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https://github.com/DanChaltiel/crosstable

Easy and thorough description of datasets
https://github.com/DanChaltiel/crosstable

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

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Easy and thorough description of datasets

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README 

        
---

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")

```





  crosstable1




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")

```





  crosstable2




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!