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README.Rmd
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README.Rmd
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---
output:
github_document:
html_preview: false
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(
collapse=TRUE,
comment="#>",
fig.path="man/figures/README-",
fig.height = 7,
out.width="100%"
)
library(crosstable)
crosstable_options(
crosstable_fontsize_body = 8,
crosstable_padding_v = 0
)
# options(Encoding="UTF-8")
# library(officer)
# library(flextable)
```
# crosstable <a href='https://DanChaltiel.github.io/crosstable/'><img src='man/figures/logo.png' align="right" height="175" /></a>
<!-- badges: start -->
[](http://www.gnu.org/licenses/gpl-3.0.html)
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://CRAN.R-project.org/package=crosstable)
[](https://r-pkg.org/pkg/crosstable)
[](https://github.com/DanChaltiel/crosstable)
[](https://app.codecov.io/gh/DanChaltiel/crosstable?branch=main)
[](https://github.com/DanChaltiel/crosstable/actions/workflows/check-standard.yaml)
[](https://cran.r-project.org/)
<!-- [](https://cran.r-project.org/package=crosstable) -->
<!-- [](https://travis-ci.org/DanChaltiel/crosstable) -->
<!-- badges: end -->
Crosstable is a package centered on a single function, `crosstable`, which easily computes descriptive statistics on datasets. It can use the `tidyverse` syntax and is interfaced with the package `officer` to create automatized reports.
## Installation
```{r run-numeric-md, include=FALSE}
last_cran = pkgsearch::cran_package("crosstable")$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")
```
<p align="center">
<img src="man/figures/ct1_mod.png" alt="crosstable1">
</p>
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")
```
<p style="text-align: center;">
<img src="man/figures/ct2_mod.png" alt="crosstable2">
</p>
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!