Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(dplyr)
library(ggplot2)
set.seed(1234)
## ----TrialAData---------------------------------------------------------------
library(PoDBAY)
data(diseased)
data(nondiseased)
str(diseased)
str(nondiseased)
## ----TrialAPoDEst, results = "hide", cache = TRUE-----------------------------
estimatedParameters <- PoDParamEstimation(diseasedTiters = diseased$titers,
nondiseasedTiters = nondiseased$titers,
nondiseasedGenerationCount = nondiseased$N,
repeatCount = 50)
## ---- echo = FALSE------------------------------------------------------------
as_tibble(estimatedParameters$resultsPriorReset)
## ---- echo = FALSE------------------------------------------------------------
as_tibble(estimatedParameters$results)
## -----------------------------------------------------------------------------
PoDParamsPointEst <- PoDParamPointEstimation(estimatedParameters$resultsPriorReset)
PoDParamsPointEst
## -----------------------------------------------------------------------------
PoDParametersCI <- PoDParamsCI(estimatedParameters$results, ci = 0.95)
unlist(PoDParametersCI)
## ---- fig.width = 5-----------------------------------------------------------
titers <- seq(from = 0, to = 15, by = 0.01)
PoDCurve <- PoDCurvePlot(titers,
estimatedParameters,
ci = 0.95)
PoDCurve
## ----TrialBData---------------------------------------------------------------
data(vaccinated)
data(control)
str(vaccinated)
str(control)
## ----EfficacyPointEstimate----------------------------------------------------
means <- list("vaccinated" = vaccinated$mean,
"control" = control$mean)
standardDeviations <- list("vaccinated" = vaccinated$stdDev,
"control" = control$stdDev)
EfficacyPointEst <- efficacyComputation(PoDParamsPointEst,
means,
standardDeviations)
EfficacyPointEst
## ----EfficacySet--------------------------------------------------------------
efficacySet <- PoDBAYEfficacy(estimatedParameters$results,
vaccinated,
control)
## ----EfficacyCI---------------------------------------------------------------
CI <- EfficacyCI(efficacySet, ci = 0.95)
unlist(CI)
## ---- fig.width = 5-----------------------------------------------------------
result <- list(
EfficacyPointEst = EfficacyPointEst,
efficacyCI = unlist(CI),
PoDParamsPointEst = PoDParamsPointEst,
PoDParametersCI = unlist(PoDParametersCI),
PoDCurve = PoDCurve
)
result
## -----------------------------------------------------------------------------
data(diseased)
data(nondiseased)
# Immunogenicity sample created
ImmunogenicitySample <- BlindSampling(diseased, nondiseased, method = list(name = "Fixed", value = 200))
nondiseasedImmunogenicitySample <- ImmunogenicitySample$ImmunogenicityNondiseased
str(diseased)
str(nondiseasedImmunogenicitySample)
## ----ApxPoDEst, results = "hide", cache = TRUE--------------------------------
estimatedParametersAP <- PoDParamEstimation(diseasedTiters = diseased$titers,
nondiseasedTiters = nondiseasedImmunogenicitySample$titers,
nondiseasedGenerationCount = nondiseased$N,
repeatCount = 50)
## ---- echo = FALSE------------------------------------------------------------
as_tibble(estimatedParametersAP$resultsPriorReset)
## ---- echo = FALSE------------------------------------------------------------
as_tibble(estimatedParametersAP$results)
## -----------------------------------------------------------------------------
PoDParamsPointEst <- PoDParamPointEstimation(estimatedParametersAP$resultsPriorReset)
PoDParamsPointEst
## -----------------------------------------------------------------------------
PoDParametersCI <- PoDParamsCI(estimatedParametersAP$results)
unlist(PoDParametersCI)
## ---- fig.width = 5-----------------------------------------------------------
titers <- seq(from = 0, to = 15, by = 0.01)
PoDCurve <- PoDCurvePlot(titers,
estimatedParametersAP,
ci = 0.95)
PoDCurve
## ----AppendixTrialBData-------------------------------------------------------
# Immunogenicity sample - vaccinated
str(ImmunogenicitySample$ImmunogenicityVaccinated)
# Immunogenicity sample - control
str(ImmunogenicitySample$ImmunogenicityControl)
## ----AppendixEfficacyPointEstimate--------------------------------------------
means <- list("vaccinated" = ImmunogenicitySample$ImmunogenicityVaccinated$mean,
"control" = ImmunogenicitySample$ImmunogenicityControl$mean)
standardDeviations <- list("vaccinated" = ImmunogenicitySample$ImmunogenicityVaccinated$stdDev,
"control" = ImmunogenicitySample$ImmunogenicityControl$stdDev)
EfficacyPointEst <- efficacyComputation(PoDParamsPointEst,
means,
standardDeviations)
EfficacyPointEst
## ----AppendixEfficacySet------------------------------------------------------
efficacySet <- PoDBAYEfficacy(estimatedParametersAP$results,
ImmunogenicitySample$ImmunogenicityVaccinated,
ImmunogenicitySample$ImmunogenicityControl)
## ----AppendixEfficacyCI-------------------------------------------------------
CI <- EfficacyCICoverage(efficacySet)
unlist(CI)
## ---- fig.width = 5-----------------------------------------------------------
result <- list(
EfficacyPointEst = EfficacyPointEst,
efficacyCI = unlist(CI),
PoDParamsPointEst = PoDParamsPointEst,
PoDParametersCI = unlist(PoDParametersCI),
PoDCurve = PoDCurve
)
result
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.