#------------------------------------------------------------------------------
# libraries
#------------------------------------------------------------------------------
library("SSN")
library('fluvgrm')
simTU <- importSSN(system.file("lsndata/simTU.ssn",
package = "fluvgrm"), o.write = TRUE)
# note, simulation code is included for reproducibility
# however, the results are stored as well
# so it is possible to just skip to graphics part of script
#------------------------------------------------------------------------------
# Simulate Network
#------------------------------------------------------------------------------
# stream network originally created using these commands
# setwd('/home/jay/Data/fluvgrm/fluvgrm/inst/lsndata')
# set.seed(1)
# simTU <- createSSN(n = 500,
# obsDesign = binomialDesign(400),
# importToR = TRUE, path = "simTU.ssn",
# treeFunction = iterativeTreeLayout)
# createDistMat(simTU)
# it takes a few minutes to create. Instead, you can
# import the object as stored in the package
# load the SpatialStreamNetwork object
# simTU <- importSSN(system.file("lsndata/simTU.ssn",
# package = "fluvgrm"), o.write = TRUE)
# now plot it
# plotSSN(simTU, pch = 19, cex = .7,
# addFuncColName = 'addfunccol')
#------------------------------------------------------------------------------
# Graphics
#------------------------------------------------------------------------------
# skip all of the simulations and just use stored data
data(storeFCWA)
data(storeFCSD)
data(FCWAlast)
data(FCSDlast)
# combine the data for plotting with boxplots
alldat = NULL
for(i in 1:length(FCWAlast[,1])) alldat = rbind(alldat,
data.frame(type = 'FCWA', dist = FCWAlast[i,'meanDist'],
svgm = storeFCWA[i,]),
data.frame(type = 'FCSD', dist = FCWAlast[i,'meanDist'],
svgm = storeFCSD[i,]))
SLDF = as.SpatialLinesDataFrame(simTU)
SPDF = as.SpatialPointsDataFrame(simTU)
# set the working directory to save the figure
setwd(tempdir())
getwd()
# create plot
pdf('FCWAvsFCSD4Fig.pdf', height = 8, width = 14)
layout(matrix(1:2, nrow = 1), widths = c(1,2.5))
par(mar = c(0,0,0,0))
plot(SLDF, asp = .65)
plot(SPDF, add =TRUE, pch = 19, cex = 1)
par(mar = c(5,5,1,1))
boxplot(svgm ~ type + dist, data = alldat, col = c('white','grey70'),
at = sort(c(1:11,(1:11)+.3)), boxwex = .25, xaxt = 'n', cex.lab = 2,
ylab = 'Semivariogram', pch = 1, cex.axis = 1.5, ylim = c(-5,10),
xlab = '')
points(1:11,apply(storeFCWA,1,mean), pch = 19)
points((1:11)+.3,apply(storeFCSD,1,mean), pch = 19)
legend(.2,-2.5, legend = c('FCWA','FCSD'), pch = c(22,15),
col = c('black','grey70'), cex = 2)
axis(side=1, (1:11)+.15, labels=
as.character(round(FCWAlast[1:11,'meanDist'],1)),
cex.axis = 1.5)
mtext('Mean Lag Distance', side=1, cex = 2, padj = 2.5)
lines(c(0,30),c(1,1), lty = 2)
dev.off()
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