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blindrecalc

Compute characteristics and plots for blinded sample size recalculation

https://github.com/imbi-heidelberg/blindrecalc

Science Score: 36.0%

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

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    CITATION.cff file
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    DOI references
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    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
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    Low similarity (15.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Compute characteristics and plots for blinded sample size recalculation

Basic Info
  • Host: GitHub
  • Owner: imbi-heidelberg
  • License: other
  • Language: R
  • Default Branch: master
  • Size: 406 KB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 2
  • Open Issues: 1
  • Releases: 6
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
editor_options: 
  chunk_output_type: console
---



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


[![R-CMD-check](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/imbi-heidelberg/blindrecalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/imbi-heidelberg/blindrecalc?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/blindrecalc)](https://cran.r-project.org/package=blindrecalc)


# blindrecalc


blindrecalc facilitates the planning of a clinical trial with an internal pilot study and blinded sample size recalculation.

## Installation

Install the current CRAN version of blindrecalc with:

``` r
install.packages("blindrecalc")
```

Or install the development version from GitHub with:

``` r
# install.packages("devtools")
devtools::install_github("imbi-heidelberg/blindrecalc")
```
## Usage

blindrecalc currently supports continuous and binary endpoints for superiority and non-inferiority test problems. Continuous endpoints are analyzed using Student's t-test, binary endpoints are analyzed using the Chi-squared test for superiority trials and the Farrington-Manning test for non-inferiority trials. Each design can be defined using a setup-function: `setupStudent`, `setupChiSquare` and `setupFarringtonManning`. For example, to setup a superiority trial with a continuous endpoint:

```{r}
library(blindrecalc)
design <- setupStudent(alpha = 0.025, beta = 0.2, r = 1, delta = 5)
```

`alpha` and `beta` refer to the type 1 and type 2 error rate, `r` is the sample size allocation ratio and `delta`is the effect size between the null and the alternative hypothesis. For a non-inferiority trial with a shifted t-test, additionally the argument `delta_NI` must be specified. 

To calculate the sample size for a fixed design, use `n_fix`:

```{r}
n_fix(design, nuisance = c(5, 10, 15))
```

`nuisance` refers to the nuisance parameter of the design, which in the case of the t-test is the common variance of the outcome variable.

To calculate the type 1 error rate of the design using blinded sample size recalculation, use `toer`:

```{r}
toer(design, n1 = c(30, 60, 90), nuisance = 10, recalculation = TRUE)
```

`n1` refers to the sample size of the internal pilot study `recalculation = TRUE` specifices that the type 1 error rate for a design with blinded sample size recalculation should be computed.

To compute the power of the design, use `pow`:

```{r}
pow(design, n1 = c(30, 60, 90), nuisance = 10, recalculation = TRUE)
```

To calculate the distribution of the total sample sizes use `n_dist`:

```{r}
n_dist(design, n1 = c(30, 60, 90), nuisance = 10)
```


## Reference

A paper describing blindrecalc can be found [here](https://journal.r-project.org/articles/RJ-2022-001/).

Owner

  • Name: Institute of Medical Biometry
  • Login: imbi-heidelberg
  • Kind: organization
  • Location: Heidelberg University, Germany

GitHub Events

Total
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 7
  • Pull request review event: 2
  • Pull request event: 2
Last Year
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 7
  • Pull request review event: 2
  • Pull request event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 148
  • Total Committers: 6
  • Avg Commits per committer: 24.667
  • Development Distribution Score (DDS): 0.622
Past Year
  • Commits: 26
  • Committers: 2
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.269
Top Committers
Name Email Commits
Maximilian Pilz 3****x 56
lbau7 l****n@a****t 35
MatheMax p****z@i****e 27
Maximilian Pilz m****z@i****e 21
MatheMax m****z@p****e 8
Baumann u****0@i****i 1
Committer Domains (Top 20 + Academic)
posteo.de: 1 itwm.fraunhofer.de: 1 imbi.uni-heidelberg.de: 1 aon.at: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 7
  • Total pull requests: 37
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 3 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 1.14
  • Average comments per pull request: 0.03
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MatheMax (6)
  • max-pilz (1)
Pull Request Authors
  • lbau7 (15)
  • MatheMax (15)
  • max-pilz (9)
Top Labels
Issue Labels
Pull Request Labels
documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 302 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: blindrecalc

Blinded Sample Size Recalculation

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 302 Last month
Rankings
Forks count: 17.8%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 30.4%
Dependent repos count: 35.5%
Downloads: 46.4%
Maintainers (1)
baumann@imbi.uni-heidelberg.de
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • Rcpp * imports
  • methods * imports
  • covr * suggests
  • testthat * suggests
.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
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite