We will practice on our continents data.frame from module 2 and the gapminder data.frame. Note how these are tidy data: We have observations at the level of continent and at the level of country, so they go in different tables. The continent column in the gapminder data.frame allows us to link them now. If continents data.frame isn’t in your Environment, load it and recall what it consists of:

  1. Left Join Merge R
  2. Left Join Vs Inner Join

We can join the two data.frames using any of the dplyr functions. We will pass the results to str to avoid printing more than we can read, and to get more high-level information on the resulting data.frames.

These operations produce slightly different results, either 1704 or 1705 observations. Can you figure out why? Antarctica contains no countries so doesn’t appear in the gapminder data.frame. When we use left_join it gets filtered from the results, but when we use right_join it appears, with missing values for all of the country-level variables:

Or copy & paste this link into an email or IM. In the previous R syntax, I applied an inner join, but of cause you could also use a right, left, or full join in this step-by-step approach. Also note that there is a very smooth way to merge multiple data frames simultaneously by combining these data frames in a list. You can learn more about this approach in this tutorial. I want to left join in STATA but due to multiple identifiers all other options except m:m don't work. Joining by 'joinby' also led to wrong merging. Is there an equivalent of R's joinby in STATA.

  • The R code implementation of these additional joins: # join datasets in r Outer Join: jointdataset merge(ChickWeight, LabResults,by = 'Diet', all=TRUE) Left Join: jointdataset merge(ChickWeight, LabResults, by = 'Diet', all.x= TRUE) Right Join: jointdataset merge(ChickWeight, LabResults, by = 'Diet', all.y=TRUE) Cross Join: jointdataset merge(ChickWeight, LabResults, by = Null).
  • In SQL database terminology, the default value of all = FALSE gives a natural join, a special case of an inner join. Specifying all.x = TRUE gives a left (outer) join, all.y = TRUE a right (outer) join, and both (all = TRUE) a (full) outer join. DBMSes do not match NULL records, equivalent to incomparables = NA in R.

There’s another problem in this data.frame – it has two population measures, one by continent and one by country and it’s not clear which is which! Let’s rename a couple of columns.

Challenge – Putting the pieces together

A colleague suggests that the more land area an individual has, the greater their gdp will be and that this relationship will be observable at any scale of observation. You chuckle and mutter “Not at the continental scale,” but your colleague insists. Test your colleague’s hypothesis by:

  • Calculating the total GDP of each continent,
    • Hint: Use dplyr’s group_by and summarize
  • Joining the resulting data.frame to the continents data.frame,
  • Calculating the per-capita GDP for each continent, and
  • Plotting per-capita gdp versus population density.

Challenge solutions

Solution to Challenge – Putting the pieces together


Arabic Vocabulary builder. This lesson is adapted from the Software Carpentry: R for Reproducible Scientific Analysis Multi-Table Joins materials and Brandon Hurr’s dplyr II: Joins and Set Ops presentation to the Davis R UsersGroup on Februrary 2, 2016.

October 27, 2018

In this post in the R:case4base series we will look at one of the most common operations on multiple data frames - merge, also known as JOIN in SQL terms.

We will learn how to do the 4 basic types of join - inner, left, right and full join with base R and show how to perform the same with tidyverse’s dplyr and data.table’s methods. A quick benchmark will also be included.

To showcase the merging, we will use a very slightly modified dataset provided by Hadley Wickham’s nycflights13 package, mainly the flights and weather data frames. Let’s get right into it and simply show how to perform the different types of joins with base R.

First, we prepare the data and store the columns we will merge by (join on) into mergeCols:

Merge

Now, we show how to perform the 4 merges (joins):

Left (outer) join

Full (outer) join

The key arguments of base merge data.frame method are:

  • x, y - the 2 data frames to be merged
  • by - names of the columns to merge on. If the column names are different in the two data frames to merge, we can specify by.x and by.y with the names of the columns in the respective data frames. The by argument can also be specified by number, logical vector or left unspecified, in which case it defaults to the intersection of the names of the two data frames. From best practice perspective it is advisable to always specify the argument explicitly, ideally by column names.
  • all, all.x, all.y - default to FALSE and can be used specify the type of join we want to perform:
    • all = FALSE (the default) - gives an inner join - combines the rows in the two data frames that match on the by columns
    • all.x = TRUE - gives a left (outer) join - adds rows that are present in x, even though they do not have a matching row in y to the result for all = FALSE
    • all.y = TRUE - gives a right (outer) join - adds rows that are present in y, even though they do not have a matching row in x to the result for all = FALSE
    • all = TRUE - gives a full (outer) join. This is a shorthand for all.x = TRUE and all.y = TRUE

Other arguments include

  • sort - if TRUE (default), results are sorted on the by columns
  • suffixes - length 2 character vector, specifying the suffixes to be used for making the names of columns in the result which are not used for merging unique
  • incomparables - for single-column merging only, a vector of values that cannot be matched. Any value in x matching a value in this vector is assigned the nomatch value (which can be passed using ..)

For this example, let us have a list of all the data frames included in the nycflights13 package, slightly updated such that they can me merged with the default value for by, purely for this exercise, and store them into a list called flightsList:

Since merge is designed to work with 2 data frames, merging multiple data frames can of course be achieved by nesting the calls to merge:

We can however achieve this same goal much more elegantly, taking advantage of base R’s Reduce function:

Note that this example is oversimplified and the data was updated such that the default values for by give meaningful joins. For example, in the original planes data frame the column year would have been matched onto the year column of the flights data frame, which is nonsensical as the years have different meanings in the two data frames. This is why we renamed the year column in the planes data frame to yearmanufactured for the above example.

Using the tidyverse

The dplyr package comes with a set of very user-friendly functions that seem quite self-explanatory:

We can also use the “forward pipe” operator %>% that becomes very convenient when merging multiple data frames:

Using data.table

The data.table package provides an S3 method for the merge generic that has a very similar structure to the base method for data frames, meaning its use is very convenient for those familiar with that method. In fact the code is exactly the same as the base one for our example use.

One important difference worth noting is that the by argument is by default constructed differently with data.table.

We however provide it explicitly, therefore this difference does not directly affect our example:

Alternatively, we can write data.table joins as subsets:

For a quick overview, lets look at a basic benchmark without package loading overhead for each of the mentioned packages:

Inner join

Full (outer) join

Visualizing the results in this case shows base R comes way behind the two alternatives, even with sort = FALSE.

Note: The benchmarks are ran on a standard droplet by DigitalOcean, with 2GB of memory a 2vCPUs.

No time for reading? Click here to get just the code with commentary

  • Animated inner join, left join, right join and full join by Garrick Aden-Buie for an easier understanding
  • Joining Data in R with dplyr by Wiliam Surles
  • Join (SQL) Wikipedia page
  • The nycflights13 package on CRAN

Left Join Merge R

Exactly 100 years ago tomorrow, October 28th, 1918 the independence of Czechoslovakia was proclaimed by the Czechoslovak National Council, resulting in the creation of the first democratic state of Czechs and Slovaks in history.

Left Join Vs Inner Join

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