abstract_screener: A GUI screener to quickly code candidate studies for...

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

Description

A GUI screener to help scan and evaluate the title and abstract of studies to be included in a systematic review or meta-analysis.

Usage

abstract_screener(
  file = file.choose(),
  aReviewer = NULL,
  reviewerColumnName = "REVIEWERS",
  unscreenedColumnName = "INCLUDE",
  unscreenedValue = "not vetted",
  abstractColumnName = "ABSTRACT",
  titleColumnName = "TITLE",
  browserSearch = "https://www.google.com/search?q=",
  fontSize = 13,
  windowWidth = 70,
  windowHeight = 16,
  theButtons = c("YES", "maybe", "NO"),
  keyBindingToButtons = c("y", "m", "n"),
  buttonSize = 10,
  highlightColor = "powderblue",
  highlightKeywords = NA
)

Arguments

file	The file name and location of a .csv file containing the abstracts and titles. The .csv file should have been initialized with effort_initialize and populated with screeners (reviewers) using effort_distribute.
aReviewer	The name (a string) of the reviewer to screen abstracts. It is used when there are multiple reviewers assigned to screen abstracts. The default column label is "REVIEWERS" as initialized with effort_distribute.
reviewerColumnName	The name of the column heading in the .csv file that contains the reviewer names that will screen abstracts. The default column label is "REVIEWERS".
unscreenedColumnName	The name of the column heading in the .csv file that contains the screening outcomes (i.e. vetting outcomes by a reviewer). Unscreened references are by default labeled as "not vetted". The reviewer then can code to "YES" (is a relevant study), "NO" is not relevant and should be excluded, or "MAYBE" if the title/abstract is missing or does not contains enough information to fully assess inclusivity. The default label of this column is "INCLUDE".
unscreenedValue	Changes the default coding (a string) of "not vetted" that designates whether an abstract remains to be screened or vetted.
abstractColumnName	The name of the column heading in the .csv file that contains the abstracts. The default label of this column is "ABSTRACT".
titleColumnName	The name of the column heading in the .csv file that contains the titles. The default label of this column is "TITLE".
browserSearch	Change the url for the browser title search; the default is Google.
fontSize	Change the font gWidgets::size of the title and abstract text.
windowWidth	Change the default width of the GUI window.
windowHeight	Change the default height of the GUI window.
theButtons	A vector of coding buttons included on the screener. The default is YES, maybe, and NO. Buttons can be removed as added by changing this vector. For example, theButtons = c("YES", "NO") to remove the maybe-button, or theButtons = c("YES", "maybe", NO", "model") to add a "model" button that tags studies specifically as "model".
keyBindingToButtons	A vector of specific keyboard bindings to buttons. They are keyboard shortcuts to buttons and the default binding is y for YES-button, m for maybe-button, and n for NO-button. If theButtons parameter is modified then these keybindings should also be modified.
buttonSize	Change the default gWidgets::size of buttons.
highlightColor	The color of keywords highlighted in title and abstract. The default is blue, but for classic yellow use "palegoldenrod".
highlightKeywords	A string or list of keywords that will be highlighted in title and abstract.

Note

Installation and troubleshooting

For Mac OS users, installation is sometimes not straighforward as this screener requires the Tcl/Tk GUI toolkit to be installed. You can get this toolkit by making sure the latest X11 application (xQuartz) is installed, see here: https://www.xquartz.org/. More information on installation is found in metagear's vignette.

How to use the screener

The GUI itself will appear as a single window with the first title/abstract listed in the .csv file. If abstracts have already been screened/coded, it will begin at the nearest reference labeled as "not vetted". The SEARCH WEB button opens the default browser and searches Google with the title of the reference. The YES, MAYBE, NO buttons, which also have keyboard shortcuts y and n, are used to code the inclusion/exclusion of the reference. Once clicked/coded the next reference is loaded. The SAVE button is used to save the coding progress of screening tasks. It will save coding progress directly to the loaded .csv file. Closing the GUI, and not saving, will result in the loss of screening efforts relative to last save.

There is also an ISSUE FIXES menu bar with quick corrections to screening errors. These include ISSUE FIXES: REFRESH TITLE AND ABSTRACT TEXT which reloads the text of the current abstract in case portions were deleted when copying and pasting sections, ISSUE FIXES: STATUS OF CURRENT ABSTRACT which provides information on whether or not the abstract was previously screened, and ISSUE FIXES: RETURN TO PREVIOUS ABSTRACT that backtracks to the previous abstract if a selection error occurred (note a warning will appear of there is a change to its inclusion/exclusion coding).

Examples

## Not run: 

data(example_references_metagear)
effort_distribute(example_references_metagear,
                  initialize = TRUE,
                  reviewers = "marc",
                  save_split = TRUE)
abstract_screener("effort_marc.csv",
                  aReviewer = "marc",
                  highlightKeywords = "and")

## End(Not run)

metagear documentation built on Feb. 15, 2021, 5:09 p.m.