get_nextclade_distribution: Get Nextclade Distribution of Sequenced Samples

In CUGBF/deidentifiedDB: Utility to Manage Clemson University COVID-19 Surveillance Data

Get Nextclade Distribution of Sequenced Samples

Description

Get Nextclade Distribution of Sequenced Samples

Usage

get_nextclade_distribution(
  viralrecon_tbl,
  sample_collection_tbl,
  start_date = "2021-01-01",
  end_date = as.character(lubridate::date(lubridate::now())),
  n_days = 30,
  time_zone = "America/New_York"
)

Arguments

viralrecon_tbl	viralrecon table from deidentifiedDB database
sample_collection_tbl	Sample Collection table from deidentifiedDB database
start_date	Filter sample collection table for samples collected after this date. Provide date as in "2021-08-01" for August 1, 2021
end_date	Filter sample collection table for samples collected on or before this date. Provide date as in "2021-08-01" for August 1, 2021
n_days	Duration of time (in days) for which only the first collected COVID-19 positive sample for a patient is retained
time_zone	Time zone for collection time (Default: "America/New_York")

Value

Tibble containing monthly count of sequenced samples in each Nextclade

CUGBF/deidentifiedDB documentation built on Sept. 13, 2023, 6:28 a.m.