Package: metagear 0.7

metagear: Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis

Functionalities for facilitating systematic reviews, data extractions, and meta-analyses. It includes a GUI (graphical user interface) to help screen the abstracts and titles of bibliographic data; tools to assign screening effort across multiple collaborators/reviewers and to assess inter- reviewer reliability; tools to help automate the download and retrieval of journal PDF articles from online databases; figure and image extractions from PDFs; web scraping of citations; automated and manual data extraction from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools to fill gaps in incomplete or missing study parameters; generation of random effects sizes for Hedges' d, log response ratio, odds ratio, and correlation coefficients for Monte Carlo experiments; covariance equations for modelling dependencies among multiple effect sizes (e.g., effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software (i.e., metawin). Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031. CITE: Lajeunesse, M.J. (2016) Facilitating systematic reviews, data extraction and meta-analysis with the metagear package for R. Methods in Ecology and Evolution 7, 323-330 <doi:10.1111/2041-210X.12472>.

Authors:Marc J. Lajeunesse [aut, cre]

metagear_0.7.tar.gz
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metagear_0.7.tgz(r-4.4-any)metagear_0.7.tgz(r-4.3-any)
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metagear_0.7.tgz(r-4.4-emscripten)metagear_0.7.tgz(r-4.3-emscripten)
metagear.pdf |metagear.html✨
metagear/json (API)
NEWS

# Install 'metagear' in R:
install.packages('metagear', repos = c('https://mjlajeunesse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mjlajeunesse/metagear/issues

Datasets:

On CRAN:

41 exports 14 stars 2.74 score 17 dependencies 8 mentions 89 scripts 1.1k downloads

Last updated 3 years agofrom:37354985d3. Checks:OK: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-winOKSep 06 2024
R-4.5-linuxOKSep 06 2024
R-4.4-winOKSep 06 2024
R-4.4-macOKSep 06 2024
R-4.3-winERRORSep 06 2024
R-4.3-macOKSep 06 2024

Exports:abstract_screenerbrowse_DOIchachicovariance_commonControleffort_distributeeffort_initializeeffort_mergeeffort_redistributeeffort_summaryfigure_addfigure_barPlotfigure_detectAllPointsfigure_detectAxisfigure_displayfigure_displayDetectedPointsfigure_displayDetectionsfigure_extractDetectedPointsfigure_readfigure_removeOutlyingPointsfigure_scatterPlotfigure_splitPlotfigure_transformByColorsfigure_transformToBinaryfigure_writeimpute_missingnessimpute_SDisPDFMA_effectsTablePDF_downloadPDF_extractImagesPDFs_collectplot_PRISMArandom_drandom_missingnessrandom_Nrandom_ORrandom_pairedNrandom_rrandom_RRreplicate_MetaWin2.0scrape_bibliography

Dependencies:cligluelatticelifecyclemagrittrMASSmathjaxrMatrixmetadatmetafornlmenumDerivpbapplyrlangstringistringrvctrs

Basic examples of screening studies, extracting data and meta-analysis with the metagear package for R

Rendered frommetagear_basic_vignette_v0.7.pdf.asisusingR.rsp::asison Sep 06 2024.

Last update: 2021-05-05
Started: 2021-05-05

Readme and manuals

Help Manual

Help pageTopics
Research synthesis tools to facilitate systematic reviews, data extraction, and meta-analysis.metagear-package
A GUI screener to quickly code candidate studies for inclusion/exclusion into a systematic review or meta-analysis.abstract_screener
Opens a web page associated with a DOI (digital object identifier).browse_DOI
A small tribute to Chachi.chachi
Generates a sampling variance-covariance matrix for modeling dependencies among effect sizes due to sharing a common control.covariance_commonControl
Assigns title/abstract screening efforts to a team.effort_distribute
Formats a reference dataset for title/abstract screening efforts.effort_initialize
Merges multiple files that had title/abstract screening efforts distributed across a team.effort_merge
Redistributes title/abstract screening efforts among a review team.effort_redistribute
Provides a text summary of screening efforts among the reviewing team.effort_summary
A collection of bibliographic referencesexample_references_metagear
Manually add/detect points to a scatter plot figure.figure_add
Detect and display all bar plot objects.figure_barPlot
Automated detection of plotted points from a scatter-plot figure image.figure_detectAllPoints
Detect an axis from a figure image.figure_detectAxis
Displays an image plot.figure_display
Displays detected points on figure.figure_displayDetectedPoints
Displays the detected figure objects.figure_displayDetections
Extracts data points from a detected image.figure_extractDetectedPoints
Reads/loads a figure image from file.figure_read
Remove outlier points from a figure.figure_removeOutlyingPoints
Detect and display all scatter plot objects.figure_scatterPlot
Splits a composite figure that contains multiple plots.figure_splitPlot
Transforms RBG figure into list of binary images.figure_transformByColors
Transforms figure to binary image.figure_transformToBinary
Saves/writes a figure image.figure_write
Provides a summary of missingness in a dataset.impute_missingness
Imputes missing standard deviations in a dataset.impute_SD
Evaluates whether a file is a PDF document.isPDF
An example image of a scatterplot figureKam_et_al_2003_Fig2.jpg
An example image of a bar plot figureKortum_and_Acymyan_2013_Fig4.jpg
Generate an ANOVA-like effects table for a meta-analysis.MA_effectsTable
Attempts to download a PDF using a DOI link.PDF_download
Attempts to extract all images from a PDFPDF_extractImages
Attempts to download PDFs from multiple DOI links.PDFs_collect
Plots and creates a PRISMA flow diagram.plot_PRISMA
Random generation of Hedges' d effect sizes.random_d
Random generation of missingness in a data frame.random_missingness
Random generation of sample sizes (N) for study outcomes.random_N
Random generation of odds ratio (OR) effect sizes.random_OR
Random generation of paired sample sizes (N) for study outcomes.random_pairedN
Random generation of correlation coefficients.random_r
Random generation of log response ratio (RR) effect sizes.random_RR
Replicate meta-analysis results and summaries from MetaWin 2.0.replicate_MetaWin2.0
Replicate phylogeneic meta-analysis results and summaries from phyloMeta 1.3.replicate_phyloMeta1.3
Attempts to scrape/extract bibliographic data from Web of Science.scrape_bibliography