Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#"
)
## ----install, eval = FALSE----------------------------------------------------
# devtools:::install_github("gunhanb/MetaStan")
## ----dataset------------------------------------------------------------------
library("MetaStan")
data("dat.Berkey1995", package = "MetaStan")
head(dat.Berkey1995)
## ----forestplot, echo=TRUE, results=TRUE--------------------------------------
library(ggplot2)
# Calculating log odds ratios and variances from data
logodds <- function(x) log((x[1] * (x[4] - x[3]))/((x[2] - x[1]) * x[3]))
stdes <- function(x) sqrt(1/x[1] + 1/(x[2] - x[1]) + 1/x[3] + 1/(x[4] - x[3]))
r_ind <- apply(cbind(dat.Berkey1995$r2, dat.Berkey1995$n2,
dat.Berkey1995$r1, dat.Berkey1995$n1), 1, logodds)
se_ind <- apply(cbind(dat.Berkey1995$r2, dat.Berkey1995$n2,
dat.Berkey1995$r1, dat.Berkey1995$n1), 1, stdes)
lower95_ind <- r_ind + qnorm(.025) * se_ind
upper95_ind <- r_ind + qnorm(.975) * se_ind
# Comparison of the results
trials <- c("1", "2" ,"3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13")
trials <- ordered(trials, levels = trials)
d <- data.frame(x = trials,
y = r_ind,
ylo = lower95_ind,
yhi = upper95_ind)
forest.plot <- ggplot(d, aes(x = x, y = y, ymin = ylo, ymax = yhi)) +
geom_pointrange() +
coord_flip() +
geom_hline(aes(yintercept=0), lty = 2) +
xlab("Studies") +
ggtitle("Forest Plot (BCG vaccines)")
plot(forest.plot)
## ----bnhmFit, results="hide"--------------------------------------------------
data('dat.Berkey1995', package = "MetaStan")
## Fitting a Binomial-Normal Hierarchical model using WIP priors
data('dat.Berkey1995', package = "MetaStan")
## Fitting a Binomial-Normal Hierarchical model using WIP priors
dat_MetaStan <- create_MetaStan_dat(dat = dat.Berkey1995,
armVars = c(responders = "r", sampleSize = "n"))
meta.BCG.stan <- meta_stan(data = dat_MetaStan,
likelihood = "binomial",
mu_prior = c(0, 10),
theta_prior = c(0, 100),
tau_prior = 0.5,
tau_prior_dist = "half-normal")
## ----shinystan, eval = FALSE--------------------------------------------------
# library("shinystan")
# ## Firstly convert "stan" object to a "shinystan" object
# bnhm1.BCG.shinystan = as.shinystan(meta.BCG.stan$fit)
# launch_shinystan(bnhm1.BCG.shinystan)
## ----print--------------------------------------------------------------------
print(meta.BCG.stan)
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