| Title: | Make Interactive 'PRISMA' Flow Diagrams |
| Version: | 1.1.1 |
| Description: | Systematic reviews should be described in a high degree of methodological detail. The 'PRISMA' Statement calls for a high level of reporting detail in systematic reviews and meta-analyses. An integral part of the methodological description of a review is a flow diagram. This package produces an interactive flow diagram that conforms to the 'PRISMA2020' preprint. When made interactive, the reader/user can click on each box and be directed to another website or file online (e.g. a detailed description of the screening methods, or a list of excluded full texts), with a mouse-over tool tip that describes the information linked to in more detail. Interactive versions can be saved as HTML files, whilst static versions for inclusion in manuscripts can be saved as HTML, PDF, PNG, SVG, PS or WEBP files. |
| Imports: | DiagrammeR, DiagrammeRsvg, htmltools, htmlwidgets, rsvg, scales, shiny, shinyjs, stats, stringr, utils, xml2, webp, DT, rio, tools, zip |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2023-02-08 23:14:33 UTC; runner |
| Author: | Neal Haddaway 
[aut],
Luke McGuinness
[aut],
Chris Pritchard
[aut, cre],
Brennan Chapman [ctb],
Hossam Hammady [ctb] |
| Maintainer: | Chris Pritchard <chris.pritchard@ntu.ac.uk> |
| Repository: | CRAN |
| Date/Publication: | 2023-02-09 11:20:15 UTC |
Add the hyperlink to the given node
Description
Generate the javascript method to insert the side labels
Usage
PRISMA_add_hyperlink_(node, url)
Arguments
node |
the relevent node |
url |
the URL the node should link to |
Value
An interactive flow diagram plot.
Calculate the correct filetime
Description
Work out the correct filetype to save the file as
Usage
PRISMA_calc_filetype_(fn, ft)
Arguments
fn |
The filename (including extension) |
ft |
The filetype (which can be NA or NULL) |
Value
the filetype taken from the filename, or overriden by the ft param
Read in PRISMA flow diagram data
Description
Read in a template CSV containing data for the flow diagram
Usage
PRISMA_data(data)
Arguments
data |
File to read in. |
Value
A list of objects needed to plot the flow diagram
Examples
csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
data <- read.csv(csvFile);
data <- PRISMA_data(data);
Plot interactive flow diagrams for systematic reviews
Description
Produces a PRISMA2020 style flow diagram for systematic reviews, with the option to add interactivity through tooltips (mouseover popups) and hyperlink URLs to each box. Data can be imported from the standard CSV template provided.
Usage
PRISMA_flowdiagram(
data,
interactive = FALSE,
previous = TRUE,
other = TRUE,
detail_databases = FALSE,
detail_registers = FALSE,
fontsize = 7,
font = "Helvetica",
title_colour = "Goldenrod1",
greybox_colour = "Gainsboro",
main_colour = "Black",
arrow_colour = "Black",
arrow_head = "normal",
arrow_tail = "none",
side_boxes = TRUE
)
Arguments
data |
List of data inputs including numbers of studies,
box text, tooltips, and urls for hyperlinks.
Data inputted via the |
interactive |
Logical argument TRUE or FALSE whether to plot interactivity (tooltips and hyperlinked boxes). |
previous |
Logical argument (TRUE or FALSE) specifying whether previous studies were sought. |
other |
Logical argument (TRUE or FALSE) specifying whether other studies were sought. |
detail_databases |
Logical argument (TRUE or FALSE) specifying whether to list specific databases. |
detail_registers |
Logical argument (TRUE or FALSE) specifying whether to list specific registers. |
fontsize |
The font size for text in each box. The default is '12'. |
font |
The font for text in each box. The default is 'Helvetica'. |
title_colour |
The colour for the upper middle title box (new studies). The default is 'Goldenrod1'. See 'DiagrammeR' colour scheme. http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors. |
greybox_colour |
The colour for the left and right column boxes. The default is 'Gainsboro'. See 'DiagrammeR' colour scheme http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors. |
main_colour |
The colour for the main box borders. The default is 'Black'. See 'DiagrammeR' colour scheme http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors. |
arrow_colour |
The colour for the connecting lines. The default is 'Black'. See 'DiagrammeR' colour scheme http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#colors. |
arrow_head |
The head shape for the line connectors. The default is 'normal'. See DiagrammeR arrow shape specification http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#arrow-shapes. #nolint |
arrow_tail |
The tail shape for the line connectors. The default is 'none'. See DiagrammeR arrow shape specification http://rich-iannone.github.io/DiagrammeR/graphviz_and_mermaid.html#arrow-shapes. #nolint |
side_boxes |
Whether or not to include the blue label boxes along the side |
Value
A flow diagram plot.
Examples
csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
data <- read.csv(csvFile);
data <- PRISMA_data(data);
plot <- PRISMA_flowdiagram(data,
fontsize = 12,
interactive = TRUE,
previous = FALSE,
other = TRUE);
plot
Format numbers with commas into numbers
Description
Turn strings containing numbers +/- commas into numbers
Usage
PRISMA_format_number_(x)
Arguments
x |
the number to format |
Value
the number with commas removed
Generate a temporary SVG from a plot object
Description
Generate and save a temporary SVG from a plot object
Usage
PRISMA_gen_tmp_svg_(obj)
Arguments
obj |
the plot object |
Value
the full path to the saved SVG
Calculate the correct height of a box from a list (e.g. of exclusion reasons)
Description
Get the correct height for a box
Usage
PRISMA_get_height_(n, offset, min = 2)
Arguments
n |
the number of rows of text in the label |
offset |
the offset height (e.g. 3.5) |
min |
the minimum number of rows before adjusting |
Value
the height of the box
Calculate the correct position of a node
Description
Get the correct position for a node
Usage
PRISMA_get_pos_(first_box_location, offset, length_orig, length_new)
Arguments
first_box_location |
the location of the first node |
offset |
the offset from the first node |
length_orig |
the width/height of the original node |
length_new |
the width/height of the new node |
Value
the position of the node
Generate / insert JS for labels
Description
Generate the javascript method to insert the side labels
Usage
PRISMA_insert_js_(plot, identification_text, screening_text, included_text)
Arguments
plot |
the plot object (without side labels) |
identification_text |
the text to use as the "identification" label |
screening_text |
the text to use as the "screening" label |
included_text |
the text to use as the "identification" label |
Value
the plot object (with JS to generate side labels)
Plot interactive flow diagram for systematic reviews
Description
Converts a PRISMA systematic review flow diagram into an interactive HTML plot, for embedding links from each box.
Usage
PRISMA_interactive_(plot, urls, previous, other)
Arguments
plot |
A plot object from |
urls |
A dataframe consisting of two columns: nodes and urls. The first column should contain 19 rows for the nodes from node1 to node19. The second column should contain a corresponding URL for each node. |
previous |
Logical argument (TRUE or FALSE) (supplied through
|
other |
Logical argument (TRUE or FALSE) (supplied through
|
Value
An interactive flow diagram plot.
See Also
Save PRISMA2020 flow diagram
Description
Save the output from PRISMA_flowdiagram() to the
working directory.
Usage
PRISMA_save(
plotobj,
filename = "PRISMA2020_flowdiagram.html",
filetype = NA,
overwrite = FALSE
)
Arguments
plotobj |
A plot produced using |
filename |
The filename to save (including extension) |
filetype |
The filetype to save the plot in, supports: HTML, ZIP, PDF, PNG, SVG, PS and WEBP (if NA, the filetype will be calculated out based on the file extension) HTML files maintain hyperlinks and tooltips The ZIP option creates an archive containing the HTML file, alongside supporting javascript and css files in an adjacent folder, instead of embedded base64 within the HTML file |
overwrite |
if TRUE, will overwrite an existing file |
Value
the absolute filename of the saved diagram plot.
Examples
csvFile <- system.file("extdata", "PRISMA.csv", package = "PRISMA2020")
data <- read.csv(csvFile);
data <- PRISMA_data(data);
plot <- PRISMA_flowdiagram(data,
fontsize = 12,
interactive = TRUE,
previous = FALSE,
other = TRUE);
PRISMA_save(plot, filename = tempfile(), filetype="html");
Defunct function - replaced by "PRISMA_data"
Description
Defunct function - replaced by "PRISMA_data"
Usage
read_PRISMAdata(data)
Arguments
data |
File to read in. |
See Also
Defunct function - replaced by "PRISMA_interactive_"
Description
Defunct function - replaced by "PRISMA_interactive_"
Usage
sr_flow_interactive(plot, urls, previous, other)
Arguments
plot |
A plot object from |
urls |
A dataframe consisting of two columns: nodes and urls. The first column should contain 19 rows for the nodes from node1 to node19. The second column should contain a corresponding URL for each node. |
previous |
Logical argument (TRUE or FALSE) (supplied through
|
other |
Logical argument (TRUE or FALSE) (supplied through
|