contour_plot

: Generates a contour plot showing the exposure-lag-response
relationship of the exposure <code>tmax</code> and <code>rainfall</code> and the diseases case type.

internal

Tools for producing climate-health indicators and supporting
official statistics from health and climate data. Implements analytical
workflows for temperature-related mortality, wildfire smoke exposure,
air pollution, suicides related to extreme heat, malaria, and
diarrhoeal disease outcomes, with utilities for descriptive statistics, model
validation, attributable fraction and attributable number estimation,
relative risk estimation, minimum mortality temperature estimation,
and plotting for reporting. These six indicators are endorsed by
the United Nations Statistical Commission for inclusion in the
Global Set of Environment and Climate Change Statistics.
Implemented methods include distributed lag non-linear models (DLNM),
quasi-Poisson time-series regression, case-crossover analysis,
Bayesian spatio-temporal models using the Integrated Nested Laplace
Approximation ('INLA'), and multivariate meta-analysis for
sub-national estimates. The package is based on methods developed
in the Standards for Official Statistics on Climate-Health
Interactions (SOSCHI) project
<https://climate-health.officialstatistics.org>. For methodologies,
see Watkins et al. (2025) <doi:10.5281/zenodo.14865904>,
Brown et al. (2024) <doi:10.5281/zenodo.14052183>,
Pearce et al. (2024) <doi:10.5281/zenodo.14050224>,
Byukusenge et al. (2025) <doi:10.5281/zenodo.15585042>,
Dzakpa et al. (2025) <doi:10.5281/zenodo.14881886>, and
Dzakpa et al. (2025) <doi:10.5281/zenodo.14871506>.

Kenechi Omeke

climatehealth

Statistical Tools for Modelling Climate-Health Impacts

Charlie Browning

Etse Yawo Dzakpa

Gladin Jose

Matt Pearce

Ellie Watkins

Claire Hunt

Beatrice Byukusenge

Cassien Habyarimana

Venuste Nyagahakwa

Felix Scarbrough

Treesa Shaji

Bonnie Lewis

Maquines Odhiambo Sewe

Vijendra Ingole

Sean Lovell

Antony Brown

Euan Soutter

Gillian Flower

David Furley

Joe Panes

Charlotte Romaniuk

Milly Powell

Wellcome 

Office for National Statistics 

contour_plot function

<dl><dt>data</dt>
<dd>Data list from <code>combine_health_climate_data()</code> function.</dd>
<dt>param_term</dt>
<dd>A character vector or list containing parameter terms such
as <code>tmax</code> (temperature exposure) and <code>rainfall</code>(rainfall exposure).
Default to <code>tmax</code>.</dd>
<dt>model</dt>
<dd>The fitted model from the <code>run_inla_models()</code> function.</dd>
<dt>level</dt>
<dd>A character vector specifying the geographical disaggregation.
Can take one of the following values: "country", "region", or "district".</dd>
<dt>case_type</dt>
<dd>Character. The type of disease that the case column refers
to. Must be one of <code>diarrhea</code> or <code>malaria</code>.</dd>
<dt>filter_year</dt>
<dd>Integer. The year to filter to data to. Defaults to NULL.</dd>
<dt>save_fig</dt>
<dd>Boolean. Whether to save the outputted plot. Defaults to
FALSE.</dd>
<dt>output_dir</dt>
<dd>The path to save the visualisation to. Defaults to NULL</dd></dl>

Arguments

Create and plot the exposure-lag-response relationship (contour plot) at country,
region or district level for each disease cases type (diarrhea and malaria). — contour_plot

<dl>

<dt>data</dt>
<dd>Data list from <code>combine_health_climate_data()</code> function.</dd>


<dt>param_term</dt>
<dd>A character vector or list containing parameter terms such
as <code>tmax</code> (temperature exposure) and <code>rainfall</code>(rainfall exposure).
Default to <code>tmax</code>.</dd>


<dt>model</dt>
<dd>The fitted model from the <code>run_inla_models()</code> function.</dd>


<dt>level</dt>
<dd>A character vector specifying the geographical disaggregation.
Can take one of the following values: "country", "region", or "district".</dd>


<dt>case_type</dt>
<dd>Character. The type of disease that the case column refers
to. Must be one of <code>diarrhea</code> or <code>malaria</code>.</dd>


<dt>filter_year</dt>
<dd>Integer. The year to filter to data to. Defaults to NULL.</dd>


<dt>save_fig</dt>
<dd>Boolean. Whether to save the outputted plot. Defaults to
FALSE.</dd>


<dt>output_dir</dt>
<dd>The path to save the visualisation to. Defaults to NULL</dd>

</dl>

Create and plot the exposure-lag-response relationship (contour plot) at country,
region or district level for each disease cases type (<code>diarrhea</code> and <code>malaria</code>).

contour_plot: Create and plot the exposure-lag-response relationship (contour plot) at country, region or district level for each disease cases type (`diarrhea` and `malaria`).

Description

Usage

Value

Arguments