Package 'MVPBT'

Title: Publication Bias Tests for Meta-Analysis of Diagnostic Accuracy Test
Description: Generalized Egger tests for detecting publication bias in meta-analysis for diagnostic accuracy test (Noma (2020) <doi:10.1111/biom.13343>, Noma (2022) <doi:10.48550/arXiv.2209.07270>). These publication bias tests are generally more powerful compared with the conventional univariate publication bias tests and can incorporate correlation information between the outcome variables.
Authors: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <[email protected]>
License: GPL-3
Version: 1.2-1
Built: 2025-02-13 04:12:12 UTC
Source: https://github.com/cran/MVPBT

Help Index


The 'MVPBT' package.

Description

Generalized Egger tests to detect publication bias in meta-analysis for diagnostic accuracy test.

References

Noma, H. (2020). Discussion of “Testing small study effects in multivariate meta-analysis” by Chuan Hong, Georgia Salanti, Sally Morton, Richard Riley, Haitao Chu, Stephen E. Kimmel, and Yong Chen. Biometrics 76: 1255-1259. doi:10.1111/biom.13343

Noma, H. (2022). MVPBT: R package for publication bias tests in meta-analysis of diagnostic accuracy studies. arXiv:2209.07270. doi:10.48550/arXiv.2209.07270


Funnel plots for the bivariate outcomes

Description

Funnel plots for the bivariate outcomes of diagnostic meta-analysis are created.

Usage

bifunnel(y,S)

Arguments

y

Summary outcome statistics

S

Covariance estimates of y

Value

Funnel plots for the logit-transformed sensitivities and false positive rates are presented.

References

Noma, H. (2020). Discussion of “Testing small study effects in multivariate meta-analysis” by Chuan Hong, Georgia Salanti, Sally Morton, Richard Riley, Haitao Chu, Stephen E. Kimmel, and Yong Chen. Biometrics 76: 1255-1259. doi:10.1111/biom.13343

Noma, H. (2022). MVPBT: R package for publication bias tests in meta-analysis of diagnostic accuracy studies. arXiv:2209.07270. doi:10.48550/arXiv.2209.07270

Examples

require(metafor)
require(mada)

data(cervical)

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

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

###

attach(LAG)

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

###

attach(dta1)

bifunnel(y,S)

Scheidler et al. (1997)'s cervical cancer data

Description

Dataset of a meta-analysis of diagnostic accuracy for radiological evaluation of lymph node metastases in patients with cervical cancer.

Usage

data(cervical)

Format

A data frame with 44 rows and 8 variables

  • id: identification number

  • author: The first author name of the corresponding study

  • year: The published year of the corresponding study

  • method: The diagnostic method; 1=CT (computed tomography), 2=LAG (lymphangiography), 3=MRI (magnetic resonance imaging)

  • TP: A vector of the number of true positives (TP)

  • FP: A vector of the number of false positives (FP)

  • FN: A vector of the number of false negatives (FN)

  • TN: A vector of the number of true negatives (TN)

References

Scheidler, J., Hricak, H., Yu, K. K., Subak, L., and Segal, M. R. (1997). Radiological evaluation of lymph node metastases in patients with cervical cancer. A meta-analysis. JAMA 278: 1096-1101.

Reitsma, J. B., Glas, A. S., Rutjes, A. W., Scholten, R. J., Bossuyt, P. M., and Zwinderman, A. H. (2005). Bivariate analysis of sensitivity and specificity produces informative summary measures in diagnostic reviews. Journal of Clinical Epidemiology 58: 982-990. doi:10.1016/j.jclinepi.2005.02.022


Transforming contingency table data to summary statistics in diagnostic studies

Description

Transforming contingency table data to summary statistics in diagnostic studies.

Usage

edta(TP,FN,TN,FP)

Arguments

TP

A vector of the number of true positives (TP)

FP

A vector of the number of false positives (FP)

FN

A vector of the number of false negatives (FN)

TN

A vector of the number of true negatives (TN)

Value

Summary statistics for meta-analysis are generated.

  • y: Logit-transformed sensitivities and false positive rates.

  • S: Within-study variances and covariances.

  • Se: Sensitivities.

  • Fp: False positive rates.

Examples

data(cervical)
LAG <- cervical[cervical$method==2,]

attach(LAG)

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

Generalized Egger test to detect publication bias in bivariate meta-analysis for diagnostic accuracy test (MSSET2)

Description

Generalized Egger test to detect publication bias in bivariate meta-analysis for diagnostic accuracy test (called MSSET2 in Noma (2020)). This test does not consider the uncertainties of heterogeneity variance-covariance parameters, so MVPBT3 is recommended in practice.

Usage

MVPBT2(y,S)

Arguments

y

Summary outcome statistics

S

Covariance estimates of y

Value

  • T: The efficient score statistic.

  • P: P-value of the publication bias test (score test).

  • b0: Constrained maximum likelihood estimates of the regression intercepts.

References

Noma, H. (2020). Discussion of “Testing small study effects in multivariate meta-analysis” by Chuan Hong, Georgia Salanti, Sally Morton, Richard Riley, Haitao Chu, Stephen E. Kimmel, and Yong Chen. Biometrics 76: 1255-1259. doi:10.1111/biom.13343

Noma, H. (2022). MVPBT: R package for publication bias tests in meta-analysis of diagnostic accuracy studies. arXiv:2209.07270. doi:10.48550/arXiv.2209.07270

Examples

require(metafor)
require(mada)

data(cervical)

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

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

###

attach(LAG)

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

oldpar <- par(mfrow=c(1,1))
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(0.4,0.1,legend=c("95% confidence region","95% prediction region"),lty=c(2,3))

###

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

###

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

par(oldpar)    # Reset the graphic parameter

Generalized Egger test to detect publication bias in bivariate meta-analysis for diagnostic accuracy test (MSSET3)

Description

Generalized Egger test to detect publication bias in bivariate meta-analysis for diagnostic accuracy test (called MSSET3 in Noma (2020)). This test adequately consider the uncertainties of heterogeneity variance-covariance parameters by bootstrapping.

Usage

MVPBT3(y,S,B=2000)

Arguments

y

Summary outcome statistics

S

Covariance estimates of y

B

Number of bootstrap resampling (default: 2000)

Value

  • T.b: Bootstrap samples of the efficient score statistic.

  • T: The efficient score statistic.

  • P: P-value of the publication bias test (bootstrap test).

References

Noma, H. (2020). Discussion of “Testing small study effects in multivariate meta-analysis” by Chuan Hong, Georgia Salanti, Sally Morton, Richard Riley, Haitao Chu, Stephen E. Kimmel, and Yong Chen. Biometrics 76: 1255-1259. doi:10.1111/biom.13343

Noma, H. (2022). MVPBT: R package for publication bias tests in meta-analysis of diagnostic accuracy studies. arXiv:2209.07270. doi:10.48550/arXiv.2209.07270

Examples

require(metafor)
require(mada)

data(cervical)

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

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

###

attach(LAG)

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

oldpar <- par(mfrow=c(1,1))
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(0.4,0.1,legend=c("95% confidence region","95% prediction region"),lty=c(2,3))

###

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

###

MVPBT3(y,S,B=20)   # Generalized Egger test (MSSET3)
# This is an example command for illustration. B should be >= 1000.

par(oldpar)    # Reset the graphic parameter

Transforming diagnostic measures to summary statistics for meta-analysis of diagnostic studies

Description

Transforming diagnostic measures to summary statistics for meta-analysis of diagnostic studies.

Usage

sdta(Se,Fp,Secl,Secu,Fpcl,Fpcu)

Arguments

Se

A vector of the sensitivity estimates

Fp

A vector of the false positive rate estimates

Secl

A vector of the lower confidence limits of sensitivities

Secu

A vector of the upper confidence limits of sensitivities

Fpcl

A vector of the lower confidence limits of false positive rates

Fpcu

A vector of the upper confidence limits of false positive rates

Value

Summary statistics for meta-analysis are generated.

  • y: Logit-transformed sensitivities and false positive rates.

  • S: Within-study variances and covariances.

  • Se: Sensitivities.

  • Fp: False positive rates.

Examples

library("mada")

MRI <- cervical[cervical$method==3,]

MRIa <- MRI[,5:8]
MRIad <- madad(MRIa)

sdta(Se=MRIad$sens$sens,Fp=MRIad$fpr$fpr,
 Secl=MRIad$sens$sens.ci[,1],Fpcl=MRIad$fpr$fpr.ci[,1])
 
sdta(Se=MRIad$sens$sens,Fp=MRIad$fpr$fpr,
 Secu=MRIad$sens$sens.ci[,2],Fpcu=MRIad$fpr$fpr.ci[,2])