joyn

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The goal of joyn is to provide the user with a set of tools to analyze the quality of merging (i.e., joining) data frames, so that it is a JOY to join tables with joyn. This is inspired on the command merge of the statistical software Stata.

Motivation

The objective joyn is to make your life easier when joining tables. As a former Stata user (I still work with Stata but not that much as I work with R now), I had missed, until now, the ability to assess the resulting data frame when joining tables in R. With one single command, merge, Stata allows the user to perform any kind of equi-join. The reason for this is that, by default, Stata merges fully both tables into one and then it is up to the user to keep the observation she needs. Most importantly, Stata forces the user to know how her joining tables relate to each other. Most tables have a one-to-one (1:1 ) relation, but it is common to find one-to-many (1:m), many-to-one (m:1), and many-to-many (m:m) relations. Finally, Stata’s merge command returns by default a variable with useful information about the table’s join. So the following features are the value added of joyn:

  1. joyn performs a full join by default (i.e., resulting table has all the observations from both original, joining tables). Yet, the user can select “left”, “right” or “inner” joins using the argument keep.

  2. In the same vain, joyn keeps all the columns form both joining tables. Two caveats are worth mentioning.

    1. If both tables have variables with the same name, by default joyn does not bring those variables from the second (i.e, right, using) table into the first (i.e., left, master) table. Yet, you can do one of two things. First, you can use arguments update_values or updateNA to update the value of those variable in the first table with the ones in the second table. Or, you can use argument keep_y_in_x = TRUE to keep both variables with a different name.

    2. You can use the argument yvars to select which variables you want to bring from the second table into the first one.

  3. joyn allows the user to perform one-to-one (1:1) , one-to-many (1:m), many-to-one (m:1), and many-to-many (m:m) joins. The default is m:m, following general R’s practice, but its is highly discouraged. Since you want to use joyn, I recommend you always specify the right relationship between your joining tables.

  4. joyn returns a reporting variable with the status of the join.

Regarding speed and flexibility

Notice the joyn is not intended to be a super fast joining tool. By construction, it does a lot of things that will make it slower than other tools out there. However, joyn is basically a wrapper around data.table’s indexed joining tools. So, the lost of speed of joyn is mainly due to evaluating several conditions, creating the reporting variable, and present a nice summary table at the end of the process. Also, keep in mind that joyn is intended to be informative, so it displays messages here and there to inform you about your join (you can silence any message in joyn, including the reporting table, by using the argument verbose = FALSE). This, of course, makes joyn a little slower than using regular data.table syntax. However, the loss of speed is not much and you’re gaining a lot of information. The main reason why joyn is a little slower is than pure data.table is that it will always perform a full join of data in the same way the Stata does it.

As of now, the flexibility of joyn is limited to the basic joins, yet the most used and useful ones. If you want to learn more about different kinds of joins available in data.table and how they relate to dplyr, I recommend you start with this blog post.

Installation

You can install the stable version of joyn from CRAN with:

install.packages("joyn")

The development version from GitHub with:

# install.packages("devtools")
devtools::install_github("randrescastaneda/joyn")

Example

library(joyn)
#> 
#> Attaching package: 'joyn'
#> The following object is masked from 'package:base':
#> 
#>     merge

x1
#>    id  t  x
#> 1:  1  1 11
#> 2:  1  2 12
#> 3:  2  1 13
#> 4:  3  2 14
#> 5: NA NA 15
y1
#>    id  y
#> 1:  1 11
#> 2:  2 15
#> 3:  4 16

# using commong variable `id` as key.
merge(x1, y1)[]
#> > removing key variables `id` from yvars
#> 
#> -- JOYn Report --
#> 
#>    report n percent
#> 1:      x 2   33.3%
#> 2:  x & y 3     50%
#> 3:      y 1   16.7%
#> 4:  total 6    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  t  x  y report
#> 1:  1  1 11 11  x & y
#> 2:  1  2 12 11  x & y
#> 3:  2  1 13 15  x & y
#> 4:  3  2 14 NA      x
#> 5:  4 NA NA 16      y
#> 6: NA NA 15 NA      x

# keep just those observations that match
merge(x1, y1, keep = "inner")[]
#> > removing key variables `id` from yvars
#> -- JOYn Report --
#> 
#>    report n percent
#> 1:  x & y 3    100%
#> 2:  total 3    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id t  x  y report
#> 1:  1 1 11 11  x & y
#> 2:  1 2 12 11  x & y
#> 3:  2 1 13 15  x & y


x2 
#>    id  t  x
#> 1:  1  1 16
#> 2:  4  2 12
#> 3:  2  1 NA
#> 4:  3  2 NA
#> 5: NA NA 15

y2
#>    id yd  y  x
#> 1:  1  1 11 16
#> 2:  2  2 15 17
#> 3:  5  5 20 18
#> 4:  6  6 13 19
#> 5:  3  3 10 20


# Bad merge for not specifying by argument
merge(x2, y2)[]
#> > removing key variables `id` and `x` from yvars
#> -- JOYn Report --
#> 
#>    report n percent
#> 1:      x 4   44.4%
#> 2:  x & y 1   11.1%
#> 3:      y 4   44.4%
#> 4:  total 9    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  x  t yd  y report
#> 1:  1 16  1  1 11  x & y
#> 2:  2 17 NA  2 15      y
#> 3:  2 NA  1 NA NA      x
#> 4:  3 20 NA  3 10      y
#> 5:  3 NA  2 NA NA      x
#> 6:  4 12  2 NA NA      x
#> 7:  5 18 NA  5 20      y
#> 8:  6 19 NA  6 13      y
#> 9: NA 15 NA NA NA      x

# good merge, ignoring variable x from y
merge(x2, y2, by = "id")[]
#> > removing key variables `id` from yvars
#> i variable `x` in table y is ignored because arguments `update_NAs` and
#>   `update_values` are FALSE.
#> 
#> -- JOYn Report --
#> 
#>    report n percent
#> 1:      x 2   28.6%
#> 2:  x & y 3   42.9%
#> 3:      y 2   28.6%
#> 4:  total 7    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  t  x yd  y report
#> 1:  1  1 16  1 11  x & y
#> 2:  2  1 NA  2 15  x & y
#> 3:  3  2 NA  3 10  x & y
#> 4:  4  2 12 NA NA      x
#> 5:  5 NA NA  5 20      y
#> 6:  6 NA NA  6 13      y
#> 7: NA NA 15 NA NA      x

# update NAs in x variable form x
merge(x2, y2, by = "id", update_NAs = TRUE)[]
#> > removing key variables `id` from yvars
#> -- JOYn Report --
#> 
#>        report n percent
#> 1: NA updated 2   28.6%
#> 2:          x 2   28.6%
#> 3:      x & y 1   14.3%
#> 4:          y 2   28.6%
#> 5:      total 7    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  t  x yd  y     report
#> 1:  1  1 16  1 11      x & y
#> 2:  2  1 17  2 15 NA updated
#> 3:  3  2 20  3 10 NA updated
#> 4:  4  2 12 NA NA          x
#> 5:  5 NA 18  5 20          y
#> 6:  6 NA 19  6 13          y
#> 7: NA NA 15 NA NA          x

# Update values in x with variables from y
merge(x2, y2, by = "id", update_values = TRUE)[]
#> > removing key variables `id` from yvars
#> -- JOYn Report --
#> 
#>         report n percent
#> 1:  NA updated 2   28.6%
#> 2: not updated 2   28.6%
#> 3:       x & y 1   14.3%
#> 4:           y 2   28.6%
#> 5:       total 7    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  t  x yd  y      report
#> 1:  1  1 16  1 11       x & y
#> 2:  2  1 17  2 15  NA updated
#> 3:  3  2 20  3 10  NA updated
#> 4:  4  2 12 NA NA not updated
#> 5:  5 NA 18  5 20           y
#> 6:  6 NA 19  6 13           y
#> 7: NA NA 15 NA NA not updated


# do not bring any variable from Y into x, just the report
merge(x2, y2, by = "id", yvars = NULL)[]
#> 
#> -- JOYn Report --
#> 
#>    report n percent
#> 1:      x 2   28.6%
#> 2:  x & y 3   42.9%
#> 3:      y 2   28.6%
#> 4:  total 7    100%
#> ---------------------------------------------------------- End of JOYn report --
#>    id  t  x report
#> 1:  1  1 16  x & y
#> 2:  2  1 NA  x & y
#> 3:  3  2 NA  x & y
#> 4:  4  2 12      x
#> 5:  5 NA NA      y
#> 6:  6 NA NA      y
#> 7: NA NA 15      x