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map_tb_burden.html
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map_tb_burden.html
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<meta property="og:description" content="Map measures of TB burden by country by specifying a metric from the TB burden data.
Specify a country or vector of countries in order to map them (the default is to map all countries).
Various other options are available for tuning the plot further." />
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<h1>Map TB Burden</h1>
<small class="dont-index">Source: <a href='https://github.com/seabbs/getTBinR/blob/master/R/map_tb_burden.R'><code>R/map_tb_burden.R</code></a></small>
<div class="hidden name"><code>map_tb_burden.Rd</code></div>
</div>
<div class="ref-description">
<p>Map measures of TB burden by country by specifying a metric from the TB burden data.
Specify a country or vector of countries in order to map them (the default is to map all countries).
Various other options are available for tuning the plot further.</p>
</div>
<pre class="usage"><span class='fu'>map_tb_burden</span>(
<span class='kw'>df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>dict</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>metric</span> <span class='kw'>=</span> <span class='st'>"e_inc_100k"</span>,
<span class='kw'>metric_label</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>fill_var_type</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>countries</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>compare_to_region</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>legend</span> <span class='kw'>=</span> <span class='st'>"bottom"</span>,
<span class='kw'>year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>annual_change</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>trans</span> <span class='kw'>=</span> <span class='st'>"identity"</span>,
<span class='kw'>interactive</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>download_data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>viridis_palette</span> <span class='kw'>=</span> <span class='st'>"viridis"</span>,
<span class='kw'>viridis_direction</span> <span class='kw'>=</span> -<span class='fl'>1</span>,
<span class='kw'>viridis_end</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>df</th>
<td><p>Dataframe of TB burden data, as sourced by <code><a href='get_tb_burden.html'>get_tb_burden</a></code>.
If not specified then will source the WHO TB burden data, either locally if available
or directly from the WHO (if <code>download_data = TRUE</code>).</p></td>
</tr>
<tr>
<th>dict</th>
<td><p>A tibble of the data dictionary. See <code><a href='get_data_dict.html'>get_data_dict</a></code>
for details. If not supplied the function will attempt to load a saved version of the
dictionary. If this fails and <code>download_data = TRUE</code> then the dictionary will be downloaded.</p></td>
</tr>
<tr>
<th>metric</th>
<td><p>Character string specifying the metric to plot</p></td>
</tr>
<tr>
<th>metric_label</th>
<td><p>Character string specifying the metric label to use.</p></td>
</tr>
<tr>
<th>fill_var_type</th>
<td><p>A character string, defaults to <code>NULL</code>. To set the fill variable type to be
discrete use "discrete" and to be continuous use "continuous".</p></td>
</tr>
<tr>
<th>countries</th>
<td><p>A character string specifying the countries to target.</p></td>
</tr>
<tr>
<th>compare_to_region</th>
<td><p>Logical, defaults to <code>FALSE</code>. If <code>TRUE</code> all
countries that share a region with those listed in <code>countries</code> will be plotted.
Note that this will override settings for <code>facet</code>, unless it is set to "country".</p></td>
</tr>
<tr>
<th>facet</th>
<td><p>Character string, the name of the variable to facet by.</p></td>
</tr>
<tr>
<th>legend</th>
<td><p>Character string, defaults to <code>"bottom"</code>. Position of the legend see <code><a href='https://ggplot2.tidyverse.org/reference/theme.html'>?ggplot2::theme</a></code> for defaults but known
options are: <code>"none"</code>, <code>"top"</code>, <code>"right"</code> and <code>"bottom"</code>.</p></td>
</tr>
<tr>
<th>year</th>
<td><p>Numeric, indicating the year of data to map. Defaults to the latest year in the data.
If <code>interactive = TRUE</code> then multiple years may be passed as a vector, the result will then be animated over years.</p></td>
</tr>
<tr>
<th>annual_change</th>
<td><p>Logical, defaults to <code>FALSE</code>. If <code>TRUE</code> then the
percentage annual change is computed for the specified metric.</p></td>
</tr>
<tr>
<th>trans</th>
<td><p>A character string specifying the transform to use on the specified metric. Defaults to no
transform ("identity"). Other options include log scaling ("log") and log base 10 scaling
("log10"). For a complete list of options see <code>ggplot2::continous_scale</code>.</p></td>
</tr>
<tr>
<th>interactive</th>
<td><p>Logical, defaults to <code>FALSE</code>. If <code>TRUE</code> then an interactive plot is
returned.</p></td>
</tr>
<tr>
<th>download_data</th>
<td><p>Logical, defaults to <code>TRUE</code>. If not found locally should the data be
downloaded from the specified URL?</p></td>
</tr>
<tr>
<th>save</th>
<td><p>Logical, should the data be saved for reuse during the current R session. Defaults to
<code>TRUE</code>. If <code>TRUE</code> then the data is saved to the temporary directory specified by <code><a href='https://rdrr.io/r/base/tempfile.html'>tempdir</a></code>.</p></td>
</tr>
<tr>
<th>viridis_palette</th>
<td><p>Character string indicating the <code>viridis</code> colour palette to use. Defaults
to "viridis". Options include "cividis", "magma", "inferno", "plasma", and "viridis". For additional details
see <code><a href='https://rdrr.io/pkg/viridis/man/viridis_pal.html'>viridis_pal</a></code> for additional details.</p></td>
</tr>
<tr>
<th>viridis_direction</th>
<td><p>Numeric, indicating the direction for the colour palette (1 or -1), defaults to -1.
See <code><a href='https://rdrr.io/pkg/viridis/man/scale_viridis.html'>scale_color_viridis</a></code> for additional details.</p></td>
</tr>
<tr>
<th>viridis_end</th>
<td><p>Numeric between 0 and 1, defaults to 0.9. The end point of the viridis scale to use.
#' See <code><a href='https://rdrr.io/pkg/viridis/man/scale_viridis.html'>scale_color_viridis</a></code> for additional details.</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>Logical, defaults to <code>FALSE</code>. Should additional status and progress messages
be displayed.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Additional arguments to pass to <code><a href='get_tb_burden.html'>get_tb_burden</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A plot of TB Incidence Rates by Country</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>plot_tb_burden plot_tb_burden_overview get_tb_burden search_data_dict</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'>
<span class='co'>## Map raw incidence rates</span>
<span class='fu'>map_tb_burden</span>()</div><div class='img'><img src='map_tb_burden-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>#' ## Map raw incidence rates</span>
<span class='fu'>map_tb_burden</span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>2014</span>:<span class='fl'>2017</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"year"</span>)
<span class='co'>## Map log10 scaled incidence rates</span>
<span class='fu'>map_tb_burden</span>(<span class='kw'>trans</span> <span class='kw'>=</span> <span class='st'>"log10"</span>)
<span class='co'>## Map percentage annual change in incidence rates</span>
<span class='fu'>map_tb_burden</span>(<span class='kw'>annual_change</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'>## Find variables relating to mortality in the WHO dataset</span>
<span class='fu'><a href='search_data_dict.html'>search_data_dict</a></span>(<span class='kw'>def</span> <span class='kw'>=</span> <span class='st'>"mortality"</span>)
<span class='co'>## Map mortality rates (exc HIV) - without progress messages</span>
<span class='fu'>map_tb_burden</span>(<span class='kw'>metric</span> <span class='kw'>=</span> <span class='st'>"e_mort_exc_tbhiv_100k"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'>## Can also use a discrete metric if one is available</span>
<span class='fu'>map_tb_burden</span>(<span class='kw'>metric</span> <span class='kw'>=</span> <span class='st'>"g_whoregion"</span>, <span class='kw'>metric_label</span> <span class='kw'>=</span> <span class='st'>"WHO world region"</span>)
}</div></pre>
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