Pulls what is available on the COVID-19 lineage website: https://cov-lineages.org/lineage_list.html.
As of the recent changes in late 2022, this website only has a annual subset of lineages. Since
the table is embedded within the web-page the rvest package is used to read the HTML content.
To provide the full lineage name, the *Description* column is searched for Alias information based upon
the regular expression passed to the pattern parameter. If this parameter is set to NULL,
the alias search will be ignored and the full_name column will be excluded.
Usage
fetch_pango_summary_tbl(
url = "https://cov-lineages.org/lineage_list.html",
pattern = "^([Aa]lias of)\\s?([A-Z\\.\\d]*)[,]?\\s?.*$",
description_col = "Description",
slice = 1,
...
)Arguments
- url
Character value defining the location of the summary table from PANGOLIN.
- pattern
Regular expression to search description column for alias details.
- description_col
Name of the description column (default: 'Description').
- slice
Integer value (default: 1), controls which table from the page to extract.
- ...
Additional parameters to send to
read_html.