metagear package - RDocumentation

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metagear package

purpose of the metagear package

metagear is a comprehensive, multifunctional toolbox with capabilities aimed to cover much of the research synthesis taxonomy: from applying a systematic review approach to objectively assemble and screen the literature, to extracting data from studies, and to finally summarize and analyze these data with the statistics of meta-analysis. More information about metagear can be found at http://lajeunesse.myweb.usf.edu.

installation instructions and dependencies

metagear has an external dependency that needs to be installed and loaded prior to use in R. This is the EBImage R package (Pau et al. 2010) available only from the Bioconductor repository: https://www.bioconductor.org. To properly install metagear, start with the following R script that loads the Bioconductor resources needed to install the EBImage (also accept all dependencies):

install.packages("BiocManager"); 
BiocManager::install("EBImage")
library(metagear)

How to 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. Download PDF here: http://lajeunesse.myweb.usf.edu.

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Version

Install

install.packages('metagear')

Monthly Downloads

983

Version

0.6

License

GPL (>= 2)

Maintainer

Marc J Lajeunesse

Last Published

April 11th, 2020

Functions in metagear (0.6)

Kam_et_al_2003_Fig2

An example image of a scatterplot figure

effort_initialize

Formats a reference dataset for title/abstract screening efforts.

covariance_commonControl

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

effort_distribute

Assigns title/abstract screening efforts to a team.

A small tribute to Chachi.

MA_effectsTable

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

Attempts to download a PDF using a DOI link.

figure_scatterPlot

Detect and display all scatter plot objects.

Manually add/detect points to a scatter plot figure.

figure_splitPlot

Splits a composite figure that contains multiple plots.

abstract_screener

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

Detect and display all bar plot objects.

figure_displayDetectedPoints

Displays detected points on figure.

Displays an image plot.

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

figure_detectAllPoints

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

Saves/writes a figure image.

figure_displayDetections

Displays the detected figure objects.

figure_extractDetectedPoints

Extracts data points from a detected image.

Imputes missing standard deviations in a dataset.

figure_detectAxis

Detect an axis from a figure image.

random_missingness

Random generation of missingness in a data frame.

metagear-package

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

Random generation of correlation coefficients.

Plots and creates a PRISMA flow diagram.

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

Random generation of odds ratio (OR) effect sizes.

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

replicate_MetaWin2.0

Replicate meta-analysis results and summaries from MetaWin 2.0.

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

effort_redistribute

Redistributes title/abstract screening efforts among a review team.

figure_transformToBinary

Transforms figure to binary image.

PDF_extractImages

Attempts to extract all images from a PDF

figure_transformByColors

Transforms RBG figure into list of binary images.

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

Random generation of Hedges' d effect sizes.

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

Evaluates whether a file is a PDF document.

figure_removeOutlyingPoints

Remove outlier points from a figure.

Attempts to download PDFs from multiple DOI links.

example_references_metagear

A collection of bibliographic references

impute_missingness

Provides a summary of missingness in a dataset.

replicate_phyloMeta1.3

Replicate phylogeneic meta-analysis results and summaries from phyloMeta 1.3.

scrape_bibliography

Attempts to scrape/extract bibliographic data from Web of Science.

Reads/loads a figure image from file.

Kortum_and_Acymyan_2013_Fig4

An example image of a bar plot figure