crosstable

Easy and thorough description of datasets

https://github.com/danchaltiel/crosstable

Science Score: 26.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Low similarity (19.1%) to scientific vocabulary

Keywords

descriptive-statistics flextable frequency-table html-report msword officer r rstats

Keywords from Contributors

interpretability ropensci standardization literate-programming pandoc hack

Last synced: 6 months ago · JSON representation

Repository

Easy and thorough description of datasets

Basic Info

Host: GitHub
Owner: DanChaltiel
Language: R
Default Branch: main
Homepage: https://danchaltiel.github.io/crosstable/
Size: 41.8 MB

Statistics

Stars: 116
Watchers: 3
Forks: 8
Open Issues: 12
Releases: 17

Topics

descriptive-statistics flextable frequency-table html-report msword officer r rstats

Created almost 6 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Codemeta

README.Rmd

---
output: 
  github_document:
    html_preview: false
---



```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(
  collapse=TRUE,
  comment="#>",
  fig.path="man/figures/README-",
  fig.height = 7,
  out.width="100%"
)
library(crosstable)
crosstable_options(
  crosstable_fontsize_body = 8,
  crosstable_padding_v = 0
)
# options(Encoding="UTF-8")
# library(officer)
# library(flextable)
```


# crosstable 


[![Package-License](http://img.shields.io/badge/license-GPL--3-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html) 
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![CRAN status](https://www.r-pkg.org/badges/version/crosstable)](https://CRAN.R-project.org/package=crosstable)
[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/crosstable?color=blue)](https://r-pkg.org/pkg/crosstable)
[![Last Commit](https://img.shields.io/github/last-commit/DanChaltiel/crosstable)](https://github.com/DanChaltiel/crosstable)
[![Codecov test coverage](https://codecov.io/gh/DanChaltiel/crosstable/branch/main/graph/badge.svg)](https://app.codecov.io/gh/DanChaltiel/crosstable?branch=main)
[![R-CMD-check](https://github.com/DanChaltiel/crosstable/actions/workflows/check-standard.yaml/badge.svg?branch=main)](https://github.com/DanChaltiel/crosstable/actions/workflows/check-standard.yaml)
[![minimal R version](https://img.shields.io/badge/R-%E2%89%A53.1-blue.svg)](https://cran.r-project.org/)






Crosstable is a package centered on a single function, `crosstable`, which easily computes descriptive statistics on datasets. It can use the `tidyverse` syntax and is interfaced with the package `officer` to create automatized reports.

## Installation

```{r run-numeric-md, include=FALSE}
last_cran = pkgsearch::cran_package("crosstable")$Version
# last_tag = dplyr::last(names(git2r::tags()))
last_tag = purrr::map_dbl(git2r::tags(), ~{
  if(is.null(.x$tagger)) return(NA)
  as.POSIXct(.x$tagger$when)
}) %>% sort() %>% names() %>% dplyr::last()
git_head = git2r::revparse_single(git2r::repository(),"HEAD") #sapply(git_head, print)
last_commit = substr(git_head$sha, 1,7)
out = c(
  "```{r install, eval=FALSE}",
  '# Install last version available on CRAN',
  'install.packages("crosstable")',
  '', 
  '# Install development version on Github',
  'devtools::install_github("DanChaltiel/crosstable", build_vignettes=TRUE)',
  '', 
  '# Install specific commit or tagged version (for reproducibility purpose)',
  knit_expand(text='devtools::install_github("DanChaltiel/crosstable@{{last_commit}}", build_vignettes=TRUE)'),
  knit_expand(text='devtools::install_github("DanChaltiel/crosstable@{{last_tag}}", build_vignettes=TRUE)'),
"```"
)
```
`r paste(knit(text = out), collapse = '\n')`

Note that, for reproducibility purpose, an even better solution would be to use [`renv`](https://rstudio.github.io/renv/articles/renv.html).

## Overview

Here are 2 examples to try and show you the main features of `crosstable`. See the [documentation website](https://danchaltiel.github.io/crosstable/) for more.

#### Example #1

> Dear crosstable, using the `mtcars2` dataset, please describe columns `disp` and `vs` depending on the levels of column `am`, with totals in both rows and columns, and with proportions formatted with group size, percent on row and percent on column, with no decimals.

```{r usage1, eval=TRUE, echo=TRUE, results="hide", warning=FALSE, message=FALSE}
library(crosstable)
ct1 = crosstable(mtcars2, c(disp, vs), by=am, total="both", 
                 percent_pattern="{n} ({p_row}/{p_col})", percent_digits=0) %>%
  as_flextable()
ct1
```

```{r, include=FALSE}
flextable::save_as_image(ct1, "man/figures/ct1.png")
```


  


With only a few arguments, we did select which column to describe (`c(disp, vs)`), define a grouping variable (`by=am`), set the percentage calculation in row/column (`percent_pattern=`), and ask for totals (`total=`). 

Since `mtcars2` is a dataset with labels, they are displayed instead of the variable name (see [here](https://danchaltiel.github.io/crosstable/articles/crosstable.html#dataset-modified-mtcars) for how to add some). 

As `crosstable()` is returning a `data.frame`, we use `as_flextable()` to output a beautiful HTML table. This one can even be exported to MS Word with a few more lines of code (see [here](https://danchaltiel.github.io/crosstable/articles/crosstable-report.html) to learn how).

#### Example #2

Here is a more advanced example. 

> Dear crosstable, using the `mtcars2` dataset again, please describe all columns whose name starts with "cy" and those whose name ends with "at", depending on the levels of both columns `am` and `vs`, without considering labels, applying `mean()` and `quantile()` as summary function, with `probs` 25% and 75% defined for this latter function, and with 3 decimals for numeric variables:

```{r usage2, eval=TRUE, echo=TRUE, results="hide", warning=FALSE, message=FALSE}
ct2 = crosstable(mtcars2, c(starts_with("cy"), ends_with("at")), by=c(am, vs), 
                 label=FALSE, num_digits=3, funs=c(mean, quantile), 
                 funs_arg=list(probs=c(.25,.75))) %>% 
  as_flextable(compact=TRUE, header_show_n=1:2)
ct2
```

```{r, include=FALSE}
flextable::save_as_image(ct2, "man/figures/ct2.png")
file.remove("man/figures/README-usage1-1.png")
file.remove("man/figures/README-usage2-1.png")
```


  



Here, the variables were selected using `tidyselect` helpers and the summary functions `mean` and `quantile` were specified, along with argument `probs` for the latter. Using `label=FALSE` allowed to see which variables were selected but it is best to keep the labels in the final table. 

In `as_flextable()`, the `compact=TRUE` option yields a longer output, which may be more suited in some contexts (for instance for publication), and `header_show_n=1:2` adds the group sizes for both rows of the header.

## Documentation

You can find the whole documentation on the [dedicated website](https://danchaltiel.github.io/crosstable/): 

+ `vignette("crosstable")` for a first step-by-step guide on how to use `crosstable` ([link](https://danchaltiel.github.io/crosstable/articles/crosstable.html))
+ `vignette("crosstable-report")` for more on creating MS Word reports using either `{officer}` or `Rmarkdown` ([link](https://danchaltiel.github.io/crosstable/articles/crosstable-report.html))
+ `vignette("pertent_pattern")` for more on how to use `percent_pattern` ([link](https://danchaltiel.github.io/crosstable/articles/crosstable-selection.html))
+ `vignette("crosstable-selection")` for more on variable selection ([link](https://danchaltiel.github.io/crosstable/articles/crosstable-selection.html)), although you should better read https://tidyselect.r-lib.org/articles/syntax.html.


There are lots of other features you can learn about there, for instance (non-exhaustive list):

- description of correlation, dates, and survival data ([link](https://danchaltiel.github.io/crosstable/articles/crosstable.html#miscellaneous-1))
- variable selection with functions, e.g. `is.numeric` ([link](https://danchaltiel.github.io/crosstable/articles/crosstable-selection.html#select-with-predicate-functions))
- formula interface, allowing to describe more mutated columns, e.g. `sqrt(mpg)` or `Surv(time, event)` ([link](https://danchaltiel.github.io/crosstable/articles/crosstable-selection.html#select-with-a-formula))
- automatic computation of statistical tests ([link](https://danchaltiel.github.io/crosstable/articles/crosstable.html#tests)) and of effect sizes ([link](https://danchaltiel.github.io/crosstable/articles/crosstable.html#effects))
- global options to avoid repeating arguments ([link](https://danchaltiel.github.io/crosstable/reference/crosstable_options.html))



## Getting help and giving feedback

If you have a question about how to use `crosstable`, please ask on [StackOverflow](https://stackoverflow.com/) with the tag `crosstable`. You can `@DanChaltiel` in a comment if  you are struggling to get answers. Don't forget to add a minimal **repr**oducible **ex**ample to your question, ideally using the [reprex](https://reprex.tidyverse.org/) package.

If you miss any feature that you think would belong in `crosstable`, please fill a [Feature Request](https://github.com/DanChaltiel/crosstable/issues/new/choose) issue.

If you encounter an unexpected error while using `crosstable`, please fill a [Bug Report](https://github.com/DanChaltiel/crosstable/issues/new/choose) issue. In case of any installation problem, try the solutions proposed in [this article](https://danchaltiel.github.io/crosstable/articles/crosstable-install.html) first.

## Acknowledgement

In its earliest development phase, `crosstable` was based on the awesome package [`biostat2`](https://github.com/eusebe/biostat2) written by David Hajage. Thanks David!

Owner

Name: Dan Chaltiel
Login: DanChaltiel
Kind: user
Location: France
Company: @gustaveroussy

Twitter: DanChaltiel
Repositories: 4
Profile: https://github.com/DanChaltiel

Data analyst (PharmD, PhD) and programming enthusiast. I love to code in R (tidyverse FTW!) but also in Kotlin/Java (Android), Python, PHP, JS, Arduino...

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  "releaseNotes": "https://github.com/DanChaltiel/crosstable/blob/master/NEWS.md",
  "readme": "https://github.com/DanChaltiel/crosstable/blob/main/README.md",
  "contIntegration": [
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  ]
}

GitHub Events

Total

Issues event: 15
Watch event: 6
Issue comment event: 2
Push event: 14
Create event: 6

Last Year

Issues event: 15
Watch event: 6
Issue comment event: 2
Push event: 14
Create event: 6

Committers

Last synced: 9 months ago

All Time

Total Commits: 1,060
Total Committers: 7
Avg Commits per committer: 151.429
Development Distribution Score (DDS): 0.133

Past Year

Commits: 115
Committers: 2
Avg Commits per committer: 57.5
Development Distribution Score (DDS): 0.217

Top Committers

Name	Email	Commits
Dan Chaltiel	d**l@g**m	919
github-actions	4****]	96
David Hajage	d**e@g**m	36
David Hajage	d**d@l**n	4
Hadley Wickham	h**m@g**m	3
Jim Hester	j**r@g**m	1
DavisVaughan	d**s@r**m	1

Committer Domains (Top 20 + Academic)

rstudio.com: 1 localhost.localdomain: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 84
Total pull requests: 8
Average time to close issues: 2 months
Average time to close pull requests: 15 days
Total issue authors: 20
Total pull request authors: 5
Average comments per issue: 1.21
Average comments per pull request: 1.5
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 17
Pull requests: 0
Average time to close issues: 2 months
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 0
Average comments per issue: 0.29
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

DanChaltiel (59)
sda030 (8)
davidgohel (3)
philipmgrant (2)
lionel- (1)
DanChartrand (1)
TonisOrmisson (1)
linem7 (1)
bberger94 (1)
linusgun (1)
kathrynagnas (1)
Lpierott (1)
tokofran (1)
hadley (1)
technocrat (1)

Pull Request Authors

hadley (3)
DanChaltiel (2)
jimhester (1)
DavisVaughan (1)
lionel- (1)

Top Labels

Issue Labels

bug (43) enhancement (28) bug 🐞 (6) enhancement ✨ (6) questionning (2) installation (1) test (1) questionning ❓ (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 5,146 last-month
Total docker downloads: 55

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 13
Total maintainers: 1

cran.r-project.org: crosstable

Crosstables for Descriptive Analyses

Homepage: https://danchaltiel.github.io/crosstable/
Documentation: http://cran.r-project.org/web/packages/crosstable/crosstable.pdf
License: GPL-3
Latest release: 0.8.1
published over 1 year ago

Versions: 13
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 5,146 Last month
Docker Downloads: 55

Rankings

Stargazers count: 3.7%

Forks count: 7.3%

Downloads: 8.4%

Average: 12.3%

Dependent packages count: 18.2%

Dependent repos count: 24.0%

Maintainers (1)

dan.chaltiel@gmail.com

Last synced: about 1 year ago

Dependencies

DESCRIPTION cran

R >= 3.1.0 depends
checkmate * imports
cli * imports
dplyr >= 1.0.0 imports
flextable >= 0.5.8 imports
forcats * imports
glue * imports
lifecycle * imports
officer >= 0.4 imports
purrr * imports
rlang >= 0.4.7 imports
stats * imports
stringr * imports
tibble * imports
tidyr * imports
tidyselect * imports
Hmisc * suggests
callr * suggests
covr * suggests
crayon * suggests
digest * suggests
expss * suggests
ggplot2 * suggests
gmodels * suggests
gt * suggests
jsonlite * suggests
knitr * suggests
openxlsx * suggests
rmarkdown * suggests
sloop * suggests
stringi * suggests
survival * suggests
systemfonts * suggests
testthat >= 3.0.0 suggests
waldo * suggests
withr * suggests
xml2 * suggests

.github/workflows/bump_version_dev.yaml actions

EndBug/add-and-commit v7.5.0 composite
actions/checkout v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/check-standard.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

.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

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite