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skimr

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A frictionless, pipeable approach to dealing with summary statistics

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- devcontainer.json
- - R-CMD-check.yaml
  - rhub.yaml
  - test-coverage.yaml
- .gitignore
- CONTRIBUTING.md
- dependabot.yml
- - skimmer_hex.png
- - blog.html
  - blog.md
  - blog.Rmd
  - blog_v2.html
  - blog_v2.md
  - blog_v2.Rmd
  - skimr_in_jupyter.ipynb
- - logo.png
- deprecated-v1.Rd
- fix_windows_histograms.Rd
- focus.Rd
- get_default_skimmers.Rd
- get_skimmers.Rd
- knit_print.Rd
- mutate.skim_df.Rd
- partition.Rd
- print.Rd
- repr.Rd
- sfl.Rd
- skim-attr.Rd
- skim-obj.Rd
- skim.Rd
- skim_with.Rd
- skimr-package.Rd
- skimr-vctrs.Rd
- stats.Rd
- summary.skim_df.Rd
- to_long.Rd
- deprecated.R
- dplyr.R
- get_skimmers.R
- package.R
- reshape.R
- sfl.R
- skim.R
- skim_obj.R
- skim_print.R
- skim_with.R
- skimr-package.R
- stats.R
- summary.R
- utils.R
- vctrs.R
- .gitignore
- cran.md
- data.sqlite
- failures.md
- problems.md
- README.md
- - helper-expectations.R
  - test-data-table.R
  - test-dplyr.R
  - test-get_skimmers.R
  - test-reshape.R
  - test-sfl.R
  - test-skim.R
  - test-skim_obj.R
  - test-skim_print.R
  - test-skim_tee.R
  - test-skim_with.R
  - test-stats.R
  - test-summary.R
  - test-vctrs.R
- testthat.R
- extending_skimr.Rmd
- Skimr_defaults.Rmd
- Using_fonts.Rmd
- using_skimr.Rmd
.gitignore
.lintr
.pre-commit-config.yaml
.Rbuildignore
codemeta.json
cran-comments.md
DESCRIPTION
NAMESPACE
NEWS.md
README.md
README.Rmd
skimr.Rproj

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Print the prime factorization of a number.

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echo {{number}} | factor

Take the input from `stdin` if no argument is specified:

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<img src='https://docs.ropensci.org/skimr/reference/figures/logo.png'
align="right" height="139" /></a>

[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/)
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[![Codecov test
coverage](https://codecov.io/gh/ropensci/skimr/graph/badge.svg)](https://app.codecov.io/gh/ropensci/skimr)
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package](https://badges.ropensci.org/175_status.svg)](https://github.com/ropensci/software-review/issues/175)
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[![cran
checks](https://badges.cranchecks.info/worst/skimr.svg)](https://badges.cranchecks.info/worst/skimr.svg)

`skimr` provides a frictionless approach to summary statistics which
conforms to the [principle of least
surprise](https://en.wikipedia.org/wiki/Principle_of_least_astonishment),
displaying summary statistics the user can skim quickly to understand
their data. It handles different data types and returns a `skim_df`
object which can be included in a pipeline or displayed nicely for the
human reader.

**Note: `skimr` version 2 has major changes when skimr is used
programmatically. Upgraders should review this document, the release
notes and vignettes carefully.**

## Installation

The current released version of `skimr` can be installed from CRAN. If
you wish to install the current build of the next release you can do so
using the following:

# install.packages("devtools")
    devtools::install_github("ropensci/skimr")

The APIs for this branch should be considered reasonably stable but
still subject to change if an issue is discovered.

To install the version with the most recent changes that have not yet
been incorporated in the main branch (and may not be):

devtools::install_github("ropensci/skimr", ref = "develop")

Do not rely on APIs from the develop branch, as they are likely to
change.

## Skim statistics in the console

`skimr`:

-   Provides a larger set of statistics than `summary()`, including
    missing, complete, n, and sd.
-   reports each data types separately
-   handles dates, logicals, and a variety of other types
-   supports spark-bar and spark-line based on the [pillar
    package](https://github.com/r-lib/pillar).

### Separates variables by class:

skim(chickwts)

## ── Data Summary ────────────────────────
    ##                            Values  
    ## Name                       chickwts
    ## Number of rows             71      
    ## Number of columns          2       
    ## _______________________            
    ## Column type frequency:             
    ##   factor                   1       
    ##   numeric                  1       
    ## ________________________           
    ## Group variables            None    
    ## 
    ## ── Variable type: factor ───────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate ordered n_unique top_counts                        
    ## 1 feed                  0             1 FALSE          6 soy: 14, cas: 12, lin: 12, sun: 12
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate mean   sd  p0  p25 p50  p75 p100 hist 
    ## 1 weight                0             1 261. 78.1 108 204. 258 324.  423 ▆▆▇▇▃

### Presentation is in a compact horizontal format:

skim(iris)

## ── Data Summary ────────────────────────
    ##                            Values
    ## Name                       iris  
    ## Number of rows             150   
    ## Number of columns          5     
    ## _______________________          
    ## Column type frequency:           
    ##   factor                   1     
    ##   numeric                  4     
    ## ________________________         
    ## Group variables            None  
    ## 
    ## ── Variable type: factor ───────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate ordered n_unique top_counts               
    ## 1 Species               0             1 FALSE          3 set: 50, ver: 50, vir: 50
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate mean    sd  p0 p25  p50 p75 p100 hist 
    ## 1 Sepal.Length          0             1 5.84 0.828 4.3 5.1 5.8  6.4  7.9 ▆▇▇▅▂
    ## 2 Sepal.Width           0             1 3.06 0.436 2   2.8 3    3.3  4.4 ▁▆▇▂▁
    ## 3 Petal.Length          0             1 3.76 1.77  1   1.6 4.35 5.1  6.9 ▇▁▆▇▂
    ## 4 Petal.Width           0             1 1.20 0.762 0.1 0.3 1.3  1.8  2.5 ▇▁▇▅▃

### Built in support for strings, lists and other column classes

skim(dplyr::starwars)

## ── Data Summary ────────────────────────
    ##                            Values         
    ## Name                       dplyr::starwars
    ## Number of rows             87             
    ## Number of columns          14             
    ## _______________________                   
    ## Column type frequency:                    
    ##   character                8              
    ##   list                     3              
    ##   numeric                  3              
    ## ________________________                  
    ## Group variables            None           
    ## 
    ## ── Variable type: character ────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate min max empty n_unique whitespace
    ## 1 name                  0         1       3  21     0       87          0
    ## 2 hair_color            5         0.943   4  13     0       11          0
    ## 3 skin_color            0         1       3  19     0       31          0
    ## 4 eye_color             0         1       3  13     0       15          0
    ## 5 sex                   4         0.954   4  14     0        4          0
    ## 6 gender                4         0.954   8   9     0        2          0
    ## 7 homeworld            10         0.885   4  14     0       48          0
    ## 8 species               4         0.954   3  14     0       37          0
    ## 
    ## ── Variable type: list ─────────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate n_unique min_length max_length
    ## 1 films                 0             1       24          1          7
    ## 2 vehicles              0             1       11          0          2
    ## 3 starships             0             1       16          0          5
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate  mean    sd p0   p25 p50   p75 p100 hist 
    ## 1 height                6         0.931 175.   34.8 66 167   180 191    264 ▂▁▇▅▁
    ## 2 mass                 28         0.678  97.3 169.  15  55.6  79  84.5 1358 ▇▁▁▁▁
    ## 3 birth_year           44         0.494  87.6 155.   8  35    52  72    896 ▇▁▁▁▁

### Has a useful summary function

skim(iris) |>
      summary()

## ── Data Summary ────────────────────────
    ##                            Values
    ## Name                       iris  
    ## Number of rows             150   
    ## Number of columns          5     
    ## _______________________          
    ## Column type frequency:           
    ##   factor                   1     
    ##   numeric                  4     
    ## ________________________         
    ## Group variables            None

### Individual columns can be selected using tidyverse-style selectors

skim(iris, Sepal.Length, Petal.Length)

## ── Data Summary ────────────────────────
    ##                            Values
    ## Name                       iris  
    ## Number of rows             150   
    ## Number of columns          5     
    ## _______________________          
    ## Column type frequency:           
    ##   numeric                  2     
    ## ________________________         
    ## Group variables            None  
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate mean    sd  p0 p25  p50 p75 p100 hist 
    ## 1 Sepal.Length          0             1 5.84 0.828 4.3 5.1 5.8  6.4  7.9 ▆▇▇▅▂
    ## 2 Petal.Length          0             1 3.76 1.77  1   1.6 4.35 5.1  6.9 ▇▁▆▇▂

### Handles grouped data

`skim()` can handle data that has been grouped using
`dplyr::group_by()`.

iris |>
      dplyr::group_by(Species) |>
      skim()

## ── Data Summary ────────────────────────
    ##                            Values                      
    ## Name                       dplyr::group_by(iris, Spe...
    ## Number of rows             150                         
    ## Number of columns          5                           
    ## _______________________                                
    ## Column type frequency:                                 
    ##   numeric                  4                           
    ## ________________________                               
    ## Group variables            Species                     
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##    skim_variable Species    n_missing complete_rate  mean    sd  p0  p25  p50  p75 p100 hist 
    ##  1 Sepal.Length  setosa             0             1 5.01  0.352 4.3 4.8  5    5.2   5.8 ▃▃▇▅▁
    ##  2 Sepal.Length  versicolor         0             1 5.94  0.516 4.9 5.6  5.9  6.3   7   ▂▇▆▃▃
    ##  3 Sepal.Length  virginica          0             1 6.59  0.636 4.9 6.22 6.5  6.9   7.9 ▁▃▇▃▂
    ##  4 Sepal.Width   setosa             0             1 3.43  0.379 2.3 3.2  3.4  3.68  4.4 ▁▃▇▅▂
    ##  5 Sepal.Width   versicolor         0             1 2.77  0.314 2   2.52 2.8  3     3.4 ▁▅▆▇▂
    ##  6 Sepal.Width   virginica          0             1 2.97  0.322 2.2 2.8  3    3.18  3.8 ▂▆▇▅▁
    ##  7 Petal.Length  setosa             0             1 1.46  0.174 1   1.4  1.5  1.58  1.9 ▁▃▇▃▁
    ##  8 Petal.Length  versicolor         0             1 4.26  0.470 3   4    4.35 4.6   5.1 ▂▂▇▇▆
    ##  9 Petal.Length  virginica          0             1 5.55  0.552 4.5 5.1  5.55 5.88  6.9 ▃▇▇▃▂
    ## 10 Petal.Width   setosa             0             1 0.246 0.105 0.1 0.2  0.2  0.3   0.6 ▇▂▂▁▁
    ## 11 Petal.Width   versicolor         0             1 1.33  0.198 1   1.2  1.3  1.5   1.8 ▅▇▃▆▁
    ## 12 Petal.Width   virginica          0             1 2.03  0.275 1.4 1.8  2    2.3   2.5 ▂▇▆▅▇

### Behaves nicely in pipelines

iris |>
      skim() |>
      dplyr::filter(numeric.sd > 1)

## ── Data Summary ────────────────────────
    ##                            Values
    ## Name                       iris  
    ## Number of rows             150   
    ## Number of columns          5     
    ## _______________________          
    ## Column type frequency:           
    ##   numeric                  1     
    ## ________________________         
    ## Group variables            None  
    ## 
    ## ── Variable type: numeric ──────────────────────────────────────────────────────────────────────────
    ##   skim_variable n_missing complete_rate mean   sd p0 p25  p50 p75 p100 hist 
    ## 1 Petal.Length          0             1 3.76 1.77  1 1.6 4.35 5.1  6.9 ▇▁▆▇▂

## Knitted results

Simply skimming a data frame will produce the horizontal print layout
shown above. We provide a `knit_print` method for the types of objects
in this package so that similar results are produced in documents. To
use this, make sure the `skimmed` object is the last item in your code
chunk.

faithful |>
      skim()

<table>
<caption>Data summary</caption>
<tbody>
<tr class="odd">
<td style="text-align: left;">Name</td>
<td style="text-align: left;">faithful</td>
</tr>
<tr class="even">
<td style="text-align: left;">Number of rows</td>
<td style="text-align: left;">272</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Number of columns</td>
<td style="text-align: left;">2</td>
</tr>
<tr class="even">
<td style="text-align: left;">_______________________</td>
<td style="text-align: left;"></td>
</tr>
<tr class="odd">
<td style="text-align: left;">Column type frequency:</td>
<td style="text-align: left;"></td>
</tr>
<tr class="even">
<td style="text-align: left;">numeric</td>
<td style="text-align: left;">2</td>
</tr>
<tr class="odd">
<td style="text-align: left;">________________________</td>
<td style="text-align: left;"></td>
</tr>
<tr class="even">
<td style="text-align: left;">Group variables</td>
<td style="text-align: left;">None</td>
</tr>
</tbody>
</table>

Data summary

**Variable type: numeric**

<table style="width:100%;">
<colgroup>
<col style="width: 17%" />
<col style="width: 12%" />
<col style="width: 17%" />
<col style="width: 7%" />
<col style="width: 7%" />
<col style="width: 6%" />
<col style="width: 7%" />
<col style="width: 4%" />
<col style="width: 7%" />
<col style="width: 6%" />
<col style="width: 7%" />
</colgroup>
<thead>
<tr class="header">
<th style="text-align: left;">skim_variable</th>
<th style="text-align: right;">n_missing</th>
<th style="text-align: right;">complete_rate</th>
<th style="text-align: right;">mean</th>
<th style="text-align: right;">sd</th>
<th style="text-align: right;">p0</th>
<th style="text-align: right;">p25</th>
<th style="text-align: right;">p50</th>
<th style="text-align: right;">p75</th>
<th style="text-align: right;">p100</th>
<th style="text-align: left;">hist</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">eruptions</td>
<td style="text-align: right;">0</td>
<td style="text-align: right;">1</td>
<td style="text-align: right;">3.49</td>
<td style="text-align: right;">1.14</td>
<td style="text-align: right;">1.6</td>
<td style="text-align: right;">2.16</td>
<td style="text-align: right;">4</td>
<td style="text-align: right;">4.45</td>
<td style="text-align: right;">5.1</td>
<td style="text-align: left;">▇▂▂▇▇</td>
</tr>
<tr class="even">
<td style="text-align: left;">waiting</td>
<td style="text-align: right;">0</td>
<td style="text-align: right;">1</td>
<td style="text-align: right;">70.90</td>
<td style="text-align: right;">13.59</td>
<td style="text-align: right;">43.0</td>
<td style="text-align: right;">58.00</td>
<td style="text-align: right;">76</td>
<td style="text-align: right;">82.00</td>
<td style="text-align: right;">96.0</td>
<td style="text-align: left;">▃▃▂▇▂</td>
</tr>
</tbody>
</table>

## Customizing skimr

Although skimr provides opinionated defaults, it is highly customizable.
Users can specify their own statistics, change the formatting of
results, create statistics for new classes and develop skimmers for data
structures that are not data frames.

### Specify your own statistics and classes

Users can specify their own statistics using a list combined with the
`skim_with()` function factory. `skim_with()` returns a new `skim`
function that can be called on your data. You can use this factory to
produce summaries for any type of column within your data.

Assignment within a call to `skim_with()` relies on a helper function,
`sfl` or `skimr` function list. By default, functions in the `sfl` call
are appended to the default skimmers, and names are automatically
generated as well.

my_skim <- skim_with(numeric = sfl(mad))
    my_skim(iris, Sepal.Length)

But you can also helpers from the `tidyverse` to create new anonymous
functions that set particular function arguments. The behavior is the
same as in `purrr` or `dplyr`, with both `.` and `.x` as acceptable
pronouns. Setting the `append = FALSE` argument uses only those
functions that you’ve provided.

my_skim <- skim_with(
      numeric = sfl(
        iqr = IQR,
        p01 = ~ quantile(.x, probs = .01)
        p99 = ~ quantile(., probs = .99)
      ),
      append = FALSE
    )
    my_skim(iris, Sepal.Length)

And you can remove default skimmers by setting them to `NULL`.

my_skim <- skim_with(numeric = sfl(hist = NULL))
    my_skim(iris, Sepal.Length)

### Skimming other objects

`skimr` has summary functions for the following types of data by
default:

-   `numeric` (which includes both `double` and `integer`)
-   `character`
-   `factor`
-   `logical`
-   `complex`
-   `Date`
-   `POSIXct`
-   `ts`
-   `AsIs`

`skimr` also provides a small API for writing packages that provide
their own default summary functions for data types not covered above. It
relies on R S3 methods for the `get_skimmers` function. This function
should return a `sfl`, similar to customization within `skim_with()`,
but you should also provide a value for the `class` argument. Here’s an
example.

get_skimmers.my_data_type <- function(column) {
      sfl(
        .class = "my_data_type",
        p99 = quantile(., probs = .99)
      )
    }

## Limitations of current version

We are aware that there are issues with rendering the inline histograms
and line charts in various contexts, some of which are described below.

### Support for spark histograms

With versions of R before 4.2.1, there are known issues with printing
the spark-histogram characters when printing a data frame. For example,
`"▂▅▇"` is printed as `"<U+2582><U+2585><U+2587>"`. This longstanding
problem [originates in the low-level
code](https://stat.ethz.ch/pipermail/r-devel/2015-May/071250.html) for
printing dataframes. While some cases have been addressed, there are,
for example, reports of this issue in Emacs ESS. While this is a deep
issue, there is [ongoing work to address it in base
R](https://blog.r-project.org/2020/05/02/utf-8-support-on-windows/). We
recommend upgrading to at least R 4.2.1 to address this issue.

This means that while `skimr` can render the histograms to the console
and in RMarkdown documents, it cannot in other circumstances. This
includes:

-   converting a `skimr` data frame to a vanilla R data frame, but
    tibbles render correctly
-   in the context of rendering to a pdf using an engine that does not
    support utf-8.

One workaround for showing these characters in Windows is to set the
CTYPE part of your locale to Chinese/Japanese/Korean with
`Sys.setlocale("LC_CTYPE", "Chinese")`. The helper function
`fix_windows_histograms()` does this for you.

And last but not least, we provide `skim_without_charts()` as a
fallback. This makes it easy to still get summaries of your data, even
if unicode issues continue.

### Printing spark histograms and line graphs in knitted documents

Spark-bar and spark-line work in the console, but may not work when you
knit them to a specific document format. The same session that produces
a correctly rendered HTML document may produce an incorrectly rendered
PDF, for example. This issue can generally be addressed by changing
fonts to one with good building block (for histograms) and Braille
support (for line graphs). For example, the open font “DejaVu Sans” from
the `extrafont` package supports these. You may also want to try
wrapping your results in `knitr::kable()`. Please see the vignette on
using fonts for details.

Displays in documents of different types will vary. For example, one
user found that the font “Yu Gothic UI Semilight” produced consistent
results for Microsoft Word and Libre Office Write.

## Inspirations

-   [TextPlots](https://github.com/sunetos/TextPlots.jl) for use of
    Braille characters

-   [spark](https://github.com/holman/spark) for use of block
    characters.

The earliest use of unicode characters to generate sparklines appears to
be [from
2009](https://blog.jonudell.net/2009/01/13/fuel-prices-and-pageviews/).

Exercising these ideas to their fullest requires a font with good
support for block drawing characters.
[PragamataPro](https://fsd.it/shop/fonts/pragmatapro/) is one such font.

## Contributing

We welcome issue reports and pull requests, including potentially adding
support for commonly used variable classes. However, in general, we
encourage users to take advantage of skimr’s flexibility to add their
own customized classes. Please see the
[contributing](https://docs.ropensci.org/skimr/CONTRIBUTING.html) and
[conduct](https://ropensci.org/code-of-conduct/) documents.

[![ropenci\_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)