Vignette: Intro to healthiar

Hi there!

This vignette will tell you about healthiar and show you how to use healthiar with the help of examples.

Note: Before using healthiar, please read carefully the information provided in the readme file or the welcome webpage. By using healthiar, you agree to the terms of use and disclaimer.


About healthiar

The healthiar functions allow you to quantify and monetize the health impacts (or burden of disease) attributable to exposure. The main focus of the EU project that initiated the development of healthiar (BEST-COST) has been two environmental exposures: air pollution and noise. However, healthiar could be used for other exposures such as green spaces, chemicals, physical activity…

See below a an overview of the healthiar, which is the first page of the cheat sheet. The whole list of functions included in healthiar is linked there and available in the reference.

Figure: Overview of healthiar
Figure: Overview of healthiar

Input & output data

Input

You can enter data in healthiar functions using: - hard coded values or - columns inside pre-loaded data frames or tibbles.

Let’s see some examples calling the most important function in healthiar: attribute_health().

Hard coded vs. columns

Hard coded

Depending on the function argument, you will need to enter numeric or character values.

results_pm_copd <- attribute_health(
  exp_central = 8.85, 
  rr_central = 1.369, 
  rr_increment = 10,  
  erf_shape = "log_linear",
  cutoff_central = 5,
  bhd_central = 30747 
)

Columns

healthiar comes with some example data that start with exdat_ that allow you to test functions. Some of these example data will be used in some examples in this vignette.

Now let’s attribute_health() with input data from the healthiar example data. Note that you can easily provide input data to the function argument using the $ operator.

results_pm_copd <- attribute_health(
  erf_shape = "log_linear",
  rr_central = exdat_pm$relative_risk, 
  rr_increment = 10, 
  exp_central = exdat_pm$mean_concentration,
  cutoff_central = exdat_pm$cut_off_value,
  bhd_central = exdat_pm$incidence
)

Tidy data

Be aware that healthiar functions are easier to use if your data is prepared in a tidy format, i.e.:

  • Each variable is a column; each column is a variable.

  • Each observation is a row; each row is an observation.

  • Each value is a cell; each cell is a single value.

To know more about the concept of tidy format, see the article by (Wickham 2014).

For example, in attribute health() the length of the input vectors to be entered in the arguments must be either 1 or the result of the combinations of the different values of:

  • geo_id_micro

  • exp_...

  • sex

  • age

  • (info for further sub-group analysis)

Output

Structure

The output of the healthiarfunction attribute_health() and attribute_lifetable consists of two lists (“folders”):

  • health_main contains the main results

  • health_detailed contained detailed results and additional info about the assessment.

In other healthiar functions you can find a similar output structure but using different prefixes. E.g., social_in socialize() and monetization_in monetitize().

Access

A similar structure can be found in other large functions in helathiar, e.g., attribute_lifetable(), compare(), socialize() or monetize(). In some functions, different elements are available in the output. For instance, attribute_lifetable() creates additional output that is specific to life table calculations.

There exist different, equivalent ways of accessing the output:

  • With $ operator: results_pm_copd$health_main$impact_rounded (as in the example above)

  • By mouse: go to the Environment tab in RStudio and click on the variable you want to inspect, and then open the health_main results table

  • With [[]] operator results_pm_copd[["health_main"]]

  • With pluck() & pull(): use the purrr::pluck function to select a list and then the dplyr::pull function extract values from a specified column, e.g. results_pm_copd |> purrr::pluck("health_main") |> dplyr::pull("impact_rounded")


Function examples

The descriptions of the healthiar functions provide examples that you can execute (with healthiar loaded) by running example("function_name"), e.g. example("attribute_health"). In the sections below in this vignette, you find additional examples and more detailed explanations.

Relative risk

Goal

E.g., to quantify the COPD cases attributable to PM2.5 (air pollution) exposure in a country.

Methodology

The comparative risk assessment approach (C. J. Murray et al. 2003) is applied obtaining the population attributable fraction (percent of cases that are attributable to the exposure) based on the relative risk. The exposure scenario is compared with a counter-factual scenario.

This approach has been extensive documented and applied (e.g., WHO 2003; Steenland and Armstrong 2006; Soares et al. 2022; Pozzer et al. 2023; GBD 2019 Risk Factors Collaborators 2020; Lehtomäki et al. 2025).

Figure: Relative risk approach
Figure: Relative risk approach

Population attributable fraction

General integral form for the population attributable fraction (PAF):

\[PAF = \frac{\int rr\_at\_exp(x) \times PE(x)dx - 1}{\int rr\_at\_exp(x) \times pop\_exp(x)dx}\]

Where:

  • \(x\) = exposure level

  • \(PE(x)\) = population distribution of exposure

  • \(rr\_at\exp(x)\) = relative risk at exposure level compared to reference

Simplified for categorical exposure distribution

If exposure is categorical, the integrals are converted to sums:

\[PAF = \frac{\sum rr\_at\_exp_i \times PE_i - 1}{\sum rr\_at\_exp_i \times PE_i}\]

Alternatively, an equivalent form is:

\[PAF = \frac{\sum PE_i \times (rr\_at\_exp_i - 1)}{\sum PE_i\times (rr\_at\_exp_i - 1) + 1}\]

Simplified for single exposure value

If there is one single single exposure value, corresponding to the population weighted mean concentration, the equation can be simplified as follows:

\[PAF = \frac{rr\_at\_exp - 1}{rr\_at\_exp }\] #### Scaling relative risk How to get this relative risk at exposure level (rr_at_exp)? This is normally different to the relative risk published in the epidemiological literature (rr) together with the (concentration/dose) increment that corresponds to this relative risk. The equations used for scaling relative risk depend on the chosen exposure-response function shapes:

  • linear (Lehtomäki et al. 2025) \[RRexp = 1 + \frac{rr - 1}{increment} \times (exp - cutoff)\]

  • log-linear (Lehtomäki et al. 2025) \[RRexp = e^{\frac{\log(rr)}{increment} \times (exp - cutoff)}\]

  • log-log (Lehtomäki et al. 2025) \[RRexp = \left( \frac{exp + 1}{cutoff + 1} \right)^{\frac{\log(rr)}{\log(increment + cutoff + 1) - \log(cutoff + 1)}}\]

  • linear-log (Pozzer et al. 2023) \[RRexp = 1 + \frac{\log(rr - 1)}{\log(increment + cutoff + 1) - \log(cutoff + 1)} \times \frac{\log(exp + 1)}{\log(cutoff + 1)}\]

The relative risk at exposure level (rr_at_exp) and is part of the output of attribute_health() and attribute_lifetable(). rr_at_exp can also be calculated using get_risk().

For conversion of hazard ratios and/or odds ratios to relative risks refer to (VanderWeele 2019) and/or use the conversion tools developed by the Teaching group in EBM in 2022 for hazard ratios (https://ebm-helper.cn/en/Conv/HR_RR.html) and/or odds ratios (https://ebm-helper.cn/en/Conv/OR_RR.html).

Function call

results_pm_copd <- attribute_health(
  approach_risk = "relative_risk", # If you do not call this argument, "relative_risk" will be assigned by default.
  erf_shape = "log_linear",
  rr_central = exdat_pm$relative_risk, 
  rr_increment = 10, 
  exp_central = exdat_pm$mean_concentration,
  cutoff_central = exdat_pm$cut_off_value,
  bhd_central = exdat_pm$incidence
)

Main results

results_pm_copd$health_main
#> # A tibble: 1 × 24
#>   geo_id_micro erf_ci  exp_ci  bhd_ci  cutoff_ci exp_category sex   age_group
#>   <chr>        <chr>   <chr>   <chr>   <chr>            <int> <chr> <chr>    
#> 1 a            central central central central              1 all   all      
#> # ℹ 16 more variables: impact <dbl>, impact_rounded <dbl>, approach_risk <chr>,
#> #   rr_increment <dbl>, erf_shape <chr>, prop_pop_exp <dbl>, exp_length <int>,
#> #   exp_type <chr>, exp <dbl>, bhd <dbl>, cutoff <dbl>, rr <dbl>,
#> #   is_lifetable <lgl>, pop_fraction_type <chr>, rr_at_exp <dbl>,
#> #   pop_fraction <dbl>

It is a table of the format tibble of 3 rows and 23 columns. Be aware that this main output contains input data, some intermediate steps and the final results in different formats.

Let’s zoom in on some relevant aspects.

results_pm_copd$health_main |> 
  dplyr::select(exp, bhd, rr, erf_ci, pop_fraction, impact_rounded) |> 
  knitr::kable() # For formatting reasons only: prints tibble in nice layout
exp bhd rr erf_ci pop_fraction impact_rounded
8.85 30747 1.369 central 0.1138961 3502

Interpretation: this table shows us that exposure was 8.85 \(\mu g/m^3\), the baseline health data (bhd_central) was 30747 (COPD incidence in this instance). The 1st row further shows that the impact attributable to this exposure using the central relative risk (rr_central) estimate of 1.369 is 3502 COPD cases, or ~11% of all baseline cases.

Some of the most results columns include:

Absolute risk

Goal

E.g., to quantify the number incidence cases of high annoyance attributable to (road traffic) noise exposure.

Methodology

In the absolute risk calculation pathway, estimates are based on the size and distribution of the exposed population, rather than on baseline health data, as is the case in the relative risk pathway (WHO 2011).

Figure: Absolute risk approach
Figure: Absolute risk approach

\[N = \sum AR_i \times PE_i\]

Where:

healthiar consistently handles cut-off values across both relative and absolute risk approaches. When a cutoff_ argument is specified alongside an exposure–response function (erf_eq_), the function evaluates exposure as excess exposure relative to the cut-off (c as \(\text{exp} - \text{cutoff}\)), effectively shifting the function by the cut-off. However, many absolute risk curves published in the literature are parameterized on raw exposure levels that already incorporate the cut-off directly into the function definition. Therefore, healthiar issues an informative warning if both erf_eq_ and a cutoff_ are specified when using attribute_health(). If your absolute risk function uses an unshifted policy threshold rather than an epidemiological cut-off, see chapter Threshold additional to cut-off.

Function call

results_noise_ha <- attribute_health(
  approach_risk = "absolute_risk", # default is "relative_risk"
  exp_central = c(57.5, 62.5, 67.5, 72.5, 77.5), # mean of the exposure categories
  pop_exp = c(387500, 286000, 191800, 72200, 7700), # population exposed per exposure category
  erf_eq_central = "78.9270-3.1162*c+0.0342*c^2" # exposure-response function
)

The erf_eq_central argument can digest other types of functions (see section on user-defined ERF).

Main results

erf_eq erf_ci impact_rounded
78.9270-3.1162c+0.0342c^2 central 174232

Results per noise exposure band

results_noise_ha$health_detailed$results_raw
exp_category exp pop_exp impact
1 57.5 387500 49674.594
2 62.5 286000 50788.595
3 67.5 191800 46813.105
4 72.5 72200 23657.232
5 77.5 7700 3298.314

Remember, that if the equation of the exposure-response function (erf_eq_...) requires taking a maximum in a vectorised context, pmax() must be used instead of max(). pmax() should be used whenever an element-wise maximum is required (the output will be a vector), while max() returns a single global maximum for the entire vector. For example:

erf_eq_central <- 
  "exp(0.2969*log((pmax(0,c-2.4)/1.9+1))/(1+exp(-(pmax(0,c-2.4)-12)/40.2)))"  

One exposure category

Alternatively, it’s also possible to only assess the absolute risk impacts for one exposure category (e.g., a single noise exposure band).

results_noise_ha <- attribute_health(
  approach_risk = "absolute_risk",
  exp_central = 57.5,
  pop_exp = 387500,
  erf_eq_central = "78.9270-3.1162*c+0.0342*c^2"
)
exp_category impact
1 49674.59

Multiple geographic units

using relative risk

Goal

E.g., to quantify the disease cases attributable to PM2.5 exposure in multiple cities using one single command.

Function call

  • Enter unique ID’s as a vector (numeric or character) to the geo_id_micro argument (e.g., municipality names or province abbreviations)

  • Optional: aggregate unit-specific results by providing higher-level ID’s (e.g., region names or country abbreviations) as a vector (numeric or character) to the geo_id_macro argument

Input to the other function arguments is specified as usual, either as a vector or a single values (which will be recycled to match the length of the other input vectors).

results_iteration <- attribute_health(
    # Names of Swiss cantons
    geo_id_micro = c("Zurich", "Basel", "Geneva", "Ticino", "Jura"),
    # Names of languages spoken in the selected Swiss cantons
    geo_id_macro = c("German","German","French","Italian","French"),
    rr_central = 1.369,
    rr_increment = 10, 
    cutoff_central = 5,
    erf_shape = "log_linear",
    exp_central = c(11, 11, 10, 8, 7),
    bhd_central = c(4000, 2500, 3000, 1500, 500)
)

In this example we want to aggregate the lower-level geographic units (municipalities) by the higher-level language region ("German", "French", "Italian").

Main results

The main output contains aggregated results

geo_id_macro impact_rounded erf_ci exp_ci bhd_ci
German 1116 central central central
French 466 central central central
Italian 135 central central central

In this case health_main contains the cumulative / summed number of stroke cases attributable to PM2.5 exposure in the 5 geo units, which is 1717 (using a relative risk of 1.369).

Detailed results

The geo unit-specific information and results are stored under health_detailed>results_raw .

geo_id_micro impact_rounded geo_id_macro
Zurich 687 German
Basel 429 German
Geneva 436 French
Ticino 135 Italian
Jura 30 French

health_detailed also contains impacts obtained through all combinations of input data central, lower and upper estimates (as usual), besides the results per geo unit (not shown above).

using absolute risk

Goal

E.g., to quantify high annoyance cases attributable to noise exposure in rural and urban areas.

Function call

data <- exdat_noise |> 
  ## Filter for urban and rural regions
  dplyr::filter(region == "urban" | region == "rural")
results_iteration_ar <- attribute_health( 
    # Both the rural and urban areas belong to the higher-level "total" region
    geo_id_macro = "total",
    geo_id_micro = data$region,
    approach_risk = "absolute_risk",
    exp_central = data$exposure_mean,
    pop_exp = data$exposed,
    erf_eq_central = "78.9270-3.1162*c+0.0342*c^2"
)

Note: the length of the input vectors fed to geo_id_micro, exp_central, pop_exp must match and must be

(number of geo units) x (number of exposure categories) = 2 x 5 = 10,

because we have 2 geo units ("rural" and "urban") and 5 exposure categories.

Main results

health_main contains the aggregated results (i.e. sum of impacts in rural and urban areas).

geo_id_macro impact_rounded erf_ci exp_ci
total 174232 central central

Detailed results

Impact by geo unit, in this case impact in the rural and in the urban area.

geo_id_micro geo_id_macro impact
urban total 150904.00
rural total 23327.84

Uncertainty

Confidence interval

Goal

E.g., to quantify the COPD cases attributable to PM2.5 exposure taking into account uncertainty (lower and upper bound of confidence interval) in several input arguments: relative risk, exposure and baseline health data.

Function call

results_pm_copd <- attribute_health(
    erf_shape = "log_linear",
    rr_central = 1.369, 
    rr_lower = 1.124, # lower 95% confidence interval (CI) bound of RR
    rr_upper = 1.664, # upper 95% CI bound of RR
    rr_increment = 10, 
    exp_central = 8.85, 
    exp_lower = 8, # lower 95% CI bound of exposure
    exp_upper = 10, # upper 95% CI bound of exposure
    cutoff_central = 5,
    bhd_central = 30747, 
    bhd_lower = 28000, # lower 95% confidence interval estimate of BHD
    bhd_upper = 32000 # upper 95% confidence interval estimate of BHD
) 

Detailed results

Let’s inspect the detailed results:

erf_ci exp_ci bhd_ci impact_rounded
central central central 3502
lower central central 1353
upper central central 5474
central central lower 3189
lower central lower 1232
upper central lower 4985
central central upper 3645
lower central upper 1408
upper central upper 5697

Each row contains the estimated attributable cases (impact_rounded) obtained by the input data specified in the columns ending in “_ci” and the other calculation pathway specifications in that row (not shown).

  • The 1st contains the estimated attributable impact when using the central estimates of relative risk, exposure and baseline health data.

  • The 2nd row shows the impact when using the central estimates of the relative risk, exposure in combination with the lower estimate of the baseline health data.

Note: only 9 of the 27 possible combinations are displayed due to space constraints.

Note: only a selection of columns are shown.

Monte Carlo simulation

Goal

E.g., to summarize uncertainty of attributable health impacts (i.e. to get a single confidence interval instead of many combinations) by using a Monte Carlo simulation.

Methodology

General concepts

A Monte Carlo simulation is a statistical method that generates repeated random sampling (Robert and Casella 2004; Rubinstein and Kroese 2016). In healthiar, you can use the function summarize_uncertainty() to simulate values in the arguments with uncertainty and estimate a single confidence interval in the results.

For each entered input argument that includes a (95%) confidence interval (i.e. _lower and _upper bound value) a distribution is fitted (see distributions below). The median of the simulated attributable impacts is reported as the central estimate. The 2.5th and 97.5th percentiles of these simulated impacts define the lower and upper bounds of the 95% summary uncertainty interval. Aggregated central, lower and upper estimates are obtained by summing the corresponding values of each lower level unit.

Distributions used for simulation

summarize_uncertainty() assumes the following shapes of the distributions in the simulations:

  • Relative risk: The values are simulated based on an optimized gamma distribution, which fits well as relative risks are positive and their distributions are usually right-skewed. The gamma distribution is parametrized such that its mean is equal to the central relative risk estimate (rate= shape/rr_central). The shape parameter is then optimized using stats::optimize() to match the inputed 95% confidence interval bounds, with stats::qgamma() used to evaluate candidate distributions. Finally, n_sim relative risk values are simulated using stats::rgamma().

  • Exposure, cutoff, baseline health data and duration: The values are simulated based on a normal distribution using stats::rnorm() with mean = exp_central, mean = cutoff_central, mean = bhd_central or mean = duration_central and a standard deviation based on corresponding lower and upper 95% exposure confidence interval values. The standard deviation is calculated as \[(upper-lower)/(2*1.96)\], since for a normal distribution the 95% CI spans approximately two standard deviations on either side of the mean.

  • Disability weights: The values are simulated based on a beta distribution, as both the disability weights and the beta distribution are bounded by 0 and 1. The beta distribution best fitting the inputted central disability weight estimate and corresponding lower and upper 95% confidence interval values is fitted using stats::qbeta() (the best fitting distribution parameters shape1 and shape2 are determined using stats::optimize()). For this purpose, we partly adapted the R function prevalence::beta_expert with permission of one of the authors (Devleesschauwer et al. 2022). Finally, n_sim disability weight values are simulated using stats::rbeta().

For stability of the 95% confidence interval, a large number of simulations (e.g., 10,000) is recommended in practice. The example below uses n_sim = 100 for brevity.

Function call

results_pm_copd_summarized <- 
  summarize_uncertainty(
    output_attribute = results_pm_copd,
    n_sim = 100
)

Main results

The outcome of the Monte Carlo analysis is added to the variable entered as the results argument, which is results_pm_copd in our case.

Two lists (“folders”) are added:

  • uncertainty_main contains the central estimate and the corresponding 95% confidence intervals obtained through the Monte Carlo assessment and

  • uncertainty_detailed contains all n_sim simulations of the Monte Carlo assessment.

geo_id_micro impact_ci impact impact_rounded
a central_estimate 3654.885 3655
a lower_estimate 1589.442 1589
a upper_estimate 5600.248 5600

Detailed results

The folder uncertainty_detailed contains all single simulations. Let’s look at the impact of the first 10 simulations.

The columns erf_ci, exp_ci, bhd_ci, and cutoff_ci indicate the source of uncertainty component used for that simulation (in the first 10 simulations, all use central estimates).

geo_id_micro erf_ci exp_ci bhd_ci cutoff_ci exp_category sex age_group sim_id impact impact_rounded approach_risk rr_increment erf_shape prop_pop_exp exp_length exp_type cutoff is_lifetable geo_id_number rr exp bhd pop_fraction_type rr_at_exp pop_fraction
a central central central central 1 all all 1 2629.951 2630 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.276850 8.740519 30103.82 paf 1.095725 0.0873627
a central central central central 1 all all 2 4628.066 4628 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.551852 8.758388 30399.07 paf 1.179584 0.1522437
a central central central central 1 all all 3 4493.994 4494 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.543406 8.798881 29566.80 paf 1.179238 0.1519946
a central central central central 1 all all 4 4474.906 4475 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.419867 9.213612 32586.97 paf 1.159181 0.1373219
a central central central central 1 all all 5 1650.331 1650 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.157613 8.812466 30409.10 paf 1.057385 0.0542710
a central central central central 1 all all 6 3728.251 3728 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.430150 8.830799 29108.69 paf 1.146895 0.1280803
a central central central central 1 all all 7 3879.688 3880 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.465879 8.502208 30948.22 paf 1.143328 0.1253606
a central central central central 1 all all 8 3917.858 3918 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.442681 8.684553 31015.55 paf 1.144583 0.1263191
a central central central central 1 all all 9 3038.873 3039 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.320146 8.880695 29741.04 paf 1.113806 0.1021778
a central central central central 1 all all 10 2145.128 2145 relative_risk 10 log_linear 1 1 population_weighted_mean 5 FALSE 1 1.253879 8.549538 27799.07 paf 1.083618 0.0771655

User-defined ERF

Goal

E.g., to quantify COPD cases attributable to air pollution exposure by applying a user-defined exposure-response function (ERF), such as the MR-BRT curves from Global Burden of Disease study.

Function call

In this case, the function arguments erf_eq_... require a function as input, so we use an auxiliary function (splinefun()) to transform the points on the ERF into type function.

results_pm_copd_mr_brt <- attribute_health(
  exp_central = 8.85,
  bhd_central = 30747,
  cutoff_central = 0,
  # Specify the function based on x-y point pairs that lie on the ERF
  erf_eq_central = splinefun(
    x = c(0, 5, 10, 15, 20, 25, 30, 50, 70, 90, 110),
    y = c(1.00, 1.04, 1.08, 1.12, 1.16, 1.20, 1.23, 1.35, 1.45, 1.53, 1.60),
    method = "natural")
)

The ERF curve created looks as follows

ERF curve

Alternatively, other functions (e.g. approxfun()) can be used to create the ERF

Sub-group analysis

by age group

Goal

E.g., to quantify health impacts attributable to air pollution in a country by age group.

Function call

To obtain age-group-specific results, the baseline health data (and possibly exposure) must be available by age group.

If the age argument was specified, age-group-specific results are available under health_detailed in the sub-folder results_by_age_group.

results_age_group <- attribute_health(
        approach_risk = "relative_risk",
        age = c("below_65", "65_plus"),
        exp_central = c(8, 7),
        cutoff_central = c(5, 5),
        bhd_central = c(1000, 5000),
        rr_central = 1.06,
        rr_increment = 10,
        erf_shape = "log_linear"
      )

Results by age group

results_age_group$health_detailed$results_by_age_group |> 
  dplyr::select(age_group, impact_rounded, exp, bhd) |> 
  knitr::kable()
age_group impact_rounded exp bhd
below_65 17 8 1000
65_plus 58 7 5000

by sex

Goal

E.g., to quantify health impacts attributable to air pollution in a country by sex.

Function call

The baseline health data (and possibly exposure) must be entered by sex.

results_sex <- attribute_health(
        approach_risk = "relative_risk",
        sex = c("female", "male"),
        exp_central = c(8, 8),
        cutoff_central = c(5, 5),
        bhd_central = c(1000, 1100),
        rr_central = 1.06,
        rr_increment = 10,
        erf_shape = "log_linear"
      )

Results by sex

If the sex argument was specified, sex-specific results are available under health_detailed in the sub-folder results_by_sex.

results_sex$health_detailed$results_by_sex |> 
  dplyr::select(sex, impact_rounded, exp, bhd) |> 
  knitr::kable()
sex impact_rounded exp bhd
female 17 8 1000
male 19 8 1100

by other sub-groups

Goal

E.g., to quantify attributable health impacts stratified by a sub-group different to age and sex, e.g., education level.

Function call

A single vector (or a data frame / tibble with multiple columns) to group the results by can be entered to the info argument. In this example, this will be information about the education level.

In a second step one can group the results based on one or more columns and so summarize the results by the preferred sub-groups.

output_attribute <- healthiar::attribute_health(
    rr_central = 1.063,
    rr_increment = 10,
    erf_shape = "log_linear",
    cutoff_central =  0,
    exp_central = c(6, 7, 8,
                    7, 8, 9,
                    8, 9, 10,
                    9, 10, 11),
    bhd_central = c(600, 700, 800,
                    700, 800, 900,
                    800, 900, 1000,
                    900, 1000, 1100),
    geo_id_micro = rep(c("a", "b", "c", "d"), each = 3),
    info = data.frame(
      education = rep(c("secondary", "bachelor", "master"), times = 4)) # education level
  )

Results by other sub-group

output_stratified <- output_attribute$health_detailed$results_raw |>
      dplyr::group_by(info_column_1) |>
      dplyr::summarize(mean_impact = mean(impact))|>
      dplyr::pull(mean_impact) |>
      print()
#> [1] 43.72087 54.26844 34.30332

by age, sex and other sub-groups

Goal

E.g., to quantify attributable health impacts stratified by age, sex and additional sub-group e.g. education level.

Function call

output_attribute <- healthiar::attribute_health(
    rr_central = 1.063,
    rr_increment = 10,
    erf_shape = "log_linear",
    cutoff_central =  0,
    age_group = base::rep(c("50_and_younger", "50_plus"), each = 4, times= 2),
    sex = base::rep(c("female", "male"), each = 2, times = 4),
    exp_central = c(6, 7, 8, 7, 8, 9, 8, 9,
                    10, 9, 10, 11, 10, 11, 12, 13),
    bhd_central = c(600, 700, 800, 700, 800, 900, 800, 900,
                    1000, 900, 1000, 1100, 1000, 1100, 1200, 1000),
    geo_id_micro = base::rep(c("a", "b"), each = 8),
    info = base::data.frame(
      education = base::rep(c("without_master", "with_master"), times = 8)) # education level
  )

Results by all sub-groups

output_stratified <- output_attribute$health_detailed$results_raw |>
      dplyr::group_by(info_column_1) |>
      dplyr::summarize(mean_impact = mean(impact))|>
      dplyr::pull(mean_impact) |>
      print()
#> [1] 52.80090 49.83826

YLL & deaths with life table

Data preparation

The life table approach to obtain YLL and deaths requires population and baseline mortality data to be stratified by one year age groups. However, in some cases these data are only available for larger age groups (e.g., 5-year data: 0-4 years old, 5-9 years old, …). What to do?

age_groups <- c(0, 5, 10, 15)
pop <- c(438200, 445100, 439800, 421500)
bhd_counts <- c(1420, 45, 50, 125)

# Standard uniform disaggregation (fraction_lived = 0.5)
prepared_data <- healthiar::prepare_lifetable(
  age_group = age_groups,
  population = pop,
  bhd = bhd_counts
  # fraction_lived = 0.5 (default)
)

# Demographic adjustment for low infant mortality (first fraction_lived = 0.1)
prepared_data_adjusting_for_low_infant_mortality <- healthiar::prepare_lifetable(
  age_group = age_groups,
  population = pop,
  bhd = bhd_counts,
  fraction_lived = c(0.1, 0.5, 0.5, 0.5)
)

YLL

Goal

E.g., to quantify the years of life lost (YLL) due to deaths from COPD attributable to PM2.5 exposure during one year.

Methodology

General concept

The life table methodology of attribute_lifetable() follows that of the WHO tool AirQ+ (WHO 2020), which is described in more detail by Miller and Hurley (2003). The generalized formulas, which do not assume a fixed fraction of life lived (fraction_lived = 0.5), are based on the foundational work by Chiang (1984). In short, two scenarios are compared:

  1. a scenario with the exposure level specified in the function (“exposed scenario”) and

  2. a scenario with no exposure (“unexposed scenario”).

First, the entry and mid-year populations of the (first) year of analysis in the unexposed scenario are determined using modified survival probabilities. Second, age-specific population projections using scenario-specific survival probabilities are done for both scenarios. Third, by subtracting the populations in the unexposed scenario from the populations in the exposed scenario the premature deaths/years of life lost attributable to the exposure are determined. An expansive life table case study for is available in a report by Miller (2010).

Use the two arguments approach_exposure and approach_newborns to modify the life table calculation:

  • approach_exposure

    • "single_year" (default): Population is exposed for only one year (year of analysis) and attributable health impacts reflect the single-year snapshot. Applicable only for deaths. AirQ+ approach for deaths in 2025.

    • "constant" : Population is exposed every year, i.e. air pollution exposure is sustained across the full projection horizon and attributable health impacts are projected and cumulated across the full lifetime period. Applicable for both deaths and YLL. AirQ+ approach for YLL in 2025.

  • approach_newborns

    • "without_newborns" (default): Population in the year of analysis is followed over time, without considering newborns being born.

    • "with_newborns": For each year after the year of analysis n babies are born, with n being equal to the (male and female) population aged 0 that is provided in the argument population.

Note: Although healthiar tries to align with AirQ+ methodologically, the results using the life table marginally differ slightly (AirQ+ results are around 0.02% higher per 1,000 attributable deaths or 0.05% per 1,000 YLL). The reason for this minor variance is unknown. A different rounding strategy might be behind (at least in part).

Determination of populations in the (first) year of analysis

Entry population

The entry (i.e. start of year) populations in both scenarios (exposed and unexposed) is determined as follows:

\[entry\_population_{year_1} = midyear\_population_{year_1} + (1 - fraction\_lived) \times deaths_{year_1}\]

Survival probabilities
Exposed scenario

The survival probabilities in the exposed scenario from start of year \(i\) to start of year \(i+1\) are calculated as follows:

\[prob\_survival = \frac{midyear\_population_i - fraction\_lived \times deaths_i}{midyear\_population_i + (1 - fraction\_lived) \times deaths_i}\]

Analogously, the probability of survival from start of year \(i\) to mid-year \(i\):

\[prob\_survival\_until\_midyear = 1 - (1 - fraction\_lived) \times (1 - prob\_survival)\]

Unexposed scenario

The survival probabilities in the unexposed scenario are calculated as follows:

First, the age-group specific hazard rate in the exposed scenario is calculated using the inputted age-specific mid-year populations and deaths.

\[hazard\_rate = \frac{deaths}{mid\_year\_population}\]

Second, the hazard rate is multiplied by the modification factor (\(= 1 - PAF\)) to obtain the age-specific hazard rate in the unexposed scenario.

\[hazard\_rate\_mod = hazard\_rate \times modification\_factor\]

Third, the age-specific survival probabilities (from the start until the end in a given age group) in the unexposed scenario are calculated as follows:

\[prob\_survival\_mod = \frac{1 - fraction\_lived \times hazard\_rate\_mod}{1 + (1 - fraction\_lived) \times hazard\_rate\_mod}\]

Mid-year population

The mid-year population of the (first) year of analysis (year_1) in the unexposed scenario are determined as follows:

First, the survival probabilities from start of year \(i\) to mid-year \(i\) in the unexposed scenario is calculated as:

\[prob\_survival\_until\_midyear_{mod} = 1 - (1 - fraction\_lived) \times (1 - prob\_survival\_mod)\]

Second, the mid-year populations of the (first) year of analysis (year_1) in the unexposed scenario is calculated:

\[midyear\_population\_unexposed_{year_1} = entry\_population_{year_1} \times prob\_survival\_until\_midyear_{mod}\]

Population projection

Using the age group-specific and scenario-specific survival probabilities calculated above, future populations of each age-group under each scenario are calculated.

Exposed scenario

The population projections for the two possible options of approach_exposure ("single_year" and "constant") for the unexposed scenario are different. In the case of "single_year" exposure, the population projection for the years after the year of exposure is the same as in the unexposed scenario.

In the case of "constant" the population projection is done as follows:

First, the entry population of year \(i+1\) is calculated (which is the same as the end of year population of year \(i\)) using the entry population of year \(i\).

\[entry\_population_{i+1} = entry\_population_i \times prob\_survival\]

Second, the mid-year population of year \(i+1\) is calculated.

\[midyear\_population_{i+1} = entry\_population_{i+1} \times prob\_survival\_until\_midyear\]

Unexposed scenario

The entry and mid-year population projections in the unexposed scenario are done as follows:

First, the entry population of year \(i+1\) is calculated (which is the same as the end of year population of year \(i\)) by multiplying the entry population of year \(i\) and the modified survival probabilities.

\[entry\_population_{i+1} = entry\_population_i \times prob\_survival\_mod\]

Second, the mid-year population of year \(i+1\) is calculated.

\[midyear\_population_{i+1} = entry\_population_{i+1} \times prob\_survival\_until\_midyear\]

Function call

We can use attribute_lifetable() combined with life table input data to determine YLL attributable to an environmental stressor.

results_pm_yll <- attribute_lifetable(
  year_of_analysis = 2019, 
  health_outcome = "yll",
  rr_central =  1.118, 
  rr_increment = 10,
  erf_shape = "log_linear",
  exp_central = 8.85,
  cutoff_central = 5,
  min_age = 20, # age from which population is affected by the exposure
  # Life table information
  age_group = exdat_lifetable$age_group,
  sex = exdat_lifetable$sex,
  population = exdat_lifetable$midyear_population,
  # In the life table case, BHD refers to deaths
  bhd_central = exdat_lifetable$deaths
) 

Main results

Total YLL attributable to exposure (sum of sex-specific impacts).

impact_rounded erf_ci exp_ci bhd_ci
28810 central central central

Detailed results

Attributable YLL results

  • per year

  • per age (group)

  • per sex (if sex-specific life table data entered)

are available.

Note: We will inspect the results for females; male results are also available.

Results per year

Note: only a selection of years is shown.

results_pm_yll$health_detailed$results_raw |>
  dplyr::summarize(
    .by = year, 
    impact = sum(impact, na.rm = TRUE)
  )
#> # A tibble: 100 × 2
#>    year  impact
#>    <chr>  <dbl>
#>  1 2019   1300.
#>  2 2020   2422.
#>  3 2021   2221.
#>  4 2022   2033.
#>  5 2023   1858.
#>  6 2024   1695.
#>  7 2025   1545.
#>  8 2026   1409.
#>  9 2027   1284.
#> 10 2028   1171.
#> # ℹ 90 more rows
results_pm_yll$health_detailed$results_raw |>
  dplyr::summarize(
    .by = year, 
    impact = sum(impact, na.rm = TRUE)) |>
  knitr::kable()
year impact
2019 1299.683
2020 2421.604
2021 2221.148
2022 2032.978
2023 1857.582
2024 1694.959
2025 1545.430
2026 1408.650
2027 1284.054
2028 1170.668

YLL

age_start age_end impact_2019
91 92 29.480668
92 93 27.542091
93 94 25.166285
94 95 22.111703
95 96 18.514777
96 97 14.505077
97 98 11.222461
98 99 8.170093
99 100 31.772534

Population (baseline scenario)

Baseline scenario refers to the scenario with exposure (i.e. the scenario specified in the assessment).

age_start midyear_population_2019 midyear_population_2020 midyear_population_2021 midyear_population_2022
91 10560 10980.4178 11536.8448 11815.045
92 8728 9105.4297 9498.3206 9979.643
93 7140 7377.6106 7725.1173 8058.449
94 5655 5910.7546 6133.2128 6422.105
95 4332 4582.9334 4813.1037 4994.250
96 3118 3436.4582 3654.9171 3838.479
97 2234 2419.2261 2682.1499 2852.657
98 1520 1695.7730 1848.4164 2049.304
99 2246 879.8714 988.6583 1077.651

Population (unexposed scenario)

Impacted scenario refers to the scenario without exposure.

age_start midyear_population_2019 midyear_population_2020 midyear_population_2021 midyear_population_2022
91 10589.481 11037.9003 11589.268 11861.323
92 8755.542 9160.1507 9548.044 10024.990
93 7165.166 7428.2700 7771.543 8100.635
94 5677.112 5956.6019 6175.327 6460.700
95 4350.515 4622.8492 4850.437 5028.544
96 3132.505 3469.5619 3686.750 3868.253
97 2245.222 2444.9150 2707.987 2877.502
98 1528.170 1715.4685 1868.044 2069.045
99 2277.773 890.9436 1000.141 1089.095

Deaths

Goal (e.g.)

E.g., to determine premature deaths from COPD attributable to PM2.5 exposure during one year.

Function call

See example on YLL for additional info on attribute_lifetable() calculations and its output.

results_pm_deaths <- attribute_lifetable(
  health_outcome = "deaths",
  year_of_analysis = 2019,
  rr_central =  1.118, 
  rr_increment = 10,
  erf_shape = "log_linear",
  exp_central = 8.85,
  cutoff_central = 5,
  min_age = 20, # age from which population is affected by the exposure   
  # Life table information
  age_group = exdat_lifetable$age_group,   
  sex = exdat_lifetable$sex,
  population = exdat_lifetable$midyear_population, 
  bhd_central = exdat_lifetable$deaths
)

Main results

Total premature deaths attributable to exposure (sum of sex-specific impacts).

impact_rounded erf_ci exp_ci bhd_ci
2599 central central central

Detailed results

Attributable premature deaths results

  • per year (if argument approach_exposure = "constant")

  • per age (group)

  • per sex (if sex-specific life table data entered)

are available.

Note: We inspect below the results for females; male results are also available.

Note: Because we set the function argument approach_exposure = "constant" results are projected and accumulated across the full time_horizon. If you set approach_exposure = “single_year”, results for premature deaths are available for one year (the year of analysis).

yoa age_group age_start age_end bhd deaths population fraction_lived modification_factor prob_survival prob_survival_until_midyear hazard_rate is_exposed_age prob_survival_mod prob_survival_until_midyear_mod hazard_rate_mod midyear_population_yoa entry_population_yoa end_population_yoa deaths_yoa entry_population_yoa_plus_1
2019 91 91 92 1498 1498 10560 0.5 0.9579656 0.8675391 0.9337696 0.1418561 TRUE 0.8727528 0.9363764 0.1358932 10589.481 11309.0 9869.961 1439.0387 11787.888
2019 92 92 93 1412 1412 8728 0.5 0.9579656 0.8503286 0.9251643 0.1617782 TRUE 0.8561675 0.9280837 0.1549779 8755.542 9434.0 8077.084 1356.9158 9869.961
2019 93 93 94 1302 1302 7140 0.5 0.9579656 0.8328841 0.9164420 0.1823529 TRUE 0.8393444 0.9196722 0.1746878 7165.166 7791.0 6539.333 1251.6674 8077.084
2019 94 94 95 1155 1155 5655 0.5 0.9579656 0.8146811 0.9073406 0.2042440 TRUE 0.8217767 0.9108884 0.1956588 5677.112 6232.5 5121.723 1110.7766 6539.333
2019 95 95 96 976 976 4332 0.5 0.9579656 0.7975104 0.8987552 0.2253001 TRUE 0.8051929 0.9025964 0.2158297 4350.515 4820.0 3881.030 938.9704 5121.723
2019 96 96 97 772 772 3118 0.5 0.9579656 0.7796804 0.8898402 0.2475946 TRUE 0.7879595 0.8939798 0.2371871 3132.505 3504.0 2761.010 742.9898 3881.030
2019 97 97 98 603 603 2234 0.5 0.9579656 0.7621771 0.8810885 0.2699194 TRUE 0.7710294 0.8855147 0.2585735 2245.222 2535.5 1954.945 580.5551 2761.010
2019 98 98 99 443 443 1520 0.5 0.9579656 0.7456216 0.8728108 0.2914474 TRUE 0.7550044 0.8775022 0.2791965 1528.170 1741.5 1314.840 426.6598 1954.945
2019 99 99 100 2231 2231 2246 0.5 0.9579656 0.3363082 0.6681541 0.9933215 TRUE 0.3552120 0.6776060 0.9515678 2277.773 3361.5 1194.045 2167.4549 1314.840

YLD

Goal

E.g., to quantify the years lived with disability (YLD) attributable to air pollution exposure using disability weights.

Methodology

To quantify the YLDs, you can use a prevalence-based or an incidence-based approach (Kim et al. 2022).

Function call

results_pm_copd_yld  <- attribute_health(
  rr_central = 1.1, 
  rr_increment = 10, 
  erf_shape = "log_linear",  
  exp_central = 8.85,
  cutoff_central = 5,
  bhd_central = 1000,
  duration_central = 10,
  dw_central = 0.2
)

Main results

erf_ci impact
central 72.05868

DALY

Goal (e.g.)

E.g., to obtain the disability-adjusted life years (DALY) as the sum of YLLs and YLDs.

Methodology

To obtain the attributable DALY, its two components, i.e. years of life lost (YLL) and years lived with disability (YLD), must be summed (GBD 2019 Risk Factors Collaborators 2020).

\[DALY = YLL + YLD\]

Function call

This is possible using the function daly().

results_daly <- daly(
     output_attribute_yll = results_pm_yll,
     output_attribute_yld = results_pm_copd_yld
)

Main results

YLL, YLD & DALY

impact_yll_rounded impact_yld_rounded impact_rounded
28810 72 28882

Modification of scenarios

Goal

E.g., to quantify health impacts using attribute_healthin an scenario B very similar to a previous scenario A.

Function call

scenario_A <- attribute_health(
    exp_central = 8.85,   # EXPOSURE 1
    cutoff_central = 5, 
    bhd_central = 25000,
    approach_risk = "relative_risk",
    erf_shape = "log_linear",
    rr_central = 1.118,
    rr_increment = 10)

The function attribute_mod() can be used to modify one or multiple arguments of attribute_healthin an existing scenario, e.g. scenario_A.

scenario_B <- attribute_mod(
  output_attribute = scenario_A, 
  exp_central = 6
)

This is equivalent to building the whole scenario again (see below), but more time and code efficient.

scenario_B <- attribute_health(
    exp_central = 6,     # EXPOSURE 2
    cutoff_central = 5, 
    bhd_central = 25000,
    approach_risk = "relative_risk",
    erf_shape = "log_linear",
    rr_central = 1.118,
    rr_increment = 10)

Comparison of two health scenarios

Goal

E.g., to compare the health impacts in the scenario “before intervention” vs. “after intervention”.

Methodology

Two approaches can be used for the comparison of scenarios:

Note that the PIF comparison approach assumes same baseline health data for scenario 1 and 2 (e.g., comparison of two scenarios at the same time point), while the delta comparison approach, the difference between two scenarios is obtained by subtraction. Therefore, the delta approach is suited for comparison of scenarios in different time points.

IMPORTANT If your aim is to quantify health impacts from a policy intervention, be aware that you should use the same year of analysis and therefore same health baseline data in both scenarios. The only variable that should change in the second scenario is the exposure (change as a result of the intervention).

Population Impact Fraction (PIF)

The Population Impact Fraction (PIF) is defined as the proportional change in disease or mortality when exposure to a risk factor is changed, for instance due to an intervention.

General Integral Form

The most general equation describing this mathematically is an integral form (WHO 2003; C. J. L. Murray et al. 2003):

\[PIF = \frac{\int rr\_at\_exp(x)PE(x)dx - \int rr\_at\_exp(x)PE'(x)dx}{\int rr\_at\_exp(x)PE(x)dx}\]

Where:

  • \(x\) = exposure level
  • \(PE(x)\) = population distribution of exposure
  • \(PE'(x)\) = alternative population distribution of exposure
  • \(rr\_at\_exp(x)\) = relative risk at exposure level compared to the reference level
Categorical Exposure Form

If the population exposure is described as a categorical rather than continuous exposure, the integrals may be converted to sums (WHO 2003; Murray2003-spbm?):

\[PIF = \frac{\sum rr\_at\_exp_{i} \times PE_{i} - \sum rr\_at\_exp_{i}PE'_{i}}{\sum rr\_at\_exp_{i}PE_{i}}\]

Where:

  • \(i\) = the exposure category (e.g., in bins of 1 \(\mu g/m^3\) \(PM_{2.5}\) or 5 dB noise exposure)
  • \(PE_i\) = fraction of population in exposure category \(i\)
  • \(PE'_i\) = fraction of population in category \(i\) for alternative (ideal) exposure scenario
  • \(rr\_at\_exp_i\) = relative risk for exposure category level \(i\) compared to the reference level
Population weighted mean concentration form

Finally, if the exposure is provided as the population weighted mean concentration, the equation for the PIF is reduced to:

\[PIF = \frac{rr\_at\_exp - rr\_at\_exp_{alt}}{rr}\]

Where:

  • \(rr\_at\_exp\) = relative risk at the exposure level
  • \(rr\_at\_exp_{alt}\) = relative risk at the exposure level for the alternative exposure scenario

Function call

  1. Use attribute_health() to calculate burden of scenarios A & B.
scenario_A <- attribute_health(
    exp_central = 8.85,   # EXPOSURE 1
    cutoff_central = 5, 
    bhd_central = 25000,
    approach_risk = "relative_risk",
    erf_shape = "log_linear",
    rr_central = 1.118,
    rr_increment = 10)
scenario_B <- attribute_mod(
  output_attribute = scenario_A, 
  exp_central = 6
)
  1. Use compare() to compare scenarios A & B.

results_comparison <- healthiar::compare(
  approach_comparison = "delta", # or "pif" (population impact fraction)
  output_attribute_scen_1 = scenario_A,
  output_attribute_scen_2 = scenario_B
)

The default value for the argument approach_comparison is "delta". The alterntive is "pif" (population impact fraction). See the function documentation of compare() for more details.

Main results

impact impact_rounded impact_scen_1 impact_scen_2 bhd exp_category exp_length exp_type exp_scen_1 exp_scen_2
773.5564 774 1050.86 277.304 25000 1 1 population_weighted_mean 8.85 6

Detailed results

The compare() results contain two additional outputs in addition to those we have already seen:

Two correlated exposures

Goal

E.g., to quantify the total health impact attributable to PM2.5 and NO2.

Methodology

A methodological report of the EU project BEST-COST (Strak et al. 2024) identified three approaches to add up attributable health impacts from correlated exposures:

\[PAF_{additive} = PAF_{exposure1} + PAF_{exposure2}\]

\[PAF_{multiplicative} = \frac{\sum PE \times (rr\_at\_exp_{multiplicative} - 1)}{\sum PE \times (rr\_at\_exp_{multiplicative}-1) + 1}\]

\[rr\_at\_exp_{multiplicative} = rr\_at\_exp_{exposure1} * rr\_at\_exp_{exposure2}\]

\[PAF_{combined} = 1-[(1-PAF_{exposure1}) \times (1-PAF_{exposure2})]\]

Attention: To apply any of these approaches, the relative risks for one exposure must be adjusted for the second exposure and the way round.

Function call

For this purpose, you can use the function multiexpose().

results_pm <- attribute_health(
  erf_shape = "log_linear",
  rr_central = 1.369, 
  rr_increment = 10,
  exp_central = 8.85,
  cutoff_central = 5,
  bhd_central = 30747
) 

results_no2 <- attribute_mod(
  output_attribute = results_pm,
  exp_central = 10.9,
  rr_central = 1.031
)

results_multiplicative <- multiexpose(
  output_attribute_exp_1 = results_pm,
  output_attribute_exp_2 = results_no2,
  exp_name_1 = "pm2.5",
  exp_name_2 = "no2",
  approach_multiexposure = "multiplicative"
)

Main results

results_multiplicative$health_main
impact_rounded
3988

Standardization

Goal

E.g., to obtain the age-standardized attributable health impacts of two age groups.

Methodology

Age standardization involves adjusting the observed rates of a particular outcome to a standard population with a specific age structure. This is a technique used to allow the comparison of populations with different age structures (GBD 2019 Demographics Collaborators 2020; Ahmad et al. 2001). In healthiar, the function standardize() applies the direct method, where the age-specific rates observed in a study population are applied to a standard (reference) population distribution.

The standardized health impact rate is computed as \[ impact\_per\_100k\_inhab_{std} = \sum_{i=1}^{k} (impact\_per\_100k\_inhab_i \times ref\_prop\_pop_i) \]

where:

Function call

output_attribute <- attribute_health(
  rr_central = 1.063,
  rr_increment = 10,
  erf_shape = "log_linear",
  cutoff_central =  0,
  age_group = c("below_40", "above_40"),
  exp_central = c(8.1, 10.9),
  bhd_central = c(1000, 4000),
  population = c(100000, 500000)
  )

results <- standardize(
  output_attribute = output_attribute,
  age_group = c("below_40", "above_40"),
  ref_prop_pop = c(0.5, 0.5)
  )

Main results

Age-standardized impact rate:

print(results$health_main$impact_per_100k_inhab)  
#> [1] 49.91113

Age group-specific impact rate:

print(results$health_detailed$results_raw$impact_per_100k_inhab)  
#> [1] 48.28250 51.53977

Preparation of exposure data

Goal

E.g., to determine population-weighted mean PM2.5 exposure for several neighborhoods of Brussels (Belgium)

Methodology

The healthiarfunction prepare_exposure() helps users that do not have the exposure data (needed for healthiar functions), but only spatial concentration and population data. The function calculates an average concentration value in each geographic unit, weighted with population at each location.

\[ exp = \frac{\sum_{i=1}^{n} (C_i \times population_i)}{\sum_{i=1}^{n} population_i} \]

where:

In case population is entered as count by geographic sub-unit, the function calculates the mean concentration in each sub-unit and aggregates it to higher-level geographic units. If no population data is entered, the function calculates a simple spatial mean concentration as exposure value.

The output of prepare_exposure() can be entered in the argument exp_mean, exp_lower and/or exp_upper in healthiar functions such as attribute_health().

Function call

# exdat_pwm_1 = Pollution grid data
exdat_pwm_1 <- terra::rast(system.file("extdata", "exdat_pwm_1.tif", package = "healthiar"))

# exdat_pwm_2 = Data with the geo units and population data. This is pre-loaded in healthiar.
# If your raw data are in .gpkg format, you can use e.g.  sf::st_read() 

pwm <- healthiar::prepare_exposure(
  poll_grid = exdat_pwm_1, # Formal class SpatRaster,
  geo_units = exdat_pwm_2, # sf of the geographic sub-units
  population = sf::st_drop_geometry(exdat_pwm_2$population), # population per geographic sub-unit
  geo_id_macro = sf::st_drop_geometry(exdat_pwm_2$region)) # higher-level IDs to aggregate

Main results

Within the function output, the list main contains the population-weighted mean exposures for the (higher-level) geographic units in the column exposure_mean and the total population in each unit in column population_total.

Threshold additional to cut-off

Goal

E.g., to quantify health impacts in the exposure group 55dB+ (calculation threshold) that are affected by a exposure above the effect threshold of 45 dB (cut-off).

Function call

The function arguments erf_eq_... require a function as input. Instead of using a splinefun() this can also be fulfilled by using a ‘function(c)’ which is of type ‘function’.

#setting up function parameters
threshold_effect <- 45
RR <- 1.055
threshold_calculation <- 55
rr_increment <- 10

# define categorical function, the ifelse condition enables the case distinction
erf_function <- function(c){
  output <- ifelse(c<threshold_calculation, 1, exp((log(RR)/rr_increment)*(c-threshold_effect)))
  return(output)
}
# attribute_health
results_catERF_different_calc_thesh <- healthiar::attribute_health(
  approach_risk = "relative_risk",
  erf_eq_central = erf_function,
  prop_pop_exp = c(300000,200000,150000,120000,100000,70000,60000)/10000000,
  exp_central = c(47,52,57,62,67,72,77),
  cutoff_central=0,
  bhd_central=50000)$health_main$impact_rounded

The used function is equal to \[ f(c) = \begin{cases} 1, & c < \text{threshold} \\ \exp\left( \frac{\log(RR)}{rr_{increment}} (c - threshold_{effect}) \right), & c \ge \text{threshold} \end{cases} \]

The categorical ERF curve created looks as follows.

ERF curve

It is important to distinguish between an epidemiological cut-off (which shifts the exposure-response function) and a policy or evaluation threshold (which truncates exposure without shifting the underlying curve shape):

  1. Shifted Epidemiological Cut-off (Default healthiar behavior): Passing cutoff shifts the exposure axis so that \(c = \text{exp} - \text{cutoff}\) and grounds the excess risk at zero at the cut-off point.

  2. Unshifted Policy Threshold: If you wish to calculate attributable risk using a raw exposure-response function where exposure below a policy threshold does not contribute to health outcomes, but without shifting the curve horizontally, set cutoff = 0 and pre-truncate your exposure vector or incorporate pmax() directly into your string formula.

# Case A: Epidemiological Cut-off (Curve shifted by healthiar)
epi_cutoff <- healthiar::attribute_health(
  approach_risk = "absolute_risk",
  exp_central = c(50, 60, 70),
  pop_exp = c(300000,200000,150000),
  cutoff_central = 53,
  erf_eq_central = "78.9270 - 3.1162 * (c + 53) + 0.0342 * (c + 53)^2"
)
#> Warning: You entered a value for: cutoff_central alongside absolute risk.
#> Be aware that healthiar shifts the exposure in 'erf_eq' as c = (exp - cutoff).

# Case B: Unshifted Policy Threshold (Exposure truncated, curve unshifted)
policy_threshold <- healthiar::attribute_health(
  approach_risk = "absolute_risk",
  exp_central = c(50, 60, 70),
  pop_exp = c(300000,200000,150000),
  cutoff_central = 0,
  erf_eq_central = "ifelse(c >= 53, 78.9270 - 3.1162 * c + 0.0342 * c^2, 0)"
)

Economic dimension

Monetization

Goal

E.g., to monetize the attributable health impact of a policy that will have health benefits five years from now.

Methodology

In health economic evaluations and economic burden of disease assessments, health impacts may need to be converted into monetary values. For this purpose, you can use monetize().

Several valuation metrics are available, depending on how outcomes are quantified in natural or health units (e.g. cases reduced, deaths prevented, reductions in mortality risk, life-years gained, QALYs gained, DALYs averted). Common metrics include the Value of a Statistical Life (VSL) (OECD 2025) , the Value of a Life-Year (VOLY) (Hammitt 2007) and the Value of a Quality-Adjusted Life-Year (VAQALY) (Bobinac et al. 2010).

Discounting is the practice of converting future costs (or health impacts as previous step to valuating them) into their present value. The underlying rationale is that the value placed on outcomes declines as they occur further in the future. Therefore, future costs and effects are converted into present-value terms to make them comparable over time (Attema et al. 2018).

Discounting is implemented by selecting a discount rate, which is used to compute a discount factor for each time period. This factor is then multiplied by the corresponding future cost (or effect) to express it in present-value terms.

If you need the discounted values of a cost or health outcome, you can call the healthiar function discount(). If you just need the discount factor, you can alternatively call get_discount_factor() (entering is_deflation = TRUE). If you just need the inflation factor, you can get_inflation_factor().

Different functional forms can be used to apply discounting. The most common is exponential discounting, also referred to as constant discounting, since outcomes are discounted proportionally as time increases. An alternative is hyperbolic discounting, which tends to better capture human behavior by discounting the near present more heavily than outcomes further in the future (Lipman and Attema 2024)

See below the equations that are used behind these functions.

\[monetized\_impact = impact \times valuation \times discount\_factor \times deflator\_factor \times real\_growth\_factor\] The arguments discount_factor, deflator_factor and real_growth_factor are only used if a value is entered in the arguments discount_rate, ingflation_rate and real_growth_rate respectively
(otherwise ignored).

Discount factor

Exponential discounting

As suggested by Frederick et al. (2002)

\[discount\_factor = \frac{1}{(1 + discount\_rate)^{n\_years}}\]

Hyperbolic discounting Harvey

As suggested by Harvey (1986)

\[discount\_factor = \frac{1}{(1 + n\_years)^{discount\_rate}}\]

Hyperbolic discounting Mazur

As suggested by Mazur (1987)

\[discount\_factor = \frac{1}{1 + (discount\_rate \times n\_years)}\]

Deflation factor

Inflation can be handled in monetize() by applying a deflator on future values, projected in nominal terms, in order to convert them into real values (i.e., express these values in terms of constant prices of a single base year). Therefore, if the user of the function provides a value for the inflation_rate argument, a deflator factor (HM Treasury 2022; Brealey et al. 2023; Samuelson 1937) is applied according to the following formulas

\[deflator\_factor = \frac{1}{(1 + inflation\_rate)^{n\_years}}\]

Real valuation growth

If a rising societal value of health over time is required in the monetization, unlike inflation, this represents a “real” increase in value. Thus, as societies become wealthier, their willingness to pay to avoid mortality and morbidity risks tends to rise (OECD 2012).

For this use case, you have enter a value in the argument real_growth_rate in monetize(), which allows you to project this growth by applying a valuation growth factor to base-year unit values:

\[real\_growth\_factor =(1 + real\_growth\_rate)^{n\_years}\]

Where \(real\_growth\_rate\) represents the annual real growth rate in health valuation. This ensures that long-term environmental impacts are not undervalued.

Function call

monetized_pm_copd <- monetize(
    output_attribute = results_pm_copd,
    discount_shape = "exponential",
    discount_rate = 0.03,
    n_years = 5,
    valuation = 50000 # E.g. EURO
)

Main results

The outcome of the monetization is added to the variable entered to the output_attribute argument, which is results_pm_copd in our case.

Two folders are added:

  • monetization_main contains the central monetization estimate and the corresponding 95% confidence intervals obtained through the specified monetization.

  • monetization_detailed contains the monetized results for each unique combination of the input variable estimates that were provided to the initial attribute_health() call.

erf_ci monetized_impact
central 151041153
lower 58358321
upper 236091201

We see that the monetized impact (discounted) is more than 160 million EURO.

Alternatively, you can also monetize (attributable) health impacts from a non-healthiar source.

results <- monetize(
  impact = 1151,
  valuation = 100
)

Cost-benefit analysis

Goal (e.g.)

E.g., to perform an economic evaluation for an intervention by comparing its benefits and costs via Cost-Benefit Analysis (CBA).

Methodology

The CBA is a type of economic evaluation that compares the costs and the benefits of an intervention, considering both measures expressed in monetary terms.

To perform a CBA, you can use the function cba(). This approach requires monetizing benefits so they can be directly compared with costs. Since interventions typically generate costs and benefits over multi-year time horizons, discounting is a common practice to obtain the present value of future costs and benefits. Depending on the reference guidelines, the discount rate can be specified as the same for costs and benefits or different across them. The outputs of a Cost-Benefit Analysis can be expressed as three main indicators (Boardman et al. 2018): - intervention’s net benefit: the difference between monetized benefits and costs - Cost-Benefit Ratio (CBR): monetized benefits divided by costs and - Return on Investment (ROI): return generated per unit of expenditure by relating net benefits to the intervention’s costs.

An intervention is recommended from a Cost-Benefit Analysis perspective, if it yields a positive net benefit or a positive ROI, or equivalently, a CBR greater than one, meaning that the intervention’s monetized benefits exceed its costs. These three outputs are available when running cba() and are calculated considering the following formulas.

Net Benefit \[net\_benefit = benefit - cost\]

Cost-Benefit Ratio (CBR) \[cbr = \frac{benefit}{cost}\]

Return on Investment (ROI) \[roi = \frac{benefit - cost}{cost} \times 100\]

Function call

Let’s imagine we design a policy that would reduce air pollution to 5 \(\mu g/m^3\), which is the concentration specified in the cutoff_central argument in the initial attribute_health() call. So we could avoid all COPD cases attributed to air pollution.

Considering the cost to implement the policy (estimated at 100 million EURO), what would be the monetary net benefit of such a policy? We can find out using the functions healthiar and cba()

cba <- cba(
    output_attribute = results_pm_copd,
    valuation = 50000,
    cost = 100000000,
    discount_shape = "exponential",
    discount_rate_benefit = 0.03,
    discount_rate_cost = 0.03,
    n_years_benefit = 5,
    n_years_cost = 5
)

Main results

The outcome of the CBA is contained in two folders, which are added to the existing assessment:

  • cba_main contains the central estimate and the corresponding 95% confidence intervals obtained

  • cba_detailed contains additional intermediate results for both cost and benefit

    • benefit contains results by_year and raw results health_raw

    • cost contains the costs of the policy at the end of the period specified in the n_years_cost argument

cba$cba_main |>  
  dplyr::select(benefit, cost, net_benefit) |> 
  knitr::kable()
benefit cost net_benefit
151041153 86260878 64780274
58358321 86260878 -27902557
236091201 86260878 149830323

We see that the central and upper 95% confidence interval estimates of avoided attributable COPD cases result in a net monetary benefit of the policy, while the lower 95% confidence interval estimate results in a net cost!

Social aspects

Health impact attributable to social indicator

Goal

E.g., to estimate the health impact that is theoretically attributable to the difference in degree of deprivation of the population exposed.

Methodology

Taking into account socio-economic indicators, e.g. a multiple deprivation index (Mogin et al. 2025), the differences in attributable health impacts across the study areas can be estimated (Renard et al. 2019; Otavova et al. 2022).

Social inequalities are quantified as the difference between the least deprived areas (the last n-quantile) and

  • the most deprived areas or

  • the population overall.

These differences can be

  • absolute or

  • relative.

Difference most deprived vs. least deprived

\[ absolute\_quantile = first - last \] Where:

  • \(absolute\_quantile\) = Absolute difference between quantiles.
  • \(first\) = Average health impacts in most deprived quantile.
  • \(last\) = Average health impacts in least deprived quantile.

\[ relative\_quantile = \frac{absolute\_quantile}{last} \]

Difference overall vs. least deprived

\[ absolute\_overall = overall - last \] Where:

  • \(absolute\_overall\) = Absolute difference regarding the overall average.
  • \(overall\) = Overall average health impacts in the study area.
  • \(last\) = Average health impacts in least deprived quantile.

If you assume that the least deprived areas are similar to counter-factual cases (no exposure to deprivation), the relative difference regarding the overall average health impact could be interpreted as some kind of relative risk attributable to social inequalities.

Function call

First, quantify health impacts.

 health_impact <- healthiar::attribute_health(
   age_group = exdat_socialize$age_group,
   exp_central = exdat_socialize$pm25_mean,
   cutoff_central = 0,
   rr_central = exdat_socialize$rr,
   erf_shape = "log_linear",
   rr_increment = 10,
   bhd_central = exdat_socialize$mortality,
   population = exdat_socialize$population,
   geo_id_micro = exdat_socialize$geo_unit)

Second, use the function socialize() entering the whole output of attribute_health() in the argument output_attribute.

social_t <- healthiar::socialize(
  output_attribute = health_impact,
  age_group = exdat_socialize$age_group, # They have to be the same in socialize() and in attribute_health()
  ref_prop_pop = exdat_socialize$ref_prop_pop, # Population already provided in output_attribute
  geo_id_micro = exdat_socialize$geo_unit,
  social_indicator = exdat_socialize$score,
  n_quantile = 10,
  increasing_deprivation = TRUE)

Alternatively, you can directly enter the health impact in the socialize() argument impact.

social <- healthiar::socialize(
  impact = health_impact$health_detailed$results_by_age_group$impact,
  age_group = exdat_socialize$age_group, # They have to be the same in socialize() and in attribute_health()
  ref_prop_pop = exdat_socialize$ref_prop_pop,
  geo_id_micro = exdat_socialize$geo_unit,
  social_indicator = exdat_socialize$score,
  population = exdat_socialize$population, # Population has to be provided because no output_attribute
  n_quantile = 10,
  increasing_deprivation = TRUE)

Main results

#> # A tibble: 4 × 5
#>   parameter      difference_type difference_compared_…¹ difference_value comment
#>   <chr>          <chr>           <chr>                             <dbl> <chr>  
#> 1 impact_rate_s… absolute        last_quantile                   11.5    <NA>   
#> 2 impact_rate_s… relative        last_quantile                    0.193  <NA>   
#> 3 impact_rate_s… absolute        overall                         -0.834  It can…
#> 4 impact_rate_s… relative        overall                         -0.0143 It can…
#> # ℹ abbreviated name: ¹​difference_compared_with

Multiple deprivation index

Goal

E.g., to estimate the multiple deprivation index (MDI) to use it for the argument social_indicator in the function socialize().

Methodology

Socio-economic indicators (e.g., education level, employment status and family structure) can be condensed into a multiple deprivation index (MDI) (Mogin et al. 2025). For this purpose, the indicators can be normalized using min-max scaling.

The reliability of the MDI can be assessed using Cronbach’s alpha (Cronbach 1951).

\[ \alpha = \frac{k}{k - 1} \left( 1 - \frac{\sum_{i=1}^{k} \sigma^2_{y_i}}{\sigma^2_x} \right) \] where:

  • \(k\) is the number of items/variables.
  • \(\sigma^2_{y_i}\) is the variance of the \(i\)-th item.
  • \(\sum_{i=1}^{k} \sigma^2_{y_i}\) is the sum of the variances of all items.
  • \(\sigma^2_x\) is the total variance of the observed total scores (the sum of all items).

To apply this approach, you should ensure that the data set is as complete as possible. Otherwise, you can try to impute missing data using: - Time-Based Imputation: Linear regression based on historical trends if prior years’ data is complete. - Indicator-Based Imputation: Multiple linear regression if the missing indicator correlates strongly with others.

Imputation models should have an R^2 greater than or equal to 0.7. If R^2 lower than 0.7, consider alternative data sources or methods.

Function call

mdi <- prepare_mdi(
  geo_id_micro = exdat_prepare_mdi$id,
  edu = exdat_prepare_mdi$edu,
  unemployed = exdat_prepare_mdi$unemployed,
  single_parent = exdat_prepare_mdi$single_parent,
  pop_change = exdat_prepare_mdi$pop_change,
  no_heating = exdat_prepare_mdi$no_heating,
  n_quantile = 10,
  verbose = FALSE
)

Note: verbose = FALSE suppresses any output to the console (default: verbose = TRUE, i.e. with printing turned on).

Main results

Function output includes:

  • mdi_main, a tibble containing the BEST-COST MDI
mdi$mdi_main |> 
  select(geo_id_micro, MDI, MDI_index)
geo_id_micro MDI MDI_index
11001 0.2117721 1
11002 0.4319924 8
11004 0.1847750 1
11005 0.3787937 7
11007 0.3121354 5
11008 0.2565185 2
11009 0.2245822 1
11013 0.2140148 1
11016 0.2656597 3
11018 0.3566141 6

The function assesses the reliability of the MDI based on the Cronbach’s alpha value as follows: - 0.9 and higher: Excellent reliability - between 0.8 (included) and 0.9: Good reliability - between 0.7 (included) and 0.8: Acceptable reliability - between 0.6 (included) and 0.7: Questionable reliability - lower than 0.6: Poor reliability

Detailed results

  • mdi_detailed

    • DESCRIPTIVE STATISTICS

    • PEARSON’S CORRELATION COEFFICIENTS

    • CRONBACH’S α, including the reliability rating this value indicates

    • Code for boxplots of the single indicators

    • Code for histogram of the MDI’s for the geo units with a normal distribution curve

To reproduce the boxlots run

eval(mdi$mdi_detailed$boxplot)

Boxplot of Normalized Indicators and MDI Analogeously, to reproduce the histogram run

eval(mdi$mdi_detailed$histogram)

Histogram of MDI with normal curve


Inside pipes

Pipe |>

healthiar can be used inside the native pipes |>. See the example below.

exdat_noise |>
  (\(df) {
    healthiar::attribute_health(
      approach_risk = df$risk_estimate_type,
      exp_central = df$exposure_mean,
      pop_exp = df$exposed,
      erf_eq_central = df$erf
      )$health_main$impact_rounded
    })()

Shorter making used of the base R function with().

exdat_noise |>
      (\(df) {
        with(df, healthiar::attribute_health(
         approach_risk = risk_estimate_type,
         exp_central = exposure_mean,
         pop_exp = exposed,
         erf_eq_central = erf
         ))$health_main$impact_rounded
        })()
#> [1] 348464

Pipe %>%

healthiar can also be used inside magrittr pipes %>% as follows.

exdat_noise %>%
  {
    healthiar::attribute_health(
      approach_risk = .$risk_estimate_type,
      exp_central = .$exposure_mean,
      pop_exp = .$exposed,
      erf_eq_central = .$erf
    )$health_main$impact_rounded
  }

Export and visualize

Exporting and visualizing results is out of scope of healthiar. To export and visualize, you can make use of existing functions in other packages beyond healthiar as indicated below.

Export results

Export as .csv file

Save as .Rdata file

Export to Excel (as .xlsx file)

Visualize results

Visualization is out of scope of healthiar. You can visualize in:


Abbreviations

BHD/bhd = baseline health data

CI = confidence interval

CBA/cba = cost-benefit analysis

exp = exposure

ERF = exposure-response function

RR/rr = relative risk

WHO = World Health Organization

YLL/yll = years of life lost


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