survHE
Survival analysis in health economic evaluation Contains a suite of functions to systematise the workflow involving survival analysis in health economic evaluation. survHE can fit a large range of survival models using both a frequentist approach (by calling the R package flexsurv) and a Bayesian perspective.
Science Score: 36.0%
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Survival analysis in health economic evaluation Contains a suite of functions to systematise the workflow involving survival analysis in health economic evaluation. survHE can fit a large range of survival models using both a frequentist approach (by calling the R package flexsurv) and a Bayesian perspective.
Basic Info
- Host: GitHub
- Owner: giabaio
- Language: R
- Default Branch: main
- Homepage: https://gianluca.statistica.it/software/survhe/
- Size: 130 MB
Statistics
- Stars: 45
- Watchers: 8
- Forks: 19
- Open Issues: 11
- Releases: 4
Topics
Metadata Files
README.md
survHE
Survival analysis in health economic evaluation
:rocket: This is the development version of the R package survHE
(currently at version 2.0.51). A “stable” version (as of 11 July 2025:
2.0.5) is packaged and available from
CRAN.
Contains a suite of functions to systematise the workflow involving survival analysis in health economic evaluation. survHE can fit a large range of survival models using both a frequentist approach (by calling the R package flexsurv) and a Bayesian perspective. For a selected range of models, both Integrated Nested Laplace Integration (via the R package INLA) and Hamiltonian Monte Carlo (via the R package rstan) are possible. HMC models are pre-compiled so that they can run in a very efficient and fast way. In addition to model fitting, survHE provides a set of specialised functions, for example to perform Probabilistic Sensitivity Analysis, export the results of the modelling to a spreadsheet, plotting survival curves and uncertainty around the mean estimates.
NB: To run the Bayesian models, as of version 2.0 of survHE, it is
necessary to install the additional packages
survHEinla and/or
survHEhmc, which are available
from this GitHub repository. The reason for this structural change is
that in this way, the basic backbone of survHE (available from this
main branch of the repo) becomes a very lean package, whose
installation is very quick. More details
here.
All the functionalities are in place for survHE to easily extend to
the Bayesian versions, once one or both of the additional “modules” is
also installed.
Installation
The most updated version can be installed using the following code.
r
install.packages(
"survHE",
repos = c("https://giabaio.r-universe.dev", "https://cloud.r-project.org")
)
To run the Bayesian versions of the models, you also need to install the ancillary packages
``` r
Bayesian models using HMC/Stan
install.packages( "survHEhmc", repos = c("https://giabaio.r-universe.dev", "https://cloud.r-project.org"), dependencies=TRUE )
Bayesian models using INLA
install.packages( "survHEinla", repos = c( "https://giabaio.r-universe.dev", "https://cloud.r-project.org", "https://inla.r-inla-download.org/R/stable" ), dependencies=TRUE ) ```
(these two are optional, in some sense, so you don’t have to, unless you want to do the right thing and be Bayesian about it… :wink:)
Owner
- Name: Gianluca Baio
- Login: giabaio
- Kind: user
- Location: United Kingdom
- Company: University College London
- Website: https://gianluca.statistica.it
- Twitter: gianlubaio
- Repositories: 46
- Profile: https://github.com/giabaio
I'm a professor of Statistics & Health Economics and the head of department @stats-ucl. I work on Bayesian stats (with applications to @r-hta and @convoigroup)
GitHub Events
Total
- Release event: 1
- Watch event: 3
- Delete event: 3
- Issue comment event: 2
- Push event: 12
- Pull request event: 1
- Create event: 4
Last Year
- Release event: 1
- Watch event: 3
- Delete event: 3
- Issue comment event: 2
- Push event: 12
- Pull request event: 1
- Create event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gianluca Baio | g****o@u****k | 172 |
| Gianluca Baio | g****o@g****m | 169 |
| lemna | p****s@g****m | 19 |
| Gianluca Baio | g****a@s****t | 7 |
| Andrea Berardi | a****i@p****m | 5 |
| Dr Nathan Green | n****n@y****k | 5 |
| Andrew Johnson | a****n@p****u | 3 |
| Ben Goodrich | g****n@g****m | 1 |
| andbe | a****e@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 36
- Total pull requests: 25
- Average time to close issues: 3 months
- Average time to close pull requests: about 18 hours
- Total issue authors: 23
- Total pull request authors: 6
- Average comments per issue: 3.69
- Average comments per pull request: 1.04
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: about 1 hour
- Average time to close pull requests: 1 minute
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 4.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lemna (7)
- Geoff-Holmes (4)
- andbe (3)
- rianmiller (2)
- n8thangreen (2)
- David-Andrew-Jones (1)
- IlariaPiergentili (1)
- NatalieSoto (1)
- fair21comic (1)
- Programming-Skills (1)
- canuckafar (1)
- OBaerenbold-Lumanity (1)
- albertocarm (1)
- fthielen (1)
- giabaio (1)
Pull Request Authors
- lemna (10)
- n8thangreen (5)
- andrjohns (5)
- andbe (3)
- giabaio (2)
- bgoodri (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 657 last-month
- Total dependent packages: 0
- Total dependent repositories: 3
- Total versions: 13
- Total maintainers: 1
cran.r-project.org: survHE
Survival Analysis in Health Economic Evaluation
- Homepage: https://github.com/giabaio/survHE
- Documentation: http://cran.r-project.org/web/packages/survHE/survHE.pdf
- License: GPL (≥ 3)
-
Latest release: 2.0.5
published 12 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- Rcpp >= 0.12.19 depends
- dplyr * depends
- flexsurv * depends
- ggplot2 * depends
- methods * depends
- rms * imports
- rstan >= 2.18.1 imports
- tibble * imports
- tools * imports
- xlsx * imports
- INLA * suggests
- shinystan * suggests