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Zenodo basics

Source: vignettes/10-zenodo.Rmd
10-zenodo.Rmd

dissmapr

A Novel Framework for Automated Compositional Dissimilarity and Biodiversity Turnover Analysis

1. Deposit all results into Zenodo

All data frames, tables, maps, and standard metadata can be deposited into Zenodo using zen4R or Zenodo UI.

Below is a minimal zen4R workflow showing how to create a new deposition, upload a file, and publish it to Zenodo:

  • Make sure ZENODO_TOKEN is set in your environment with deposit:write (and if plan to publish, deposit:actions) scope.
  • createDeposition(), uploadFile(), and publishDeposition() are all methods of the R6 ZenodoManager object.
  • Use downloadFiles() to pull back any/all files from a given record ID.

NOTE: This will only work if you have an existing Zenodo account. For step‐by‐step guidance on creating and managing your personal access token, consult the official Zenodo Developers documentation under Authentication.

For a tutorial on using zen4R to upload (and download) data, see the official zen4R vignette.

# # Install and load zen4R if you haven’t already
# # install.packages("zen4R")
# library(zen4R)
# 
# # 1. Authenticate (expects your token in ZENODO_TOKEN)
# token  = Sys.getenv("ZENODO_TOKEN")
# zenodo = ZenodoManager$new(token = token)
# 
# # 2. Create a new (empty) deposition with basic metadata
# dep = zenodo$createDeposition(
#   metadata = list(
#     title       = "My Example Dataset",
#     upload_type = "dataset",
#     description = "A demo upload via zen4R",
#     creators    = list(list(name = "Doe, Jane"))
#   )
# )
# 
# # 3. Upload your local file into that deposition
# zenodo$uploadFile(deposition = dep, file = "path/to/my_data.csv")
# 
# # 4. Publish the deposition (this mints a DOI)
# published = zenodo$publishDeposition(deposition = dep)
# message("Published DOI: ", published$doi)
# 
# # 5. Later on: download all files from that record into a folder
# zenodo$downloadFiles(record_id = dep$id, path = "downloads/")