read_lineage_counts: Read lineage count data from a CSV file

In lineagefreq: Lineage Frequency Dynamics from Genomic Surveillance Counts

Read lineage count data from a CSV file

Description

A convenience wrapper for reading surveillance count data from CSV files into lfq_data format. Expects a file with at least columns for date, lineage, and count.

Usage

read_lineage_counts(
  file,
  date = "date",
  lineage = "lineage",
  count = "count",
  ...
)

Arguments

file	Path to CSV file.
date	Name of the date column. Default "date".
lineage	Name of the lineage column. Default "lineage".
count	Name of the count column. Default "count".
...	Additional arguments passed to lfq_data().

Value

An lfq_data object.

Examples

# Read the bundled example CSV
f <- system.file("extdata", "example_counts.csv",
                 package = "lineagefreq")
x <- read_lineage_counts(f)
x

lineagefreq documentation built on April 3, 2026, 9:09 a.m.