knitr::opts_chunk$set(echo = TRUE)
summary(factor(ann_caps$status.focals)) ann_caps[is.na(ann_caps$status.focals),"spp.code"] ann_caps$hab1 <- as.character(ann_caps$hab1) ann_caps$hab1 <- gsub("D$","DF",ann_caps$hab1) summary(factor(ann_caps$hab1 )) hab_matrix <- dcast(data = ann_caps, formula = site + year + year.num + site.age + site.age.init + site.age.cent ~ hab1, value.var = "spp.code", fun.aggregate = length) #names(hab_matrix)[dim(hab_matrix)[2]] <- "hab.NA" hab.tot <- apply(hab_matrix[,c("DF","EF","SF")],1,sum) diet_matrix <- dcast(data = ann_caps, formula = site + year + year.num + site.age + site.age.init + site.age.cent ~ diet, value.var = "spp.code", fun.aggregate = length) #names(diet_matrix)[dim(diet_matrix)[2]] <- "diet.NA" diets <- c("C","F","G","I","N","O") diet.tot <- apply(diet_matrix[,diets],1,sum) trait_dat <- cbind(hab_matrix, diet_matrix[,diets]) #check that row totals match plot(diet.tot , hab.tot) habs <- c("DF","EF","SF") names(trait_dat)[which(names(trait_dat) %in% habs)] <- paste("hab",habs,sep = ".") names(trait_dat)[which(names(trait_dat) %in% diets)] <- paste("diet",diets,sep = ".") trait_dat$tot <- diet.tot
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