variable_frequency_epiweek: Simple log odds freqency plot for given variable. Does not...

In emvolz-phylodynamics/variantAnalysis: sarscov2 variant analysis

Description

If the column 'weight' is in the input data frame, this will use the values to weight each observation. If computing for genotypes you will want to remove gaps and 'X' before passing to this function; also deduplicate by patient id.

Usage

variable_frequency_epiweek(
  s,
  variable = "genotype",
  value = "mutant",
  mint = -Inf,
  maxt = Inf,
  detailed = TRUE,
  form = y ~ s(sample_time, bs = "gp", k = 5)
)

Arguments

s	data frame which must contain sample_time and 'variable' for each sequence
variable	Column of s which contains variable to split the data
value	The value in conlumn 'variable' for which we will compute frequency
mint	Minimum sample time to include
maxt	Max time to include
form	formula passed to mgcv::gam for estimating frequencies

Value

list with data, plots, and estimated frequencies

emvolz-phylodynamics/variantAnalysis documentation built on Nov. 13, 2021, 7:16 p.m.