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(v1.5.0.9019) use functions without loading AMR pkg

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dr. M.S. (Matthijs) Berends
2021-02-17 10:58:13 +01:00
parent 2dd0656355
commit 601ea7377c
30 changed files with 90 additions and 74 deletions
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data-raw/AMR_1.5.0.9018.tar.gz → data-raw/AMR_1.5.0.9019.tar.gz
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data-raw/reproduction_of_microorganisms.R
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@ -25,8 +25,9 @@
# Reproduction of the `microorganisms` data set
# Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
# https://opendata.eol.org/dataset/catalogue-of-life/
# Data retrieved from the Catalogue of Life (CoL):
# https://download.catalogueoflife.org/col/monthly/life/
# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2020-12-01_dwca.zip)
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
# https://doi.org/10.15468/rffz4x
#
@ -38,7 +39,7 @@ library(AMR)
# also needed: data.table, httr, jsonlite, cleaner, stringr
# unzip and extract taxa.txt (both around 1.5 GB, 3.7-3.9M rows) from Col and GBIF, then:
data_col_raw <- data.table::fread("data-raw/taxon.tab", quote = "")
data_col_raw <- data.table::fread("data-raw/taxon.tsv", quote = "")
data_gbif <- data.table::fread("data-raw/taxa.txt", quote = "")
# merge the two