get_table_pathways: Pathway count indicator table

In trias-project/trias: Process Data for the Project Tracking Invasive Alien Species (TrIAS)

Pathway count indicator table

Description

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: #' Chordata 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

## Not run: 
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"
)

## End(Not run)

trias-project/trias documentation built on Sept. 18, 2024, 11:50 a.m.