set_cross_basis

Generates cross-basis matrices for lagged climate variables in a dataset,
for use in Distributed Lag Nonlinear Models (DLNM).

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 

set_cross_basis function

<dl><dt>data</dt>
<dd>A dataset returned from <code>combine_health_climate_data()</code>,
including lagged variables like <code>tmax_lag1</code>, <code>tmin_lag1</code>, etc.</dd>
<dt>max_lag</dt>
<dd>Character. Number corresponding to the maximum lag to be
considered for the delay effect. It should be between 2 an 4. Defaults to 2.</dd>
<dt>nk</dt>
<dd>Numeric. Number of internal knots for the natural spline of
each predictor, controlling its flexibility: <code>nk = 0</code> produces a linear
effect with one basis column, <code>nk = 1</code> generates a simple spline with two
columns, <code>nk = 2</code> yields a more flexible spline with three columns,
and higher values of <code>nk</code> further increase flexibility but may also
raise collinearity among spline terms. Defaults to 1</dd></dl>

Arguments

Create a cross-basis matrix set for DLNM analysis — set_cross_basis

<dl>

<dt>data</dt>
<dd>A dataset returned from <code>combine_health_climate_data()</code>,
including lagged variables like <code>tmax_lag1</code>, <code>tmin_lag1</code>, etc.</dd>


<dt>max_lag</dt>
<dd>Character. Number corresponding to the maximum lag to be
considered for the delay effect. It should be between 2 an 4. Defaults to 2.</dd>


<dt>nk</dt>
<dd>Numeric. Number of internal knots for the natural spline of
each predictor, controlling its flexibility: <code>nk = 0</code> produces a linear
effect with one basis column, <code>nk = 1</code> generates a simple spline with two
columns, <code>nk = 2</code> yields a more flexible spline with three columns,
and higher values of <code>nk</code> further increase flexibility but may also
raise collinearity among spline terms. Defaults to 1</dd>

</dl>

Create a cross-basis matrix set for DLNM analysis

set_cross_basis: Create a cross-basis matrix set for DLNM analysis

Description

Usage

Value

Arguments