estimate_rt: Estimate reproduction over time by group

In mrc-ide/pika: Evaluate Correlation Between Time Series

Description

This function estimates reproduction number by group using EpiEstim's estimate_R() and then binds the results together into a single data frame

Usage

estimate_rt(
  dat,
  grp_var,
  date_var,
  incidence_var,
  est_method = "parametric_si",
  si_mean = 6.48,
  si_std = 3.83
)

Arguments

dat	data frame with columns that correspond to two time series and grouping variable(s)
grp_var	character string of column names in dat to be used as grouping variable(s)
date_var	primary time series (should be a column in dat)
incidence_var	secondary time series (should be a column in dat)
est_method	estimation method to be used to estimate R in EpiEstim: c("non_parametric_si","parametric_si","uncertain_si","si_from_data","si_from_sample")
si_mean	mean of serial interval distribution to be specified when est_method = "parametric_si"
si_std	standard deviation of serial interval distribution to be specified when est_method = "parametric_si"

Value

data frame of mean, median, and 95

mrc-ide/pika documentation built on May 18, 2020, 8:55 p.m.