---
title: "Getting Started with climatehealth"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with climatehealth}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  eval     = FALSE
)
```

## What is climatehealth?

The **climatehealth** package provides R functions for calculating climate–health
indicators following the statistical framework developed under the
[SOSCHI (Standards for Official Statistics on Climate–Health Interactions)](https://climate-health.officialstatistics.org)
project. It covers indicators for six climate-health topic areas:

| Topic | Lead |
|---|---|
| Temperature-related health effects | ONS |
| Health effects of wildfires | ONS |
| Mental health (suicides and heat) | ONS |
| Water-borne diseases (diarrhoea) | AIMS |
| Health effects of air pollution | AIMS |
| Vector-borne diseases (malaria) | RIPS/AIMS |

Each topic has a dedicated analysis function that takes a data file path and
column mappings, fits the appropriate statistical models, and returns results
and optional plots.

---

## Installation

### From CRAN

```{r install-cran}
install.packages("climatehealth")
```

### From GitHub (latest development version)

```{r install-github}
install.packages("remotes")
remotes::install_github("onssoschi/climatehealth")
```

### Optional dependencies

Two indicators (malaria and diarrhoea) depend on **INLA** and **terra**
respectively, which are not on CRAN and must be installed separately if needed:

```{r install-optional}
climatehealth::install_INLA()
climatehealth::install_terra()
```

Once installed, load the package:

```{r load}
library(climatehealth)
```

---

## Package workflow

All six indicator functions follow the same pattern:

1. **Provide a path** to your input CSV.
2. **Map your column names** to the function's expected arguments (or use the
   defaults if your data already matches them).
3. **Choose optional extras**: covariates, meta-analysis, output saving.
4. **Inspect the returned list** for model results, plots, and summary tables.

```
your_data.csv  -->  indicator_do_analysis()  -->  results list
                                              -->  figures (optional)
                                              -->  CSV outputs (optional)
```

---

## Your first analysis: temperature and mortality

`temp_mortality_do_analysis()` estimates the association between ambient
temperature and mortality using a distributed lag non-linear model (DLNM).

```{r temp-mortality-basic}
res <- climatehealth::temp_mortality_do_analysis(
  data_path        = "path/to/your/data.csv",
  date_col         = "date",
  region_col       = "region",
  temperature_col  = "tmean",
  health_outcome_col = "deaths",
  population_col   = "population",
  meta_analysis    = FALSE,
  save_fig         = FALSE,
  save_csv         = FALSE
)
```

The returned object `res` is a named list. Common fields include:

```{r temp-mortality-results}
res$data_raw          # the input data as loaded
res$analysis_results  # model coefficients and confidence intervals
res$meta_results      # pooled estimates (when meta_analysis = TRUE)
```

### Adding covariates

Pass extra column names via `independent_cols` (continuous exposures) and
`control_cols` (factors such as day-of-week or public holidays):

```{r temp-mortality-covariates}
res <- climatehealth::temp_mortality_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "deaths",
  population_col     = "population",
  independent_cols   = c("humidity", "ozone"),
  control_cols       = c("dow", "holiday_flag"),
  meta_analysis      = FALSE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

### Pooling across regions with meta-analysis

Set `meta_analysis = TRUE` to pool region-level estimates into a single
national estimate:

```{r temp-mortality-meta}
res <- climatehealth::temp_mortality_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "deaths",
  population_col     = "population",
  country            = "National",
  meta_analysis      = TRUE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

---

## The six indicators

### Air pollution

`air_pollution_do_analysis()` estimates attributable mortality burden from
PM2.5 exposure. By default it expects columns named `date`, `region`, `pm25`,
`deaths`, `population`, `humidity`, `precipitation`, `tmax`, and `wind_speed`.

```{r air-pollution}
res <- climatehealth::air_pollution_do_analysis(
  data_path       = "path/to/your/data.csv",
  save_outputs    = FALSE,
  run_descriptive = TRUE,
  run_power       = TRUE
)
```

Compare against multiple PM2.5 reference thresholds in a single run:

```{r air-pollution-standards}
res <- climatehealth::air_pollution_do_analysis(
  data_path         = "path/to/your/data.csv",
  reference_standards = list(
    list(value = 15, name = "WHO"),
    list(value = 25, name = "National")
  ),
  save_outputs = FALSE,
  run_power    = TRUE
)
```

### Wildfires

`wildfire_do_analysis()` estimates the health impact of wildfire smoke exposure.

```{r wildfire}
res <- climatehealth::wildfire_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  exposure_col       = "pm25_fire",
  health_outcome_col = "respiratory_admissions",
  population_col     = "population",
  meta_analysis      = FALSE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

### Mental health (suicides and heat)

`suicides_heat_do_analysis()` models the association between temperature and
suicide counts.

```{r suicides}
res <- climatehealth::suicides_heat_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "suicides",
  population_col     = "population",
  meta_analysis      = FALSE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

### Water-borne diseases (diarrhoea)

`diarrhea_do_analysis()` estimates climate-driven diarrhoea burden.

```{r diarrhea}
res <- climatehealth::diarrhea_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "diarrhea_cases",
  population_col     = "population",
  meta_analysis      = FALSE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

### Vector-borne diseases (malaria)

`malaria_do_analysis()` requires the **INLA** package (see Installation above).

```{r malaria}
res <- climatehealth::malaria_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "malaria_cases",
  population_col     = "population",
  meta_analysis      = FALSE,
  save_fig           = FALSE,
  save_csv           = FALSE
)
```

---

## Descriptive statistics

Before running an indicator analysis, use `run_descriptive_stats()` to explore
your data: distributions, correlations, missing values, outliers, and seasonal
patterns.

```{r descriptive-basic}
df <- read.csv("path/to/your/data.csv")

desc <- climatehealth::run_descriptive_stats(
  data               = df,
  output_path        = "path/to/output/folder",
  aggregation_column = "region",
  dependent_col      = "deaths",
  independent_cols   = c("tmean", "humidity", "rainfall"),
  plot_corr_matrix   = TRUE,
  plot_dist          = TRUE,
  plot_na_counts     = TRUE,
  plot_scatter       = TRUE,
  plot_box           = TRUE,
  create_base_dir    = TRUE
)
```

Add units for cleaner plot labels, and enable time-series and rate calculations:

```{r descriptive-advanced}
desc <- climatehealth::run_descriptive_stats(
  data               = df,
  output_path        = "path/to/output/folder",
  aggregation_column = "region",
  population_col     = "population",
  dependent_col      = "deaths",
  independent_cols   = c("tmean", "humidity", "rainfall"),
  units = c(
    deaths    = "count",
    tmean     = "C",
    humidity  = "%",
    rainfall  = "mm"
  ),
  timeseries_col     = "date",
  plot_corr_matrix   = TRUE,
  plot_dist          = TRUE,
  plot_ma            = TRUE,
  ma_days            = 30,
  plot_seasonal      = TRUE,
  plot_regional      = TRUE,
  plot_total         = TRUE,
  detect_outliers    = TRUE,
  calculate_rate     = TRUE,
  create_base_dir    = TRUE
)
```

The returned list includes paths to all generated plots:

```{r descriptive-results}
desc$run_output_path      # folder where all outputs were saved
desc$region_output_paths  # per-region output sub-folders
```

---

## Saving outputs

Every indicator function accepts `save_fig` and `save_csv` arguments (or
`save_outputs` for air pollution). Set these to `TRUE` and supply
`output_folder_path` to write results to disk. The function creates a
timestamped sub-folder automatically.

```{r saving}
res <- climatehealth::temp_mortality_do_analysis(
  data_path          = "path/to/your/data.csv",
  date_col           = "date",
  region_col         = "region",
  temperature_col    = "tmean",
  health_outcome_col = "deaths",
  population_col     = "population",
  meta_analysis      = TRUE,
  save_fig           = TRUE,
  save_csv           = TRUE,
  output_folder_path = "path/to/output/folder"
)
```

---

## Error handling

The package uses structured conditions. You can catch them with `tryCatch`:

```{r error-handling}
result <- tryCatch(
  climatehealth::temp_mortality_do_analysis(
    data_path          = "path/to/your/data.csv",
    date_col           = "wrong_column_name",
    health_outcome_col = "deaths",
    population_col     = "population"
  ),
  climate_error = function(e) {
    message("climatehealth error: ", conditionMessage(e))
    NULL
  }
)
```

Use `is_climate_error()` to test whether a caught condition came from this
package:

```{r is-climate-error}
climatehealth::is_climate_error(e)
```

---

## Next steps

- **Full example scripts** for each indicator are in
  `system.file("examples", package = "climatehealth")`.
- **Function reference**: see `?temp_mortality_do_analysis` and related help
  pages.
- **Methodology documents** for each SOSCHI topic are linked from the
  [SOSCHI project website](https://climate-health.officialstatistics.org).
- **Report issues** by emailing <climate.health@ons.gov.uk> or via the
  [Contact Us page](https://climate-health.officialstatistics.org).
