load_and_process_data

Read in a csv file containing a monthly time series of health
outcomes and population data. Renames columns and creates time variables for
spatiotemporal analysis.

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 

load_and_process_data function

<dl><dt>health_data_path</dt>
<dd>Path to a csv file containing a monthly time series of data
for health outcome case type, which may be disaggregated by sex (under five case or
above five case), and by Region and District.</dd>
<dt>region_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the region names.</dd>
<dt>district_col</dt>
<dd>Character. Name of the column in the dataframe that
contains the district names.</dd>
<dt>date_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the date. Defaults to NULL.</dd>
<dt>year_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the year.</dd>
<dt>month_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the month.</dd>
<dt>case_col</dt>
<dd>Character. Name of the column in the dataframe
that contains the disease cases to be considered.</dd>
<dt>case_type</dt>
<dd>Character. The type of disease that the case column refers
to. Must be one of 'diarrhea' or 'malaria'.</dd>
<dt>tot_pop_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the total population.</dd></dl>

Arguments

Read in and format health data - diseases cases type — load_and_process_data

<dl>

<dt>health_data_path</dt>
<dd>Path to a csv file containing a monthly time series of data
for health outcome case type, which may be disaggregated by sex (under five case or
above five case), and by Region and District.</dd>


<dt>region_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the region names.</dd>


<dt>district_col</dt>
<dd>Character. Name of the column in the dataframe that
contains the district names.</dd>


<dt>date_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the date. Defaults to NULL.</dd>


<dt>year_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the year.</dd>


<dt>month_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the month.</dd>


<dt>case_col</dt>
<dd>Character. Name of the column in the dataframe
that contains the disease cases to be considered.</dd>


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


<dt>tot_pop_col</dt>
<dd>Character. Name of the column in the dataframe that contains
the total population.</dd>

</dl>

Read in and format health data - diseases cases type

load_and_process_data: Read in and format health data - diseases cases type

Description

Usage

Value

Arguments