Directory Structure

Here is the current structure (20/09/2019).

ITHIM-R package¶ ↑

The key components of the package are in

R/ – all the functions for ITHIM-R, with (generally) one file per function and the filename the same as the function name
- inst/extdata/ – all the processed data we use for case studies, which is subdivided into local/ and global/.
- global/ – the dose–response relationships and, for now at least, emissions. (These data could potentially be moved to data/ and be loaded automatically with the library.)
local/ – are location-specific folders, e.g. accra/. Within each folder should be the same input files - same naming conventions, same structures.
docs/ – pkgdown documentation
man/ – Rd documentation

Internal¶ ↑

The things that are just for us/for our development:

tests/testthat/ – old tests, not in use
code/ – our data processing scripts - subdivided by module and city
data/ – some of our raw data, to be processed by ‘code’ and saved in ‘inst/extdata/’
results/ – our own results
diagnostic/ – another internal testing place
project_mgmt/ – files to help us organise our project

WIP¶ ↑

below contents are produced in this gdoc:docs.google.com/document/d/1K1CAymRdae3Dx8ReNB6VVqFr2PbbAmaj38JCzZf1BzU/edit#heading=h.gjdgxs (I use Rdoc format for proper - more or less - display of indented structure)

(indent using 4 spaces for each sub-level. Also 2 spaces after each line)

(the numbered text is from ITHIM R modules …and could be removed/cleaned eventually)

** Generic R-Package components**

Code (R/)  
Package Metadata (DESCRIPTION)  
Object documentation (man/)  
Vignettes (vignettes/)  
Testing (tests/)  
Namespaces (NAMESPACE)  
Data (data/)  
Compiled code (src/)  
Installed files (inst/)  
_Other components_  
User interface (shiny/)

**Folder/Directory structure ITHIM-R**

Root-directory

ITHIM-R/

Data Sources

(Everything related to external data, i.e. user input data, generic data used by the tool, and their various formats, implications, metadata)

DATASOURCES/

R/  
shiny/  
data/  
    international_data/  
       demographics/  
       travel/  
       physical_activity/  
       other/  
    local_data/  
       demographics/  
           case_study_name/  
           zurich/  
       travel/  
           case_study_name/  
           zurich/  
       physical_activity/  
           case_study_name/  
           zurich/  
       other/

Data Localization

(The process of adjustments, calibration of international, national data to local settings of a specific ITHIM application. This may include spatial scaling, temporal extrapolation, adjustment for population attributes, etc.)

LOCALIZATION/

R/  
shiny/  
data/  
    localized_data/  
       demographics/  
           case_study_name/  
           zurich/  
       travel/  
           case_study_name/  
           zurich/  
       physical_activity/  
           case_study_name/  
           zurich/  
       other/

Data Harmonization

(The process of conversion or matching of various data formats and variable definitions of external data to the generic data formats used in ITHIM (e.g. mode categories))

HARMONIZATION/

R/  
shiny/  
data/  
    harmonized_data/
       demographics/  
           case_study_name/  
           zurich/  
       travel/  
           case_study_name/  
           zurich/  
       physical_activity/  
           case_study_name/  
           zurich/  
       other/

**Synthetic Baseline Data** (i.e. individual data, vehicle data, crash data)

1. The process of creating a **[[Synthetic population]]** (sample of 10k individuals), through probabilistic matching of separate input data from  population, travel, and health surveys, for baseline.

SYNTHPOP/

R/  
shiny/  
data/  
    synthpop_data/  
       baseline/  
           case_study_name/  
           zurich/  

2. The creation of a **[[Vehicle distance dataset]]** based on travel behaviour, occupancy factors, and transport statistics, for baseline.

VEHDIST/

R/  
shiny/  
data/  
    vehdist_data/  
       baseline/  
           case_study_name/  
           zurich/  

3. The creation of a **[[Who-hit-whom matrix]]** based on crash statistics, for baseline.

CRASHMATRIX/

R/  
shiny/  
data/  
    crashmatrix_data/  
       baseline/  
           case_study_name/  
           zurich/

**Scenario Definition** (Creation of “Synthetic counterfactual data”) (2 options:)

1. Manipulation of baseline data through a **[[Scenario definition module]]** (interface or code).  
2. Creation of  **[[Synthetic scenario data]]**, based on local data sources, analogous to steps for baseline data above.

SCENARIO/

R/  
shiny/  
data/  
    synthpop_data/
       baseline/  
       scenario/  
           case_study_name/  
           zurich/  
    vehdist_data/  
       baseline/  
       scenario/  
           case_study_name/  
           zurich/  
    crashmatrix_data/  
       baseline/  
       scenario/  
           case_study_name/  
           zurich/

**Environmental Impacts Calculations**
```
1. **[[Carbon emissions]]**
```

CARBON/

R/  
shiny/  
data/  
    carbon_data/  

1. **[[Background AP concentration]]** (i.e. as affected under scenario conditions)

APBG/

R/  
shiny/  
data/  
    AP_data/

**Exposure Calculations** for each scenario (for baseline only as needed beyond Synthetic Baseline Data)
```
1. [[Exposure calculation for PA]] (calculation of total METhrs/week or similar)
```

PAEXP/

R/  
shiny/  
data/  
    PAexp_data/  

1. [[Exposure calculation for AP]] (calculation of long term exposure equivalents, PM2.5,..)

APEXP/

R/  
shiny/  
data/  
    APexp_data/

**Impact Calculations**

A. **[[Health Impact Calculations (PA, AP)]]** 
1. Calculation of Potential Impact Fractions (**PIF**s)  
2. Application of PIFs (or PAFs) to either:  
    1. GBD-derived rates of various outcomes (YLL, YLD, deaths), or  
    2. Proportionate Multi-State Life Table calculations

IMPACTS_PA_AP/

R/  
    PAF/  
    PIF/  
    MSLT/  

B. **[[Injury Impact Calculations (Crashes)]]**   
1. Events Calculation based on Who-hit-whom matrix
1. Conversion of injury events into various units of disease burdens (e.g YLLs)

IMPACTS_INJ/

R/  
    injevents/  
    injimpactunits/

Impacts Presentations

(outcome definitions, level of detail, aggregation, visualization)

1. combined pathway results
1. pathway specific

RESULTS/

R/  
shiny/  
data/  
    pathway_results/  
    combined_results/

**Overarching modules**
1. User interface (including data visualization, explortation and validation features)
2. Website contents/documentation
3. Tool Parameters (“is the math being done in miles or km?” A central place for default values, units, constants, assumptions to be called by various tool elements)

WEBSITE/

.…various/TBD

TOOLPARAMETERS/

.…data/

**Overarching project domains**
1. Coding guidelines
2. Documentation
3. Scientific publications
4. Dissemenination
5. Case studies/applications

OTHER/..

ITHIM-R-modules

Data Sources
1. trips (travel survey) source
2. physical activity source
3. air pollution source
4. injuries source
5. GBD source
6. population source
Data Harmonization
1. trips (travel survey) process
2. physical activity process
3. air pollution process
4. injuries process
5. GBD process
6. population process
Processed Data
1. trips (travel survey) processed
2. physical activity processed
3. air pollution processed
4. injuries processed
5. GBD processed
6. population processed
Synthetic population
Scenario Definition
Exposure and Impact Calculations
1. Air pollution exposure and impact
2. Physical activity exposure and impact
3. Injury exposure and impact
4. Health impact calculations
Uncertain Parameters
Impacts Presentations
Overarching modules
Overarching project domains
1. Coding guidelines
2. Documentation
3. Scientific publications
4. Dissemination
5. Case studies/applications

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Directory Structure

ITHIM-R package¶ ↑

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