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; 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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software. Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031.

Author
Marc J. Lajeunesse [aut, cre]
Date of publication
2015-08-19 13:49:41
Maintainer
Marc J. Lajeunesse <lajeunesse@usf.edu>
License
GPL (>= 2)
Version
0.2
URLs

View on CRAN

Man pages

abstract_screener
A GUI screener to quickly code candidate studies for...
browse_DOI
Opens a web page associated with a DOI (digital object...
covariance_commonControl
Generates a sampling variance-covariance matrix for modeling...
effort_distribute
Assigns title/abstract screening efforts to a team.
effort_initialize
Formats a reference dataset for title/abstract screening...
effort_merge
Merges multiple files that had title/abstract screening...
effort_redistribute
Redistributes title/abstract screening efforts among a review...
effort_summary
Provides a text summary of screening efforts among the...
example_references_metagear
A collection of bibliographic references
figure_add
Manually add/detect points to a scatter plot figure.
figure_barPlot
Detect and display all bar plot objects.
figure_detectAllPoints
Automated detection of plotted points from a scatter-plot...
figure_detectAxis
Detect an axis from a figure image.
figure_display
Displays an image plot.
figure_displayDetectedPoints
Displays detected points on figure.
figure_displayDetections
Displays the detected figure objects.
figure_extractDetectedPoints
Extracts data points from a detected image.
figure_read
Reads/loads a figure image from file.
figure_removeOutlyingPoints
Remove outlier points from a figure.
figure_scatterPlot
Detect and display all scatter plot objects.
figure_transformByColors
Transforms RBG figure into list of binary images.
figure_transformToBinary
Transforms figure to binary image.
figure_write
Saves/writes a figure image.
impute_missingness
Provides a summary of missingness in a dataset.
impute_SD
Imputes missing standard deviations in a dataset.
isPDF
Evaluates whether a file is a PDF document.
Kam_et_al_2003_Fig2
An example image of a scatterplot figure
Kortum_and_Acymyan_2013_Fig4
An example image of a bar plot figure
MA_effectsTable
Generate an ANOVA-like effects table for a meta-analysis.
metagear-package
Research synthesis tools to facilitate systematic reviews,...
PDF_download
Attempts to download a PDF using a DOI link.
PDFs_collect
Attempts to download PDFs from multiple DOI links.
plot_PRISMA
Plots and creates a PRISMA flow diagram.
random_d
Random generation of Hedges' d effect sizes.
random_missingness
Random generation of missingness in a data frame.
random_N
Random generation of sample sizes (N) for study outcomes.
random_OR
Random generation of odds ratio (OR) effect sizes.
random_pairedN
Random generation of paired sample sizes (N) for study...
random_r
Random generation of correlation coefficients.
random_RR
Random generation of log response ratio (RR) effect sizes.
replicate_MetaWin2.0
Replicate meta-analysis results and summaries from MetaWin...

Files in this package

metagear
metagear/inst
metagear/inst/CITATION
metagear/NAMESPACE
metagear/NEWS.md
metagear/data
metagear/data/Kam_et_al_2003_Fig2.rda
metagear/data/Kortum_and_Acymyan_2013_Fig4.rda
metagear/data/example_references_metagear.rda
metagear/R
metagear/R/PDFs_collect.R
metagear/R/metagear_data.R
metagear/R/figure_transformToBinary.R
metagear/R/metagear_utils.R
metagear/R/random_N.R
metagear/R/effort_summary.R
metagear/R/random_RR.R
metagear/R/figure_detectAxis.R
metagear/R/random_OR.R
metagear/R/plot_PRISMA_utils.R
metagear/R/figure_write.R
metagear/R/figure_removeOutlyingPoints.R
metagear/R/effort_initialize.R
metagear/R/PDF_download.R
metagear/R/figure_read.R
metagear/R/random_d.R
metagear/R/impute_SD.R
metagear/R/figure_utils.R
metagear/R/random_pairedN.R
metagear/R/figure_barPlot.R
metagear/R/figure_detectAllPoints.R
metagear/R/effort_merge.R
metagear/R/figure_displayDetections.R
metagear/R/plot_PRISMA.R
metagear/R/effort_distribute.R
metagear/R/browse_DOI.R
metagear/R/figure_scatterPlot.R
metagear/R/MA_effectsTable.R
metagear/R/random_missingness.R
metagear/R/figure_transformByColors.R
metagear/R/impute_utils.R
metagear/R/metagear.R
metagear/R/effort_utils.R
metagear/R/covariance_commonControl.R
metagear/R/impute_missingness.R
metagear/R/replicate_MetaWin2.0.R
metagear/R/figure_display.R
metagear/R/figure_extractDetectedPoints.R
metagear/R/figure_add.R
metagear/R/figure_displayDetectedPoints.R
metagear/R/abstract_screener.R
metagear/R/effort_redistribute.R
metagear/R/PDF_utils.R
metagear/R/isPDF.R
metagear/R/random_utils.R
metagear/R/random_r.R
metagear/vignettes
metagear/vignettes/metagear_basic_vignette_v0.2.Rmd
metagear/MD5
metagear/DESCRIPTION
metagear/man
metagear/man/figure_read.Rd
metagear/man/random_r.Rd
metagear/man/effort_initialize.Rd
metagear/man/PDF_download.Rd
metagear/man/effort_redistribute.Rd
metagear/man/MA_effectsTable.Rd
metagear/man/figure_detectAllPoints.Rd
metagear/man/metagear-package.Rd
metagear/man/figure_barPlot.Rd
metagear/man/effort_merge.Rd
metagear/man/figure_transformByColors.Rd
metagear/man/figure_removeOutlyingPoints.Rd
metagear/man/figure_scatterPlot.Rd
metagear/man/effort_summary.Rd
metagear/man/impute_SD.Rd
metagear/man/random_OR.Rd
metagear/man/replicate_MetaWin2.0.Rd
metagear/man/example_references_metagear.Rd
metagear/man/figure_displayDetectedPoints.Rd
metagear/man/effort_distribute.Rd
metagear/man/Kam_et_al_2003_Fig2.Rd
metagear/man/abstract_screener.Rd
metagear/man/figure_extractDetectedPoints.Rd
metagear/man/random_N.Rd
metagear/man/figure_write.Rd
metagear/man/random_missingness.Rd
metagear/man/figure_display.Rd
metagear/man/covariance_commonControl.Rd
metagear/man/figure_add.Rd
metagear/man/random_d.Rd
metagear/man/impute_missingness.Rd
metagear/man/browse_DOI.Rd
metagear/man/PDFs_collect.Rd
metagear/man/isPDF.Rd
metagear/man/figure_detectAxis.Rd
metagear/man/Kortum_and_Acymyan_2013_Fig4.Rd
metagear/man/figure_transformToBinary.Rd
metagear/man/figure_displayDetections.Rd
metagear/man/random_RR.Rd
metagear/man/random_pairedN.Rd
metagear/man/plot_PRISMA.Rd