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 0.7 (2/12/21)
Removed some testThat tests that use random numbers: randomly got
errors and CRAN will not like it (since they won’t rerun tests)
Moved many dependencies from Imports to Suggest – in particular
focusing on minimizing EBImage package footprint and limiting
installation from Bioconductor until a figure extraction function is
called
Added external dependency checks when package is loaded
Converted image data examples from .rda to orginal jpg formats
(keeps package size small) [also modified vignette to reflect new way of
loading packaged images]
Updated some of the PDF_download() ad-hoc searches for PDFs.
typo fixes
metagear 0.6 (4/11/20)
removed version requirements for EBImage package (CRAN binary
compilers may not always have the latest version from Bioconductor)
typo fixes
metagear 0.5 (3/20/20)
Added zzz.R file with major dependency error catching during first
installation: message to install EBImage from bioconductor and message
to check if Tcl/Tk GUI toolkit is installed
Completely migrated non-R GUI dependencies of abstract_screener();
it now uses the base package tcltk rather than gWidgets and
gWidgetsRGtk2 to build the GUI. The later packages required users to
install non-R dependency GTK+; it also always lead to failed CRAN checks
for MacOS (resulting in no CRAN OS X binary builds for more than a year)
since the gWidgetsRGtk2 package has not been updated since 2014 and
consequently no longer helps mac users to install GTK+. I think Tcl/Tk
is included by default in windows and linux (but mac users still need to
get XQuartz X11), so this should really improve installation and
dependency rot since tcltk is part of base R. TESTED on 1/10/19 in
Windows 7 & 10, and Mac OS Mojave. NOTE: since this change,
gWidgetsRGtk2 has been updated and old version now works for Mac Os, but
will keep new one since it uses base…
Updated abstract_screener() to dynamically generate coding buttons
as needed. Thanks to Matt Jones for this suggestion. Now you can remove
or add screening buttons beyond the typical YES, NO, MAYBE for coding
studies
Updated abstract_screener() to have flexible keyboard key-bindings
to coding buttons
Updated abstract_screener() to include menu dropdown options for
reversing coding decisions, backtrack previous coding decisions, refresh
abstract/title text (if text was accidentally deleted; now replaces
previous protect option), and peek into what previous coding decisions
were made. These are found under the new dropdown menu called “Issue
fixes”
Updated abstract_screener() to include highlighted keywords
Fixed bug in effort_summary() that did not properly sort screening
outcomes among the paired Reviewers from dual screening efforts
Added Crossref DOI searches to browse_DOI()
Updated replicate_phyloMeta1.3() to include tree shape statistics
and original VCV calculation as in the C++ (2011) version
Fixed PDF download templates for Elsiver which broke vignette
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
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