library(joyn)
#>
#> Attaching package: 'joyn'
#> The following object is masked from 'package:base':
#>
#> mergeOverview
📌 In joyn, there are two major sets of tools to join
data tables:
The primary function
joyn()Dplyr-like join functions:
left_join(),right_join(),full_join(),inner_join()
This vignette will explore the main function joyn(). You
can read about dplyr-joins in the “dplyr-joins” article
instead.
General use
library(joyn)
library(data.table)
x1 <- data.table(id = c(1L, 1L, 2L, 3L, NA_integer_),
t = c(1L, 2L, 1L, 2L, NA_integer_),
x = 11:15)
y1 <- data.table(id = c(1,2, 4),
y = c(11L, 15L, 16))
x2 <- data.table(id = c(1, 4, 2, 3, NA),
t = c(1L, 2L, 1L, 2L, NA_integer_),
x = c(16, 12, NA, NA, 15))
y2 <- data.table(id = c(1, 2, 5, 6, 3),
yd = c(1, 2, 5, 6, 3),
y = c(11L, 15L, 20L, 13L, 10L),
x = c(16:20))
x3 <- data.table(id = c("c","b", "d", "d"),
v = 8:11,
foo = c(4,2, 7, 3))
y3 <- data.table(id = c("c","b", "c", "a"),
y = c(11L, 15L, 18L, 20L))
x4 <- data.table(id1 = c(1, 1, 2, 3, 3),
id2 = c(1, 1, 2, 3, 4),
t = c(1L, 2L, 1L, 2L, NA_integer_),
x = c(16, 12, NA, NA, 15))
y4 <- data.table(id = c(1, 2, 5, 6, 3),
id2 = c(1, 1, 2, 3, 4),
y = c(11L, 15L, 20L, 13L, 10L),
x = c(16:20))
x5 <- data.table(id = c(1, 4, 2, 3, NA),
t = c(1L, 2L, 1L, 2L, NA),
country = c(16, 12, 3, NA, 15))
y5 <- data.table(id = c(1, 2, 2, 6, 3),
gdp = c(11L, 15L, 20L, 13L, 10L),
country = 16:20)The basics
Let’s suppose that you want to join the two tables x1
and y1.
# Calling joyn() to join x1 and y1
joyn(x = x1,
y = y1,
match_type = "m:1" ) #Note RT: remove this argument once fixing the default value
#> id t x y .joyn
#> <num> <int> <int> <num> <fctr>
#> 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: NA NA 15 NA x
#> 6: 4 NA NA 16 yThe output table is the result of a full join -which is what
joyn always executes by the default. This means that the
returning table will retains both matching and non matching rows from
both x1 and y1. Notice that the resulting
table also contains an additional variable called .joyn,
which is the reporting variable. (Read below ⬇️)
Reporting variable
A particular feature of joyn is that it includes the
reportvar in the returning table, which
informs you about the status of the join. You can modify both the name
and the format of the reporting variable as follows:
Name: by default
reportvar = ".joyn", but you can modify it withreportvar = "myname"specifying the name you want to assignFormat: by default
reporttype = "character", but you can also set it to numeric usingreporttype = "numeric"
You can see the difference between the two types in the table below1:
| numeric | character | meaning |
|---|---|---|
| 1 | x | Obs only available in x table |
| 2 | y | Obs only available in y table |
| 3 | x & y | Matching obs available in both tables |
| 4 | NA updated | NAs in x updated with actual values in variables with same names in y |
| 5 | value updated | Actual values and NAs in x updated with actual values in variables with same names in y |
| 6 | not updated | Actual values and NAs in x are NOT updated with actual values in y |
Key variables
When performing a join, you might want to specify which variable(s)
joyn should join by.
While by default joyn will consider the variable(s) in
common between x and y as key(s) for the join,
our suggestion is to make the keys explicit - i.e., specifying it/them
in the by argument
# Join with one variable in common
joyn(x = x1,
y = y1,
by = "id",
match_type = "m:1")
#> id t x y .joyn
#> <num> <int> <int> <num> <fctr>
#> 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: NA NA 15 NA x
#> 6: 4 NA NA 16 yIf you don’t want to join by all variables in common between
x and y, you can alternately use equivalency
as an element of by vector. This specification allows you
to join on different variables between x and
y.
joyn(x = x4,
y = y4,
by = c("id1 = id", "id2"),
match_type = "m:m")
#> id1 id2 t x y .joyn
#> <num> <num> <int> <num> <int> <fctr>
#> 1: 1 1 1 16 11 x & y
#> 2: 1 1 2 12 11 x & y
#> 3: 2 2 1 NA NA x
#> 4: 3 3 2 NA NA x
#> 5: 3 4 NA 15 10 x & y
#> 6: 2 1 NA NA 15 y
#> 7: 5 2 NA NA 20 y
#> 8: 6 3 NA NA 13 yAlso, notice that joyn will sort the
resulting table by key variables in by. This is because
sort = TRUE by default.
Match type
💡Match type refers to the relationship that exists between the
observations of the joining tables. The possibility to perform joins
based on the match type is one of the value added of using
joyn.
Following Stata’s convention, we can have four different match types:
1:1 (one to one): the default2, the variables specified in
byvariables uniquely identify single observations in both table –> each observation in left table has a unique match in the right table and viceversa1:m (one to many): only left table is uniquely identified by
byvariables –> each observation inbyvar of the left table can have multiple matches inbyvar of the right tablem:1 (many to one): only right table is uniquely identified by
byvar -> each observation in left table can have only one match in the right table but observations in the right table might have multiple matches in the left tablem:m (many to many): variables in
bydoes not uniquely identify the observations in either table –> both tables can have multiple matches for each observation
We recommend you always specify the match type when joining tables to ensure the output is correct.
# Many to one match type
joyn(x = x1,
y = y1,
by = "id",
match_type = "m:1")
#> id t x y .joyn
#> <num> <int> <int> <num> <fctr>
#> 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: NA NA 15 NA x
#> 6: 4 NA NA 16 y
# Many to many match type
joyn(x = x3,
y = y3,
by = "id",
match_type = "m:m")
#> id v foo y .joyn
#> <char> <int> <num> <int> <fctr>
#> 1: c 8 4 11 x & y
#> 2: c 8 4 18 x & y
#> 3: b 9 2 15 x & y
#> 4: d 10 7 NA x
#> 5: d 11 3 NA x
#> 6: a NA NA 20 y
# One to one match type - the default
joyn(x = x2,
y = y2,
by = "id",
match_type = "1:1")
#> id t x yd y .joyn
#> <num> <int> <num> <num> <int> <fctr>
#> 1: 1 1 16 1 11 x & y
#> 2: 4 2 12 NA NA x
#> 3: 2 1 NA 2 15 x & y
#> 4: 3 2 NA 3 10 x & y
#> 5: NA NA 15 NA NA x
#> 6: 5 NA NA 5 20 y
#> 7: 6 NA NA 6 13 y
# Same join as:
joyn(x = x2,
y = y2,
by = "id")
#> id t x yd y .joyn
#> <num> <int> <num> <num> <int> <fctr>
#> 1: 1 1 16 1 11 x & y
#> 2: 4 2 12 NA NA x
#> 3: 2 1 NA 2 15 x & y
#> 4: 3 2 NA 3 10 x & y
#> 5: NA NA 15 NA NA x
#> 6: 5 NA NA 5 20 y
#> 7: 6 NA NA 6 13 y
# One to many match type
joyn(x = x5,
y = y5,
by = "id",
match_type = "1:m")
#> id t country gdp .joyn
#> <num> <int> <num> <int> <fctr>
#> 1: 1 1 16 11 x & y
#> 2: 4 2 12 NA x
#> 3: 2 1 3 15 x & y
#> 4: 2 1 3 20 x & y
#> 5: 3 2 NA 10 x & y
#> 6: NA NA 15 NA x
#> 7: 6 NA NA 13 yHowever, if are unsure/wrong about the relationships between the
observations in your tables, joyn will let you know that
something is not right. Suppose you think your data is uniquely
identified by variable id, while it is not. By setting
match_type = "1:1" you will get and error, informing you
that the match type is not as expected.
# Merging correctly but getting error because something is not right in the data
joyn(x3, y3, by = "id", match_type = "1:1")
#> ✖ Error: table x is not uniquely identified by id
#> ✖ Error: table y is not uniquely identified by id
#> Error in `check_match_type()`:
#> ! match type inconsistency
#> ℹ set verbose to TRUE to see where the issue is
# Merging wrongly but getting NO errors because you did not use match_type
joyn(x3, y3, by = "id")
#> ✖ Error: table x is not uniquely identified by id
#> ✖ Error: table y is not uniquely identified by id
#> Error in `check_match_type()`:
#> ! match type inconsistency
#> ℹ set verbose to TRUE to see where the issue isIf instead you don’t care about match types or you don’t think it is
necessary to use them for your particular needs, you might be fine
without joyn.
Type of join
Join type determines which observations will be kept after the join.
joyn() allows you to choose which type of join to execute
via the keep argument.
This argument is called keep rather than
join_type to avoid confusion with the argument
match_type, and in order to reflect that what you are
specifying in the end is which observations you want to keep. This
argument plays the role of allowing joyn() to mimic the
behavior of dplyr’s functions left_join,
right_join, inner_join, and
full_join, the default.
keep can be of four types:
-
keep = "full": the default, which keeps all the observations in x and y, regardless of whether they match or not.# Full join joyn(x = x1, y = y1, match_type = "m:m") #> id t x y .joyn #> <num> <int> <int> <num> <fctr> #> 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: NA NA 15 NA x #> 6: 4 NA NA 16 y -
keep = "left"orkeep = "master": keeps all observations inx, both matching and non, and only those observations inythat match inx# keep obs in x joyn(x = x1, y = y1, keep = "left", match_type = "m:m") #> id t x y .joyn #> <num> <int> <int> <num> <fctr> #> 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: NA NA 15 NA x -
keep = "right"orkeep = "using"keeps all observations iny, both matching and non, and only those observations inxthat match iny# keep obs in y joyn(x = x1, y = y1, keep = "right", match_type = "m:m") #> id t x y .joyn #> <num> <int> <int> <num> <fctr> #> 1: 1 1 11 11 x & y #> 2: 1 2 12 11 x & y #> 3: 2 1 13 15 x & y #> 4: 4 NA NA 16 y -
keep = "inner"keeps only those observations that match in both tables.# keep matching obs in both tables joyn(x1, y1, keep = "inner", match_type = "m:m") #> id t x y .joyn #> <num> <int> <int> <num> <fctr> #> 1: 1 1 11 11 x & y #> 2: 1 2 12 11 x & y #> 3: 2 1 13 15 x & y
An important feature: JOYn report and info display
Recall that joyn is intended to be informative about the
status and quality of the merging.
📊 JOYn report
By default, joyn returns the JOYn report ,
i.e., a summary table of the merging. This includes the reporting
variable, the number of rows that come from x, the number
of rows that come from y and those that are common to both
x and y. This info is also shown in percentage
form in the percent column.
joyn(x = x3,
y = y3,
by = "id",
match_type = "m:m",
verbose = TRUE)
#>
#> ── JOYn Report ──
#>
#> .joyn n percent
#> 1 x 2 33.3%
#> 2 y 1 16.7%
#> 3 x & y 3 50%
#> 4 total 6 100%
#> ────────────────────────────────────────────────────────── End of JOYn report ──
#> ℹ Note: Joyn's report available in variable .joyn
#> ℹ Note: Removing key variables id from id and y
#> id v foo y .joyn
#> <char> <int> <num> <int> <fctr>
#> 1: c 8 4 11 x & y
#> 2: c 8 4 18 x & y
#> 3: b 9 2 15 x & y
#> 4: d 10 7 NA x
#> 5: d 11 3 NA x
#> 6: a NA NA 20 y📝 Displaying messages
One of the value added of joyn is that it produces a
number of messages that are intended to inform you about the status of
the join. The display of such messages is controlled by the argument
verbose, which allows you to show
(verbose = TRUE) or silent (verbose = FALSE)
any messages.
To further explore messages in joyn, please refer to the
“Messages” article.