Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(dplyr)
library(PoDBAY)
set.seed(1)
## -----------------------------------------------------------------------------
populationEmpty <- generatePopulation()
populationEmpty
## -----------------------------------------------------------------------------
vaccinated <- generatePopulation()
vaccinated$N <- 1000
vaccinated$mean <- 7
vaccinated$stdDev <- 2
str(vaccinated)
control <- generatePopulation()
control$N <- 1000
control$mean <- 5
control$stdDev <- 2
str(control)
## -----------------------------------------------------------------------------
vaccinated <- generatePopulation(N = 1000,
mean = 7,
stdDev = 2)
str(vaccinated)
control <- generatePopulation(N = 1000,
mean = 5,
stdDev = 2)
str(control)
## -----------------------------------------------------------------------------
vaccinated <- generatePopulation()
vaccinated$N <- 1000
vaccinated$mean <- 7
vaccinated$stdDev <- 2
str(vaccinated)
control <- generatePopulation()
control$N <- 1000
control$mean <- 5
control$stdDev <- 2
str(control)
## ---- results = "hide"--------------------------------------------------------
vaccinated$getTiters()
control$getTiters()
## -----------------------------------------------------------------------------
str(vaccinated)
str(control)
## -----------------------------------------------------------------------------
# Define PoD curve parameters
PoDParams <- data.frame("pmax" = 0.05, "et50" = 5, "slope" = 7)
# Assign PoD
vaccinated$assignPoD(
PoD(titer = vaccinated$titers,
pmax = PoDParams$pmax,
et50 = PoDParams$et50,
slope = PoDParams$slope,
adjustTiters = FALSE
))
control$assignPoD(
PoD(titer = control$titers,
pmax = PoDParams$pmax,
et50 = PoDParams$et50,
slope = PoDParams$slope,
adjustTiters = FALSE
))
str(vaccinated)
str(control)
## ---- eval = FALSE------------------------------------------------------------
# vaccinated$assignPoD(
# rep(0.05, vaccinated$N))
#
# control$assignPoD(
# rep(0.1, control$N))
## -----------------------------------------------------------------------------
CaseCount <- ClinicalTrial(vaccinated, control, CI = 0.95)
str(vaccinated)
str(control)
## ---- warning = FALSE---------------------------------------------------------
vaccinated$getDiseasedCount()
vaccinated$getNondiseasedCount()
vaccinated$getDiseasedTiters()
as_tibble(vaccinated$getNondiseasedTiters())
## -----------------------------------------------------------------------------
dataTrial <- data.frame("patno" = 1:20,
"treatment" = c(rep(FALSE, 10), rep(TRUE, 10)),
"titers" = as.numeric(c(rnorm(10, 5, 2),
rnorm(10, 7, 2)))
)
dataTrial
## -----------------------------------------------------------------------------
# vaccinated
vacc <- dataTrial %>% filter(treatment)
vaccinated <- generatePopulation()
vaccinated$N <- nrow(vacc)
vaccinated$mean <- mean(vacc$titers)
vaccinated$stdDev <- sd(vacc$titers)
vaccinated$titers <- vacc$titers
vaccinated
# control
ctrl <- dataTrial %>% filter(!treatment)
control <- generatePopulation()
control$N <- nrow(ctrl)
control$mean <- mean(ctrl$titers)
control$stdDev <- sd(ctrl$titers)
control$titers <- ctrl$titers
control
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