R/HERBIV.R

In ZhuLeZi/leplant: Description of community characteristics

HERBIV<-function (x, method = 3)
{
  sh <- x
  xdz <- function(x) {
    total <- apply(x, 1, sum, na.rm = TRUE)
    x <- sweep(x, 1, total, "/")
    return(x)
  }
  if (method == 3.1) {
    sp_high <- tapply(sh$hight, list(sh$plot, sh$sp), sum) %>%
      xdz()
    sp_biomass <- tapply(sh$biomass, list(sh$plot, sh$sp),
                         sum) %>% xdz()
    sp_cover <- tapply(sh$cover, list(sh$plot, sh$sp), sum) %>%
      xdz()
    plotIV <- (sp_high + sp_biomass + sp_cover)/3
  }
  if (method == 3) {
    sp_high <- tapply(sh$hight, list(sh$plot, sh$sp), sum) %>%
      xdz()
    sp_biomass <- tapply(sh$biomass, list(sh$plot, sh$sp),
                         sum) %>% xdz()
    sp_abun <- tapply(sh$abun, list(sh$plot, sh$sp), sum) %>%
      xdz()
    plotIV <- (sp_high + sp_biomass + sp_abun)/3
  }
  if (method == 1) {
    sp_biomass <- tapply(sh$biomass, list(sh$plot, sh$sp),
                         sum) %>% xdz()
    plotIV <- sp_biomass
  }
  if (method == 2) {
    sp_biomass <- tapply(sh$biomass, list(sh$plot, sh$sp),
                         sum) %>% xdz()
    sp_high <- tapply(sh$hight, list(sh$plot, sh$sp), sum) %>%
      xdz()
    plotIV <- (sp_biomass + sp_high)/2
  }
  plotIV <- as.data.frame(plotIV)
  plotiv <- t(plotIV)
  lq <- melt(plotiv, id.vars = c(colnames(plotiv)))
  names(lq)[1:3] <- c("sp", "plot", "iv")
  lq$site <- word(as.character(lq$plot), 1, sep = fixed("."))
  la <- tapply(lq$iv, list(lq$site, lq$sp), sum, na.rm = TRUE)
  yfn <- sh %>% group_by(site) %>% summarise(yfn = length(unique(plot)))
  yfn$site<-as.character(yfn$site)
  yfn<-arrange(yfn,site)
  yfn <- yfn[, 2]
  newl <- length(la[1, ]) + 1
  la <- as.data.frame(la)
  la[, newl] <- yfn
  la <- as.matrix(la)
  siteiv <- la/la[, newl]
  siteiv <- siteiv[, 1:newl - 1]
  siteiv[which(siteiv == 0)] <- NA
  siteiv
}