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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software.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


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 two external dependencies that need to be installed and loaded prior to use in R. The first 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 of its dependencies):

source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")
library(metagear)

The second is associated with metagear’s abstract_screener function that generates a GUI to help quickly sift bibliographic data from multiple studies. The first loading of metagear with library(metagear) will trigger the download of the gWidgets package and associated toolkits needed to build GUI interfaces. A small window will also prompt you to download GTK+ asking "Need GTK+ ?". From the listed options answer: "Install GTK+" and click "OK". Once installed, these will not be downloaded again.

Finally, sometimes the installation will freeze; however, re-starting the R session can fix this issue.

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.

News

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.

metagear 0.4 (3/14/17)

  • As of Jan/2017, Elsevier added numerous redirects and cookies for their PDF downloads; consequently, metagear is (sometimes) no longer able to extract PDFs from this publisher; this also broke an entire vignette section :(
  • Updated vignette to reflect low download success of Elsevier journal articles
  • Fixed effort_redistribute() bug that incorrectly calculated effort % for distribution of references (thanks to Melanie Hartley for making me aware of this issue)
  • Added new color and style themes for PRISMA flow charts via the plot_PRISMA(); this includes several flat schemes
  • Fixed PDF_extractImages() bug preventing some of the extracted images from being recognized as image files (was an SOI file signature problem for some jpg formats)
  • Fixed bug in abstract_screener() that continuously prompted a validation check when screening abstracts
  • Added figure_split() to automatically split-up a figure image with multiple inlaid plots

metagear 0.3 (01/03/17)

  • Updated abstract_screener() to include options for changing the default settings of GUI window size, font size, button sizes, url of search engine, or text protection (thanks to Maria Gatta for this suggestion). A menu bar was also added to help quickly fix screening errors.
  • Total reworking of plot_PRISMA() since previous version could not plot phase grobs when loaded from within the package (although works fine when loaded separately from metagear). Thanks to Hautahi Kingi for making me aware of this problem. Unfortunately, this new version is not as flexible since it no longer makes use of 'drawDetails' functionality of grid objects that allow for rescaling of plots/objects as the window size gets adjusted by the user. This mostly results in the spacing among the phase labels to change with window size. In case high quality plots are needed, the previous plot_PRISMA() function with the nice scaling abilities was added as a supplementary to metagear's vignette. TO DO: reintroduce the 'drawDetails' function approach and get it to load within the package!
  • Fixed plot_PRISMA() not properly connecting phases when only a single START_PHASE is included in the phase list.
  • Added poorman's bibliographic scraper using Web of Science's OpenUrl
  • Added extra examples in vignette (PRISMA plot, acknowledgments, installation tips, WOS citations scrape)
  • Updated all figure_ functions that used depreciated R calls from EBImage bioconductor package
  • Added Chachi tribute
  • Added installation guide to R manual that includes troubleshooting links
  • Added unit tests for: datasets, effort_initialize, effort_summary, effort_distribute, effort_merge, effort_redistribute, random_d, random_missingness, random_N, random_OR, random_pairedN, random_r, random_RR
  • Fixed scrape_bibliography to extract multiline abstracts from WOS (still not perfect)
  • Fixed PDFs_collect() directory name issue and now defaults to working directory
  • Added to PDFs_collect() an option to randomize the download order of PDFs. Also added a random time-delay between downloads to decrease the likelihood of being blocked by website hosts.
  • Updated some of the PDF_download() ad-hoc searches for PDFs.
  • Fixed "In file(con, "r") : InternetOpenUrl failed: 'The operation timed out'" error when trying to download > 40 PDFs with PDFs_collect(). Establishing connections via wininet largely fixes this issue on Windows computers.
  • Added PDF figure/image extractor
  • Updated replicate_metawin2.0: fixed issues with resampling analyses, and confidence interval estimation

metagear 0.2 (8/18/15)

  • Added vignette (v. 0.2, version 0.1 not included in previous metagear versions)
  • Added figure_add() for manual extractions of data points on a figure image
  • Added figure_barPlot() for extracting data from vertical or horizontal bar-plots
  • Added figure_display() for visualizing the loaded figure image
  • Added example image data for a bar plot: Kortum_and_Acymyan_2013_Fig4
  • Fixed summary bug for non-dual screening outcomes in effort_summary()
  • Corrected typos in descriptions for: abstract_screener, effort_initialize, figure_removeOutlyingPoints, isPDF

metagear 0.1 (5/20/15)

  • Released package

Reference manual

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install.packages("metagear")

0.4 by Marc J. Lajeunesse, 2 years ago


http://lajeunesse.myweb.usf.edu


Browse source code at https://github.com/cran/metagear


Authors: Marc J. Lajeunesse [aut, cre]


Documentation:   PDF Manual  


Task views: Meta-Analysis


GPL (>= 2) license


Imports EBImage, gWidgetsRGtk2, gWidgets, hexView, Matrix, MASS, metafor, RCurl, stringr

Suggests testthat, R.rsp


See at CRAN