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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software.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

AuthorMarc J. Lajeunesse [aut, cre]
Date of publication2017-01-03 16:25:57
MaintainerMarc J. Lajeunesse <lajeunesse@usf.edu>
LicenseGPL (>= 2)
Version0.3
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_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...

Files in this package

metagear
metagear/inst
metagear/inst/CITATION
metagear/inst/doc
metagear/inst/doc/metagear_basic_vignette_v0.31.pdf.asis
metagear/inst/doc/metagear_basic_vignette_v0.31.pdf
metagear/tests
metagear/tests/testthat.R
metagear/tests/testthat
metagear/tests/testthat/test-random_OR.R
metagear/tests/testthat/test-effort_merge.R
metagear/tests/testthat/test-random_RR.R
metagear/tests/testthat/test-effort_summary.R
metagear/tests/testthat/test-effort_redistribute.R
metagear/tests/testthat/test-datasets.R
metagear/tests/testthat/test-effort_distribute.R
metagear/tests/testthat/test-random_N.R
metagear/tests/testthat/test-random_missingness.R
metagear/tests/testthat/test-random_r.R
metagear/tests/testthat/test-random_d.R
metagear/tests/testthat/test-random_pairedN.R
metagear/tests/testthat/test-effort_initialize.R
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/chachi.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_extractImages.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/scrape_utils.R metagear/R/random_pairedN.R metagear/R/figure_barPlot.R metagear/R/figure_detectAllPoints.R metagear/R/scrape_bibliography.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/MA_phylogenetic.R metagear/R/impute_missingness.R metagear/R/MA_utils.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_v0.31.Rmd
metagear/vignettes/metagear_basic_vignette_v0.31.pdf.asis
metagear/MD5
metagear/build
metagear/build/vignette.rds
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/chachi.Rd metagear/man/figure_scatterPlot.Rd metagear/man/effort_summary.Rd metagear/man/impute_SD.Rd metagear/man/PDF_extractImages.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/scrape_bibliography.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

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