Skip to content

Latest commit

 

History

History
96 lines (67 loc) · 3.51 KB

README.md

File metadata and controls

96 lines (67 loc) · 3.51 KB
Raw

Repo to accompany

Unevenly distributed biological invasion costs among origin and recipient regions

in Nature Sustainability.

Emma J. Hudgins*, Ross N. Cuthbert*, Phillip J. Haubrock*, Nigel G. Taylor, Melina Kourantidou, Dat Nguyen, Alok Bang, Anna J. Turbelin, Desika Moodley, Elizabeta Briski, Syrmalenia G. Kotronaki, Franck Courchamp

* equivalent contribution

code written by Dat Nguyen and Emma J Hudgins

SCRIPTS

  1. 001-get_range_EH.R
  • provides the functions getRangeGISD, getRangeCABI and trim to retrieve dataset
  1. 002-native_ranges_countries_fourpointone.R
  • using all invacost species in invacost package (version 4.1), attempts to download the ranges
  • also checks whether it has an accepted name or synonyms and attempts the process on those as well

see our extended InvaCost region-to-country designation:

  • 6 unique cases were manually mapped:

    kosovo = "Europe"
    tropical america = "Central America"
    pacific northwest = "Asia"
    north america = "North America"
    atlantic coast (north america) = "North America"
    indian ocean - western = "Africa"

  1. 003-data_cleaning_fourpointone.R
  • joins double-checked origin list (givers_takers_doublecheck_.csv) to invacost data
  1. 004-assign_con_DN_fourpointone.R
  • standardizes continent designations with pre-defined list
  1. 0041-add4p1Countries.R
  • additional code to add continent designations for new data entries not present in the first version of our analysis (Invacost 3.0)
  1. 005_analysis_script.R
  • performs analyses of the manuscript at the continent level (Figs 1-2)
  1. 006_countrylevel_script.R
  • performs country-level analyses of the manuscript (Figs 3-4)

KEY FILES

see also old_data_givers_takers folder for Invacost 3.0 files

  1. Datasheet_201911240709.csv
  • Full list of species with datasheets from CABI
  • Used in get_native.R to supplement the downloading process, to reduce error as getRangeCABI would have to Google the species without a match
  1. country-origin-ref_4p1_DN.csv
  • reference for continent designation by country and iso3c code
  1. givers_takers_doublecheck_fourpointone.csv
  • result of manual double checking of web scraped origin data
  1. Gravity_V202102.Rds
  • CEPII Gravity database as of February 2022
  1. island.nations.csv
  • pre-determined continent designations for island nations
  1. Invacost_database_v4.1.csv
  • equivalent to calling data(invacost) from the invacost package with the version argument set to 4.1
  1. invacost_origin_expanded_fourpointone_DN2.csv
  • expanded invacost database joined to origin country designations
  1. soc_econ_country.rds
  • socioeconomic predictors from Sardain et al. 2019
  1. sTwist_database.csv
  • IAS first record and country occurrence information from Seebens et al. (2022)

10.turbelinetal_2017_IAS.csv

  • IAS load for each country by iso3c code from Turbelin et al. 2017

KEY OUTPUT

  1. tax_accepted_fourpointone.rds and tax_synonyms_fourpointone.rds
  • output from native_ranges_countriesnew.R
  • list of accepted names and synonyms for species that were originally missing from first pass using invacost species names
  1. trade_averaged.RDS, trade_historical.RDS
  • average yearly pairwise trade for 21st and 20th century
  1. senders.RDS, receivers.RDS, top_pairs.RDS
  • flows at country level
  1. given., received.
  • flows at continent level
  1. invacost_givers_data., invacost_takers_data.
  • decadal flows at continent level
  1. pubs_per_receiving_continent.csv
  • number of publications by which cost per publication was derived per receiving continent