Package: metamisc 0.4.0.9000

Thomas Debray

metamisc: Meta-Analysis of Diagnosis and Prognosis Research Studies

Facilitate frequentist and Bayesian meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance (Debray et al., 2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry (Debray et al., 2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering (de Jong et al., 2021) <doi:10.1002/sim.8981>.

Authors:Thomas Debray [aut, cre], Valentijn de Jong [aut]

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metamisc/json (API)
NEWS

# Install 'metamisc' in R:
install.packages('metamisc', repos = c('https://smartdata-analysis-and-statistics.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/smartdata-analysis-and-statistics/metamisc/issues

Datasets:
  • Collins - Collins data
  • DVTipd - Hypothetical dataset for diagnosis of Deep Vein Thrombosis
  • DVTmodels - Risk prediction models for diagnosing Deep Venous Thrombosis
  • Daniels - Daniels and Hughes data
  • EuroSCORE - Predictive performance of EuroSCORE II
  • Fibrinogen - Meta-analysis of the association between plasma fibrinogen concentration and the risk of coronary heath disease
  • Framingham - Predictive performance of the Framingham Risk Score in male populations
  • Kertai - Kertai data
  • Roberts - Roberts data
  • Scheidler - Diagnostic accuracy data
  • Tzoulaki - The incremental value of cardiovascular risk factors
  • Zhang - Meta-analysis of the prognostic role of hormone receptors in endometrial cancer
  • impact - IMPACT data

On CRAN:

meta-analysisprognosisprognostic-models

7.24 score 6 stars 102 scripts 1.0k downloads 7 mentions 25 exports 45 dependencies

Last updated 9 months agofrom:d3aef8e71b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:acplotccalccor2covdplotfatforestgelmanplotgengeneralizabilityimpute_conditional_meanmametapredoecalcperfperformancerecalibraterileyrmplotsestackedglmtautau2uvmetavalmetavariances

Dependencies:bootclicolorspacedplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSmathjaxrMatrixmetadatmetaformgcvminqamunsellmvtnormnlmenloptrnumDerivpbapplypillarpkgconfigplyrpROCR6RColorBrewerRcppRcppEigenrlangscalestibbletidyselectutf8vctrsviridisLitewithr

Meta-analysis of prediction model performance

Thomas Debray

Rendered fromma-pm.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-08-25
Started: 2023-05-14

Meta-analysis of prognostic factors

Thomas Debray

Rendered fromma-pf.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-08-25
Started: 2023-05-15

Readme and manuals

Help Manual

Help pageTopics
Meta-Analysis of Diagnosis and Prognosis Research Studiesmetamisc-package
Plot the autocorrelation of a Bayesian meta-analysis modelacplot
Plot the autocorrelation of a Bayesian meta-analysis modelacplot.mcmc.list
Plot the autocorrelation of a Bayesian meta-analysis modelacplot.uvmeta
Plot the autocorrelation of a Bayesian meta-analysis modelacplot.valmeta
Calculate the concordance statisticccalc
Collins dataCollins
Convert a correlation matrix into a covariance matrixcor2cov
Daniels and Hughes dataDaniels
Posterior distribution of estimated model parametersdplot
Posterior distribution of estimated model parametersdplot.mcmc.list
Plot the prior and posterior distribution of a meta-analysis modeldplot.uvmeta
Plot the prior and posterior distribution of a meta-analysis modeldplot.valmeta
Hypothetical dataset for diagnosis of Deep Vein Thrombosis (DVT)DVTipd
Risk prediction models for diagnosing Deep Venous Thrombosis (DVT)DVTmodels
Predictive performance of EuroSCORE IIEuroSCORE
Regression tests for detecting funnel plot asymmetryfat
Meta-analysis of the association between plasma fibrinogen concentration and the risk of coronary heath diseaseFibrinogen
Extract Model Fitted Valuesfitted.metapred
Forest plotforest
Forest plotforest.default
Forest plot of a metapred fitforest.metapred
Forest plot of a validation object.forest.mp.cv.val forest.perf
Predictive performance of the Framingham Risk Score in male populationsFramingham
Gelman-Rubin-Brooks plotgelmanplot
Gelman-Rubin-Brooks plotgelmanplot.mcmc.list
Gelman-Rubin-Brooks plotgelmanplot.uvmeta
Gelman-Rubin-Brooks plotgelmanplot.valmeta
Generalizability estimatesgen generalizability
IMPACT dataimpact
Impute missing values by their conditional meanimpute_conditional_mean
Apply the inverse logit tranformationinv.logit
Kertai dataKertai
Apply logit tranformationlogit
Print the log-likelihoodlogLik.riley
Random effects meta-analysisma
Generalized Stepwise Regression for Prediction Models in Clustered Datametapred
Calculate the total O:E ratiooecalc
Performance estimatesperf performance
Display results from the funnel plot asymmetry testplot.fat
Forest Plotsplot.mm_perf
Plot the summary of the bivariate model from Riley et al. (2008).plot.riley
Forest Plotsplot.uvmeta
Forest Plotsplot.valmeta
Prediction Intervalpredict.riley
Recalibrate a Prediction Modelrecalibrate
Fit the alternative model for bivariate random-effects meta-analysisriley
Plot the running means of a Bayesian meta-analysis modelrmplot
Plot the running means of a Bayesian meta-analysis modelrmplot.mcmc.list
Plot the running means of a Bayesian meta-analysis modelrmplot.uvmeta
Plot the running means of a Bayesian meta-analysis modelrmplot.valmeta
Roberts dataRoberts
Diagnostic accuracy dataScheidler
Standard errors and variancesse tau tau2 variances
Stacked Regressionstackedglm
Subsetting metapred fitssubset.metapred
Parameter summaries Provides the summary estimates of the alternative model for bivariate random-effects meta-analysis by Riley et al. (2008) with their corresponding standard errors (derived from the inverse Hessian). For confidence intervals, asymptotic normality is assumed.summary.riley
Summarizing Univariate Meta-Analysis Modelssummary.uvmeta
The incremental value of cardiovascular risk factorsTzoulaki
Univariate meta-analysisuvmeta
Class "uvmeta". Result of a univariate meta-analysis.uvmeta-clas
Meta-analysis of prediction model performancevalmeta
Calculate Variance-Covariance Matrix for a Fitted Riley Model Objectvcov.riley
Meta-analysis of the prognostic role of hormone receptors in endometrial cancerZhang