Summaries of eucalypt taxa and their traits

knitr::opts_chunk$set(cache = TRUE, dev = c("png", "pdf"))
library(eucs)
library(here)
library(xtable)

grampians_taxa_tab <- subset(
  medians_grampians,
  select = c(taxon, sla_mm2_per_mg, seed_mass_mg, max_height_m)
)

sla_n_samples <- subset(
  traits_grampians,
  select = c(tree, taxon, sla_mm2_per_mg)
)

sla_n_samples <- sla_n_samples[complete.cases(sla_n_samples), ]

sm_n_samples <- subset(
  traits_grampians,
  select = c(taxon, seed_mass_mg)
)

sm_n_samples <- sm_n_samples[complete.cases(sm_n_samples), ]

nplots <- table(subset(modeldata_grampians, occupancy, taxon))

names(nplots)[
  names(nplots) %in%
    c(
      "Eucalyptus (goniocalyx|nortonii)",
      "Eucalyptus leucoxylon",
      "Eucalyptus radiata",
      "Eucalyptus viminalis subsp. (pryoriana|viminalis)"
    )
  ] <- c(
    "Eucalyptus goniocalyx subsp. (goniocalyx|viridissima)",
    "Eucalyptus leucoxylon subsp. (leucoxylon|pruinosa)",
    "Eucalyptus radiata subsp. radiata",
    "Eucalyptus viminalis subsp. viminalis"
  )

grampians_taxa_tab <- data.frame(
  "\\vtop{\\hbox{\\strut }\\hbox{\\strut Taxon}}" = paste0(
    "\\textit{",
    gsub("subsp.", "ssp.", gsub("Eucalyptus", "E.", grampians_taxa_tab$taxon)),
    "}"
  ),
  "\\vtop{\\hbox{\\strut No.}\\hbox{\\strut of}\\hbox{\\strut plots}}" =
    as.character(nplots[grampians_taxa_tab$taxon]),
  "\\vtop{\\hbox{\\strut SLA}\\hbox{\\strut (mm$^2$/mg)}}" = paste0(
    round(grampians_taxa_tab$sla_mm2_per_mg, 1),
    " (", table(sla_n_samples$taxon)[grampians_taxa_tab$taxon],
    "/", table(unique(sla_n_samples[1:2])$taxon)[grampians_taxa_tab$taxon], ")"
  ),
  "\\vtop{\\hbox{\\strut Seed}\\hbox{\\strut mass}\\hbox{\\strut (mg)}}" =
    paste0(
      round(grampians_taxa_tab$seed_mass_mg, 1),
      " (", table(sm_n_samples$taxon)[grampians_taxa_tab$taxon], ")"
    ),
  "\\vtop{\\hbox{\\strut Max}\\hbox{\\strut height}\\hbox{\\strut (m)}}" =
    as.character(round(grampians_taxa_tab$max_height_m, 0)),
  check.names = FALSE,
  stringsAsFactors = FALSE
)

grampians_taxa_tab[
    grampians_taxa_tab[, 1]%in%
      c(
        "\\textit{E. goniocalyx ssp. (goniocalyx|viridissima)}",
        "\\textit{E. leucoxylon ssp. (leucoxylon|pruinosa)}"
      ), 1
  ] <- c(
    "\\textit{E. goniocalyx}",
    "\\textit{E. leucoxylon}"
  )

dir.create(
  here("notebooks/eucalypt_taxa_summaries_files"),
  showWarnings = FALSE
)

print(
  xtable(
    grampians_taxa_tab, caption =
      "Grampians taxa. Number of plots at which each taxa occurred.
      Median SLA (number of leaves/number of trees). Median seed mass (number of
      samples). Maximum attainable height.",
    label = "tab:grampianstaxasummary"
  ),
  file = here(
    "notebooks/eucalypt_taxa_summaries_files/grampianssummarytab.tex"
  ),
  include.rownames = FALSE,
  table.placement = "htbp!",
  caption.placement = "top",
  sanitize.text.function = identity
)

southeast_taxa_tab <- subset(
  combine_taxa_traits(medians_southeast, euctils::taxa_groups),
  select = c(taxon, sla_mm2_per_mg, seed_mass_mg, max_height_m)
)

southeast_samples <- local({
    df <- traits_southeast
    for (i in seq_along(taxa_groups)) {
      df[
        grepl(taxa_groups[i], df$taxon) |
        grepl(taxa_groups[i], df$taxon, fixed = TRUE),
        "taxon"
      ] <- names(taxa_groups)[i]
    }
    df
  })

sla_n_samples <- subset(
  southeast_samples,
  select = c(tree, taxon, sla_mm2_per_mg)
)

sla_n_samples <- sla_n_samples[complete.cases(sla_n_samples), ]

sm_n_samples <- subset(
  southeast_samples,
  select = c(tree, taxon, seed_mass_mg)
)

sm_n_samples <- sm_n_samples[complete.cases(sm_n_samples), ]

nplots <- table(subset(modeldata_southeast, occupancy, taxon))

nregs <- table(
  unique(subset(modeldata_southeast, occupancy, c(taxon, ibra_subregion)))$taxon
)

southeast_taxa_tab <- southeast_taxa_tab[complete.cases(southeast_taxa_tab), ]

southeast_taxa_tab <- data.frame(
   taxon = southeast_taxa_tab$taxon,
  "\\vtop{\\hbox{\\strut No.}\\hbox{\\strut of}\\hbox{\\strut regions}}" =
    as.character(nregs[southeast_taxa_tab$taxon]),
  "\\vtop{\\hbox{\\strut No.}\\hbox{\\strut of}\\hbox{\\strut plots}}" =
    as.character(nplots[southeast_taxa_tab$taxon]),
  "\\vtop{\\hbox{\\strut SLA}\\hbox{\\strut (mm$^2$/mg)}}" = paste0(
    round(southeast_taxa_tab$sla_mm2_per_mg, 1),
    " (", table(sla_n_samples$taxon)[southeast_taxa_tab$taxon],
    "/", table(unique(sla_n_samples[1:2])$taxon)[southeast_taxa_tab$taxon], ")"
  ),
  "\\vtop{\\hbox{\\strut Seed}\\hbox{\\strut mass}\\hbox{\\strut (mg)}}" =
    paste0(
      round(southeast_taxa_tab$seed_mass_mg, 1),
      " (", table(sm_n_samples$taxon)[southeast_taxa_tab$taxon],
      "/", table(unique(sm_n_samples[1:2])$taxon)[southeast_taxa_tab$taxon], ")"
    ),
  "\\vtop{\\hbox{\\strut Max}\\hbox{\\strut height}\\hbox{\\strut (m)}}" =
    as.character(round(southeast_taxa_tab$max_height_m, 0)),
  check.names = FALSE,
  stringsAsFactors = FALSE
)

southeast_taxa_tab$taxon <- gsub("subsp.", "ssp.", southeast_taxa_tab$taxon)
southeast_taxa_tab$taxon <- gsub("(", "", southeast_taxa_tab$taxon, fixed = T)
southeast_taxa_tab$taxon <- gsub(")", "", southeast_taxa_tab$taxon, fixed = T)
southeast_taxa_tab$taxon <- gsub("|", "/", southeast_taxa_tab$taxon, fixed = T)
southeast_taxa_tab$taxon <- paste0("\\textit{", southeast_taxa_tab$taxon, "}")
southeast_taxa_tab <- southeast_taxa_tab[order(southeast_taxa_tab$taxon), ]

colnames(southeast_taxa_tab)[1] <-
  "\\vtop{\\hbox{\\strut }\\hbox{\\strut Taxon}}"

southeast_taxa_tab <- southeast_taxa_tab[complete.cases(southeast_taxa_tab), ]

print(
  xtable(
    southeast_taxa_tab,
    caption =
      "Southeast taxa. Number of IBRA subregions in which the taxon occurs.
      Number of plots at which each taxa occurred. Median SLA (number of
      leaves/number of trees). Median seed mass (number of samples/number of
      trees). Maximum attainable height.",
    label = "tab:southeasttaxasummary",
    align = c(
      "l", "P{.42\\textwidth}", "P{.07\\textwidth}", "P{.045\\textwidth}",
      "P{.11\\textwidth}", "P{.11\\textwidth}", "P{.06\\textwidth}"
    )
  ),
  file = here(
    "notebooks/eucalypt_taxa_summaries_files/southeastsummarytab.tex"
  ),
  tabular.environment = 'longtable',
  size = "\\fontsize{8pt}{8pt}\\selectfont",
  hline.after = -1,
  include.colnames = TRUE,
  floating = FALSE,
  add.to.row = list(pos = list(0), command = "\\hline \\endhead "),
  include.rownames = FALSE,
  table.placement = "htbp!",
  caption.placement = "top",
  sanitize.text.function = identity
)

Correlations among traits

par(mar = rep(.5, 4), oma = c(3, 4, 4, 3), mfrow = c(2, 2))
rgns <- c("South-east Australia" = FALSE, "Grampians" = TRUE)
vars <- list()
vars[[1]] <- c("sla_mm2_per_mg", "seed_mass_mg")
vars[[2]] <- c("max_height_m", "seed_mass_mg")
labels <- c(
  sla_mm2_per_mg = "SLA (mm\u00b2/mg)",
  seed_mass_mg   = "Seed mass (mg)",
  max_height_m   = "Maximum height (m)"
)

trait_data <- list()
trait_data$southeast <-
  unique(modeldata_southeast[, c("taxon", names(labels))])[-1]
trait_data$grampians <-
  unique(modeldata_grampians[, c("taxon", names(labels))])[-1]

for (i in seq(vars[[1]])) {
  for (j in seq(vars[[2]])) {
    if (sum(i, j) > 3) {
      plot.new()
      if (i == j) {
        legend(
          "center", c("Southeast","Grampians"),
          fill = c("black", "white"),
          bty = "n", cex = 1, xpd = NA
        )
      }
    } else {
      plot(
        subset(trait_data[[1]], select = c(vars[[1]][j], vars[[2]][i])),
        xaxt = "n", yaxt = "n", pch = 19, log = "xy",
        panel.first = grid(col = "grey"),
        xlim = range(do.call(rbind, trait_data)[vars[[1]][j]], na.rm = TRUE) * c(.9, 1.2),
        ylim = range(do.call(rbind, trait_data)[vars[[2]][i]], na.rm = TRUE) * c(.9, 1.2)
      )
      points(
        subset(trait_data[[2]], select = c(vars[[1]][j], vars[[2]][i])),
        bg = "white", pch = 21
      )
      if (sum(i, j) == 3) {
        axis(1, cex.axis = .8)
        axis(4, las = 1, cex.axis = .8)
      }
      if (i == 1) mtext(labels[vars[[1]][j]], 3, 1)
      if (j == 1) mtext(labels[vars[[2]][i]], 2, 1)
    }
  }
}