This document describes how to estimate PoD curve parameters using PoDBAY package. This process can be applied when user doesn’t have individual level data about vaccinated and control populations, but only summary statistics data and corresponding estimatedcase-count vaccine efficacy.
The goal of this document is to show how to estimate point estimate of PoD curve parameters in two steps
Required input:
Required input:
Function PoDEfficacySquaredError()
is used to estimate et50 and γ. As the inputs to the function we use vaccinated
and control
mock-up population class objects together with artificially chosen TrueEfficacy
parameter.
Note: To convert your data in to the population
class object use generatePopulation()
function from PoDBAY package. See vignette vignette("population", package = "PoDBAY")
for further details.
# Mockup vaccinated and control population class objects
data(vaccinated)
data(control)
# Observed vaccine efficacy
0.53
TrueEfficacy <-
# PoD curve parameter estimation
PoDEfficacySquaredError(TrueEfficacy,
params_et50_slope <-
vaccinated,
control,initialSlope = 6)
params_et50_slope#> et50 slope
#> 5.268031 6.179620
NOTE
Once we have et50 and γ estimated we can proceed with pmax estimation using PmaxEstimation
. As the inputs to the function we use estimated et50 and γ, control
mock-up population class object together with artificially chosen IncidenceRate
parameter.
# Incidence rate for low titer population
0.02
IncidenceRate <-
# pmax estimation
PmaxEstimation(IncidenceRate, params_et50_slope, control)
pmax <-
# combining PoD curve parameters
unlist(c(params_et50_slope, pmax))
PoDParams <-
PoDParams#> et50 slope pmax
#> 5.26803128 6.17962043 0.03552708