climatehealth
Statistical Tools for Modelling Climate-Health Impacts
Description
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>.
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CRAN Check Status
Show all 12 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | ERROR |
| r-devel-linux-x86_64-fedora-gcc | ERROR |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-x86_64 | NOTE |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (3 non-OK)
tests
Running ‘testthat.R’ [5m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(patrick)
> library(climatehealth)
>
> test_check("climatehealth")
This is dlnm 2.4.10. For details: help(dlnm) and vignette('dlnmOverview').
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD
...[truncated]...
only.hyperparam, inla.call = inla.call, inla.arg = inla.arg, num.threads = num.threads, keep = keep, working.directory = working.directory, silent = silent, inla.mode = inla.mode, safe = FALSE, debug = debug, .parent.frame = .parent.frame)`: 16 simultaneous processes spawned
The inla program failed and the maximum number of tries has been reached.
Backtrace:
▆
1. ├─climatehealth:::suppress_plot(...) at test_malaria.R:104:3
2. │ └─base::force(expr) at ./helper-utils.R:11:3
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─climatehealth::malaria_do_analysis(...)
6. └─climatehealth:::run_inla_models(...)
7. └─climatehealth (local) fit(base_formula)
8. ├─INLA::inla.rerun(...)
9. │ └─base::stopifnot(any(inherits(object, "inla")))
10. └─INLA::inla(...)
11. └─INLA:::inla.core.safe(...)
[ FAIL 2 | WARN 14 | SKIP 2 | PASS 2315 ]
Error:
! Test failures.
Execution halted
tests
Running ‘testthat.R’ [4m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(patrick)
> library(climatehealth)
>
> test_check("climatehealth")
This is dlnm 2.4.10. For details: help(dlnm) and vignette('dlnmOverview').
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD
...[truncated]...
only.hyperparam, inla.call = inla.call, inla.arg = inla.arg, num.threads = num.threads, keep = keep, working.directory = working.directory, silent = silent, inla.mode = inla.mode, safe = FALSE, debug = debug, .parent.frame = .parent.frame)`: 16 simultaneous processes spawned
The inla program failed and the maximum number of tries has been reached.
Backtrace:
▆
1. ├─climatehealth:::suppress_plot(...) at test_malaria.R:104:3
2. │ └─base::force(expr) at ./helper-utils.R:11:3
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─climatehealth::malaria_do_analysis(...)
6. └─climatehealth:::run_inla_models(...)
7. └─climatehealth (local) fit(base_formula)
8. ├─INLA::inla.rerun(...)
9. │ └─base::stopifnot(any(inherits(object, "inla")))
10. └─INLA::inla(...)
11. └─INLA:::inla.core.safe(...)
[ FAIL 2 | WARN 14 | SKIP 2 | PASS 2315 ]
Error:
! Test failures.
Execution halted
package dependencies
Package suggested but not available for checking: ‘INLA’
Check History
ERROR 4 OK · 1 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 31, 2026
tests
Running ‘testthat.R’ [5m/13m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(patrick)
> library(climatehealth)
>
> test_check("climatehealth")
This is dlnm 2.4.10. For details: help(dlnm) a
...[truncated]...
::inla.rerun(...)
9. │ └─base::stopifnot(any(inherits(object, "inla")))
10. └─INLA::inla(...)
11. └─INLA:::inla.core.safe(...)
[ FAIL 2 | WARN 14 | SKIP 2 | PASS 2315 ]
Error:
! Test failures.
Execution halted
tests
Running ‘testthat.R’ [294s/418s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(patrick)
> library(climatehealth)
>
> test_check("climatehealth")
This is dlnm 2.4.10. For details: help(dlnm
...[truncated]...
::inla.rerun(...)
9. │ └─base::stopifnot(any(inherits(object, "inla")))
10. └─INLA::inla(...)
11. └─INLA:::inla.core.safe(...)
[ FAIL 2 | WARN 14 | SKIP 2 | PASS 2315 ]
Error:
! Test failures.
Execution halted
package dependencies
Package suggested but not available for checking: ‘INLA’