Counts over time

You have counts per week from a surveillance programme, or of mutations per passage from an evolution experiment, and perhaps an estimate over the same time: a reproductive number, a population size.

karyon --frequencies lineages.tsv \
  --phylodynamics reproduction.tsv --threshold 1 -o time.svg

No place is named: the tables are their own place, and the ruler counts their weeks. Each week's lineages fill the band to 100%, and under them is the estimate with its interval and a dashed line at 1.

Your tables

One row per group per time, under a header:

week    lineage  count  total
1       A        106    124
1       B.1      6      124

The columns are found by their names: the time as week, day, month, year or time, the group as lineage, mutation or variant, then count and total. The estimate is a time, a mean, median or estimate, and lower and upper where there is an interval. Tabs, commas or spaces separate the columns. A time is a number of weeks, days, months or years, as week 12 or year 2015; a skyline in decimal years, as BEAST writes one, is drawn as the continuous time it is, to a thousandth of a year.

Change it

To	Write
A line per group, each read against the whole	--style line after the counts
Some of the weeks	week:10-30 as the place, before the files
A population size on a log scale	--phylodynamics skyline.tsv --log
Only the counts, or only the estimate	leave the other file out

The example files: lineages.tsv and reproduction.tsv. Every option: karyon help frequencies and karyon help phylodynamics, or the command line reference.