Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
opt <- options()
options(continue=" ", width=70, prompt=" ")
on.exit(options(opt))
library(iDOVE, quietly=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# intCens(entry_time, left_time, right_time, vaccination_time)
## ----usage, eval=FALSE--------------------------------------------------------
# idove(formula, data, constantVE = FALSE, plots = TRUE,
# changePts = NULL, timePts = NULL, tol = 0.0001, maxit = 2000)
## ----intCens-usage, eval=FALSE------------------------------------------------
# intCens(entry_time, left_time, right_time, vaccination_time) ~ covariates
## ----data-load----------------------------------------------------------------
data(idoveData)
## ----data-head----------------------------------------------------------------
head(idoveData)
## ----data-summary-------------------------------------------------------------
summary(idoveData)
summary(idoveData$right.time[is.finite(idoveData$right.time)])
## ----idove-noaic, fig.show='hide', echo=TRUE, eval=FALSE----------------------
# model <- intCens(entry.time, left.time, right.time, vaccine.time) ~ priority + sex
# result1 <- idove(formula = model,
# data = idoveData,
# changePts = 4*7,
# timePts = c(4, 16, 28, 40)*7)
## ----idove-noaic-read, echo = FALSE, eval = TRUE------------------------------
result1 <- readRDS(file="result1.rds")
## ----idove-noaic-return-call--------------------------------------------------
result1$call
## ----idove-noaic-return-changePts---------------------------------------------
result1$changePts
## ----idove-noaic-return-covariates--------------------------------------------
result1$covariates
## ----idove-noaic-return-VE----------------------------------------------------
head(result1$vaccine$VE_a)
tail(result1$vaccine$VE_a)
head(result1$vaccine$VE_h)
tail(result1$vaccine$VE_h)
## ----idove-naic-return-interval-----------------------------------------------
result1$vaccine$VE_period
## ----idove-noaic-plot, eval=FALSE---------------------------------------------
# plot(x = result1)
## ----idove-noaic-show-plot, echo=FALSE, out.width='49%',fig.cap='\\label{fig:idoveFigs}Plots auto-generated by \\textit{idove()}. On the left, the estimated $VE_a(t)$ curve (black) and its $95\\%$ confidence intervals (green) are shown as a function of the time since vaccination. On the right, the estimated $VE_h(t)$ curve (black) and its $95\\%$ confidence intervals (green) are shown as a function of the time since vaccination.' , fig.show='hold', fig.align='center'----
knitr::include_graphics(
path=c("idove1a.pdf","idove1b.pdf"),
auto_pdf = getOption("knitr.graphics.auto_pdf", FALSE),
dpi = NULL,
error = getOption("knitr.graphics.error", TRUE)
)
## ----idove-constantVE, echo=TRUE, eval=FALSE----------------------------------
# result2 <- idove(formula = model, data = idoveData, constantVE = TRUE)
## ----idove-constantVE-read, echo = FALSE, eval = TRUE-------------------------
result2 <- readRDS(file="result2.rds")
## ----idove-constantVE-return-covariates---------------------------------------
result2$covariates
## ----idove-aic-return-VE------------------------------------------------------
result2$vaccine$VE
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.