Create neon-information-test.R

misc/NEON/neon-information-test.R

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+library(aqp)
+library(lattice)
+library(tactile)
+library(hexbin)
+
+#### profileInformationIndex, NEON Data  ####
+
+
+soildata.url <- "https://github.com/swsalley/NEONsoil/blob/master/DistributedAnalysis/SSSA-J_Variability/NEON_Lab_clean_20230127.csv?raw=true"
+
+x <- read.csv(soildata.url)
+
+depths(x) <- plotID ~ horizonTopDepth + horizonBottomDepth  
+
+hzdesgnname(x) <- 'horizonName'
+
+sdc <- getSoilDepthClass(x)
+
+site(x) <- sdc
+
+table(x$depth.class)
+hist(x$depth)
+
+
+i.sum.t <- profileInformationIndex(x, vars = c('clayTotal'), method = 'sum', baseline = TRUE)
+i.mean.t <- profileInformationIndex(x, vars = c('clayTotal'), method = 'mean', baseline = TRUE)
+i.sum.f <- profileInformationIndex(x, vars = c('clayTotal'), method = 'sum', baseline = FALSE)
+i.mean.f <- profileInformationIndex(x, vars = c('clayTotal'), method = 'mean', baseline = FALSE)
+
+neon.info <- data.frame(
+  plotID = site(x)[[idname(x)]],
+  depth = x$depth,
+  depth.class = x$depth.class,
+  i.sum.t, 
+  i.mean.t, 
+  i.sum.f, 
+  i.mean.f
+)
+
+neon.info$site <- substr(neon.info$plotID , start = 1, stop = 4)
+rownames(neon.info) <- NULL
+head(neon.info)
+
+# write.csv(neon.info, "E:/Publications/NEON/R/Neon_info_index.csv")
+# this file is at: https://github.com/swsalley/NEONsoil/blob/master/NCSP/Neon_info_index.csv
+
+v <- c('depth', 'i.sum.t', 'i.mean.t', 'i.sum.f', 'i.mean.f')
+round(cor(neon.info[, v]), 2)
+
+nm <- names(sort(tapply(neon.info$i.mean.t, neon.info$site, median)))
+neon.info$g <- factor(neon.info$site, levels = nm)
+
+bwplot(g ~ i.mean.t, data = neon.info, par.settings = tactile.theme(), panel = function(...) {
+  panel.grid(-1, -1)
+  panel.bwplot(...)
+})
+
+bwplot(g ~ i.mean.f, data = neon.info, par.settings = tactile.theme(), panel = function(...) {
+  panel.grid(-1, -1)
+  panel.bwplot(...)
+})
+
+
+bwplot(depth.class ~ i.sum.t, data = neon.info, par.settings = tactile.theme(), panel = function(...) {
+  panel.grid(-1, -1)
+  panel.bwplot(...)
+})
+
+bwplot(depth.class ~ i.sum.f, data = neon.info, par.settings = tactile.theme(), panel = function(...) {
+  panel.grid(-1, -1)
+  panel.bwplot(...)
+})
+
+
+
+hsd <- TukeyHSD(aov(i.sum.f ~ depth.class, data = neon.info))
+
+par(mar = c(4, 8, 3, 1))
+plot(hsd, cex.axis = 0.66, las = 1)
+
+hexplom(neon.info[, v], par.settings = tactile.theme(), colramp = viridisLite::viridis, nbins = 30)
+
+
+hexplom(neon.info[, c('depth', 'i.sum.t', 'i.sum.f')], par.settings = tactile.theme(), colramp = viridisLite::viridis, nbins = 30)
+
+
+