How to merge data in R using R merge, dplyr, or data.table

See how to join two data sets by one or more common columns using base R’s merge function, dplyr join functions, and the speedy data.table package

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Joins with data.table

The data.table package is best known for its speed, so it can be a good choice for dealing with large data sets.

In the code below, I load data.table and then use data.table’s fread() function to import the zip file. To read the zipped file, I use fread’s ability to call shell commands directly. That’s what the unzip -cq part of the argument is doing in fread() — you wouldn’t need that unless your file is zipped.

mydt <- fread('unzip -cq')
mylookup_dt <- fread("L_UNIQUE_CARRIERS.csv_")

fread() creates a data.table object — a data frame with extra functionality, especially within brackets after the object name. There are several ways to do joins with data.table.

One is to use the exact same merge() syntax as base R. You write it the same way, but it executes a lot faster. 

joined_dt1 <- merge(mydt, mylookup_dt, 
by.x = "OP_UNIQUE_CARRIER", by.y = "Code",
all.x = TRUE, all.y = FALSE)

If you want to use specific data.table syntax, you can first use the setkey() function to specify which columns you want to join on. Then, the syntax is simply mylookup_dt[mydt] as you can see in the code below. 

setkey(mydt, "OP_UNIQUE_CARRIER")
setkey(mylookup_dt, "Code")
joined_dt2 <- mylookup_dt[mydt]

data.table creator Matt Dowle explained the format as “X[Y] looks up X rows using Y as an index.” But note that if you think of mylookup_dt as a lookup table, the lookup table is outside the brackets while the primary data is within the brackets

There’s another data.table syntax that doesn’t require setkey(), and that’s adding an on argument within brackets. The syntax for the on vector is on = c(lookupColName = "dataColName"), with the lookup column name unquoted and the data column name in quotation marks:

dt3 <- mylookup_dt[mydt, on = c(Code = "OP_UNIQUE_CARRIER")]

Joins with dtplyr: dplyr syntax and data.table speed

I want to mention one other option: using dplyr syntax but with data.table on the back-end. You can do that with the dtplyr package, which is ideal for people who like dplyr syntax, or who are used to SQL database syntax, but want the speedy data.table performance. 

To use dtplyr, you need to turn data frames or tibbles into special lazy datatable objects. You do that with dtplyr’s lazy_dt() function.

In the code below, I use a %>% pipe to send the result of read_csv to the lazy_dt() function and then join the two objects the usual dplyr left_join() way:

lazy_dt <- readr::read_csv("") %>%
lazy_lookup <- readr::read_csv("L_UNIQUE_CARRIERS.csv_") %>%

joined_lazy_dt <- left_join(my_lazy_dt, my_lazy_lookup,
by = c("OP_UNIQUE_CARRIER" = "Code"))

That joined_lazy_dt variable is a special dtplyr step object. If you print it, you can see the data.table code that created the object — look at the Call: line in the print() results below. That can be handy! You also see the first few rows of data, and a message that you need to turn that object into a data frame, tibble, or data.table if you want to use the data in there.

Source: local data table [?? x 8]
Call:   `_DT4`[`_DT3`, on = .(Code = OP_UNIQUE_CARRIER), allow.cartesian = TRUE]

  Code  Description          FL_DATE    ORIGIN DEST  DEP_DELAY_NEW X6   
  <chr> <chr>                <date>     <chr>  <chr>         <dbl> <lgl>
1 DL    Delta Air Lines Inc. 2019-08-01 ATL    DFW              31 NA   
2 DL    Delta Air Lines Inc. 2019-08-01 DFW    ATL               0 NA   
3 DL    Delta Air Lines Inc. 2019-08-01 IAH    ATL              40 NA   
4 DL    Delta Air Lines Inc. 2019-08-01 PDX    SLC               0 NA   
5 DL    Delta Air Lines Inc. 2019-08-01 SLC    PDX               0 NA   
6 DL    Delta Air Lines Inc. 2019-08-01 DTW    ATL              10 NA   

# Use to access results

My complete code using pipes:

joined_tibble <- left_join(my_lazy_dt, my_lazy_lookup, 
by = c("OP_UNIQUE_CARRIER" = "Code")) %>%

After running some rather crude benchmarking, data.table code was fastest; dtplyr was almost as fast; dplyr took about twice as long; and base R was 15 or 20 times slower. Major caution here: That performance depends on the structure and size of your data and can vary wildly depending on your task. But it’s safe to say that base R isn’t a great choice for large data sets.

How to merge when you only want rows with matches

For the rest of these examples, I’m going to use two new data sets: Home values by U.S. Zip code from Zillow and some population and other data by Zip code from Simplemaps. If you’d like to follow along, download Median Home Values per Square Foot by Zip code from the Zillow research data page and the free basic database from Simplemaps' US Zip Codes Database page. (Because of licensing issues surrounding this private data, it is not included in the code and data download.)

In the code below, I’ve renamed files. If your data has different names or locations, adjust the code accordingly. 

Base R and data.table

For both base R and data.table, if you want only rows that match, tell the merge() function all = FALSE. The code below reads in files and then runs merge() with all = FALSE:

# Import data
home_values_dt <- fread("Zip_MedianValuePerSqft_AllHomes.csv",
colClasses = c(RegionName = "character"))
pop_density_dt <- fread("simplemaps_uszips_basicv1.6/uszips.csv",
colClasses = c(zip = "character"))
# Merge data
matches1 <- merge(home_values_dt, pop_density_dt,
by.x = "RegionName",
by.y = "zip", all = FALSE)

Note that I set column classes as "character" when using fread() so that five-digit ZIP codes starting with 0 didn’t end up as four-digit numbers.


With dplyr, selecting only rows that match is an inner join.

inner join IDG

Inner join keeps just rows that match in both data sets.

Code is:

# Import data
home_values <- read_csv("Zip_MedianValuePerSqft_AllHomes.csv")
pop_density <- read_csv("simplemaps_uszips_basicv1.6/uszips.csv")
# Merge data with inner join
matches2 <- inner_join(home_values, pop_density,
c("RegionName" = "zip"))

With readr’s read_csv(), the Zip code columns automatically come in as character strings.

data.table bracket syntax

If you want to use data.table’s bracket syntax, add the argument nomatch=0 to exclude rows that don’t have a match:

matchesdt <- home_values_dt[pop_density_dt, nomatch = 0]

How to merge when you want all rows

Base R and data.table

With base R or data.table, use merge() with all = TRUE:

all_rows1 <- merge(home_values_dt, pop_density_dt, 
by.x = "RegionName", by.y = "zip", all = TRUE)


With dplyr, this is a full join: 

full join IDG

Full join keeps all rows in both data sets.

all_rows2 <- full_join(home_values, pop_density, 
by = c("RegionName" = "zip"))

How to view rows in a data set without a match

It can be useful to check for rows in a data set that didn’t match, since that can help you understand the limitations of your data and whether something you expected is missing.


In dplyr, finding rows that didn’t match is an anti join.

anti join IDG

Anti join keeps rows from the left data frame without a match.

Here, as with left joins, order matters. To see all the rows in home_values without a match in pop_density:

home_values_no_match <- anti_join(home_values, pop_density, 
by = c("RegionName" = "zip"))

And, to see all rows in pop_density that don’t have a match in home_values:

pop_density_no_match <- anti_join(pop_density, home_values, 
by = c("zip" = "RegionName"))


While merge() syntax is fairly easy for most types of merges, in this case it gets a bit complex if you want rows without a match. I use dplyr’s anti_join() for this type of task, never merge().

If you want to use data.table bracket syntax, use this code to see all the rows in home_values_dt that don’t have a match in pop_density_dt:

home_values_no_match <- home_values_dt[!pop_density_dt]

Note that the code above assumes I’ve already run setkey() on both data sets. And pay attention to the order.  

As we saw earlier, all rows in home_values including those that have a match:



Only rows in home_values that don't have a match: 



Dowle’s full explanation to me about this syntax: “X[Y] looks up X rows using Y as an index. X[!Y] returns all the rows in X that don’t match the Y index. Analogous to X[-c(3,6,10), ] returns all X rows except rows 3, 6, and 10.”

How to merge on multiple columns

Finally, one question I often see: How do you combine data sets on two common columns? 


To use merge() on multiple columns, the syntax is merge(dt1, dt2, by.x = c(”dt1_ColA", dt1_ColB"), by.y = c("dt2_cola", "dt2_colb")).

So, to merge home_values_dt and pop_density_dt on the Zip code and city columns, the code is:

merge2_dt <- merge(home_values_dt, pop_density_dt, 
by.x = c("RegionName", "City"),
by.y = c("zip", "city"),
all.x = TRUE, all.y = FALSE)

setting all.x and all.y as needed.


data.table has a couple of ways to set multiple keys in a data set. There’s setkey() to refer to column names unquoted, and setkeyv() if you want the names quoted in a vector (useful for when this task is within a function).

The formats are

setkey(pop_density_dt, ZipCode, City)
# or
setkeyv(pop_density_dt, c("ZipCode", "City"))


setkey(pop_density_dt, zip, city)
# or
setkeyv(pop_density_dt, c("zip", "city"))

Then use your bracket syntax as usual, such as pop_density_dt[home_values_dt] .

Want more R tips? Head to the Do More With R page!

Copyright © 2019 IDG Communications, Inc.

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