Pollution to health

morie.envhealth (Python) and morie_envhealth_* (R) turn an ambient exposure into a disease burden. Every function cites the paper whose formula it implements, and the two arms agree on fixed inputs to 1e-12 (the parity test ships with the packages). The command verify-pollution runs the chain end to end and logs its assumptions.

Concentration-response

PM2.5, all-cause mortality, log-linear with the pooled cohort estimate of the WHO 2021 guideline review (Chen & Hoek 2020: RR 1.08, 95% CI 1.06-1.09, per 10 \(\mu g/m^3\)):

\[RR(z) = \exp\!\left(\ln(1.08) \, \frac{z - z_{cf}}{10}\right) \quad (z > z_{cf}), \qquad RR(z) = 1 \text{ otherwise}\]

with the counterfactual \(z_{cf} = 5.8\ \mu g/m^3\) (WHO 2021 interim target). The cause-specific outcomes (IHD, stroke) keep the Integrated Exposure-Response curve of Burnett et al. (2014, Eq. 1), \(RR(z) = 1 + \alpha (1 - e^{-\gamma (z - z_{cf})^{\delta}})\), with the GBD 2013 triples IHD \((1.91, 0.14, 0.49)\) and stroke \((1.46, 0.13, 0.61)\); the IER was fit per cause and has no all-cause form.

NO2, log-linear (Huangfu & Atkinson 2020, the WHO 2021 review):

\[RR(z) = \exp\!\left(\beta \, \frac{z - z_{cf}}{10}\right)\]

with \(\beta\) per 10 \(\mu g/m^3\) of \(\ln(1.02) = 0.0198\) (all-cause mortality: RR 1.02, 95% CI 1.01-1.04), 0.029 (respiratory) or 0.039 (childhood asthma), \(z_{cf} = 10\).

from morie import envhealth
envhealth.concentration_response_pm25(12.0).rr        # 1.0489...
envhealth.concentration_response_no2(25.0, outcome="respiratory").log_rr

rmorie::morie_envhealth_crf_pm25(12)$rr
rmorie::morie_envhealth_crf_no2(25, outcome = "respiratory")$log_rr

Attributable fraction

Levin’s formula (Rothman, Greenland and Lash 2008, chapter 5), with \(p\) the exposure prevalence:

\[PAF = \frac{p\,(RR - 1)}{1 + p\,(RR - 1)}\]

Deaths displaced

The BenMAP-CE health-impact function (US EPA 2018; Anenberg et al. 2010):

\[\Delta Y = y_0 \, N \, \left(1 - e^{-\beta \Delta x}\right)\]

with \(y_0\) the baseline rate per person-year, \(N\) the population and \(\beta\) the log-RR per unit of exposure.

Burden

burden_of_pollution / morie_envhealth_burden() chain the three: RR at the mean exposure, PAF at the prevalence, attributable cases \(= PAF \times y_0 N\) (GBD 2019 Risk Factors Collaborators 2020). burden_by_fsa applies it per area and sorts the worst first.

Equity

The concentration index (Wagstaff, Paci and van Doorslaer 1991), with \(R_i\) the fractional income rank \((rank_i - 0.5)/n\) and the population covariance:

\[CI = \frac{2}{\mu}\,\mathrm{cov}(h_i, R_i)\]

Negative values mean lower-income units bear more exposure.

Sensitivity

exposure_response_sensitivity / morie_envhealth_sensitivity() fit the partially linear double-ML model (Chernozhukov et al. 2018, section 4.2) with the exposure as a continuous treatment and add a percentile bootstrap over resamples (Efron and Tibshirani 1993).

The command

morie verify-pollution --pollutant no2 --demo
morie verify-pollution --pollutant pm25 --exposure-csv exposure.csv --baseline-rate 500 --population 1000000
rmorie verify-pollution --pollutant no2 --exposure-mean 25 --exposure-prevalence 0.9 --json

The report prints the inputs, an assumption log (exposure above the reference, prevalence in [0, 1], non-negative baseline, positive population, supported pollutant), then the RR with its citation, the PAF, the deaths displaced, the attributable cases and, when an income column is present, the concentration index. Exit status 0 when every assumption holds, 1 when one fails (the pipeline is skipped), 2 on a data error.

References

  • Burnett, R. T. et al. (2014). An integrated risk function for estimating the global burden of disease attributable to ambient fine particulate matter exposure. Environmental Health Perspectives, 122(4), 397-403.

  • Chen, J. and Hoek, G. (2020). Long-term exposure to PM and all-cause and cause-specific mortality: a systematic review and meta-analysis. Environment International, 143, 105974.

  • Huangfu, P. and Atkinson, R. (2020). Long-term exposure to NO2 and O3 and all-cause and respiratory mortality: a systematic review and meta-analysis. Environment International, 144, 105998.

  • WHO (2021). Global Air Quality Guidelines.

  • Rothman, K. J., Greenland, S. and Lash, T. L. (2008). Modern Epidemiology, 3rd ed., chapter 5.

  • US EPA (2018). BenMAP-CE User’s Manual Appendices; Anenberg, S. C. et al. (2010). Environmental Health Perspectives, 118(9), 1189-1195.

  • Wagstaff, A., Paci, P. and van Doorslaer, E. (1991). On the measurement of inequalities in health. Social Science and Medicine, 33(5), 545-557.

  • Chernozhukov, V. et al. (2018). Double/debiased machine learning. Econometrics Journal, 21(1), C1-C68.