knitr::opts_chunk$set(echo = TRUE)
library(compositions) id.cols <- c("site","year", "year.num","site.age", "site.age.init", "site.age.cent") diet.cols <- qc(diet.C,diet.F,diet.G,diet.I,diet.N,diet.O) ## centered log ratio diet.clr <- clr(diet.clo) #isometric log ratio diet.ilr <- ilr(diet.clo) diet.clo2 <- cbind(diet.clo, trait_dat[,id.cols]) diet.clr2 <- cbind(diet.clr, trait_dat[,id.cols]) diet.ilr2 <- cbind(diet.ilr, trait_dat[,id.cols])
m.diet.clr <- manova(diet.clr[,1:3] ~ trait_dat$site.age) m.diet.ilr.site <- manova(diet.ilr[,1:3] ~ trait_dat$site) m.ilr.site.age <- manova(hab.ilr[,1:3] ~ trait_dat$site.age) # # x <- adonis(hab.ilr[,1:3] ~ site.age, # #strata = site, # data = trait_dat[,id.cols])
Note: can't really use "strata" w/ Aceitillar b/c there is only 1 measurement per year for Aceitillar
For information on compsitional data analysis see http://r-sig-ecology.471788.n2.nabble.com/Measurement-distance-for-proportion-data-td7578891.html
i.not.Aceit <- which(trait_dat$site != "Aceitillar") acomp.hab <- acomp(trait_dat[i.not.Aceit,diet.cols])# proportions closed between 0 and 1 acomp.hab.ilr <- ilr(acomp.hab)# isometric log-ratios acomp.hab.ilr.dist = vegdist(acomp.hab.ilr, method="euclidean")# Aitchison dissimilarity matrix #betadisper() homogen of dispersion acomp.hab.ilr.dist.adonis <- adonis2(acomp.hab.ilr.dist ~ trait_dat$site[i.not.Aceit], strata = factor(trait_dat$year[i.not.Aceit]) ) acomp.hab.ilr.dist.anosim <- anosim(acomp.hab.ilr.dist, trait_dat$site[i.not.Aceit], strata = factor(trait_dat$year[i.not.Aceit]) ) summary(acomp.hab.ilr.dist.adonis)
i.diet.I <- which(diet.clo.melt$diet == "diet.I") #i.SF <- which(diet.clo.melt$Habitat == "hab.SF") # ef.lims <- c(0.4,0.9) # sf.lims <- c(0.0,0.6) gg.ef <- ggplot(data = diet.clo.melt[i.diet.I,], aes(y = Percent, x = site.age, group = site, color = site)) + geom_point() + # ylim(ef.lims) + ylab("Proportion") + #facet_wrap(~Habitat,nrow = 2) + theme(legend.position="none")+ theme(#strip.background = element_blank(), strip.text = element_blank()) + xlab("") # gg.sf <- ggplot(data = diet.clo.melt[i.SF,], # aes(y = Percent, # x = site.age # color = site)) + # geom_point() + # ylim(sf.lims)+ # ylab("Proportion") + # #facet_wrap(~Habitat,nrow = 2) + # theme(legend.position="none")+ # theme(#strip.background = element_blank(), # strip.text = element_blank()) i.ef.Aceit <- which(diet.clo.melt$diet == "diet.I" & diet.clo.melt$site == "Aceitillar") # i.sf.Aceit <- which(diet.clo.melt$Habitat == "hab.SF" & # diet.clo.melt$site == "Aceitillar") aceit.ef <- ggplot(data = diet.clo.melt[i.ef.Aceit,], aes(y = Percent, x = site, #group = Habitat, color = site)) + geom_point() + xlab("") + ylab("") + #ylim(ef.lims) + #facet_wrap(~Habitat,nrow = 2)+ theme(legend.position="none") + theme(#strip.background = element_blank(), strip.text = element_blank()) + theme(axis.title.y=element_blank(), axis.line.y=element_blank(), axis.text.y=element_blank(), axis.ticks.y=element_blank()) + xlab("") # aceit.sf <- ggplot(data = diet.clo.melt[i.sf.Aceit,], # aes(y = Percent, # x = site, # group = Habitat, # color = site)) + # geom_point() + # ylim(sf.lims)+ # xlab("") + ylab("") + # #facet_wrap(~Habitat,nrow = 2)+ # theme(legend.position="none") + # theme(#strip.background = element_blank(), # strip.text = element_blank()) + # # theme(axis.title.y=element_blank(), # axis.line.y=element_blank(), # axis.text.y=element_blank(), # axis.ticks.y=element_blank()) cowplot::plot_grid(gg.ef,aceit.ef, #gg.sf,aceit.sf, rel_widths = c(3,1), labels = c("Insectivores",""))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.