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Accessing GitHub Data

Source: vignettes/github_data.Rmd
github_data.Rmd

Description

The original accessions for the data sets included within datamuseum are also available on GitHub. These are from the Global Biodiversity Information Facility (GBIF), Invert-E-Base (InvBase), the Biological Information System for Marine Life (BISMAL), Ocean Biodiversity Information System (OBIS), and one data set obtained by direct request from the National Museum of Nature and Science, Japan (NSMT).

In this workflow, accessing the GBIF-sourced data directly from the GitHub repository for datamuseum will be demonstrated.

Due to the size of the data, the files are stored within a .zip folder. Luckily, R is capable of downloading and unzipping the files directly from a GitHub link!


rawzip <- tempfile()

download.file("https://github.com/btorgovitsky00/datamuseum/raw/master/data-raw.zip", rawzip, 
  mode = "wb")

temp <- tempdir()

unzip(rawzip, exdir = temp)

list.files(file.path(temp, "data-raw"))

Each data set in datamuseum has two associated parent files: the actual original accession from the respective repository (denoted as “raw”), and a version with some columns removed for improved visibility (“trim”).


#Raw Original Data

GBIF_raw <- read.csv(file.path(temp, "data-raw", "GBIF_Octopodoidea_raw.csv")) #88256 Observations


#Trimmed Original Data

GBIF_clean <- read.csv(file.path(temp, "data-raw", "GBIF_Octopodoidea_trim.csv")) #88256 Observations

The GBIF data sets were obtained and refined from the following occurrence download:

Global Biodiversity Information Facility (GBIF). GBIF.org (30 March 2026) GBIF Occurrence Download. https://www.gbif.org. doi: 10.15468/dl.2379hj