In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

# Look up plant occurrence data for Oregon
library(rgbif)
occ <- rgbif::occ_data(stateProvince = "Oregon",
                       scientificName = "Plantae")

# Parse data with taxa
library(taxa)
obj <- parse_tax_data(occ$data,
                      class_cols = c(22:26, 28),
                      named_by_rank = TRUE)

# Plot number of occurrences for each taxon
library(metacoder)
obj %>% 
  filter_obs("tax_data",
             basisOfRecord == "PRESERVED_SPECIMEN",
             drop_taxa = TRUE) %>%
  filter_taxa(taxon_ranks != "specificEpithet") %>%
  filter_taxa(! is.na(taxon_names)) %>%
  filter_taxa(taxon_names == "Tracheophyta",
              subtaxa = TRUE) %>%
  filter_taxa(taxon_ranks == "order", n_subtaxa > 10,
              subtaxa = TRUE, supertaxa = TRUE) %>%
  heat_tree(node_label = taxon_names,
            node_color = n_obs,
            node_size = n_obs,
            node_color_axis_label = "# occurrences",
            output_file = c("example_analysis_figure.eps",
                            "example_analysis_figure.pdf",
                            "example_analysis_figure.tiff"))

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.