This package provides functions for calculating climate–health indicators and supporting the production of climate–health statistics. The methods implemented in the package follow the statistical framework for climate–health indicators developed under the Standards for Official Statistics on Climate–Health Interactions (SOSCHI) project. You can find out more and stay up to date with the SOSCHI project here.
This package contains scientific functions dedicated to the following topics in the SOSCHI framework. Please note the final methods documents are still in development, so the versions linked below are earlier alpha versions.
| Topic | Topic Owner | Methods |
|---|---|---|
| Temperature-related health effects | ONS | Methodology Document |
| Health effects of wildfires | ONS | Methodology Document |
| Mental health | ONS | Methodology Document |
| Water-borne diseases | AIMS | Methodology Document |
| Health effects of air pollution | AIMS | Methodology Document |
| Vector-borne diseases | RIPS/AIMS | Methodology Document |
[!NOTE] Please note that there may be some inconsistencies between the indicators and methods included in the Github code/R package, and those described in the corresponding SOSCHI topic documents, and/or related analysis publications. This is because the final methods documents are still in development, so those linked below in the section ‘SOSCHI Topics and Indicators’ are an earlier alpha version.
For information on how to use this R package, check here
To install and use the package, you need an R environment. This package has been developed primarily with R 4.4.1, and that version is recommended where possible. R-4.4.1 can be downloaded here
You can use the package in several ways, depending on whether you want a stable release or want to work with the source code.
Use this option if you want to inspect the source code, make changes locally, test updates, or contribute to the package.
First clone the repository from GitHub to your machine. Then in R:
install.packages("devtools")
devtools::load_all(path = "{path/to/climatehealth}")This loads the package directly from the local source directory into
your current R session. This is useful for development, but won’t make
the climatehealth package available as a standard installed
package in your library. Once the source code changes, run
devtools::load_all() again to reload the updated functions.
If you are an end user, follow the standard installation procedure
outlined below for your operating system.
If you want to install the latest development version of the package
directly from GitHub without cloning the repository, you can use
remotes::install_github().
First install the remotes package in R if needed:
install.packages("remotes")Then install the package with:
remotes::install_github("onssoschi/climatehealth")This installs the package from the GitHub repository into your R library in the usual way. This option is useful if you want the latest development version of the package but do not need to edit the source code locally.
If you would like to install the latest official release of the
package, download the .zip file from the latest GitHub
release here.
Then install it in R with:
install.packages(path = "{path/to/climatehealth_<version>.zip}", repos = NULL, type = "win.binary")where <version> is the version number of the
release you downloaded.
If you are using MacOS and would like to install from the source,
download the .tar.gz file from the latest GitHub release here.
Then install it in R with:
install.packages(path = "{path/to/climatehealth_<version>.tar.gz}", repos = NULL, type = "source")where <version> is the version number of the
release you downloaded.
Once the package is installed or loaded, you can run any of the main analysis entry points depending on your use case.
Most indicator modules are run through a top-level
*_do_analysis() function. For example:
result <- climatehealth::air_pollution_do_analysis(
data_path = "{path/to/your_data.csv}"
)Other indicators follow the same pattern, for example:
temp_mortality_do_analysis()
wildfire_do_analysis()
malaria_do_analysis()
diarrhea_do_analysis()
suicides_heat_do_analysis()Each analysis function expects specific input data and parameters for that indicator, so refer to the package documentation for the relevant module before running it.
Example usage scripts for the main indicator workflows are provided
in inst/examples/, including: -
air_pollution_usage.R - temp_mortality_usage.R
- wildfires_usage.R - malaria_usage.R -
diarrhea_usage.R - suicides_heat_usage.R -
descriptive_stats_usage.R
You can also run the descriptive statistics workflow directly:
result <- climatehealth::run_descriptive_stats(
data = my_data,
output_path = "{path/to/output}"
)This is useful for checking data quality, exploring variables, and generating summary outputs before running an indicator-specific workflow.
We welcome contributions from public users, collaborators, and developers who want to improve the package. If you want to contribute code, documentation, tests, or bug fixes, please start by reading the CONTRIBUTING guide CONTRIBUTING. This includes guidance on setting up a local development workflow, making changes safely, and submitting updates through GitHub.
The package authors reflect direct intellectual and technical contributions to the package architecture, module methods, and reproducible analytical workflows.
The following contributors supported the package through bug fixes, minor features, testing, documentation, and review work: - Sean Lovell - Antony Brown - Euan Soutter - Gillian Flower - David Furley - Joe Panes - Charlotte Romaniuk - Milly Powell
We acknowledge the Topic Expert Group members and Expert Advisory Group members for higher-level leadership, methodological input, and subject-area support to the SOSCHI climate-health work. We also acknowledge the use of external data and code examples that informed testing and early prototyping.
This is an open access R package published under a UK Open Government Licence 3.0 which is compatible with the Creative Commons CC-BY-SA 4.0 licence. You are free to copy, publish, distribute and adapt the information, provided you acknowledge the source and link to this R package (see citation below). Enquiries concerning the application of this R package can be made to the project team at climate.health@ons.gov.uk.
If you use climatehealth in publications, cite the
package as:
Browning, C., Omeke, K., Dzakpa, E. Y., Jose, G., Pearce, M.,
Watkins, E., Hunt, C., Byukusenge, B., Habyarimana, C., Nyagahakwa, V.,
Scarbrough, F., Shaji, T., Lewis, B., and Ingole, V. (2026).
climatehealth: Epidemiological Tools for Climate-Health Impact Assessment.
R package.
An R package citation file is provided at
inst/CITATION.
This work was supported by Wellcome.