query: Query GISAID Database

In Wytamma/GISAIDR: R wrapper for GISAID "API"

Query GISAID Database

Description

Query GISAID Database

Usage

query(
  credentials,
  location = NULL,
  lineage = NULL,
  from = NULL,
  from_subm = NULL,
  to = NULL,
  to_subm = NULL,
  start_index = 0,
  nrows = 50,
  load_all = FALSE,
  low_coverage_excl = FALSE,
  complete = FALSE,
  high_coverage = FALSE,
  collection_date_complete = FALSE,
  total = FALSE
)

Arguments

credentials	GISAID credentials.
location	search for entries based on geographic location.
lineage	search for entries based on pango lineage designations.
from	search from specific collection date.
from_subm	search from specific submission date.
to	search to specific collection date.
to_subm	search to specific submission date.
start_index	page through results.
nrows	number of results to return.
load_all	return all results.
low_coverage_excl	exclude low coverage entries from the results.
complete	include only complete entries in the results.
high_coverage	include only high coverage entries in the results.
collection_date_complete	include only entries with complete in collection date the results.
total	returns the total number of sequences matching the query.

Value

Dataframe.

Wytamma/GISAIDR documentation built on April 14, 2025, 1:50 p.m.