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pammtools

Piece-wise exponential Additive Mixed Modeling tools

https://github.com/adibender/pammtools

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

additive-models pamm pammtools piece-wise-exponential r rstats survival-analysis

Keywords from Contributors

geo tidy-data
Last synced: 6 months ago · JSON representation

Repository

Piece-wise exponential Additive Mixed Modeling tools

Basic Info
Statistics
  • Stars: 49
  • Watchers: 4
  • Forks: 11
  • Open Issues: 20
  • Releases: 20
Topics
additive-models pamm pammtools piece-wise-exponential r rstats survival-analysis
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

```{r options, echo = FALSE}
library(knitr)
opts_chunk$set(warning = FALSE)
```



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[![MIT license](https://img.shields.io/badge/license-MIT-brightgreen.svg)]( https://opensource.org/license/mit)


# **`pammtools`**: Piece-Wise Exponential Additive Mixed Modeling Tools


### Installation

Install from CRAN or GitHub using:

```{r eval = FALSE}
# CRAN
install.packages("pammtools")
# Development version
remotes::install_github("adibender/pammtools")
```

### Overview
**`pammtools`** facilitates the estimation of Piece-wise exponential Additive Mixed Models (PAMMs) for time-to-event data. PAMMs can be represented as generalized additive models and can therefore be estimated using GAM software (e.g. **`mgcv`**), which, compared to other packages for survival analysis, often offers more flexibility w.r.t. to the specification of covariate effects (e.g. non-linear, time-varying effects, cumulative effects, etc.). The package supports single-event analysis, left-truncation, recurrent events, competing risks and multi-state models.

To get started, see the [Articles](https://adibender.github.io/pammtools/articles/) section.

Owner

  • Name: Andreas Bender
  • Login: adibender
  • Kind: user
  • Company: LMU

GitHub Events

Total
  • Issues event: 7
  • Watch event: 3
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 7
  • Push event: 51
  • Pull request event: 14
  • Fork event: 1
  • Create event: 7
Last Year
  • Issues event: 7
  • Watch event: 3
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 7
  • Push event: 51
  • Pull request event: 14
  • Fork event: 1
  • Create event: 7

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 997
  • Total Committers: 9
  • Avg Commits per committer: 110.778
  • Development Distribution Score (DDS): 0.198
Past Year
  • Commits: 88
  • Committers: 2
  • Avg Commits per committer: 44.0
  • Development Distribution Score (DDS): 0.307
Top Committers
Name Email Commits
adibender b****R@g****m 800
Piller J****r@l****e 91
fabian-s f****l@g****m 41
Philipp Kopper p****r@a****e 32
Lukas Burk l****s@q****e 18
Hadley Wickham h****m@g****m 8
Gavin Simpson u****s@g****m 3
fabian-s f****l@g****m 3
Staffan Betnér s****n@b****u 1
Committer Domains (Top 20 + Academic)
betner.nu: 1 quantenbrot.de: 1 am-ammersee.de: 1 lmu.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 59
  • Total pull requests: 75
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 18
  • Total pull request authors: 9
  • Average comments per issue: 1.56
  • Average comments per pull request: 0.61
  • Merged pull requests: 62
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 13
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 14 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.69
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adibender (34)
  • fabian-s (6)
  • jonas-schropp (3)
  • iMSQ (2)
  • romainfrancois (1)
  • eds-slim (1)
  • pkopper (1)
  • sckott (1)
  • AngelaCar (1)
  • meriops (1)
  • ningyile (1)
  • lona-k (1)
  • StaffanBetner (1)
  • gavinsimpson (1)
  • RenzoTale88 (1)
Pull Request Authors
  • adibender (60)
  • johannespiller (5)
  • xu-lisa (3)
  • jemus42 (2)
  • jc-espinosa (2)
  • gavinsimpson (2)
  • fabian-s (2)
  • lzumeta (1)
  • StaffanBetner (1)
Top Labels
Issue Labels
bug (15) priority: low (11) enhancement (8) feature (7) documentation (6) discussion (5) CRAN (5) priority: high (4) priority:urgent (4) addition (3) data transformation (2) deprecation (1) tidyverse (1)
Pull Request Labels
enhancement (11) addition (5) feature (4) priority: high (2) bug (1) data transformation (1) documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 3,905 last-month
  • Total docker downloads: 42,106
  • Total dependent packages: 6
  • Total dependent repositories: 11
  • Total versions: 17
  • Total maintainers: 1
cran.r-project.org: pammtools

Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

  • Versions: 17
  • Dependent Packages: 6
  • Dependent Repositories: 11
  • Downloads: 3,905 Last month
  • Docker Downloads: 42,106
Rankings
Docker downloads count: 0.6%
Forks count: 6.3%
Average: 6.6%
Dependent packages count: 7.3%
Stargazers count: 7.5%
Dependent repos count: 8.8%
Downloads: 9.3%
Maintainers (1)
andreas.bender@stat.uni-muenchen.de
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • Formula * imports
  • checkmate * imports
  • dplyr >= 1.0.0 imports
  • ggplot2 >= 3.2.2 imports
  • lazyeval * imports
  • magrittr * imports
  • mgcv * imports
  • mvtnorm * imports
  • pec * imports
  • purrr >= 0.2.3 imports
  • rlang * imports
  • survival >= 2.39 imports
  • tibble * imports
  • tidyr >= 1.0.0 imports
  • vctrs >= 0.3.0 imports
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite