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alien-birds-checklist's Introduction

Checklist of non-native birds in Belgium

Rationale

This repository contains the functionality to standardize the Checklist of alien birds in Belgium to a Darwin Core checklist that can be harvested by GBIF.

Workflow

source data (maintained as a Google Spreadsheet) β†’ Darwin Core mapping script β†’ generated Darwin Core files

Published dataset

Repo structure

The repository structure is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.

β”œβ”€β”€ README.md              : Description of this repository
β”œβ”€β”€ LICENSE                : Repository license
β”œβ”€β”€ checklist-recipe.Rproj : RStudio project file
β”œβ”€β”€ .gitignore             : Files and directories to be ignored by git
β”‚
β”œβ”€β”€ data
β”‚   β”œβ”€β”€ raw                : Source data, input for mapping script
β”‚   └── processed          : Darwin Core output of mapping script GENERATED
β”‚
β”œβ”€β”€ docs                   : Repository website GENERATED
β”‚
└── src
    β”œβ”€β”€ dwc_mapping.Rmd    : Darwin Core mapping script, core functionality of this repository
    β”œβ”€β”€ _site.yml          : Settings to build website in docs/
    └── index.Rmd          : Template for website homepage

Installation

  1. Clone this repository to your computer
  2. Open the RStudio project file
  3. Open the dwc_mapping.Rmd R Markdown file in RStudio
  4. Install any required packages
  5. Click Run > Run All to generate the processed data
  6. Alternatively, click Build > Build website to generate the processed data and build the website in docs/ (advanced)

Contributors

List of contributors

License

MIT License for the code and documentation in this repository. The included data is released under another license.

alien-birds-checklist's People

Contributors

lienreyserhove avatar peterdesmet avatar sannegovaert avatar

Watchers

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alien-birds-checklist's Issues

Clean up sources

  1. Many (202) sources are empty and should be completed as much as possible
  2. For several records, the source states GBIF (data download not possible on (date) - gbif download error): Could you please check whether the download is possible now and supplement the dataset with a working link?
  3. The following sources could be cleaned somewhat:
  • GBIF occurrence downloads: should be refered to as

GBIF.org (14 August 2018) GBIF Occurrence Download https://doi.org/10.15468/dl.example-donotcite

  • wnm.be is a website for audiovisual solutions. I assume you mean https://waarnemingen.be :-)

  • observations.be and Observations.be: change to https://observations.be and preferably link to the observation (if applicable)

  • Try to use consistent format for reference (e.g. Author N. (year) Title. Journal, volume: pages

Separate records for different localities

To integrate different localities for one species, I found two approaches in the dataset:

  1. Two different lines, one line per location (e.g. for Oxyura jamaicensis)
  2. One line for two loations (e.g. Poicephalus senegalus), with localities separated by a comma

The specifications in the legend say that only one value for location information is allowed. I will integrate this accordingly, and make two (or more) different lines with only one piece of location information per species

institutionCode and rightsHolder

Which organization can be considered as the rightsholder of the published data?
I'm now using INBO for both the institutionCode and rightsHolder as the publication falls under the TrIAS project, but perhaps we need to change this?

Update checklist birds 2024

We will release a new publication. I moved the data from the old spreadsheet to the new big spreadsheet with all checklists together, so it is easier to manage. Can you check wether the current checklist is up to date?

Most important is to check:

  • In the old checklist, row 212 - 245 are marked in red. What is the meaning of this, and is it still relevant?
  • In the old checklist, there are several tabs, e.g. removed and not included. I did not copy those to the new spreadsheet. Check if this is ok. See #2
  • Is it correct that the line with Poephila guttata can be deleted? See #15
  • add the species that were introduced since the last publication
  • There is many missing data. Please fill in as much as possible, especially for degree of establishment, introduction pathway, date first observation (see #11, but this counts for all species) , date last observation and source.
  • clean up source, see #6. The original source of an observation cannot be the unified checklist. The original source is a publication, unpublished observation, or an observation that has a link (e.g. a specific link to observation.org).
  • Make sure all data is correct/updated.

Removed and not included taxa in gsheets file

The googlesheets file contains 5 different tabs:

  • checklist
  • legend
  • removed
  • not included
  • alien birds in unified checklist

With respect to the last three, it's not clear to me why there's a distinction between removed and not included, and why there's a need for a tab alien birds in unified checklist. Especially with respect to the last, you will need to maintain both in case of updates which is not very efficient.

Add date of introduction for Columba livia

While working on occurrence indicators I noticed that the datacube has a taxon which refers to the pigeon, Columba livia.

Moving backwards in the processing chain I found this taxon in the unified checklist and there I found that it has been published in the Alien birds checklist:
https://www.gbif.org/species/159498341

I am not an expert and I didn't know it is an alien species in Belgium. @timadriaens ? Any comment about?

By the way, it seems it is considered alien even in GRIIS of Denmark and UK:
https://www.gbif.org/species/148742092
https://www.gbif.org/species/148704311

Form as taxon rank correct?

Lonchura striata domestica has a taxon rank form attached to it. Is this correct?
My feeling is that this should be subspecies.

species that should not be on the unified checklist

Hi, scrolling through some emerging species products further down the pipeline and through the unified checklist itself, there are still a number of species that should not occur on the unified checklist. I use this issue to report them:

  • Carex pendula (Hangende zegge is a native species, the reference given in the unified is https://doi.org/10.15468/wtda1m which is the MAP, but this species in not on MAP): see trias-project/unified-checklist#53

  • Anser anser (mixed populations, should be excluded from alien bird checklist)

  • Branta leucopsis (mixed populations, should be excluded from alien bird checklist)

  • Junco hyemalis (vagrant, should be excluded from alien bird checklist) see this issue

Clean up remarks

I cleaned up some of the remarks:

  • occ --> occurrence or occurrences
  • observations.be --> https://observations.be
  • gbif --> GBIF
  • waarnemingne.be dataset: removed dataset
  • IUCN to IUCN red list

remove Junco hyemalis from alien bird checklist

see this issue, which popped up when drafting indicators, for justification. The species occurs on the alien bird checklist (and rightly so < escapes) Γ nd in the dataset of (native) bird observations of waarnemingen.be (link).

Yet, we have decided to discard such species from the checklist: "Species with populations of mixed origin (escaped and wild) in Belgium (e.g. barnacle goose Branta leucopsis, greylag goose Anser anser) were not considered true alien species and were excluded from the list. Also excluded are native species that are used for restocking (e.g. grey partridge Perdix perdix) or birds that might have popped up occasionally as escapes from collections but that also occur as rare migrants or occur as native breeders. "

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