inst/doc/community-analysis.R

In fishtree: Interface to the Fish Tree of Life API

## ----setup, echo = FALSE------------------------------------------------------
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
knitr::opts_chunk$set(
  echo = TRUE,
  eval = NOT_CRAN,
  collapse = TRUE,
  comment = "#>"
)

## ----load-packages------------------------------------------------------------
library(ape)
library(fishtree)
loadNamespace("rfishbase")
loadNamespace("picante")
loadNamespace("geiger")

## ----get-data-----------------------------------------------------------------
# Get reef-associated species from the `species` table
reef_species <- rfishbase::species(fields = c("Species", "DemersPelag"))
reef_species <- reef_species[reef_species$DemersPelag == "reef-associated", ]

# Get native and endemic species from the Atlantic, Pacific, and Indian Oceans
eco <- rfishbase::ecosystem(species_list = reef_species$Species)
valid_idx <- eco$Status %in% c("native", "endemic") & eco$EcosystemName %in% c("Atlantic Ocean", "Pacific Ocean", "Indian Ocean") 
eco <- eco[valid_idx, c("Species", "EcosystemName")]

# Retrieve the phylogeny of only native reef species across all three oceans.
phy <- fishtree_phylogeny(species = eco$Species)

## ----data-cleaning-1----------------------------------------------------------
sample_matrix <- unclass(table(eco))
dimnames(sample_matrix)$Species <- gsub(" ", "_", dimnames(sample_matrix)$Species, fixed = TRUE)

## ----data-cleaning-2----------------------------------------------------------
nc <- geiger::name.check(phy, sample_matrix)
sample_matrix <- sample_matrix[!rownames(sample_matrix) %in% nc$data_not_tree, ]

## ----data-cleaning-3----------------------------------------------------------
cophen <- cophenetic(phy)
sample_matrix <- t(sample_matrix)

## ----results------------------------------------------------------------------
picante::ses.mpd(sample_matrix, cophen, null.model = "taxa.labels", runs = 99)
picante::ses.mntd(sample_matrix, cophen, null.model = "taxa.labels", runs = 99)

## ----plot, fig.width = 7, fig.height = 20-------------------------------------
plot(phy, show.tip.label = FALSE, no.margin = TRUE)
obj <- get("last_plot.phylo", .PlotPhyloEnv)

matr <- t(sample_matrix)[phy$tip.label, ]
xx <- obj$xx[1:obj$Ntip]
yy <- obj$yy[1:obj$Ntip]
cols <- c("#1b9e77", "#d95f02", "#7570b3")
for (ii in 1:ncol(matr)) {
  present_idx <- matr[, ii] == 1
  points(xx[present_idx] + ii, yy[present_idx], col = cols[ii], cex = 0.1)
}