## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(DAISIEprep) library(ape) library(phylobase) ## ----sim-data, fig.height=5, fig.width=8-------------------------------------- set.seed(1) tree <- ape::rcoal(10) tree$tip.label <- paste("Plant", letters[1:10], sep = "_") tree$tip.label[4] <- "Plant_d_a" tree$tip.label[5] <- "Plant_d_b" phylo <- phylobase::phylo4(tree) endemicity_status <- c("not_present", "not_present", "not_present", "nonendemic", "nonendemic", "not_present", "not_present", "not_present", "endemic", "not_present") phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status)) plot_phylod(phylod) ## ----------------------------------------------------------------------------- island_tbl <- extract_island_species(phylod = phylod, extraction_method = "min") island_tbl ## ----sample-label, fig.height=5, fig.width=8---------------------------------- endemicity_status <- c("not_present", "not_present", "not_present", "nonendemic", "not_present", "not_present", "not_present", "not_present", "endemic", "not_present") phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status)) plot_phylod(phylod) ## ----------------------------------------------------------------------------- island_tbl <- extract_island_species(phylod = phylod, extraction_method = "min") island_tbl ## ----species-encode-endemic, fig.height=5, fig.width=8------------------------ endemicity_status <- c("not_present", "not_present", "not_present", "endemic", "endemic", "not_present", "not_present", "not_present", "endemic", "not_present") phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status)) plot_phylod(phylod) island_tbl <- extract_island_species(phylod = phylod, extraction_method = "min") island_tbl ## ----species-encode-endemic-3, fig.height=5, fig.width=8---------------------- phylobase::tipLabels(phylo) <- c("Plant_a", "Plant_d_a", "Plant_d_b", "Plant_d_c", "Plant_d_d", "Plant_b", "Plant_c", "Plant_e", "Plant_f", "Plant_g") endemicity_status <- c("not_present", "endemic", "endemic", "endemic", "endemic", "not_present", "not_present", "not_present", "endemic", "not_present") phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status)) plot_phylod(phylod) island_tbl <- extract_island_species(phylod = phylod, extraction_method = "min") island_tbl ## ----geo-encode-2-island, fig.height=5, fig.width=8--------------------------- phylobase::tipLabels(phylo) <- c("Plant_a", "Plant_b", "Plant_c", "Plant_d", "Plant_e", "Plant_f", "Plant_g_mainland", "Plant_g_island_b", "Plant_g_island_a", "Plant_h") endemicity_status <- c("not_present", "not_present", "not_present", "not_present", "not_present", "not_present", "not_present", "nonendemic", "nonendemic", "not_present") phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status)) plot_phylod(phylod) island_tbl <- extract_island_species(phylod = phylod, extraction_method = "min") island_tbl