In allanecology/BetaDivMultifun: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality

Depends on analysis_nonpublic.R to load the raw dataset rawlui and plotNAset

# Load requirements from <..>nonpublic.R file
sections_to_be_loaded <- c("raw_lui")
source("vignettes/analysis_nonpublic.R")

Combining LUI over 11 years

Years 2006 to 2016. We have information until 2017, but the range of functions is until 2016.

$$LUI = \frac{1}{11} \left( \sum_{i = 2006}^{2016} \sqrt{\frac{G_i}{mean(G_i)}+ \frac{M_i}{mean(M_i)} + \frac{F_i}{mean(F_i)}} \right)$$

code by Caterina Penone

luiy <- data.table::copy(rawlui)
luiy <- luiy[Year != "2017", ]

# calculate the global means
luiy[,MeanF:=mean(TotalFertilization,na.rm = T)]
luiy[,MeanM:=mean(TotalMowing,na.rm = T)]
luiy[,MeanG:=mean(TotalGrazing,na.rm = T)]

# calculate the LUI and its components for each year and each plot, using the global mean
luiy[ , LUI := sqrt((TotalFertilization/MeanF) + (TotalMowing/MeanM) +(TotalGrazing / MeanG)), by=EP_PlotID]
luiy[ ,Fstd := TotalFertilization / MeanF, by = EP_PlotID]
luiy[ ,Mstd := TotalMowing / MeanM, by = EP_PlotID]
luiy[ ,Gstd := TotalGrazing / MeanG , by = EP_PlotID]

# calculate DELTA LUI and DELTA COMPONENTS
luiy[ , deltaLUI := sd(LUI), by = EP_PlotID]
luiy[ , deltaFstd := sd(Fstd), by = EP_PlotID]
luiy[ , deltaMstd := sd(Mstd), by = EP_PlotID]
luiy[ , deltaGstd := sd(Gstd), by = EP_PlotID]

# clean and format
luiy <- luiy[,.(EP_PlotID,LUI, Gstd, Mstd, Fstd, deltaLUI, deltaGstd, deltaMstd, deltaFstd)]
data.table::setnames(luiy, old = "EP_PlotID", new = "Plot")
luiy <- merge(luiy, usefulplotids, by = "Plot")
luiy[, Plot := NULL]

# calculate the means over 11 years
lui <- aggregate(LUI~Plotn, luiy, mean)
lui <- merge(lui, aggregate(Gstd~Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(Mstd ~ Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(Fstd ~ Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(deltaLUI ~ Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(deltaGstd ~ Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(deltaMstd ~ Plotn, luiy, mean), by = "Plotn")
lui <- merge(lui, aggregate(deltaFstd ~ Plotn, luiy, mean), by = "Plotn")

Select set of plots

lui <- lui[which(lui$Plotn %in% plotNAset),]

Save for analysis

saveRDS(lui, "LUI.rds")

Prepare LUI euclidean distance

test <- as.matrix(lui[, .(LUI)])
rownames(test) <- lui$Plotn
test <- vegan::vegdist(test, method = "euclid")
test <- as.matrix(test)
test[!lower.tri(test)] <- NA
test <- reshape2::melt(test, value.name = "distLUI")
test <- test[!is.na(test[, 3]),]
test <- data.table::data.table(test)

saveRDS(test, "distLUI.rds")

allanecology/BetaDivMultifun documentation built on Nov. 9, 2023, 8:47 p.m.