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spsurv

An R package for semiparametric survival analysis.

https://github.com/rvpanaro/spsurv

Science Score: 26.0%

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    Low similarity (18.7%) to scientific vocabulary

Keywords

bernstein-polynomial cran-r r-package rstan rstats-package survival-analysis survival-regression
Last synced: 9 months ago · JSON representation

Repository

An R package for semiparametric survival analysis.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Topics
bernstein-polynomial cran-r r-package rstan rstats-package survival-analysis survival-regression
Created about 7 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License

README.md

spsurv

CRAN status CRAN RStudio mirror downloads R build status Travis build status Codecov test coverage

Overview

spsurv: An R package for semi-parametric survival analysis. The **spsurv** package was designed to contribute with a flexible set of semi-parametric survival regression options, including proportional hazards (PH), proportional odds (PO), and accelerated failure time (AFT) models for right-censored data. The proposed package provides: - Survival classes (PH, PO, AFT) extensions based on a fully likelihood-based approach for either Bayesian or maximum likelihood (ML) estimation procedures, - smooth estimates for the unknown baseline functions based on the Bernstein polynomial (BP), - integration with Stan software aiming more flexibility in terms of user-defined modeling, - six distinct prior specification options in a Bayesian analysis. [Stan](https://mc-stan.org) is an open-source platform that has a specific language and many built-in log-probability functions that can be used to define custom likelihood functions and prior specifications. The program has extensive supporting literature available online such as reference manuals, forums, articles, and books for users and developers. The Stan currently defaults to No-U-Turn (NUTS) sampling, which consists of a Hamiltonian Monte Carlo (HMC) extension that explores the posterior distribution more efficiently, access to Stan can be established through several modules integration such as [rstan](https://mc-stan.org/users/interfaces/rstan).

Installation

  • Install the CRAN version: r install.packages("spsurv")

  • Installation using the devtools package:

r install.packages("devtools") devtools::install_github("rvpanaro/spsurv")

Usage

  • Fit a BP based survival regression PH model using:

```r library("KMsurv") data("larynx")

library(spsurv)

fit <- bpph(Surv(time, delta) ~ age + factor(stage), model = "ph", data = larynx) summary(fit)
```

  • Alternatively, one can use the spbp function:

r fit <- spbp(Surv(time, delta) ~ age + factor(stage), model = "ph", data = larynx) summary(fit) - Access to Bayesian analysis using approach argument:

```

NUTS sampling (Bayesian)

fit2 <- spbp(Surv(time, delta) ~ age + factor(stage), approach = "bayes", data = larynx, iter = 2000, chains = 1, warmup = 1000) summary(fit2) ```

See the reference manual for more examples.

Upcoming features (To do)

  • [ ] survivor class.
  • [ ] survivor ggplot method.
  • [ ] Deviance, martingale and standard residuals.
  • [ ] Frailty models coding coverage.

Troubleshooting

Please report issues at https://github.com/rvpanaro/spsurv/issues or mail it to renatovp@ime.usp.br, we will answer as soon as possible.

Owner

  • Name: Renato Valladares Panaro
  • Login: rvpanaro
  • Kind: user
  • Location: Germany
  • Company: University Medical Center Göttingen

Doctoral research assistant in medical statistics

GitHub Events

Total
  • Issue comment event: 1
  • Push event: 1
  • Fork event: 1
Last Year
  • Issue comment event: 1
  • Push event: 1
  • Fork event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 78
  • Total Committers: 4
  • Avg Commits per committer: 19.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
renatovp r****p@i****r 72
Renato r****p@i****r 3
RVP07 3****o@u****m 2
rn00bs c****s@g****m 1
Committer Domains (Top 20 + Academic)
ime.usp.br: 1 id.uff.br: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • rvpanaro (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 192 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: spsurv

Bernstein Polynomial Based Semiparametric Survival Analysis

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 192 Last month
Rankings
Stargazers count: 28.5%
Forks count: 28.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 41.3%
Downloads: 84.1%
Maintainers (1)
renatovp@ime.usp.br
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • MASS >= 7.3 depends
  • R >= 3.5.0 depends
  • coda >= 0.19 depends
  • loo >= 2.1.0 depends
  • survival >= 2.44 depends
  • Rcpp >= 0.12.0 imports
  • methods * imports
  • rstan >= 2.18.1 imports
  • rstantools >= 1.5.1 imports
  • KMsurv * suggests
  • covr * suggests
  • devtools * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat >= 2.1.0 suggests