My favourite R package for: frequency tables

Back for the next part of the “which of the infinite ways of doing a certain task in R do I most like today?” series. This time, what could more more fascinating an aspect of analysis to focus on than: frequency tables?

OK, most topics might actually be more fascinating. Especially when my definition of frequency tables here will restrict itself to 1-dimensional variations, which in theory a primary school kid could calculate manually, given time. But they are such a common tool, that analysts can use for all sorts of data validation and exploratory data analysis jobs, that finding a nice implementation might prove to be a time-and-sanity saving task over a lifetime of counting how many things are of which type.

Here’s the top of an example dataset. Imagine a “tidy” dataset, such that each row is an one observation. I would like to know how many observations (e.g. people) are of  which type (e.g. demographic – here a category between A and E inclusive)

Type	Person ID
E	1
E	2
B	3
B	4
B	5
B	6
C	7

I want to be able to say things like: “4 of my records are of type E”, or “10% of my records are of type A”. The dataset I will use in my below example is similar to the above table, only with more records, including some with a blank (missing) type.

What would I like my 1-dimensional frequency table tool to do in an ideal world?

1. Provide a count of how many observations are in which category.
2. Show the percentages or proportions of total observations that represents
3. Be able to sort by count, so I see the most popular options at the top – but only when I want to, as sometimes the order of data is meaningful for other reasons.
4. Show a cumulative %, sorted by count, so I can see quickly that, for example, the top 3 options make up 80% of the data – useful for some swift Pareto analysis and the like.
5. Deal with missing data transparently. It is often important to know how many of your observations are “missing”. Other times, you might only care about the statistics derived from those which are not missing.
6. If an external library, then be on CRAN or some other well supported network so I can be reasonably confident the library won’t vanish, given how often I want to use it.
7. Output data in a “tidy” but human-readable format. Being a big fan of the tidyverse, it’d be great if I could pipe the results directly into ggplot, dplyr, or whatever for some quick plots and manipulations. Other times, if working interactively, I’d like to be able to see the key results at a glance, without having to use further coding.
8. Work with “kable” from the Knitr package, or similar table output tools. I often use R markdown and would like the ability to show the frequency table output in reasonably presentable manner.
9. Have a sensible set of defaults (aka facilitate my laziness).

 

So what options come by default with base R?

Most famously, perhaps the “table” command.

table(data$Type)

A super simple way to count up the number of records by type. But it doesn’t show percentages or any sort of cumulation. By default it hasn’t highlighted that there are some records with missing data. It does have a useNA parameter that will show that though if desired.

table(data$Type, useNA = "ifany")

The output also isn’t tidy and doesn’t work well with Knitr.

The table command can be wrapped in the prop.table command to show proportions.

prop.table(table(data$Type))

But you’d need to run both commands to understand the count and percentages, and the latter inherits many of the limitations from the former.

So what’s available outside of base R? I tested 5 options, although there are, of course , countless more. In no particular order:

• tabyl, from the janitor package
• tab1, from epidisplay
• freq, from summarytools
• CrossTable, from gmodels
• freq, from questionr

Because I am fussy, I managed to find some slight personal niggle with all of them, so it’s hard to pick an overall personal winner for all circumstances. Several came very close. I would recommend looking at any of the janitor, summarytools and questionr package functions outlined below if you have similar requirements and tastes to me.

tabyl, from the janitor package

Documentation

library(janitor)
tabyl(data$Type, sort = TRUE)

This is a pretty good start! By default, it shows counts, percents, and percent of non-missing data. It can optionally sort in order of frequency. It the output is tidy, and works with kable just fine. The only thing missing really is a cumulative percentage option. But it’s a great improvement over base table.

I do find myself constantly misspelling “tabyl” as “taybl” though, which is annoying, but not really something I can really criticise anyone else for.

tab1, from the epidisplay package

Documentation

library(epiDisplay)
tab1(data$Type, sort.group = "decreasing", cum.percent = TRUE)

This one is pretty fully featured. It even (optionally) generates a visual frequency chart output as you can see above. It shows the frequencies, proportions and cumulative proportions both with and without missing data. It can sort in order of frequency, and has a totals row so you know how many observations you have all in.

However it isn’t very tidy by default, and doesn’t work with knitr. I also don’t really like the column names it assigns, although one can certainly claim that’s pure personal preference.

A greater issue may be that the cumulative columns don’t seem to work as I would expect when the table is sorted, as in the above example. The first entry in the table is “E”, because that’s the largest category. However, it isn’t 100% of the non-missing dataset, as you might infer from the fifth numerical column. In reality it’s 31.7%, per column 4.

As far as I can tell, the function is working out the cumulative frequencies before sorting the table – so as category E is the last category in the data file it has calculated that by the time you reach the end of category E you have 100% of the non-missing data in hand. I can’t envisage a situation where you would want this behaviour, but I’m open to correction if anyone can.

freq, from the summarytools package

Documentation

library(summarytools)
summarytools::freq(data$Type, order = "freq")

This looks pretty great. Has all the variations of counts, percents and missing-data output I want – here you can interpret the “% valid” column as “% of all non-missing”. Very readable in the console, and works well with Knitr. In fact it has some further nice formatting options that I wasn’t particularly looking for.

It it pretty much tidy, although has a minor niggle in that the output always includes the total row. It’s often important to know your totals, but if you’re piping it to other tools or charts, you may have to use another command to filter that row out each time, as there doesn’t seem to be an obvious way to prevent it being included with the rest of the dataset when running it directly.

Update 2018-04-28: thanks to Roland in the comments below pointing out that a new feature to disable the totals display has been added: set the “totals” parameter to false, and the totals row won’t show up, potential making it easier to pass on for further analysis.

CrossTable, from the gmodels library

Documentation

library(gmodels)
CrossTable(data$Type)

Here the results are displayed in a horizontal format, a bit like the base “table”. Here though, the proportions are clearly shown, albeit not with a cumulative version. It doesn’t highlight that there are missing values, and isn’t “tidy”. You can get it to display a vertical version (add the parameter max.width = 1 ) which is visually distinctive, but untidy in the usual R tidyverse sense.

It’s not a great tool for my particular requirements here, but most likely this is because, as you may guess from the command name, it’s not particularly designed for 1-way frequency tables. If you are crosstabulating multiple dimensions it may provide a powerful and visually accessible way to see counts, proportions and even run hypothesis tests.

freq, from the questionr package

Documentation

library(questionr)
questionr::freq(data$Type, cum = TRUE, sort = "dec", total = TRUE)

Counts, percentages, cumulative percentages, missing values data, yes, all here! The table can optionally be sorted in descending frequency, and works well with kable.

It is mostly tidy, but also has an annoyance in that the category values themselves (A -E are row labels rather than a standalone column. This means you may have to pop them into in a new column for best use in any downstream tidy tools. That’s easy enough with e.g. dplyr’s add_rownames command. But that is another processing step to remember, which is not a huge selling point.

There is a total row at the bottom, but it’s optional, so just don’t use the “total” parameter if you plan to pass the data onwards in a way where you don’t want to risk double-counting your totals. There’s an “exclude” parameter if you want to remove any particular categories from analysis before performing the calculations as well as a couple of extra formatting options that might be handy.