow = 2, byrow = TRUE))
# part A
npWtStd = 1 + (FUSDout[[1]][[1]]$np - min(FUSDout[[1]][[1]]$np))/
(max(FUSDout[[1]][[1]]$np) - min(FUSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUSDout[[1]][[1]]$brkDist,FUSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FUSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FUSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 4*npWtStd, xlab = 'Flow-Unconnected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
lines(c(min(FUSDout[[1]][[1]]$brkDist),max(FUSDout[[1]][[1]]$brkDist)),
rep(FUSDbar, times =2), lty = 2, col = 'grey60', lwd = 3)
mtext('A', cex = 4, adj = -.18, padj = -.4)
#part B
clrClasses = c('#f0f0f0','#d9d9d9',
'#bdbdbd','#969696','#737373','#525252','#252525')
clrBrks = min(FUDJout[[1]][[1]]$semivar) + (0:length(clrClasses))*
(max(FUDJout[[1]][[1]]$semivar) - min(FUDJout[[1]][[1]]$semivar))/
length(clrClasses)
clrBrks[1] = clrBrks[1] - 1e-5
clrBrks[length(clrClasses) + 1] = clrBrks[length(clrClasses) + 1] + 1e-5
npWtStd = 1 + (FUDJout[[1]][[1]]$np - min(FUDJout[[1]][[1]]$np))/
(max(FUDJout[[1]][[1]]$np) - min(FUDJout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, type = 'n',
xlim = c(0, max(FUDJout[[1]][[1]]$distLong)),
ylim = c(0, max(FUDJout[[1]][[1]]$distLong)),
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))],
xlab = 'Shorter Distance to Common Junction',
ylab = 'Longer Distance to Common Junction',
cex.lab = 2, cex.axis = 1.2
)
for(i in 1:(2*length(FUSDout[[1]][[1]][,1]))) {
iinc = i*max(FUDJout[[1]][[1]]$distLong)/length(FUSDout[[1]][[1]][,1])
lines(c(0,iinc),c(iinc,0), lty = 2, col = 'grey60')
}
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 19,
cex = 3*npWtStd,
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))])
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 1,
cex = 3*npWtStd, lwd = 2)
xyleg = min(FUDJout[[1]][[1]]$distLong) + (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/2
xylen = max(FUDJout[[1]][[1]]$distLong)
legWidth = (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/10
addBreakColorLegend(.7*xylen,0,.7*xylen+legWidth,.6*xylen, clrBrks, clrClasses,
'1.2', cex = 1.4)
mtext('B', cex = 4, adj = -.18, padj = -.4)
# part C
npWtStd = 1 + (FCSDout[[1]][[1]]$np - min(FCSDout[[1]][[1]]$np))/
(max(FCSDout[[1]][[1]]$np) - min(FCSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FCSDout[[1]][[1]]$brkDist,FCSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FCSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FCSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 2*npWtStd, xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
mtext('C', cex = 4, adj = -.18, padj = -.4)
# part D
par(mar = c(5,5,5,2))
plot(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist),
c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar), type = 'n',
xlim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1),
ylim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar))*1.1),
xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm1$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
pch = 19, cex = 2*npWtStd, col = '#bdbdbd')
text(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm1$np),
pos = 2, cex = 2.5, offset = .7)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm0$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
pch = 19, cex = 2*npWtStd)
text(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm0$np),
pos = 4, cex = 2.5, offset = .7)
legend(max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1, xjust = 1,
0, yjust = 0,
pch = c(19,19), col = c('black','#bdbdbd'),
legend = c('FCSD(0)','FCSD(1)'), lwd = c(3,3),
cex = 2, lty = c(0,0))
mtext('D', cex = 4, adj = -.18, padj = -.4)
dev.off()
#------------------------------------------------------------------------------
# create pdf figure in current working directory
#------------------------------------------------------------------------------
# compute the various variograms
FUSDout = FUSD(SSN4, 'STREAM_AUG', breaks = fubrks)
svgmbar = function(x) {sum(x$np*x$semivar)/sum(x$np)}
FUSDbar = svgmbar(FUSDout[[1]][[1]])
FUDJout = FUDJ(SSN4, 'STREAM_AUG', breaks = fubrks[1:10])
FCSDout = FCSD(SSN4, 'STREAM_AUG', breaks = fcbrks)
FCSD01out = FCSD01(SSN4, 'STREAM_AUG',
breaks = c(0, 600, 1200, 3000, 10000),
ReachNei = Mat)
pdf('FCFUtemp.pdf', height = 12, width = 12)
layout(matrix(1:4, nrow = 2, byrow = TRUE))
# part A
npWtStd = 1 + (FUSDout[[1]][[1]]$np - min(FUSDout[[1]][[1]]$np))/
(max(FUSDout[[1]][[1]]$np) - min(FUSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUSDout[[1]][[1]]$brkDist,FUSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FUSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FUSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 4*npWtStd, xlab = 'Flow-Unconnected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
lines(c(min(FUSDout[[1]][[1]]$brkDist),max(FUSDout[[1]][[1]]$brkDist)),
rep(FUSDbar, times =2), lty = 2, col = 'grey60', lwd = 3)
mtext('A', cex = 4, adj = -.18, padj = -.4)
#part B
clrClasses = c('#f0f0f0','#d9d9d9',
'#bdbdbd','#969696','#737373','#525252','#252525')
clrBrks = min(FUDJout[[1]][[1]]$semivar) + (0:length(clrClasses))*
(max(FUDJout[[1]][[1]]$semivar) - min(FUDJout[[1]][[1]]$semivar))/
length(clrClasses)
clrBrks[1] = clrBrks[1] - 1e-5
clrBrks[length(clrClasses) + 1] = clrBrks[length(clrClasses) + 1] + 1e-5
npWtStd = 1 + (FUDJout[[1]][[1]]$np - min(FUDJout[[1]][[1]]$np))/
(max(FUDJout[[1]][[1]]$np) - min(FUDJout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, type = 'n',
xlim = c(0, max(FUDJout[[1]][[1]]$distLong)),
ylim = c(0, max(FUDJout[[1]][[1]]$distLong)),
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))],
xlab = 'Shorter Distance to Common Junction',
ylab = 'Longer Distance to Common Junction',
cex.lab = 2, cex.axis = 1.2
)
for(i in 1:(2*length(FUSDout[[1]][[1]][,1]))) {
iinc = i*max(FUDJout[[1]][[1]]$distLong)/length(FUSDout[[1]][[1]][,1])
lines(c(0,iinc),c(iinc,0), lty = 2, col = 'grey60')
}
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 19,
cex = 3*npWtStd,
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))])
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 1,
cex = 3*npWtStd, lwd = 2)
xyleg = min(FUDJout[[1]][[1]]$distLong) + (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/2
xylen = max(FUDJout[[1]][[1]]$distLong)
legWidth = (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/10
addBreakColorLegend(.7*xylen,0,.7*xylen+legWidth,.6*xylen, clrBrks, clrClasses,
'1.2', cex = 1.4)
mtext('B', cex = 4, adj = -.18, padj = -.4)
# part C
npWtStd = 1 + (FCSDout[[1]][[1]]$np - min(FCSDout[[1]][[1]]$np))/
(max(FCSDout[[1]][[1]]$np) - min(FCSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FCSDout[[1]][[1]]$brkDist,FCSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FCSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FCSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 2*npWtStd, xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
mtext('C', cex = 4, adj = -.18, padj = -.4)
# part D
par(mar = c(5,5,5,2))
plot(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist),
c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar), type = 'n',
xlim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1),
ylim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar))*1.1),
xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm1$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
pch = 19, cex = 2*npWtStd, col = '#bdbdbd')
text(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm1$np),
pos = 2, cex = 2.5, offset = .7)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm0$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
pch = 19, cex = 2*npWtStd)
text(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm0$np),
pos = 4, cex = 2.5, offset = .7)
legend(max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1, xjust = 1,
0, yjust = 0,
pch = c(19,19), col = c('black','#bdbdbd'),
legend = c('FCSD(0)','FCSD(1)'), lwd = c(3,3),
cex = 2, lty = c(0,0))
mtext('D', cex = 4, adj = -.18, padj = -.4)
dev.off()
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#------------------------------------------------------------------------------
# libraries
#------------------------------------------------------------------------------
library('SSN')
library('fluvgrm')
library('viridis')
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
# SCRIPT
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
#------------------------------------------------------------------------------
# load the SpatialStreamNetwork object
SSN4 <- importSSN(system.file("lsndata/LewWillCol.ssn",
package = "fluvgrm"), o.write = TRUE)
# pull out the data.frame of observed data
DF = getSSNdata.frame(SSN4)
# fit a classical regression model to the observed data
lmout = lm(STREAM_AUG ~ upDist + upDist:upDist + ELEV + ELEV:ELEV,
data = DF)
# compute residuals on the fitted model and add to data.frame
DF[,'resid'] = residuals(lmout)
# put the data.frame back into the SpatialStreamNetwork object
SSN4 = putSSNdata.frame(DF, SSN4)
#------------------------------------------------------------------------------
# plot the SpatialStreamNetwork object and color response variable
#------------------------------------------------------------------------------
plotSSN(SSN4, VariableName = 'resid', pch = 19, cex = 1.2,
addFuncColName = 'afvArea', strCol = 'grey50')
# to create the neighborhood matrix from scratch, use the following command
# Mat = SSNreachNei(SSN4)
# however, it takes a long time, so it is stored as part of the package and
# can be loaded directly
load(system.file("/lsndata/reachnei/neiMatrix-72.Rdata",
package = "fluvgrm"))
# set some of the arguments for the variogram functions
nbrksfc = 12
maxbrksfc = 2.3e+05
nbrksfu = 18
maxbrksfu = 3.5e+05
fcbrks = c(-.001, (1:nbrksfc)/nbrksfc*maxbrksfc)
fubrks = c(-.001, (1:nbrksfu)/nbrksfu*maxbrksfu)
# set the working directory to R's temp directory to save figures
setwd(tempdir())
# to see where this is on your file system
getwd()
# the figures will go away with the temp directory when R quits
#------------------------------------------------------------------------------
# create pdf figure in current working directory
#------------------------------------------------------------------------------
# compute the various variograms
FUSDout = FUSD(SSN4, 'resid', breaks = fubrks)
svgmbar = function(x) {sum(x$np*x$semivar)/sum(x$np)}
FUSDbar = svgmbar(FUSDout[[1]][[1]])
FUDJout = FUDJ(SSN4, 'resid', breaks = fubrks[1:10])
FCSDout = FCSD(SSN4, 'resid', breaks = fcbrks)
FCSD01out = FCSD01(SSN4, 'resid',
breaks = c(0, 600, 1200, 3000, 10000),
ReachNei = Mat)
pdf('FCFUresid.pdf', height = 12, width = 12)
layout(matrix(1:4, nrow = 2, byrow = TRUE))
# part A
npWtStd = 1 + (FUSDout[[1]][[1]]$np - min(FUSDout[[1]][[1]]$np))/
(max(FUSDout[[1]][[1]]$np) - min(FUSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUSDout[[1]][[1]]$brkDist,FUSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FUSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FUSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 4*npWtStd, xlab = 'Flow-Unconnected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
lines(c(min(FUSDout[[1]][[1]]$brkDist),max(FUSDout[[1]][[1]]$brkDist)),
rep(FUSDbar, times =2), lty = 2, col = 'grey60', lwd = 3)
mtext('A', cex = 4, adj = -.18, padj = -.4)
#part B
clrClasses = c('#f0f0f0','#d9d9d9',
'#bdbdbd','#969696','#737373','#525252','#252525')
clrBrks = min(FUDJout[[1]][[1]]$semivar) + (0:length(clrClasses))*
(max(FUDJout[[1]][[1]]$semivar) - min(FUDJout[[1]][[1]]$semivar))/
length(clrClasses)
clrBrks[1] = clrBrks[1] - 1e-5
clrBrks[length(clrClasses) + 1] = clrBrks[length(clrClasses) + 1] + 1e-5
npWtStd = 1 + (FUDJout[[1]][[1]]$np - min(FUDJout[[1]][[1]]$np))/
(max(FUDJout[[1]][[1]]$np) - min(FUDJout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, type = 'n',
xlim = c(0, max(FUDJout[[1]][[1]]$distLong)),
ylim = c(0, max(FUDJout[[1]][[1]]$distLong)),
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))],
xlab = 'Shorter Distance to Common Junction',
ylab = 'Longer Distance to Common Junction',
cex.lab = 2, cex.axis = 1.2
)
for(i in 1:(2*length(FUSDout[[1]][[1]][,1]))) {
iinc = i*max(FUDJout[[1]][[1]]$distLong)/length(FUSDout[[1]][[1]][,1])
lines(c(0,iinc),c(iinc,0), lty = 2, col = 'grey60')
}
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 19,
cex = 3*npWtStd,
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))])
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 1,
cex = 3*npWtStd, lwd = 2)
xyleg = min(FUDJout[[1]][[1]]$distLong) + (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/2
xylen = max(FUDJout[[1]][[1]]$distLong)
legWidth = (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/10
addBreakColorLegend(.7*xylen,0,.7*xylen+legWidth,.6*xylen, clrBrks, clrClasses,
'1.2', cex = 1.4)
mtext('B', cex = 4, adj = -.18, padj = -.4)
# part C
npWtStd = 1 + (FCSDout[[1]][[1]]$np - min(FCSDout[[1]][[1]]$np))/
(max(FCSDout[[1]][[1]]$np) - min(FCSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FCSDout[[1]][[1]]$brkDist,FCSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FCSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FCSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 2*npWtStd, xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
mtext('C', cex = 4, adj = -.18, padj = -.4)
# part D
par(mar = c(5,5,5,2))
plot(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist),
c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar), type = 'n',
xlim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1),
ylim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar))*1.1),
xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm1$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
pch = 19, cex = 2*npWtStd, col = '#bdbdbd')
text(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm1$np),
pos = 2, cex = 2.5, offset = .7)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm0$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
pch = 19, cex = 2*npWtStd)
text(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm0$np),
pos = 4, cex = 2.5, offset = .7)
legend(max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1, xjust = 1,
0, yjust = 0,
pch = c(19,19), col = c('black','#bdbdbd'),
legend = c('FCSD(0)','FCSD(1)'), lwd = c(3,3),
cex = 2, lty = c(0,0))
mtext('D', cex = 4, adj = -.18, padj = -.4)
dev.off()
#------------------------------------------------------------------------------
# create pdf figure in current working directory
#------------------------------------------------------------------------------
# compute the various variograms
FUSDout = FUSD(SSN4, 'STREAM_AUG', breaks = fubrks)
svgmbar = function(x) {sum(x$np*x$semivar)/sum(x$np)}
FUSDbar = svgmbar(FUSDout[[1]][[1]])
FUDJout = FUDJ(SSN4, 'STREAM_AUG', breaks = fubrks[1:10])
FCSDout = FCSD(SSN4, 'STREAM_AUG', breaks = fcbrks)
FCSD01out = FCSD01(SSN4, 'STREAM_AUG',
breaks = c(0, 600, 1200, 3000, 10000),
ReachNei = Mat)
pdf('FCFUtemp.pdf', height = 12, width = 12)
layout(matrix(1:4, nrow = 2, byrow = TRUE))
# part A
npWtStd = 1 + (FUSDout[[1]][[1]]$np - min(FUSDout[[1]][[1]]$np))/
(max(FUSDout[[1]][[1]]$np) - min(FUSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUSDout[[1]][[1]]$brkDist,FUSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FUSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FUSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 4*npWtStd, xlab = 'Flow-Unconnected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
lines(c(min(FUSDout[[1]][[1]]$brkDist),max(FUSDout[[1]][[1]]$brkDist)),
rep(FUSDbar, times =2), lty = 2, col = 'grey60', lwd = 3)
mtext('A', cex = 4, adj = -.18, padj = -.4)
#part B
clrClasses = c('#f0f0f0','#d9d9d9',
'#bdbdbd','#969696','#737373','#525252','#252525')
clrBrks = min(FUDJout[[1]][[1]]$semivar) + (0:length(clrClasses))*
(max(FUDJout[[1]][[1]]$semivar) - min(FUDJout[[1]][[1]]$semivar))/
length(clrClasses)
clrBrks[1] = clrBrks[1] - 1e-5
clrBrks[length(clrClasses) + 1] = clrBrks[length(clrClasses) + 1] + 1e-5
npWtStd = 1 + (FUDJout[[1]][[1]]$np - min(FUDJout[[1]][[1]]$np))/
(max(FUDJout[[1]][[1]]$np) - min(FUDJout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, type = 'n',
xlim = c(0, max(FUDJout[[1]][[1]]$distLong)),
ylim = c(0, max(FUDJout[[1]][[1]]$distLong)),
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))],
xlab = 'Shorter Distance to Common Junction',
ylab = 'Longer Distance to Common Junction',
cex.lab = 2, cex.axis = 1.2
)
for(i in 1:(2*length(FUSDout[[1]][[1]][,1]))) {
iinc = i*max(FUDJout[[1]][[1]]$distLong)/length(FUSDout[[1]][[1]][,1])
lines(c(0,iinc),c(iinc,0), lty = 2, col = 'grey60')
}
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 19,
cex = 3*npWtStd,
col = clrClasses[as.integer(cut(FUDJout[[1]][[1]]$semivar, clrBrks))])
points(FUDJout[[1]][[1]]$distShrt, FUDJout[[1]][[1]]$distLong, pch = 1,
cex = 3*npWtStd, lwd = 2)
xyleg = min(FUDJout[[1]][[1]]$distLong) + (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/2
xylen = max(FUDJout[[1]][[1]]$distLong)
legWidth = (max(FUDJout[[1]][[1]]$distLong) -
min(FUDJout[[1]][[1]]$distLong))/10
addBreakColorLegend(.7*xylen,0,.7*xylen+legWidth,.6*xylen, clrBrks, clrClasses,
'1.2', cex = 1.4)
mtext('B', cex = 4, adj = -.18, padj = -.4)
# part C
npWtStd = 1 + (FCSDout[[1]][[1]]$np - min(FCSDout[[1]][[1]]$np))/
(max(FCSDout[[1]][[1]]$np) - min(FCSDout[[1]][[1]]$np))
par(mar = c(5,5,5,2))
plot(FCSDout[[1]][[1]]$brkDist,FCSDout[[1]][[1]]$semivar,
ylim = c(0,1.05*max(FCSDout[[1]][[1]]$semivar)),
xlim = c(0,1.05*max(FCSDout[[1]][[1]]$brkDist)),
pch = 19, cex = 2*npWtStd, xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
mtext('C', cex = 4, adj = -.18, padj = -.4)
# part D
par(mar = c(5,5,5,2))
plot(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist),
c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar), type = 'n',
xlim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1),
ylim = c(0,max(c(FCSD01out[[1]][['72']]$svgm0$semivar,
FCSD01out[[1]][['72']]$svgm1$semivar))*1.1),
xlab = 'Flow-Connected Distance',
ylab = 'Semivariance', cex.lab = 2, cex.axis = 1.5)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm1$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
pch = 19, cex = 2*npWtStd, col = '#bdbdbd')
text(FCSD01out[[1]][['72']]$svgm1$brkDist,
FCSD01out[[1]][['72']]$svgm1$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm1$np),
pos = 2, cex = 2.5, offset = .7)
npWtStd = 1 + (FCSD01out[[1]][['72']]$svgm0$np -
min(FCSD01out[[1]][['72']]$svgm0$np))/
(max(FCSD01out[[1]][['72']]$svgm0$np) -
min(FCSD01out[[1]][['72']]$svgm0$np))
points(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
pch = 19, cex = 2*npWtStd)
text(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm0$semivar,
labels = as.character(FCSD01out[[1]][['72']]$svgm0$np),
pos = 4, cex = 2.5, offset = .7)
legend(max(c(FCSD01out[[1]][['72']]$svgm0$brkDist,
FCSD01out[[1]][['72']]$svgm1$brkDist))*1.1, xjust = 1,
0, yjust = 0,
pch = c(19,19), col = c('black','#bdbdbd'),
legend = c('FCSD(0)','FCSD(1)'), lwd = c(3,3),
cex = 2, lty = c(0,0))
mtext('D', cex = 4, adj = -.18, padj = -.4)
dev.off()
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