Package: metagear 0.7

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effect sizes with a common control); and finally summaries that replicate analyses and outputs from widely used but no longer updated meta-analysis software (i.e., metawin). Funding for this package was supported by National Science Foundation (NSF) grants DBI-1262545 and DEB-1451031. 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 <doi:10.1111/2041-210X.12472>.

Authors:Marc J. Lajeunesse [aut, cre]

metagear_0.7.tar.gz
metagear_0.7.zip(r-4.7)metagear_0.7.zip(r-4.6)metagear_0.7.zip(r-4.5)
metagear_0.7.tgz(r-4.6-any)metagear_0.7.tgz(r-4.5-any)
metagear_0.7.tar.gz(r-4.7-any)metagear_0.7.tar.gz(r-4.6-any)
metagear_0.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metagear/json (API)

# Install 'metagear' in R:

install.packages('metagear', repos = c('https://mjlajeunesse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mjlajeunesse/metagear/issues

Datasets:

example_references_metagear - A collection of bibliographic references

On CRAN:

6.87 score 15 stars 124 scripts 864 downloads 8 mentions 41 exports 18 dependencies

Last updated from:37354985d3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	258
source / vignettes	OK	325
linux-release-x86_64	OK	186
macos-release-arm64	OK	134
macos-oldrel-arm64	OK	96
windows-devel	OK	107
windows-release	OK	119
windows-oldrel	OK	104
wasm-release	OK	124

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

Dependencies:cli digest glue lattice lifecycle magrittr MASS mathjaxr Matrix metadat metafor nlme numDeriv pbapply rlang stringi stringr vctrs

Basic examples of screening studies, extracting data and meta-analysis with the metagear package for R

Rendered frommetagear_basic_vignette_v0.7.pdf.asisusingR.rsp::asis

Last update: 2021-05-05
Started: 2021-05-05

Help page	Topics
Research synthesis tools to facilitate systematic reviews, data extraction, and meta-analysis.	metagear-package
A GUI screener to quickly code candidate studies for inclusion/exclusion into a systematic review or meta-analysis.	abstract_screener
Opens a web page associated with a DOI (digital object identifier).	browse_DOI
A small tribute to Chachi.	chachi
Generates a sampling variance-covariance matrix for modeling dependencies among effect sizes due to sharing a common control.	covariance_commonControl
Assigns title/abstract screening efforts to a team.	effort_distribute
Formats a reference dataset for title/abstract screening efforts.	effort_initialize
Merges multiple files that had title/abstract screening efforts distributed across a team.	effort_merge
Redistributes title/abstract screening efforts among a review team.	effort_redistribute
Provides a text summary of screening efforts among the reviewing team.	effort_summary
A collection of bibliographic references	example_references_metagear
Manually add/detect points to a scatter plot figure.	figure_add
Detect and display all bar plot objects.	figure_barPlot
Automated detection of plotted points from a scatter-plot figure image.	figure_detectAllPoints
Detect an axis from a figure image.	figure_detectAxis
Displays an image plot.	figure_display
Displays detected points on figure.	figure_displayDetectedPoints
Displays the detected figure objects.	figure_displayDetections
Extracts data points from a detected image.	figure_extractDetectedPoints
Reads/loads a figure image from file.	figure_read
Remove outlier points from a figure.	figure_removeOutlyingPoints
Detect and display all scatter plot objects.	figure_scatterPlot
Splits a composite figure that contains multiple plots.	figure_splitPlot
Transforms RBG figure into list of binary images.	figure_transformByColors
Transforms figure to binary image.	figure_transformToBinary
Saves/writes a figure image.	figure_write
Provides a summary of missingness in a dataset.	impute_missingness
Imputes missing standard deviations in a dataset.	impute_SD
Evaluates whether a file is a PDF document.	isPDF
An example image of a scatterplot figure	Kam_et_al_2003_Fig2.jpg
An example image of a bar plot figure	Kortum_and_Acymyan_2013_Fig4.jpg
Generate an ANOVA-like effects table for a meta-analysis.	MA_effectsTable
Attempts to download a PDF using a DOI link.	PDF_download
Attempts to extract all images from a PDF	PDF_extractImages
Attempts to download PDFs from multiple DOI links.	PDFs_collect
Plots and creates a PRISMA flow diagram.	plot_PRISMA
Random generation of Hedges' d effect sizes.	random_d
Random generation of missingness in a data frame.	random_missingness
Random generation of sample sizes (N) for study outcomes.	random_N
Random generation of odds ratio (OR) effect sizes.	random_OR
Random generation of paired sample sizes (N) for study outcomes.	random_pairedN
Random generation of correlation coefficients.	random_r
Random generation of log response ratio (RR) effect sizes.	random_RR
Replicate meta-analysis results and summaries from MetaWin 2.0.	replicate_MetaWin2.0
Replicate phylogeneic meta-analysis results and summaries from phyloMeta 1.3.	replicate_phyloMeta1.3
Attempts to scrape/extract bibliographic data from Web of Science.	scrape_bibliography

Package: metagear 0.7

metagear: Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis

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