Bayesian forest plot
bayes_forest.RdProduce a Bayesian forest plot with gemtc::forest()
Usage
bayes_forest(
model,
xmin = NULL,
xmax = NULL,
title = "",
ranking = FALSE,
logger = NULL
)
covariate_forest(...)Arguments
- model
list. Object created by
bayes_model()orcovariate_model()- xmin
numeric. Minimum x-axis value. Default
NULLin which case it is calculated internally- xmax
numeric. Maximum x-axis value. Default
NULLin which case it is calculated internally- title
character. Title for the plot. Default is no title
- ranking
logical. Whether the function is being used in
bayes_ranking- logger
Stores all notification messages to be displayed in the Log Window. Insert the logger reactive list here for running in shiny, otherwise leave the default
NULL- ...
Parameters passed to
bayes_forest()
Value
html. Contains the svg string to generate the plot. This will display
the plot when at the end of a quarto or rmarkdown chunk. To view in the viewer
panel of Rstudio, use htmltools::browsable(). The output can be saved
using write_plot().
Examples
configured_data_path <- system.file("extdata", "configured_data.Rds", package = "metainsight")
configured_data <- readRDS(configured_data_path)
# n_adapt and n_iter are set low to run quickly, but should be left as the
# default values in real use
fitted_bayes_model <- bayes_model(configured_data = configured_data,
n_adapt = 100,
n_iter = 100)
bayes_forest(model = fitted_bayes_model)
#> <?xml version="1.0" encoding="UTF-8"?>
#> <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="57 35 439 157">
#> <g class="svglite">
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#> <style type="text/css"><![CDATA[
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#> fill: none;
#> stroke: #000000;
#> stroke-linecap: round;
#> stroke-linejoin: round;
#> stroke-miterlimit: 10.00;
#> }
#> .svglite text {
#> white-space: pre;
#> }
#> .svglite g.glyphgroup path {
#> fill: inherit;
#> stroke: none;
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#> </defs>
#> <rect width="525.60" height="285.00" style="stroke: none; fill: #FFFFFF;"/>
#> <defs>
#> <clipPath id="cpMC4wMHw1MjUuNjB8MC4wMHwyODUuMDA=">
#> <rect x="0.00" y="0.00" width="525.60" height="285.00"/>
#> </clipPath>
#> </defs>
#> <g clip-path="url(#cpMC4wMHw1MjUuNjB8MC4wMHwyODUuMDA=)">
#> <text x="415.17" y="94.79" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="142.48px" lengthAdjust="spacingAndGlyphs">Mean Difference (95% CrI)</text>
#> <text x="66.42" y="112.79" style="font-size: 12.00px; font-weight: bold; font-family: "Liberation Sans";" textLength="146.00px" lengthAdjust="spacingAndGlyphs">Compared with the_Great</text>
#> <text x="66.42" y="130.79" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="64.69px" lengthAdjust="spacingAndGlyphs">the_Butcher</text>
#> <polyline points="282.27,126.66 330.15,126.66 " style="stroke-width: 0.75;"/>
#> <circle cx="306.91" cy="126.66" r="2.88" style="stroke-width: 0.75; fill: #FFFFFF;"/>
#> <text x="371.16" y="130.79" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="88.02px" lengthAdjust="spacingAndGlyphs">12.1 (8.66, 15.4)</text>
#> <text x="66.42" y="145.19" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="48.69px" lengthAdjust="spacingAndGlyphs">the_Little</text>
#> <polyline points="269.97,141.06 336.39,141.06 " style="stroke-width: 0.75;"/>
#> <circle cx="306.66" cy="141.06" r="2.88" style="stroke-width: 0.75; fill: #FFFFFF;"/>
#> <text x="371.16" y="145.19" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="88.02px" lengthAdjust="spacingAndGlyphs">12.1 (6.92, 16.3)</text>
#> <text x="66.42" y="159.59" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="67.61px" lengthAdjust="spacingAndGlyphs">the_Younger</text>
#> <polyline points="278.52,155.46 324.96,155.46 " style="stroke-width: 0.75;"/>
#> <circle cx="303.46" cy="155.46" r="2.88" style="stroke-width: 0.75; fill: #FFFFFF;"/>
#> <text x="371.16" y="159.59" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="87.12px" lengthAdjust="spacingAndGlyphs">11.6 (8.13, 14.7)</text>
#> <polyline points="220.93,169.86 220.93,97.86 " style="stroke-width: 0.75;"/>
#> <polyline points="220.93,162.66 362.66,162.66 " style="stroke-width: 0.75;"/>
#> <polyline points="220.93,169.86 220.93,162.66 " style="stroke-width: 0.75;"/>
#> <polyline points="362.66,169.86 362.66,162.66 " style="stroke-width: 0.75;"/>
#> <text x="220.93" y="181.19" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="6.67px" lengthAdjust="spacingAndGlyphs">0</text>
#> <text x="220.93" y="181.19" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="6.67px" lengthAdjust="spacingAndGlyphs">0</text>
#> <text x="362.66" y="181.19" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="13.34px" lengthAdjust="spacingAndGlyphs">20</text>
#> <text x="277.20" y="53.09" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="214.06px" lengthAdjust="spacingAndGlyphs">Between-study standard deviation: 1.62 </text>
#> <text x="277.20" y="67.49" text-anchor="middle" style="font-size: 12.00px; font-family: "Liberation Sans";" textLength="171.38px" lengthAdjust="spacingAndGlyphs"> 95% credible interval: 0.2 , 6.05</text>
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