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dabestr

Data Analysis with Bootstrap Estimation in R

https://github.com/acclab/dabestr

Science Score: 46.0%

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
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: nature.com, zenodo.org
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.5%) to scientific vocabulary

Keywords

data-analysis data-visualization estimation r statistics
Last synced: 6 months ago · JSON representation

Repository

Data Analysis with Bootstrap Estimation in R

Basic Info
Statistics
  • Stars: 217
  • Watchers: 8
  • Forks: 38
  • Open Issues: 41
  • Releases: 9
Topics
data-analysis data-visualization estimation r statistics
Created over 7 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.Rmd 

---
output: github_document
---



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

# dabestr 


[![minimal R version](https://img.shields.io/badge/R%3E%3D-2.10-6666ff.svg)](https://cran.r-project.org/) [![CRAN Download Count](https://cranlogs.r-pkg.org/badges/grand-total/dabestr?color=brightgreen)](https://cran.r-project.org/package=dabestr) [![Free-to-view citation](https://zenodo.org/badge/DOI/10.1038/s41592-019-0470-3.svg)](https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlRew%3D%3D) [![License](https://img.shields.io/badge/License-Apache_2.0-orange.svg)](https://spdx.org/licenses/BSD-3-Clause-Clear.html)
[![R-CMD-check](https://github.com/sunroofgod/dabestr-prototype/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sunroofgod/dabestr-prototype/actions/workflows/R-CMD-check.yaml)



dabestr is a package for **D**ata **A**nalysis using **B**ootstrap-Coupled **EST**imation.

[Estimation statistics](https://en.wikipedia.org/wiki/Estimation_statistics "Estimation Stats on Wikipedia") is a [simple framework](https://thenewstatistics.com/itns/ "Introduction to the New Statistics") that avoids the [pitfalls](https://www.nature.com/articles/nmeth.3288 "The fickle P value generates irreproducible results, Halsey et al 2015") of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by *P* values.

An estimation plot has two key features.

1.  It **presents all datapoints** as a swarmplot, which orders each point to display the underlying distribution.

2.  It presents the **effect size** as a **bootstrap 95% confidence interval** on a **separate but aligned axes**.

The `dabestr` package powers [estimationstats.com](http://estimationstats.com), allowing everyone access to high-quality estimation plots.

## Installation

```{r, eval = FALSE}
# Install it from CRAN
install.packages("dabestr")

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github(repo = "ACCLAB/dabestr", ref = "dev")
```

## Usage

```{r, warning = FALSE, message = FALSE, eval = FALSE}
library(dabestr)
```

```{r, include = FALSE}
devtools::load_all(".")
```

```{r, dpi = 500, warning = FALSE}
data("non_proportional_data")

dabest_obj.mean_diff <- load(
  data = non_proportional_data,
  x = Group,
  y = Measurement,
  idx = c("Control 1", "Test 1")
) %>%
  mean_diff()

dabest_plot(dabest_obj.mean_diff, TRUE)
```

Please refer to the official [tutorial](https://acclab.github.io/dabestr/articles/tutorial_basics.html) for more useful code snippets.

## Citation 

**Moving beyond P values: Everyday data analysis with estimation plots**

*Joses Ho, Tayfun Tumkaya, Sameer Aryal, Hyungwon Choi, Adam Claridge-Chang*

Nature Methods 2019, 1548-7105. [10.1038/s41592-019-0470-3](http://dx.doi.org/10.1038/s41592-019-0470-3)

[Paywalled publisher site](https://www.nature.com/articles/s41592-019-0470-3); [Free-to-view PDF](https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlRew%3D%3D)

## Contributing

Please report any bugs on the [Github issue tracker](https://github.com/ACCLAB/dabestr/issues/new).

All contributions are welcome; please read the [Guidelines for contributing](https://github.com/ACCLAB/dabestr/blob/master/CONTRIBUTING.md) first.

We also have a [Code of Conduct](https://github.com/ACCLAB/dabestr/blob/master/CODE_OF_CONDUCT.md) to foster an inclusive and productive space.

## Acknowledgements

We would like to thank alpha testers from the [Claridge-Chang lab](https://www.claridgechang.net/): [Sangyu Xu](https://github.com/sangyu), [Xianyuan Zhang](https://github.com/XYZfar), [Farhan Mohammad](https://github.com/farhan8igib), Jurga Mituzaitė, and Stanislav Ott.

## DABEST in other languages

DABEST is also available in Python ([DABEST-python](https://github.com/ACCLAB/DABEST-python "DABEST-Python on Github")) and Matlab
([DABEST-Matlab](https://github.com/ACCLAB/DABEST-Matlab "DABEST-Matlab on Github")).

Owner

  • Name: ACCLAB
  • Login: ACCLAB
  • Kind: organization
  • Location: Singapore

GitHub Events

Total
  • Issues event: 1
  • Watch event: 6
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 51
  • Pull request review event: 1
  • Pull request event: 15
  • Fork event: 3
  • Create event: 7
Last Year
  • Issues event: 1
  • Watch event: 6
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 51
  • Pull request review event: 1
  • Pull request event: 15
  • Fork event: 3
  • Create event: 7

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 399
  • Total Committers: 5
  • Avg Commits per committer: 79.8
  • Development Distribution Score (DDS): 0.218
Past Year
  • Commits: 78
  • Committers: 2
  • Avg Commits per committer: 39.0
  • Development Distribution Score (DDS): 0.179
Top Committers
Name Email Commits
Joses W. Ho j****h@g****m 312
sunroofgod e****8@u****u 64
Liao Jun Yang 1****o 14
Felicia e****4@u****u 8
Adam Claridge-Chang a****c@g****m 1
Committer Domains (Top 20 + Academic)
u.nus.edu: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 90
  • Total pull requests: 63
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 69
  • Total pull request authors: 9
  • Average comments per issue: 2.62
  • Average comments per pull request: 0.25
  • Merged pull requests: 48
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 16
  • Average time to close issues: N/A
  • Average time to close pull requests: 16 days
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lijiawei88 (4)
  • mfarrant (3)
  • Generalized (3)
  • Dallak (3)
  • josesho (3)
  • marioniepel (2)
  • brembs (2)
  • NikitaKhromov-Borisov (2)
  • heathium (2)
  • araikes (2)
  • TMax66 (2)
  • benjaminwnelson (2)
  • coopert25 (2)
  • timothysandhu (2)
  • yngmiin (1)
Pull Request Authors
  • sunroofgod (28)
  • josesho (17)
  • cyberosa (11)
  • FellowFish (8)
  • marsiwiec (3)
  • Lucas1213WZY (2)
  • JonatanFernandez (2)
  • maiyishan (1)
  • teunbrand (1)
Top Labels
Issue Labels
help wanted (14) enhancement (13) aesthetics (10) bug (9) question (9) documentation (2) wontfix (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 425 last-month
  • Total docker downloads: 76
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 28
  • Total maintainers: 1
proxy.golang.org: github.com/ACCLAB/dabestr
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/acclab/dabestr
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
cran.r-project.org: dabestr

Data Analysis using Bootstrap-Coupled Estimation

  • Versions: 10
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 425 Last month
  • Docker Downloads: 76
Rankings
Stargazers count: 2.0%
Forks count: 2.2%
Average: 11.8%
Docker downloads count: 17.3%
Dependent packages count: 18.1%
Dependent repos count: 19.1%
Maintainers (1)
maiyishan@u.duke.nus.edu
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 2.10 depends
  • boot * imports
  • brunnermunzel * imports
  • cli * imports
  • cowplot * imports
  • dplyr * imports
  • effsize * imports
  • ggbeeswarm * imports
  • ggplot2 * imports
  • ggsci * imports
  • grid * imports
  • magrittr * imports
  • methods * imports
  • rlang * imports
  • scales * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • kableExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
  • vdiffr * suggests