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Copy path05.compare_means_var.R
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05.compare_means_var.R
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#### compare means and variances to dissimilarity ####
## Load package 'distantia'
library(distantia)
## load clean data
file.to.load = list.files("data/")[grep("sn.06", list.files("data/"))]
load(paste0("data/", file.to.load))
rm(file.to.load)
str(sn.06)
## get the variance of each node
var.04r = aggregate(sn.06, by = list(sn.06$sensornode), FUN = var, na.rm = T)
plot(var.04r$soiltemp_5cm_avg ~ var.04r$Group.1, pch = 19)
points(var.04r$soilmoisture_a_5cm_avg ~ var.04r$Group.1)
nodes = unique(var.04r$Group.1)
st5 = as.matrix(dist(var.04r$soiltemp_5cm_avg, diag = TRUE, upper = T))
colnames(st5) = nodes
rownames(st5) = nodes
st5
st30 = as.matrix(dist(var.04r$soiltemp_30cm_avg, diag = TRUE, upper = T))
colnames(st30) = nodes
rownames(st30) = nodes
st30
sma5 = as.matrix(dist(var.04r$soilmoisture_a_5cm_avg, diag = TRUE, upper = T))
colnames(sma5) = nodes
rownames(sma5) = nodes
sma5
sma30 = as.matrix(dist(var.04r$soilmoisture_a_30cm_avg, diag = TRUE, upper = T))
colnames(sma30) = nodes
rownames(sma30) = nodes
sma30
smb5 = as.matrix(dist(var.04r$soilmoisture_b_5cm_avg, diag = TRUE, upper = T))
colnames(smb5) = nodes
rownames(smb5) = nodes
smb5
smb30 = as.matrix(dist(var.04r$soilmoisture_b_30cm_avg, diag = TRUE, upper = T))
colnames(smb30) = nodes
rownames(smb30) = nodes
smb30
smc5 = as.matrix(dist(var.04r$soilmoisture_c_5cm_avg, diag = TRUE, upper = T))
colnames(smc5) = nodes
rownames(smc5) = nodes
smc5
smc30 = as.matrix(dist(var.04r$soilmoisture_c_30cm_avg, diag = TRUE, upper = T))
colnames(smc30) = nodes
rownames(smc30) = nodes
smc30
file.name = paste0("data/", format(Sys.Date(), "%m.%d.%Y"), ".var.04r.Rdata")
save(sma30, sma5, smb30, smb5, smc30, smc5, st30, st5, file = file.name)
rm(sma30, sma5, smb30, smb5, smc30, smc5, st30, st5)
rm(file.name, var.04r)
## get the mean for each node
mean.04r = aggregate(sn.04r, by = list(sn.04r$sensornode), FUN = mean)
st5 = as.matrix(dist(mean.04r$soiltemp_5cm_avg, diag = TRUE, upper = T))
colnames(st5) = nodes
rownames(st5) = nodes
st5
st30 = as.matrix(dist(mean.04r$soiltemp_30cm_avg, diag = TRUE, upper = T))
colnames(st30) = nodes
rownames(st30) = nodes
st30
sma5 = as.matrix(dist(mean.04r$soilmoisture_a_5cm_avg, diag = TRUE, upper = T))
colnames(sma5) = nodes
rownames(sma5) = nodes
sma5
sma30 = as.matrix(dist(mean.04r$soilmoisture_a_30cm_avg, diag = TRUE, upper = T))
colnames(sma30) = nodes
rownames(sma30) = nodes
sma30
smb5 = as.matrix(dist(mean.04r$soilmoisture_b_5cm_avg, diag = TRUE, upper = T))
colnames(smb5) = nodes
rownames(smb5) = nodes
smb5
smb30 = as.matrix(dist(mean.04r$soilmoisture_b_30cm_avg, diag = TRUE, upper = T))
colnames(smb30) = nodes
rownames(smb30) = nodes
smb30
smc5 = as.matrix(dist(mean.04r$soilmoisture_c_5cm_avg, diag = TRUE, upper = T))
colnames(smc5) = nodes
rownames(smc5) = nodes
smc5
smc30 = as.matrix(dist(mean.04r$soilmoisture_c_30cm_avg, diag = TRUE, upper = T))
colnames(smc30) = nodes
rownames(smc30) = nodes
smc30
file.name = paste0("data/", format(Sys.Date(), "%m.%d.%Y"), ".mean.04r.Rdata")
save(sma30, sma5, smb30, smb5, smc30, smc5, st30, st5, file = file.name)
rm(sma30, sma5, smb30, smb5, smc30, smc5, st30, st5)
rm(file.name, mean.04r)