In brouwern/DRmencia: Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.

knitr::opts_chunk$set(echo = TRUE)

Calcualte simpsons div

Diversity of taxa grupsl not really

simps <- diversity(litter.comm.matrix[,-c(1:2)], MARGIN =1)

simps <- cbind(simps, litter.comm.matrix[,c(1:2)])

Model simpson's diversity

Diveristy marginally significant

library(lme4)
library(coefplot)
simps$site <- factor(simps$site,
        levels = c("La Cueva","La Caoba","Morelia","El Corral",
                                      "Broadleaf"))

m.simps.0 <- lmer(exp(simps) ~ 1 + (1|site), data = simps)
m.simps.site <- lmer(exp(simps) ~ site + (1|site), data = simps)
m.simps.means <- lmer(exp(simps) ~ -1 + site + (1|site), data = simps)

anova(m.simps.0,m.simps.site)


x <- cbind(m.simps.0@frame,
predictInterval(m.simps.0,which = "full",
                include.resid.var = FALSE))



coefplot(m.simps.means,
         xlab = "Simpson's diversity",
         horizontal = TRUE,
         ylab = "Site",
         title = "Simpson's diveristy of Taxonimic groups in Litter Samples")

library(ggpubr)
simps$exp.simps <- with(simps, exp(simps))
ggerrorplot(data = simps,x = "site",
            y="exp.simps",
            desc_stat = "mean_sd")

brouwern/DRmencia documentation built on May 6, 2019, 12:24 p.m.