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metagear (version 0.1)

Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis

Description

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 data extractions from scatter-plots; 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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software.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.

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Version

Install

install.packages('metagear')

Monthly Downloads

842

Version

0.1

License

GPL (>= 2)

Maintainer

Marc J Lajeunesse

Last Published

May 21st, 2015

Functions in metagear (0.1)

figure_displayDetections

Displays the detected figure objects.
figure_extractDetectedPoints

Extracts data points from a detected image.
effort_initialize

Formats a reference dataset for title/abstract screening efforts.
PDF_download

Attempts to download a PDF using a DOI link.
abstract_screener

A GUI screener to quickly code candidate studies for inclusion/exclusion into a systematic review or meta-analysis.
covariance_commonControl

Generates a sampling variance-covariance matrix for modeling dependencies among effect sizes due to sharing a common control.
figure_read

Reads/loads a figure image from file.
random_N

Random generation of sample sizes (N) for study outcomes.
effort_summary

Provides a text summary of screening efforts among the reviewing team.
random_d

Random generation of Hedges' d effect sizes.
replicate_MetaWin2.0

Replicate meta-analysis results and summaries from MetaWin 2.0.
random_missingness

Random generation of missingness in a data frame.
browse_DOI

Opens a web page associated with a DOI (digital object identifier).
figure_scatterPlot

Detect and display all scatter plot objects.
PDFs_collect

Attempts to download PDFs from multiple DOI links.
figure_displayDetectedPoints

Displays detected points on figure.
random_r

Random generation of correlation coefficients.
figure_detectAllPoints

Automated detection of plotted points from a scatter-plot figure image.
figure_write

Saves/writes a figure image.
plot_PRISMA

Plots and creates a PRISMA flow diagram.
impute_missingness

Provides a summary of missingness in a dataset.
metagear-package

Research synthesis tools to facilitate systematic reviews, data extraction, and meta-analysis.
effort_redistribute

Redistributes title/abstract screening efforts among a review team.
effort_merge

Merges multiple files that had title/abstract screening efforts distributed across a team.
figure_transformToBinary

Transforms figure to binary image.
isPDF

Evaluates whether a file is a PDF document.
random_RR

Random generation of log response ratio (RR) effect sizes.
random_pairedN

Random generation of paired sample sizes (N) for study outcomes.
MA_effectsTable

Generate an ANOVA-like effects table for a meta-analysis.
figure_transformByColors

Transforms RBG figure into list of binary images.
impute_SD

Imputes missing standard deviations in a dataset.
Kam_et_al_2003_Fig2

An example image of a scatterplot figure
figure_removeOutlyingPoints

Remove outlier points from a figure.
figure_detectAxis

Detect an axis from a figure image.
example_references_metagear

A collection of bibliographic references
effort_distribute

Assigns title/abstract screening efforts to a team.
random_OR

Random generation of odds ratio (OR) effect sizes.