https://github.com/dcmuller/ukbiobank_lca_model_predictions

Stata programs to calculate the predicted risk of lung cancer based on the UK Biobank prediction model.
https://github.com/dcmuller/ukbiobank_lca_model_predictions

Last synced: 4 months ago
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Stata programs to calculate the predicted risk of lung cancer based on the UK Biobank prediction model.

• Host: GitHub
• URL: https://github.com/dcmuller/ukbiobank_lca_model_predictions
• Owner: dcmuller
• License: bsd-3-clause
• Created: 2015-10-28T14:20:09.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-03-28T13:04:34.000Z (over 6 years ago)
• Last Synced: 2024-01-17T01:04:16.283Z (6 months ago)
• Language: Stata
• Homepage:
• Size: 30.3 KB
• Stars: 4
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome-uk-biobank - ukbiobank_lca_model_predictions

README

        
# Predicted risk of lung cancer based on the UK Biobank risk prediction model

This repository provides Stata code to calculate the predicted risk of

lung cancer based on supplied information and the UK Biobank risk

prediction model.

## How to use this code

You will need a copy of Stata, version 12 or higher, with the

user-written commands stpm2 and rcsgen installed (`ssc install stpm2`, `ssc install rcsgen`). Open stata

and change directory to the root of this repository. Running

```

do predict_lca_risk.do

```

will calculate the predicted risk of lung cancer. By default this will

take covariate information from the file 'input.csv', calculate the

2-year cumulative probability of lung cancer for each record therein,

and save the results in the file 'output.csv'. These default input,

output, and time-horizons can be changed by editing the parameters in

the configuration block at the beginning of the file

'predict\_lca\_risk.do'.

## Input specification

The input file must be an ASCII plain text CSV file, and must contain

the following variables:

variable name | description | type | valid values

--------------|:------------|:-----|:-------------

age | age in years | real | [40,70]

smoke\_stat | smoking status | integer | 0 (never smoker), 1 (former smoker), 2 (current smoker)

male | male sex | integer | 0 (female), 1 (male)

previous\_cancer | Previously diagnosed with an invasive cancer | integer | 0 (no), 1 (yes)

fhist\_lungca | one or more first-degree relatives who have been diagnosed with lung cancer | integer | 0 (no), 1 (yes)

emph\_bronch | history of emphysema or bronchitis | integer | 0 (no), 1 (yes)

allergy | history of hayfever, allergic rhinitis, or eczema | integer | 0 (no), 1 (yes)

fev1\_max | forced expiratory volume in one second (FEV1) | real | [0.5,10]

smkfmr\_quitage | for former smokers only, the age at which they quit | real | less than current age

ncig | for current and former smokers only, the average number of cigarettes smoked per day | real | (0,80]

stop1day\_easy | for current smokers only, how difficult would it be to not smoke for one day | integer | 0 (difficult or very difficult), 1 (easy or very easy)

Other variables can be included in the input file, but they are

ignored by the program.

## Output file

The output file contains the same variables as the input file, with

the addition of the variable 'cif\_lung' which contains the predicted

probability (Cumulative Incidence Function evaluated at a given time

horizon) for each input observation.