This vignette discusses the default usage of reshaping functions melt (wide to long) and dcast (long to wide) for data.tables as well as the new extended functionalities of melting and casting on multiple columns available from v1.9.6.

### Data

We will load the data sets directly within sections.

### Introduction

The melt and dcast functions for data.tables are for reshaping wide-to-long and long-to-wide, respectively; the implementations are specifically designed with large in-memory data (e.g. 10Gb) in mind.

In this vignette, we will

1. First briefly look at the default melting and dcasting of data.tables to convert them from wide to long format and vice versa

2. Look at scenarios where the current functionalities become cumbersome and inefficient

3. Finally look at the new improvements to both melt and dcast methods for data.tables to handle multiple columns simultaneously.

The extended functionalities are in line with data.table’s philosophy of performing operations efficiently and in a straightforward manner.

### 1. Default functionality

#### a) melting data.tables (wide to long)

Suppose we have a data.table (artificial data) as shown below:

s1 <- "family_id age_mother dob_child1 dob_child2 dob_child3
1         30 1998-11-26 2000-01-29         NA
2         27 1996-06-22         NA         NA
3         26 2002-07-11 2004-04-05 2007-09-02
4         32 2004-10-10 2009-08-27 2012-07-21
5         29 2000-12-05 2005-02-28         NA"
DT
#    family_id age_mother dob_child1 dob_child2 dob_child3
#        <int>      <int>     <IDat>     <IDat>     <IDat>
# 1:         1         30 1998-11-26 2000-01-29       <NA>
# 2:         2         27 1996-06-22       <NA>       <NA>
# 3:         3         26 2002-07-11 2004-04-05 2007-09-02
# 4:         4         32 2004-10-10 2009-08-27 2012-07-21
# 5:         5         29 2000-12-05 2005-02-28       <NA>
## dob stands for date of birth.

str(DT)
# Classes 'data.table' and 'data.frame':    5 obs. of  5 variables:
#  $family_id : int 1 2 3 4 5 #$ age_mother: int  30 27 26 32 29
#  $dob_child1: IDate, format: "1998-11-26" "1996-06-22" "2002-07-11" ... #$ dob_child2: IDate, format: "2000-01-29" NA "2004-04-05" ...
#  $dob_child3: IDate, format: NA NA "2007-09-02" ... # - attr(*, ".internal.selfref")=<externalptr> ##### - Convert DT to long form where each dob is a separate observation. We could accomplish this using melt() by specifying id.vars and measure.vars arguments as follows: DT.m1 = melt(DT, id.vars = c("family_id", "age_mother"), measure.vars = c("dob_child1", "dob_child2", "dob_child3")) DT.m1 # family_id age_mother variable value # <int> <int> <fctr> <IDat> # 1: 1 30 dob_child1 1998-11-26 # 2: 2 27 dob_child1 1996-06-22 # 3: 3 26 dob_child1 2002-07-11 # 4: 4 32 dob_child1 2004-10-10 # 5: 5 29 dob_child1 2000-12-05 # 6: 1 30 dob_child2 2000-01-29 # 7: 2 27 dob_child2 <NA> # 8: 3 26 dob_child2 2004-04-05 # 9: 4 32 dob_child2 2009-08-27 # 10: 5 29 dob_child2 2005-02-28 # 11: 1 30 dob_child3 <NA> # 12: 2 27 dob_child3 <NA> # 13: 3 26 dob_child3 2007-09-02 # 14: 4 32 dob_child3 2012-07-21 # 15: 5 29 dob_child3 <NA> str(DT.m1) # Classes 'data.table' and 'data.frame': 15 obs. of 4 variables: #$ family_id : int  1 2 3 4 5 1 2 3 4 5 ...
#  $age_mother: int 30 27 26 32 29 30 27 26 32 29 ... #$ variable  : Factor w/ 3 levels "dob_child1","dob_child2",..: 1 1 1 1 1 2 2 2 2 2 ...
#  $value : IDate, format: "1998-11-26" "1996-06-22" "2002-07-11" ... # - attr(*, ".internal.selfref")=<externalptr> • measure.vars specify the set of columns we would like to collapse (or combine) together. • We can also specify column indices instead of names. • By default, variable column is of type factor. Set variable.factor argument to FALSE if you’d like to return a character vector instead. • By default, the molten columns are automatically named variable and value. • melt preserves column attributes in result. ##### - Name the variable and value columns to child and dob respectively DT.m1 = melt(DT, measure.vars = c("dob_child1", "dob_child2", "dob_child3"), variable.name = "child", value.name = "dob") DT.m1 # family_id age_mother child dob # <int> <int> <fctr> <IDat> # 1: 1 30 dob_child1 1998-11-26 # 2: 2 27 dob_child1 1996-06-22 # 3: 3 26 dob_child1 2002-07-11 # 4: 4 32 dob_child1 2004-10-10 # 5: 5 29 dob_child1 2000-12-05 # 6: 1 30 dob_child2 2000-01-29 # 7: 2 27 dob_child2 <NA> # 8: 3 26 dob_child2 2004-04-05 # 9: 4 32 dob_child2 2009-08-27 # 10: 5 29 dob_child2 2005-02-28 # 11: 1 30 dob_child3 <NA> # 12: 2 27 dob_child3 <NA> # 13: 3 26 dob_child3 2007-09-02 # 14: 4 32 dob_child3 2012-07-21 # 15: 5 29 dob_child3 <NA> • By default, when one of id.vars or measure.vars is missing, the rest of the columns are automatically assigned to the missing argument. • When neither id.vars nor measure.vars are specified, as mentioned under ?melt, all non-numeric, integer, logical columns will be assigned to id.vars. In addition, a warning message is issued highlighting the columns that are automatically considered to be id.vars. #### b) dcasting data.tables (long to wide) In the previous section, we saw how to get from wide form to long form. Let’s see the reverse operation in this section. ##### - How can we get back to the original data table DT from DT.m1? That is, we’d like to collect all child observations corresponding to each family_id, age_mother together under the same row. We can accomplish it using dcast as follows: dcast(DT.m1, family_id + age_mother ~ child, value.var = "dob") # Key: <family_id, age_mother> # family_id age_mother dob_child1 dob_child2 dob_child3 # <int> <int> <IDat> <IDat> <IDat> # 1: 1 30 1998-11-26 2000-01-29 <NA> # 2: 2 27 1996-06-22 <NA> <NA> # 3: 3 26 2002-07-11 2004-04-05 2007-09-02 # 4: 4 32 2004-10-10 2009-08-27 2012-07-21 # 5: 5 29 2000-12-05 2005-02-28 <NA> • dcast uses formula interface. The variables on the LHS of formula represents the id vars and RHS the measure vars. • value.var denotes the column to be filled in with while casting to wide format. • dcast also tries to preserve attributes in result wherever possible. ##### - Starting from DT.m1, how can we get the number of children in each family? You can also pass a function to aggregate by in dcast with the argument fun.aggregate. This is particularly essential when the formula provided does not identify single observation for each cell. dcast(DT.m1, family_id ~ ., fun.agg = function(x) sum(!is.na(x)), value.var = "dob") # Key: <family_id> # family_id . # <int> <int> # 1: 1 2 # 2: 2 1 # 3: 3 3 # 4: 4 3 # 5: 5 2 Check ?dcast for other useful arguments and additional examples. ### 2. Limitations in current melt/dcast approaches So far we’ve seen features of melt and dcast that are implemented efficiently for data.tables, using internal data.table machinery (fast radix ordering, binary search etc..). However, there are situations we might run into where the desired operation is not expressed in a straightforward manner. For example, consider the data.table shown below: s2 <- "family_id age_mother dob_child1 dob_child2 dob_child3 gender_child1 gender_child2 gender_child3 1 30 1998-11-26 2000-01-29 NA 1 2 NA 2 27 1996-06-22 NA NA 2 NA NA 3 26 2002-07-11 2004-04-05 2007-09-02 2 2 1 4 32 2004-10-10 2009-08-27 2012-07-21 1 1 1 5 29 2000-12-05 2005-02-28 NA 2 1 NA" DT <- fread(s2) DT # family_id age_mother dob_child1 dob_child2 dob_child3 gender_child1 gender_child2 gender_child3 # <int> <int> <IDat> <IDat> <IDat> <int> <int> <int> # 1: 1 30 1998-11-26 2000-01-29 <NA> 1 2 NA # 2: 2 27 1996-06-22 <NA> <NA> 2 NA NA # 3: 3 26 2002-07-11 2004-04-05 2007-09-02 2 2 1 # 4: 4 32 2004-10-10 2009-08-27 2012-07-21 1 1 1 # 5: 5 29 2000-12-05 2005-02-28 <NA> 2 1 NA ## 1 = female, 2 = male And you’d like to combine (melt) all the dob columns together, and gender columns together. Using the current functionality, we can do something like this: DT.m1 = melt(DT, id = c("family_id", "age_mother")) DT.m1[, c("variable", "child") := tstrsplit(variable, "_", fixed = TRUE)] DT.c1 = dcast(DT.m1, family_id + age_mother + child ~ variable, value.var = "value") DT.c1 # Key: <family_id, age_mother, child> # family_id age_mother child dob gender # <int> <int> <char> <IDat> <IDat> # 1: 1 30 child1 1998-11-26 1970-01-02 # 2: 1 30 child2 2000-01-29 1970-01-03 # 3: 1 30 child3 <NA> <NA> # 4: 2 27 child1 1996-06-22 1970-01-03 # 5: 2 27 child2 <NA> <NA> # 6: 2 27 child3 <NA> <NA> # 7: 3 26 child1 2002-07-11 1970-01-03 # 8: 3 26 child2 2004-04-05 1970-01-03 # 9: 3 26 child3 2007-09-02 1970-01-02 # 10: 4 32 child1 2004-10-10 1970-01-02 # 11: 4 32 child2 2009-08-27 1970-01-02 # 12: 4 32 child3 2012-07-21 1970-01-02 # 13: 5 29 child1 2000-12-05 1970-01-03 # 14: 5 29 child2 2005-02-28 1970-01-02 # 15: 5 29 child3 <NA> <NA> str(DT.c1) ## gender column is character type now! # Classes 'data.table' and 'data.frame': 15 obs. of 5 variables: #$ family_id : int  1 1 1 2 2 2 3 3 3 4 ...
#  $age_mother: int 30 30 30 27 27 27 26 26 26 32 ... #$ child     : chr  "child1" "child2" "child3" "child1" ...
#  $dob : IDate, format: "1998-11-26" "2000-01-29" NA ... #$ gender    : IDate, format: "1970-01-02" "1970-01-03" NA ...
#  - attr(*, ".internal.selfref")=<externalptr>
#  - attr(*, "sorted")= chr [1:3] "family_id" "age_mother" "child"
##### Issues
1. What we wanted to do was to combine all the dob and gender type columns together respectively. Instead we are combining everything together, and then splitting them again. I think it’s easy to see that it’s quite roundabout (and inefficient).

As an analogy, imagine you’ve a closet with four shelves of clothes and you’d like to put together the clothes from shelves 1 and 2 together (in 1), and 3 and 4 together (in 3). What we are doing is more or less to combine all the clothes together, and then split them back on to shelves 1 and 3!

2. The columns to melt may be of different types, as in this case (character and integer types). By melting them all together, the columns will be coerced in result, as explained by the warning message above and shown from output of str(DT.c1), where gender has been converted to character type.

3. We are generating an additional column by splitting the variable column into two columns, whose purpose is quite cryptic. We do it because we need it for casting in the next step.

4. Finally, we cast the data set. But the issue is it’s a much more computationally involved operation than melt. Specifically, it requires computing the order of the variables in formula, and that’s costly.

In fact, stats::reshape is capable of performing this operation in a very straightforward manner. It is an extremely useful and often underrated function. You should definitely give it a try!

### 3. Enhanced (new) functionality

#### a) Enhanced melt

Since we’d like for data.tables to perform this operation straightforward and efficient using the same interface, we went ahead and implemented an additional functionality, where we can melt to multiple columns simultaneously.

##### - melt multiple columns simultaneously

The idea is quite simple. We pass a list of columns to measure.vars, where each element of the list contains the columns that should be combined together.

colA = paste0("dob_child", 1:3)
colB = paste0("gender_child", 1:3)
DT.m2 = melt(DT, measure = list(colA, colB), value.name = c("dob", "gender"))
DT.m2
#     family_id age_mother variable        dob gender
#         <int>      <int>   <fctr>     <IDat>  <int>
#  1:         1         30        1 1998-11-26      1
#  2:         2         27        1 1996-06-22      2
#  3:         3         26        1 2002-07-11      2
#  4:         4         32        1 2004-10-10      1
#  5:         5         29        1 2000-12-05      2
#  6:         1         30        2 2000-01-29      2
#  7:         2         27        2       <NA>     NA
#  8:         3         26        2 2004-04-05      2
#  9:         4         32        2 2009-08-27      1
# 10:         5         29        2 2005-02-28      1
# 11:         1         30        3       <NA>     NA
# 12:         2         27        3       <NA>     NA
# 13:         3         26        3 2007-09-02      1
# 14:         4         32        3 2012-07-21      1
# 15:         5         29        3       <NA>     NA

str(DT.m2) ## col type is preserved
# Classes 'data.table' and 'data.frame':    15 obs. of  5 variables:
#  $family_id : int 1 2 3 4 5 1 2 3 4 5 ... #$ age_mother: int  30 27 26 32 29 30 27 26 32 29 ...
#  $variable : Factor w/ 3 levels "1","2","3": 1 1 1 1 1 2 2 2 2 2 ... #$ dob       : IDate, format: "1998-11-26" "1996-06-22" "2002-07-11" ...
#  \$ gender    : int  1 2 2 1 2 2 NA 2 1 1 ...
#  - attr(*, ".internal.selfref")=<externalptr>
• We can remove the variable column if necessary.

• The functionality is implemented entirely in C, and is therefore both fast and memory efficient in addition to being straightforward.

##### - Using patterns()

Usually in these problems, the columns we’d like to melt can be distinguished by a common pattern. We can use the function patterns(), implemented for convenience, to provide regular expressions for the columns to be combined together. The above operation can be rewritten as:

DT.m2 = melt(DT, measure = patterns("^dob", "^gender"), value.name = c("dob", "gender"))
print(DT.m2, class=TRUE)
#     family_id age_mother variable        dob gender
#         <int>      <int>   <fctr>     <IDat>  <int>
#  1:         1         30        1 1998-11-26      1
#  2:         2         27        1 1996-06-22      2
#  3:         3         26        1 2002-07-11      2
#  4:         4         32        1 2004-10-10      1
#  5:         5         29        1 2000-12-05      2
#  6:         1         30        2 2000-01-29      2
#  7:         2         27        2       <NA>     NA
#  8:         3         26        2 2004-04-05      2
#  9:         4         32        2 2009-08-27      1
# 10:         5         29        2 2005-02-28      1
# 11:         1         30        3       <NA>     NA
# 12:         2         27        3       <NA>     NA
# 13:         3         26        3 2007-09-02      1
# 14:         4         32        3 2012-07-21      1
# 15:         5         29        3       <NA>     NA
##### - Using measure() to specify measure.vars via separator or pattern

If, as in the data above, the input columns to melt have regular names, then we can use measure, which allows specifying the columns to melt via a separator or a regex. For example consider the iris data,

(two.iris = data.table(datasets::iris)[c(1,150)])
#    Sepal.Length Sepal.Width Petal.Length Petal.Width   Species
#           <num>       <num>        <num>       <num>    <fctr>
# 1:          5.1         3.5          1.4         0.2    setosa
# 2:          5.9         3.0          5.1         1.8 virginica

The iris data has four numeric columns with a regular structure: first the flower part, then a period, then the measurement dimension. To specify that we want to melt those four columns, we can use measure with sep="." which means to use strsplit on all column names; the columns which result in the maximum number of groups after splitting will be used as measure.vars:

melt(two.iris, measure.vars = measure(part, dim, sep="."))
#      Species   part    dim value
#       <fctr> <char> <char> <num>
# 1:    setosa  Sepal Length   5.1
# 2: virginica  Sepal Length   5.9
# 3:    setosa  Sepal  Width   3.5
# 4: virginica  Sepal  Width   3.0
# 5:    setosa  Petal Length   1.4
# 6: virginica  Petal Length   5.1
# 7:    setosa  Petal  Width   0.2
# 8: virginica  Petal  Width   1.8

The first two arguments to measure in the code above (part and dim) are used to name the output columns; the number of arguments must equal the max number of groups after splitting with sep.

If we want two value columns, one for each part, we can use the special value.name keyword, which means to output a value column for each unique name found in that group:

melt(two.iris, measure.vars = measure(value.name, dim, sep="."))
#      Species    dim Sepal Petal
#       <fctr> <char> <num> <num>
# 1:    setosa Length   5.1   1.4
# 2: virginica Length   5.9   5.1
# 3:    setosa  Width   3.5   0.2
# 4: virginica  Width   3.0   1.8

Using the code above we get one value column per flower part. If we instead want a value column for each measurement dimension, we can do

melt(two.iris, measure.vars = measure(part, value.name, sep="."))
#      Species   part Length Width
#       <fctr> <char>  <num> <num>
# 1:    setosa  Sepal    5.1   3.5
# 2: virginica  Sepal    5.9   3.0
# 3:    setosa  Petal    1.4   0.2
# 4: virginica  Petal    5.1   1.8

Going back to the example of the data with families and children, we can see a more complex usage of measure, involving a function which is used to convert the child string values to integers:

DT.m3 = melt(DT, measure = measure(value.name, child=as.integer, sep="_child"))
print(DT.m3, class=TRUE)
#     family_id age_mother child        dob gender
#         <int>      <int> <int>     <IDat>  <int>
#  1:         1         30     1 1998-11-26      1
#  2:         2         27     1 1996-06-22      2
#  3:         3         26     1 2002-07-11      2
#  4:         4         32     1 2004-10-10      1
#  5:         5         29     1 2000-12-05      2
#  6:         1         30     2 2000-01-29      2
#  7:         2         27     2       <NA>     NA
#  8:         3         26     2 2004-04-05      2
#  9:         4         32     2 2009-08-27      1
# 10:         5         29     2 2005-02-28      1
# 11:         1         30     3       <NA>     NA
# 12:         2         27     3       <NA>     NA
# 13:         3         26     3 2007-09-02      1
# 14:         4         32     3 2012-07-21      1
# 15:         5         29     3       <NA>     NA

In the code above we used sep="_child" which results in melting only the columns which contain that string (six column names split into two groups each). The child=as.integer argument means the second group will result in an output column named child with values defined by plugging the character strings from that group into the function as.integer.

Finally we consider an example (borrowed from tidyr package) where we need to define the groups using a regular expression rather than a separator.

(who <- data.table(id=1, new_sp_m5564=2, newrel_f65=3))
#       id new_sp_m5564 newrel_f65
#    <num>        <num>      <num>
# 1:     1            2          3
melt(who, measure.vars = measure(
diagnosis, gender, ages, pattern="new_?(.*)_(.)(.*)"))
#       id diagnosis gender   ages value
#    <num>    <char> <char> <char> <num>
# 1:     1        sp      m   5564     2
# 2:     1       rel      f     65     3

When using the pattern argument, it must be a Perl-compatible regular expression containing the same number of capture groups (parenthesized sub-expressions) as the number other arguments (group names). The code below shows how to use a more complex regex with five groups, two numeric output columns, and an anonymous type conversion function,

print(melt(who, measure.vars = measure(
diagnosis, gender, ages,
ymin=as.numeric,
ymax=function(y)ifelse(y=="", Inf, as.numeric(y)),
pattern="new_?(.*)_(.)(([0-9]{2})([0-9]{0,2}))"
)), class=TRUE)
#       id diagnosis gender   ages  ymin  ymax value
#    <num>    <char> <char> <char> <num> <num> <num>
# 1:     1        sp      m   5564    55    64     2
# 2:     1       rel      f     65    65   Inf     3

#### b) Enhanced dcast

Okay great! We can now melt into multiple columns simultaneously. Now given the data set DT.m2 as shown above, how can we get back to the same format as the original data we started with?

If we use the current functionality of dcast, then we’d have to cast twice and bind the results together. But that’s once again verbose, not straightforward and is also inefficient.

##### - Casting multiple value.vars simultaneously

We can now provide multiple value.var columns to dcast for data.tables directly so that the operations are taken care of internally and efficiently.

## new 'cast' functionality - multiple value.vars
DT.c2 = dcast(DT.m2, family_id + age_mother ~ variable, value.var = c("dob", "gender"))
DT.c2
# Key: <family_id, age_mother>
#    family_id age_mother      dob_1      dob_2      dob_3 gender_1 gender_2 gender_3
#        <int>      <int>     <IDat>     <IDat>     <IDat>    <int>    <int>    <int>
# 1:         1         30 1998-11-26 2000-01-29       <NA>        1        2       NA
# 2:         2         27 1996-06-22       <NA>       <NA>        2       NA       NA
# 3:         3         26 2002-07-11 2004-04-05 2007-09-02        2        2        1
# 4:         4         32 2004-10-10 2009-08-27 2012-07-21        1        1        1
# 5:         5         29 2000-12-05 2005-02-28       <NA>        2        1       NA
• Attributes are preserved in result wherever possible.

• Everything is taken care of internally, and efficiently. In addition to being fast, it is also very memory efficient.

##### Multiple functions to fun.aggregate:

You can also provide multiple functions to fun.aggregate to dcast for data.tables. Check the examples in ?dcast which illustrates this functionality.