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Software, websites & apps

The following are software packages, apps and websites dedicated specifically to prognosis research.

Many generic (e.g. regression model or machine learning) packages can also be used to undertake prognosis research

The list is in development, and certainly not exhaustive.

Please get in touch to provide more recommendations to add. 

  • PM suite of modules produced by Dr Joie Ensor:

    • pmsampsize: R and Stata packages for sample size calculations for prediction model development studies

    • pmcalplot: Stata package for producing calibration plots 

  • stcoxcal: a Stata package for examining the calibration performance of a survival model at particular time-point(s)

  • metamiscan R package for conducting meta-analysis of prognosis studies by Dr Thomas Debray

  • bsvalidation: a Stata package for bootstrap internal validation command for predictive logistic regression models

  • BMJ series (forthcoming) on validation by Riley, Collins et al .... software code as follows:

- Paper 1: R code for validation of the CRASH model is here

- Paper 2: Stata example code for the external validation of the binary and time-to-event models

- Paper 3: Stata code for the sample size for external validation of the continuous and binary outcomes is given

in the paper: more generally, see pmvalsampsize)

  • Various researchers have GitHub pages offering code for prognosis and prediction research, including:

- Gary Collins: see here

- Glen Martin: see here

- Hisashi Noma: see here

- Valentijn de Jong: see here

Karandeep Singh & others: see here

- Daniele Giardiello: see here  

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