obstools: Extract measurements from observations

In rplzzz/vacovdata: COVID-19 Data for the Commonwealth of Virginia

Description

Extract measurements of growth rates and sample prevalences from observed data. The observations are relatively noisy, so windowed smoothing is used.

Usage

fitgr(
  obsdata,
  winsize = 7,
  poscol = "pos",
  totcol = "tot",
  iscumul = TRUE,
  ksmooth = 7
)

smoothprev(
  obsdata,
  winsize = 7,
  poscol = "pos",
  totcol = "tot",
  iscumul = TRUE
)

Arguments

obsdata	Data frame of observations. Date in column date daily normalized observations in column given in the col argument
winsize	Window size calculating rates and positive fractions
poscol	Name of the column holding the positive observations
totcol	Name of the column holding the total observations
iscumul	Flag indicating whether poscol and totcol are cumulative
ksmooth	Smoothing length in days for growth rates. Zero means no smoothing.

Details

If smooth is set, the smoothing is done before the growth rate bias correction is applied.

Functions

• fitgr: Measure growth rate from observations

• smoothprev: Measure sample prevalence with smoothing

rplzzz/vacovdata documentation built on June 8, 2020, 2:41 a.m.