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Pathway count indicator table

Source: R/get_table_pathways.R
get_table_pathways.Rd

Function to get number of taxa introduced by different pathways. Possible breakpoints: taxonomic (kingdom + vertebrates/invertebrates), temporal (lower limit year).

Usage

get_table_pathways(
  df,
  category = NULL,
  from = NULL,
  n_species = 5,
  kingdom_names = "kingdom",
  phylum_names = "phylum",
  first_observed = "first_observed",
  species_names = "canonicalName"
)

Arguments

df

df.

category

NULL or character. One of the kingdoms as given in GBIF:

  • "Plantae"

  • "Animalia"

  • "Fungi"

  • "Chromista"

  • "Archaea"

  • "Bacteria"

  • "Protozoa"

  • "Viruses"

  • "incertae sedis"

It can also be one of the following not kingdoms: #'

  • Not Chordata. Default: NULL.

from

NULL or numeric. Year trade-off: if not NULL select only pathways related to taxa introduced during or after this year. Default: NULL.

n_species

numeric. The maximum number of species to return as examples per pathway. For groups with less species than n_species, all species are given. Default: 5.

kingdom_names

character. Name of the column of df containing information about kingdom. Default: "kingdom".

phylum_names

character. Name of the column of df containing information about phylum. This parameter is used only if category is one of: "Chordata", "Not Chordata". Default: "phylum".

first_observed

character. Name of the column of df containing information about year of introduction. Default: "first_observed".

species_names

character. Name of the column of df containing information about species names. Default: "canonicalName".

Value

a data.frame with 4 columns: pathway_level1, pathway_level2, n (number of taxa) and examples.

Examples

if (FALSE) { # \dontrun{
library(readr)
datafile <- paste0(
  "https://raw.githubusercontent.com/trias-project/indicators/master/data/",
  "interim/data_input_checklist_indicators.tsv"
)
data <- read_tsv(datafile,
  na = "NA",
  col_types = cols(
    .default = col_character(),
    key = col_double(),
    nubKey = col_double(),
    speciesKey = col_double(),
    acceptedKey = col_double(),
    first_observed = col_double(),
    last_observed = col_double()
  )
)
get_table_pathways(data)
# Specify kingdom
get_table_pathways(data, "Plantae")
# with special categories, `Chordata` or `not Chordata`
get_table_pathways(data, "Chordata")
get_table_pathways(data, "Not Chordata")
# From 2000
get_table_pathways(data, from = 2000, first_observed = "first_observed")
# Specify number of species to include in examples
get_table_pathways(data, "Plantae", n_species = 8)
# Specify columns containing kingdom and species names
get_table_pathways(data,
  "Plantae",
  n_species = 8,
  kingdom_names = "kingdom",
  species_names = "canonicalName"
)
} # }