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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software.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

Install the latest version of this package by entering the following in R:
install.packages("metagear")
AuthorMarc J. Lajeunesse [aut, cre]
Date of publication2017-03-24 19:02:58 UTC
MaintainerMarc J. Lajeunesse <lajeunesse@usf.edu>
LicenseGPL (>= 2)
Version0.4
http://lajeunesse.myweb.usf.edu

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...

chachi: A small tribute to Chachi.

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_splitPlot: Splits a composite figure that contains multiple plots.

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.

PDF_extractImages: Attempts to extract all images from a PDF

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...

scrape_bibliography: Attempts to scrape/extract bibliographic data from Web of...

Functions

abstract_screener Man page
browse_DOI Man page
chachi Man page
covariance_commonControl Man page
effort_distribute Man page
effort_initialize Man page
effort_merge Man page
effort_redistribute Man page
effort_summary Man page
example_references_metagear Man page
figure_add Man page
figure_barPlot Man page
figure_detectAllPoints Man page
figure_detectAxis Man page
figure_display Man page
figure_displayDetectedPoints Man page
figure_displayDetections Man page
figure_extractDetectedPoints Man page
figure_read Man page
figure_removeOutlyingPoints Man page
figure_scatterPlot Man page
figure_splitPlot Man page
figure_transformByColors Man page
figure_transformToBinary Man page
figure_write Man page
impute_missingness Man page
impute_SD Man page
isPDF Man page
Kam_et_al_2003_Fig2 Man page
Kortum_and_Acymyan_2013_Fig4 Man page
MA_effectsTable Man page
metagear-package Man page
PDF_download Man page
PDF_extractImages Man page
PDFs_collect Man page
plot_PRISMA Man page
random_d Man page
random_missingness Man page
random_N Man page
random_OR Man page
random_pairedN Man page
random_r Man page
random_RR Man page
replicate_MetaWin2.0 Man page
scrape_bibliography Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/metagear_basic_vignette_v0.4.pdf
inst/doc/metagear_basic_vignette_v0.4.pdf.asis
tests
tests/testthat.R
tests/testthat
tests/testthat/test-random_OR.R tests/testthat/test-effort_merge.R tests/testthat/test-random_RR.R tests/testthat/test-effort_summary.R tests/testthat/test-effort_redistribute.R tests/testthat/test-datasets.R tests/testthat/test-effort_distribute.R tests/testthat/test-random_N.R tests/testthat/test-random_missingness.R tests/testthat/test-random_r.R tests/testthat/test-random_d.R tests/testthat/test-random_pairedN.R tests/testthat/test-effort_initialize.R
NAMESPACE
NEWS.md
data
data/Kam_et_al_2003_Fig2.rda
data/Kortum_and_Acymyan_2013_Fig4.rda
data/example_references_metagear.rda
R
R/PDFs_collect.R R/metagear_data.R R/figure_transformToBinary.R R/chachi.R R/metagear_utils.R R/random_N.R R/effort_summary.R R/random_RR.R R/figure_detectAxis.R R/random_OR.R R/plot_PRISMA_utils.R R/figure_write.R R/figure_removeOutlyingPoints.R R/effort_initialize.R R/PDF_extractImages.R R/PDF_download.R R/figure_read.R R/random_d.R R/impute_SD.R R/figure_utils.R R/scrape_utils.R R/random_pairedN.R R/figure_barPlot.R R/figure_detectAllPoints.R R/scrape_bibliography.R R/effort_merge.R R/figure_displayDetections.R R/plot_PRISMA.R R/effort_distribute.R R/browse_DOI.R R/figure_scatterPlot.R R/figure_split.R R/MA_effectsTable.R R/random_missingness.R R/figure_transformByColors.R R/impute_utils.R R/metagear.R R/effort_utils.R R/covariance_commonControl.R R/impute_missingness.R R/replicate_MetaWin2.0.R R/figure_display.R R/figure_extractDetectedPoints.R R/figure_add.R R/figure_displayDetectedPoints.R R/abstract_screener.R R/effort_redistribute.R R/PDF_utils.R R/isPDF.R R/random_utils.R R/random_r.R
vignettes
vignettes/metagear_basic_vignette_v0.4.Rmd
vignettes/metagear_basic_vignette_v0.4.pdf.asis
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/figure_read.Rd man/random_r.Rd man/effort_initialize.Rd man/PDF_download.Rd man/effort_redistribute.Rd man/MA_effectsTable.Rd man/figure_detectAllPoints.Rd man/metagear-package.Rd man/figure_barPlot.Rd man/effort_merge.Rd man/figure_transformByColors.Rd man/figure_removeOutlyingPoints.Rd man/figure_splitPlot.Rd man/chachi.Rd man/figure_scatterPlot.Rd man/effort_summary.Rd man/impute_SD.Rd man/PDF_extractImages.Rd man/random_OR.Rd man/replicate_MetaWin2.0.Rd man/example_references_metagear.Rd man/figure_displayDetectedPoints.Rd man/effort_distribute.Rd man/Kam_et_al_2003_Fig2.Rd man/abstract_screener.Rd man/figure_extractDetectedPoints.Rd man/random_N.Rd man/figure_write.Rd man/random_missingness.Rd man/figure_display.Rd man/covariance_commonControl.Rd man/figure_add.Rd man/random_d.Rd man/impute_missingness.Rd man/browse_DOI.Rd man/PDFs_collect.Rd man/isPDF.Rd man/figure_detectAxis.Rd man/Kortum_and_Acymyan_2013_Fig4.Rd man/scrape_bibliography.Rd man/figure_transformToBinary.Rd man/figure_displayDetections.Rd man/random_RR.Rd man/random_pairedN.Rd man/plot_PRISMA.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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