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bonsaiforest

https://github.com/insightsengineering/bonsaiforest

Science Score: 36.0%

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
    Links to: arxiv.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.9%) to scientific vocabulary

Keywords

statistical-engineering

Keywords from Contributors

rna-seq general-purpose nest shiny
Last synced: 9 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 1
  • Open Issues: 4
  • Releases: 2
Topics
statistical-engineering
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Codeowners

README.Rmd 

---
output: github_document
---




```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# bonsaiforest bonsaiforest website


[![Project Status: Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![CRAN status](https://www.r-pkg.org/badges/version-last-release/bonsaiforest)](https://www.r-pkg.org/badges/version-last-release/bonsaiforest)
[![CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/bonsaiforest)](https://cranlogs.r-pkg.org/badges/bonsaiforest)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/bonsaiforest)](https://cranlogs.r-pkg.org/badges/grand-total/bonsaiforest)
[![Code Coverage](https://raw.githubusercontent.com/openpharma/bonsaiforest/_xml_coverage_reports/data/main/badge.svg)](https://openpharma.github.io/bonsaiforest/latest-tag/coverage-report/)



Subgroup analyses are routinely performed in clinical trial analyses. This package implements
shrinkage methods to estimate treatment effects in overlapping subgroups with a binary or
time-to-event endpoint as described in [Wolbers et al (2024)](https://arxiv.org/pdf/2407.11729).
Both Bayesian estimation with a regularized horseshoe prior as well as penalized frequentist
methods using the lasso or ridge penalties are implemented. The Bayesian approach provides
both point estimates and credible intervals whereas only point estimates are available for the
penalized frequentist methods. The estimators are intended to completement standard
subgroup-specific estimators which are routinely displayed in forest plots. They typically have
substantially smaller overall mean squared error compared to the standard estimator.

## Installation

Please note that on Windows, you will need to install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/),
because you will need to have a working `C++` toolchain to compile the Stan models.

### Release

You can install the current release version of `bonsaiforest` from CRAN with:

```{r cran-installation, eval = FALSE, echo = TRUE}
install.packages("bonsaiforest")
```

### Development

You can install the development version of `bonsaiforest` from [GitHub](https://github.com/) with:

```{r gh-installation, eval = FALSE, echo = TRUE}
# install.packages("remotes")
remotes::install_github("insightsengineering/bonsaiforest")
```

## Getting started

See the [introductory vignette](https://insightsengineering.github.io/bonsaiforest/main/articles/introduction.html) or get started by trying out the example:

```{r bonsaiforest-horseshoe}
library(bonsaiforest)
str(example_data)

horseshoe_model <- horseshoe(
  resp = "tt_pfs", trt = "arm",
  subgr = c("x_1", "x_2", "x_3", "x_4"),
  covars = c(
    "x_1", "x_2", "x_3", "x_4", "x_5",
    "x_6", "x_7", "x_8", "x_9", "x_10"
  ),
  data = example_data, resptype = "survival",
  status = "ev_pfs", chains = 2, seed = 0,
  control = list(adapt_delta = 0.95)
)

summary_horseshoe <- summary(horseshoe_model, conf = 0.9)
summary_horseshoe

plot(summary_horseshoe)
```

Owner

  • Name: Roche/Genentech - Insights Engineering
  • Login: insightsengineering
  • Kind: organization
  • Location: Switzerland

Roche/Genentech - Insights Engineering

GitHub Events

Total
  • Issues event: 4
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 15
  • Pull request review event: 2
  • Pull request event: 4
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 4
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 15
  • Pull request review event: 2
  • Pull request event: 4
  • Fork event: 1
  • Create event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 85
  • Total Committers: 6
  • Avg Commits per committer: 14.167
  • Development Distribution Score (DDS): 0.306
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mar-vazquez M****z 59
Daniel Sabanes Bove d****e 13
gravesti g****i 6
cicdguy c****y 4
walkowif 5****f 2
Insights Engineering Bot 6****t 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 41
  • Total pull requests: 47
  • Average time to close issues: 3 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 6
  • Total pull request authors: 6
  • Average comments per issue: 0.17
  • Average comments per pull request: 2.83
  • Merged pull requests: 42
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 6
  • Average time to close issues: 13 days
  • Average time to close pull requests: about 22 hours
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 2.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Mar-vazquez (29)
  • danielinteractive (6)
  • wolbersm (4)
  • gravesti (1)
  • paul-buerkner (1)
  • brockk (1)
Pull Request Authors
  • Mar-vazquez (31)
  • gravesti (9)
  • danielinteractive (8)
  • walkowif (2)
  • llrs-roche (1)
  • cicdguy (1)
Top Labels
Issue Labels
enhancement (3) bug (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 240 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: bonsaiforest

Shrinkage Based Forest Plots

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 240 Last month
Rankings
Dependent packages count: 28.7%
Dependent repos count: 35.4%
Average: 50.1%
Downloads: 86.2%
Maintainers (1)
isaac.gravestock@roche.com
Last synced: 10 months ago

Dependencies

.github/workflows/check.yaml actions
.github/workflows/cla.yaml actions
.github/workflows/docs.yaml actions
.github/workflows/release.yaml actions
DESCRIPTION cran
  • R >= 4.1 depends
  • Rcpp * imports
  • brms * imports
  • broom * imports
  • checkmate * imports
  • dplyr * imports
  • forcats * imports
  • gbm * imports
  • ggplot2 * imports
  • glmnet * imports
  • splines2 * imports
  • stats * imports
  • survival * imports
  • tibble * imports
  • tidyr * imports
  • tidyselect * imports
  • vdiffr * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/rhub.yaml actions
  • r-hub/actions/checkout v1 composite
  • r-hub/actions/platform-info v1 composite
  • r-hub/actions/run-check v1 composite
  • r-hub/actions/setup v1 composite
  • r-hub/actions/setup-deps v1 composite
  • r-hub/actions/setup-r v1 composite