# "MVPBT: R package for publication bias tests in meta-analysis of diagnostic accuracy studies"
#  by Hisashi Noma
#  arXiv:2209.07270      available at: https://arxiv.org/abs/2209.07270

#  R example code for implementing generalized Egger tests for meta-analysis of diagnostic accuracy studies

# The "MVPBT" package
# CRAN page: https://cran.r-project.org/web/packages/MVPBT/

###

install.packages("MVPBT")			# Installation command

library("MVPBT")

require("metafor")
require("mada")


# Load the example dataset

data(cervical)

LAG <- cervical[cervical$method==2,]


# Perform the bivariate meta-analysis by the Reitsma model

fit1 <- reitsma(LAG)
summary(fit1)     # results of the bivariate meta-analysis


# Transform the dataset

attach(LAG)

dta1 <- edta(TP,FN,TN,FP)


# Create the SROC curve

par(mfrow=c(1,3))

plot(fit1, predict=TRUE, cex=1.5, pch=19, sroclty=1, sroclwd=1.5, lty=2, 
 main="(a) SROC plot", xlim=c(0,1), ylim=c(0,1))
points(dta1$Fp,dta1$Se,pch=20,col="blue")
legend(0.2,0.1,legend=c("95% confidence region","95% prediction region"),lty=c(2,3))


# Create the funnel plots

attach(dta1)

res1 <- rma(y[,1], S[,1])
funnel(res1,main="(b) Funnel plot for logit(Se)")
regtest(res1, model="lm")	# univariate Egger's test

res2 <- rma(y[,2], S[,3])
funnel(res2,main="(c) Funnel plot for logit(FPR)")
regtest(res2, model="lm")	# univariate Egger's test


# Perform the generalized Egger test (MSSET2)

MVPBT2(y,S)   # Generalized Egger test (MSSET2)


# Perform the generalized Egger test (MSSET3)

MVPBT3(y,S)   # Generalized Egger test (MSSET3)