| Title: | A `DataFrame` (`S4Vectors`) backend for `dplyr` |
|---|---|
| Description: | Provides `dplyr` verbs (`mutate`, `select`, `filter`, etc...) supporting `S4Vectors::DataFrame` objects. Importantly, this is achieved without conversion to an intermediate `tibble`. Adds grouping infrastructure to `DataFrame` which is respected by the transformation verbs. |
| Authors: | Jonathan Carroll [aut, cre] |
| Maintainer: | Jonathan Carroll <[email protected]> |
| License: | GPL-3 |
| Version: | 1.1.0 |
| Built: | 2024-10-30 05:22:17 UTC |
| Source: | https://github.com/bioc/DFplyr |
S4Vectors::DataFrame as a dplyr data sourceAdd dplyr compatibility to S4Vectors::DataFrame
for use with a selection of dplyr verbs.
x |
A |
Maintainer: Jonathan Carroll [email protected] (ORCID)
Useful links:
library(S4Vectors) library(dplyr) d <- as(mtcars, "DataFrame") mutate(d, newvar = cyl + hp) mutate_at(d, vars(starts_with("c")), ~ .^2) group_by(d, cyl, am) %>% tally(gear) count(d, gear, am, cyl) select(d, am, cyl) select(d, am, cyl) %>% rename2(foo = am) arrange(d, desc(hp)) rbind(DataFrame(mtcars[1, ], row.names = "MyCar"), d) %>% distinct() filter(d, am == 0) slice(d, 3:6)library(S4Vectors) library(dplyr) d <- as(mtcars, "DataFrame") mutate(d, newvar = cyl + hp) mutate_at(d, vars(starts_with("c")), ~ .^2) group_by(d, cyl, am) %>% tally(gear) count(d, gear, am, cyl) select(d, am, cyl) select(d, am, cyl) %>% rename2(foo = am) arrange(d, desc(hp)) rbind(DataFrame(mtcars[1, ], row.names = "MyCar"), d) %>% distinct() filter(d, am == 0) slice(d, 3:6)
arrange() orders the rows of a data frame by the values of selected
columns.
Unlike other dplyr verbs, arrange() largely ignores grouping; you
need to explicitly mention grouping variables (or use .by_group = TRUE)
in order to group by them, and functions of variables are evaluated
once per data frame, not once per group.
## S3 method for class 'DataFrame' arrange(.data, ...)## S3 method for class 'DataFrame' arrange(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< |
Unlike base sorting with sort(), NA are:
always sorted to the end for local data, even when wrapped with desc().
treated differently for remote data, depending on the backend.
An object of the same type as .data. The output has the following
properties:
All rows appear in the output, but (usually) in a different place.
Columns are not modified.
Groups are not modified.
Data frame attributes are preserved.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Other single table verbs:
filter(),
mutate(),
reframe(),
rename(),
select(),
slice(),
summarise()
arrange(mtcars, cyl, disp) arrange(mtcars, desc(disp)) # grouped arrange ignores groups by_cyl <- mtcars %>% group_by(cyl) by_cyl %>% arrange(desc(wt)) # Unless you specifically ask: by_cyl %>% arrange(desc(wt), .by_group = TRUE) # use embracing when wrapping in a function; # see ?rlang::args_data_masking for more details tidy_eval_arrange <- function(.data, var) { .data %>% arrange({{ var }}) } tidy_eval_arrange(mtcars, mpg) # Use `across()` or `pick()` to select columns with tidy-select iris %>% arrange(pick(starts_with("Sepal"))) iris %>% arrange(across(starts_with("Sepal"), desc))arrange(mtcars, cyl, disp) arrange(mtcars, desc(disp)) # grouped arrange ignores groups by_cyl <- mtcars %>% group_by(cyl) by_cyl %>% arrange(desc(wt)) # Unless you specifically ask: by_cyl %>% arrange(desc(wt), .by_group = TRUE) # use embracing when wrapping in a function; # see ?rlang::args_data_masking for more details tidy_eval_arrange <- function(.data, var) { .data %>% arrange({{ var }}) } tidy_eval_arrange(mtcars, mpg) # Use `across()` or `pick()` to select columns with tidy-select iris %>% arrange(pick(starts_with("Sepal"))) iris %>% arrange(across(starts_with("Sepal"), desc))
count() lets you quickly count the unique values of one or more variables:
df %>% count(a, b) is roughly equivalent to
df %>% group_by(a, b) %>% summarise(n = n()).
count() is paired with tally(), a lower-level helper that is equivalent
to df %>% summarise(n = n()). Supply wt to perform weighted counts,
switching the summary from n = n() to n = sum(wt).
add_count() and add_tally() are equivalents to count() and tally()
but use mutate() instead of summarise() so that they add a new column
with group-wise counts.
## S3 method for class 'DataFrame' count( x, ..., wt = NULL, sort = FALSE, name = "n", .drop = group_by_drop_default(x) )## S3 method for class 'DataFrame' count( x, ..., wt = NULL, sort = FALSE, name = "n", .drop = group_by_drop_default(x) )
x |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). |
... |
< |
wt |
<
|
sort |
If |
name |
The name of the new column in the output. If omitted, it will default to |
.drop |
Handling of factor levels that don't appear in the data, passed
on to For
|
An object of the same type as .data. count() and add_count()
group transiently, so the output has the same groups as the input.
# count() is a convenient way to get a sense of the distribution of # values in a dataset starwars %>% count(species) starwars %>% count(species, sort = TRUE) starwars %>% count(sex, gender, sort = TRUE) starwars %>% count(birth_decade = round(birth_year, -1)) # use the `wt` argument to perform a weighted count. This is useful # when the data has already been aggregated once df <- tribble( ~name, ~gender, ~runs, "Max", "male", 10, "Sandra", "female", 1, "Susan", "female", 4 ) # counts rows: df %>% count(gender) # counts runs: df %>% count(gender, wt = runs) # When factors are involved, `.drop = FALSE` can be used to retain factor # levels that don't appear in the data df2 <- tibble( id = 1:5, type = factor(c("a", "c", "a", NA, "a"), levels = c("a", "b", "c")) ) df2 %>% count(type) df2 %>% count(type, .drop = FALSE) # Or, using `group_by()`: df2 %>% group_by(type, .drop = FALSE) %>% count() # tally() is a lower-level function that assumes you've done the grouping starwars %>% tally() starwars %>% group_by(species) %>% tally() # both count() and tally() have add_ variants that work like # mutate() instead of summarise df %>% add_count(gender, wt = runs) df %>% add_tally(wt = runs)# count() is a convenient way to get a sense of the distribution of # values in a dataset starwars %>% count(species) starwars %>% count(species, sort = TRUE) starwars %>% count(sex, gender, sort = TRUE) starwars %>% count(birth_decade = round(birth_year, -1)) # use the `wt` argument to perform a weighted count. This is useful # when the data has already been aggregated once df <- tribble( ~name, ~gender, ~runs, "Max", "male", 10, "Sandra", "female", 1, "Susan", "female", 4 ) # counts rows: df %>% count(gender) # counts runs: df %>% count(gender, wt = runs) # When factors are involved, `.drop = FALSE` can be used to retain factor # levels that don't appear in the data df2 <- tibble( id = 1:5, type = factor(c("a", "c", "a", NA, "a"), levels = c("a", "b", "c")) ) df2 %>% count(type) df2 %>% count(type, .drop = FALSE) # Or, using `group_by()`: df2 %>% group_by(type, .drop = FALSE) %>% count() # tally() is a lower-level function that assumes you've done the grouping starwars %>% tally() starwars %>% group_by(species) %>% tally() # both count() and tally() have add_ variants that work like # mutate() instead of summarise df %>% add_count(gender, wt = runs) df %>% add_tally(wt = runs)
Transform a vector into a format that will be sorted in descending order.
This is useful within arrange().
desc(x)desc(x)
x |
vector to transform |
the input vector in a format that will be sorted in descending order.
desc(1:10) desc(factor(letters)) first_day <- seq(as.Date("1910/1/1"), as.Date("1920/1/1"), "years") desc(first_day) starwars %>% arrange(desc(mass))desc(1:10) desc(factor(letters)) first_day <- seq(as.Date("1910/1/1"), as.Date("1920/1/1"), "years") desc(first_day) starwars %>% arrange(desc(mass))
Keep only unique/distinct rows from a data frame. This is similar
to unique.data.frame() but considerably faster.
## S3 method for class 'DataFrame' distinct(.data, ..., .keep_all = FALSE)## S3 method for class 'DataFrame' distinct(.data, ..., .keep_all = FALSE)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< |
.keep_all |
If |
An object of the same type as .data. The output has the following
properties:
Rows are a subset of the input but appear in the same order.
Columns are not modified if ... is empty or .keep_all is TRUE.
Otherwise, distinct() first calls mutate() to create new columns.
Groups are not modified.
Data frame attributes are preserved.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
df <- tibble( x = sample(10, 100, rep = TRUE), y = sample(10, 100, rep = TRUE) ) nrow(df) nrow(distinct(df)) nrow(distinct(df, x, y)) distinct(df, x) distinct(df, y) # You can choose to keep all other variables as well distinct(df, x, .keep_all = TRUE) distinct(df, y, .keep_all = TRUE) # You can also use distinct on computed variables distinct(df, diff = abs(x - y)) # Use `pick()` to select columns with tidy-select distinct(starwars, pick(contains("color"))) # Grouping ------------------------------------------------- df <- tibble( g = c(1, 1, 2, 2, 2), x = c(1, 1, 2, 1, 2), y = c(3, 2, 1, 3, 1) ) df <- df %>% group_by(g) # With grouped data frames, distinctness is computed within each group df %>% distinct(x) # When `...` are omitted, `distinct()` still computes distinctness using # all variables in the data frame df %>% distinct()df <- tibble( x = sample(10, 100, rep = TRUE), y = sample(10, 100, rep = TRUE) ) nrow(df) nrow(distinct(df)) nrow(distinct(df, x, y)) distinct(df, x) distinct(df, y) # You can choose to keep all other variables as well distinct(df, x, .keep_all = TRUE) distinct(df, y, .keep_all = TRUE) # You can also use distinct on computed variables distinct(df, diff = abs(x - y)) # Use `pick()` to select columns with tidy-select distinct(starwars, pick(contains("color"))) # Grouping ------------------------------------------------- df <- tibble( g = c(1, 1, 2, 2, 2), x = c(1, 1, 2, 1, 2), y = c(3, 2, 1, 3, 1) ) df <- df %>% group_by(g) # With grouped data frames, distinctness is computed within each group df %>% distinct(x) # When `...` are omitted, `distinct()` still computes distinctness using # all variables in the data frame df %>% distinct()
The filter() function is used to subset a data frame,
retaining all rows that satisfy your conditions.
To be retained, the row must produce a value of TRUE for all conditions.
Note that when a condition evaluates to NA
the row will be dropped, unlike base subsetting with [.
## S3 method for class 'DataFrame' filter(.data, ..., .preserve = FALSE)## S3 method for class 'DataFrame' filter(.data, ..., .preserve = FALSE)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< |
.preserve |
Relevant when the |
The filter() function is used to subset the rows of
.data, applying the expressions in ... to the column values to determine which
rows should be retained. It can be applied to both grouped and ungrouped data (see group_by() and
ungroup()). However, dplyr is not yet smart enough to optimise the filtering
operation on grouped datasets that do not need grouped calculations. For this
reason, filtering is often considerably faster on ungrouped data.
An object of the same type as .data. The output has the following properties:
Rows are a subset of the input, but appear in the same order.
Columns are not modified.
The number of groups may be reduced (if .preserve is not TRUE).
Data frame attributes are preserved.
There are many functions and operators that are useful when constructing the expressions used to filter the data:
Because filtering expressions are computed within groups, they may yield different results on grouped tibbles. This will be the case as soon as an aggregating, lagging, or ranking function is involved. Compare this ungrouped filtering:
starwars %>% filter(mass > mean(mass, na.rm = TRUE))
With the grouped equivalent:
starwars %>% group_by(gender) %>% filter(mass > mean(mass, na.rm = TRUE))
In the ungrouped version, filter() compares the value of mass in each row to
the global average (taken over the whole data set), keeping only the rows with
mass greater than this global average. In contrast, the grouped version calculates
the average mass separately for each gender group, and keeps rows with mass greater
than the relevant within-gender average.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Other single table verbs:
arrange(),
mutate(),
reframe(),
rename(),
select(),
slice(),
summarise()
# Filtering by one criterion filter(starwars, species == "Human") filter(starwars, mass > 1000) # Filtering by multiple criteria within a single logical expression filter(starwars, hair_color == "none" & eye_color == "black") filter(starwars, hair_color == "none" | eye_color == "black") # When multiple expressions are used, they are combined using & filter(starwars, hair_color == "none", eye_color == "black") # The filtering operation may yield different results on grouped # tibbles because the expressions are computed within groups. # # The following filters rows where `mass` is greater than the # global average: starwars %>% filter(mass > mean(mass, na.rm = TRUE)) # Whereas this keeps rows with `mass` greater than the gender # average: starwars %>% group_by(gender) %>% filter(mass > mean(mass, na.rm = TRUE)) # To refer to column names that are stored as strings, use the `.data` pronoun: vars <- c("mass", "height") cond <- c(80, 150) starwars %>% filter( .data[[vars[[1]]]] > cond[[1]], .data[[vars[[2]]]] > cond[[2]] ) # Learn more in ?rlang::args_data_masking# Filtering by one criterion filter(starwars, species == "Human") filter(starwars, mass > 1000) # Filtering by multiple criteria within a single logical expression filter(starwars, hair_color == "none" & eye_color == "black") filter(starwars, hair_color == "none" | eye_color == "black") # When multiple expressions are used, they are combined using & filter(starwars, hair_color == "none", eye_color == "black") # The filtering operation may yield different results on grouped # tibbles because the expressions are computed within groups. # # The following filters rows where `mass` is greater than the # global average: starwars %>% filter(mass > mean(mass, na.rm = TRUE)) # Whereas this keeps rows with `mass` greater than the gender # average: starwars %>% group_by(gender) %>% filter(mass > mean(mass, na.rm = TRUE)) # To refer to column names that are stored as strings, use the `.data` pronoun: vars <- c("mass", "height") cond <- c(80, 150) starwars %>% filter( .data[[vars[[1]]]] > cond[[1]], .data[[vars[[2]]]] > cond[[2]] ) # Learn more in ?rlang::args_data_masking
Format an R object for pretty printing.
## S3 method for class 'DataFrame' format(x, ...)## S3 method for class 'DataFrame' format(x, ...)
x |
any R object (conceptually); typically numeric. |
... |
further arguments passed to or from other methods. |
format is a generic function. Apart from the methods described
here there are methods for dates (see format.Date),
date-times (see format.POSIXct) and for other classes such
as format.octmode and format.dist.
format.data.frame formats the data frame column by column,
applying the appropriate method of format for each column.
Methods for columns are often similar to as.character but offer
more control. Matrix and data-frame columns will be converted to
separate columns in the result, and character columns (normally all)
will be given class "AsIs".
format.factor converts the factor to a character vector and
then calls the default method (and so justify applies).
format.AsIs deals with columns of complicated objects that
have been extracted from a data frame. Character objects and (atomic)
matrices are passed to the default method (and so width does
not apply).
Otherwise it calls toString to convert the object
to character (if a vector or list, element by element) and then
right-justifies the result.
Justification for character vectors (and objects converted to
character vectors by their methods) is done on display width (see
nchar), taking double-width characters and the rendering
of special characters (as escape sequences, including escaping
backslash but not double quote: see print.default) into
account. Thus the width is as displayed by print(quote =
FALSE) and not as displayed by cat. Character strings
are padded with blanks to the display width of the widest. (If
na.encode = FALSE missing character strings are not included in
the width computations and are not encoded.)
Numeric vectors are encoded with the minimum number of decimal places
needed to display all the elements to at least the digits
significant digits. However, if all the elements then have trailing
zeroes, the number of decimal places is reduced until at least one
element has a non-zero final digit; see also the argument
documentation for big.*, small.* etc, above. See the
note in print.default about digits >= 16.
Raw vectors are converted to their 2-digit hexadecimal representation
by as.character.
format.default(x) now provides a “minimal” string when
isS4(x) is true.
The internal code respects the option
getOption("OutDec") for the ‘decimal mark’, so if
this is set to something other than "." then it takes precedence
over argument decimal.mark.
An object of similar structure to x containing character
representations of the elements of the first argument x
in a common format, and in the current locale's encoding.
For character, numeric, complex or factor x, dims and dimnames
are preserved on matrices/arrays and names on vectors: no other
attributes are copied.
If x is a list, the result is a character vector obtained by
applying format.default(x, ...) to each element of the list
(after unlisting elements which are themselves lists),
and then collapsing the result for each element with
paste(collapse = ", "). The defaults in this case are
trim = TRUE, justify = "none" since one does not usually want
alignment in the collapsed strings.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.
format.info indicates how an atomic vector would be
formatted.
formatC, paste, as.character,
sprintf, print, prettyNum,
toString, encodeString.
format(1:10) format(1:10, trim = TRUE) zz <- data.frame("(row names)"= c("aaaaa", "b"), check.names = FALSE) format(zz) format(zz, justify = "left") ## use of nsmall format(13.7) format(13.7, nsmall = 3) format(c(6.0, 13.1), digits = 2) format(c(6.0, 13.1), digits = 2, nsmall = 1) ## use of scientific format(2^31-1) format(2^31-1, scientific = TRUE) ## a list z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,10,100,1000), d = c("a", "longer", "character", "string"), q = quote( a + b ), e = expression(1+x)) ## can you find the "2" small differences? (f1 <- format(z, digits = 2)) (f2 <- format(z, digits = 2, justify = "left", trim = FALSE)) f1 == f2 ## 2 FALSE, 4 TRUE ## A "minimal" format() for S4 objects without their own format() method: cc <- methods::getClassDef("standardGeneric") format(cc) ## "<S4 class ......>"format(1:10) format(1:10, trim = TRUE) zz <- data.frame("(row names)"= c("aaaaa", "b"), check.names = FALSE) format(zz) format(zz, justify = "left") ## use of nsmall format(13.7) format(13.7, nsmall = 3) format(c(6.0, 13.1), digits = 2) format(c(6.0, 13.1), digits = 2, nsmall = 1) ## use of scientific format(2^31-1) format(2^31-1, scientific = TRUE) ## a list z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,10,100,1000), d = c("a", "longer", "character", "string"), q = quote( a + b ), e = expression(1+x)) ## can you find the "2" small differences? (f1 <- format(z, digits = 2)) (f2 <- format(z, digits = 2, justify = "left", trim = FALSE)) f1 == f2 ## 2 FALSE, 4 TRUE ## A "minimal" format() for S4 objects without their own format() method: cc <- methods::getClassDef("standardGeneric") format(cc) ## "<S4 class ......>"
Default value for .drop argument of group_by
## S3 method for class 'DataFrame' group_by_drop_default(.tbl)## S3 method for class 'DataFrame' group_by_drop_default(.tbl)
.tbl |
A data frame |
TRUE unless .tbl is a grouped data frame that was previously
obtained by group_by(.drop = FALSE)
group_by_drop_default(iris) iris %>% group_by(Species) %>% group_by_drop_default() iris %>% group_by(Species, .drop = FALSE) %>% group_by_drop_default()group_by_drop_default(iris) iris %>% group_by(Species) %>% group_by_drop_default() iris %>% group_by(Species, .drop = FALSE) %>% group_by_drop_default()
Most data operations are done on groups defined by variables.
group_by() takes an existing tbl and converts it into a grouped tbl
where operations are performed "by group". ungroup() removes grouping.
## S3 method for class 'DataFrame' group_by(.data, ..., add = FALSE, .drop = group_by_drop_default(.data))## S3 method for class 'DataFrame' group_by(.data, ..., add = FALSE, .drop = group_by_drop_default(.data))
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
In |
add |
When This argument was previously called |
.drop |
Drop groups formed by factor levels that don't appear in the
data? The default is |
A grouped data frame with class grouped_df,
unless the combination of ... and add yields a empty set of
grouping columns, in which case a tibble will be returned.
These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
Methods available in currently loaded packages:
group_by(): no methods found.
ungroup(): no methods found.
Currently, group_by() internally orders the groups in ascending order. This
results in ordered output from functions that aggregate groups, such as
summarise().
When used as grouping columns, character vectors are ordered in the C locale
for performance and reproducibility across R sessions. If the resulting
ordering of your grouped operation matters and is dependent on the locale,
you should follow up the grouped operation with an explicit call to
arrange() and set the .locale argument. For example:
data %>% group_by(chr) %>% summarise(avg = mean(x)) %>% arrange(chr, .locale = "en")
This is often useful as a preliminary step before generating content intended for humans, such as an HTML table.
Prior to dplyr 1.1.0, character vector grouping columns were ordered in the
system locale. If you need to temporarily revert to this behavior, you can
set the global option dplyr.legacy_locale to TRUE, but this should be
used sparingly and you should expect this option to be removed in a future
version of dplyr. It is better to update existing code to explicitly call
arrange(.locale = ) instead. Note that setting dplyr.legacy_locale will
also force calls to arrange() to use the system locale.
Other grouping functions:
group_map(),
group_nest(),
group_split(),
group_trim()
by_cyl <- mtcars %>% group_by(cyl) # grouping doesn't change how the data looks (apart from listing # how it's grouped): by_cyl # It changes how it acts with the other dplyr verbs: by_cyl %>% summarise( disp = mean(disp), hp = mean(hp) ) by_cyl %>% filter(disp == max(disp)) # Each call to summarise() removes a layer of grouping by_vs_am <- mtcars %>% group_by(vs, am) by_vs <- by_vs_am %>% summarise(n = n()) by_vs by_vs %>% summarise(n = sum(n)) # To removing grouping, use ungroup by_vs %>% ungroup() %>% summarise(n = sum(n)) # By default, group_by() overrides existing grouping by_cyl %>% group_by(vs, am) %>% group_vars() # Use add = TRUE to instead append by_cyl %>% group_by(vs, am, .add = TRUE) %>% group_vars() # You can group by expressions: this is a short-hand # for a mutate() followed by a group_by() mtcars %>% group_by(vsam = vs + am) # The implicit mutate() step is always performed on the # ungrouped data. Here we get 3 groups: mtcars %>% group_by(vs) %>% group_by(hp_cut = cut(hp, 3)) # If you want it to be performed by groups, # you have to use an explicit mutate() call. # Here we get 3 groups per value of vs mtcars %>% group_by(vs) %>% mutate(hp_cut = cut(hp, 3)) %>% group_by(hp_cut) # when factors are involved and .drop = FALSE, groups can be empty tbl <- tibble( x = 1:10, y = factor(rep(c("a", "c"), each = 5), levels = c("a", "b", "c")) ) tbl %>% group_by(y, .drop = FALSE) %>% group_rows()by_cyl <- mtcars %>% group_by(cyl) # grouping doesn't change how the data looks (apart from listing # how it's grouped): by_cyl # It changes how it acts with the other dplyr verbs: by_cyl %>% summarise( disp = mean(disp), hp = mean(hp) ) by_cyl %>% filter(disp == max(disp)) # Each call to summarise() removes a layer of grouping by_vs_am <- mtcars %>% group_by(vs, am) by_vs <- by_vs_am %>% summarise(n = n()) by_vs by_vs %>% summarise(n = sum(n)) # To removing grouping, use ungroup by_vs %>% ungroup() %>% summarise(n = sum(n)) # By default, group_by() overrides existing grouping by_cyl %>% group_by(vs, am) %>% group_vars() # Use add = TRUE to instead append by_cyl %>% group_by(vs, am, .add = TRUE) %>% group_vars() # You can group by expressions: this is a short-hand # for a mutate() followed by a group_by() mtcars %>% group_by(vsam = vs + am) # The implicit mutate() step is always performed on the # ungrouped data. Here we get 3 groups: mtcars %>% group_by(vs) %>% group_by(hp_cut = cut(hp, 3)) # If you want it to be performed by groups, # you have to use an explicit mutate() call. # Here we get 3 groups per value of vs mtcars %>% group_by(vs) %>% mutate(hp_cut = cut(hp, 3)) %>% group_by(hp_cut) # when factors are involved and .drop = FALSE, groups can be empty tbl <- tibble( x = 1:10, y = factor(rep(c("a", "c"), each = 5), levels = c("a", "b", "c")) ) tbl %>% group_by(y, .drop = FALSE) %>% group_rows()
This collection of functions accesses data about grouped data frames in various ways:
group_data() returns a data frame that defines the grouping structure.
The columns give the values of the grouping variables. The last column,
always called .rows, is a list of integer vectors that gives the
location of the rows in each group.
group_keys() returns a data frame describing the groups.
group_rows() returns a list of integer vectors giving the rows that
each group contains.
group_indices() returns an integer vector the same length as .data
that gives the group that each row belongs to.
group_vars() gives names of grouping variables as character vector.
groups() gives the names of the grouping variables as a list of symbols.
group_size() gives the size of each group.
n_groups() gives the total number of groups.
See context for equivalent functions that return values for the current group.
## S3 method for class 'DataFrame' group_data(.data)## S3 method for class 'DataFrame' group_data(.data)
.data |
a data.frame of group data
This collection of functions accesses data about grouped data frames in various ways:
group_data() returns a data frame that defines the grouping structure.
The columns give the values of the grouping variables. The last column,
always called .rows, is a list of integer vectors that gives the
location of the rows in each group.
group_keys() returns a data frame describing the groups.
group_rows() returns a list of integer vectors giving the rows that
each group contains.
group_indices() returns an integer vector the same length as .data
that gives the group that each row belongs to.
group_vars() gives names of grouping variables as character vector.
groups() gives the names of the grouping variables as a list of symbols.
group_size() gives the size of each group.
n_groups() gives the total number of groups.
See context for equivalent functions that return values for the current group.
## S3 method for class 'DataFrame' group_vars(x)## S3 method for class 'DataFrame' group_vars(x)
x |
a |
the grouping variables as a character vector
mutate() creates new columns that are functions of existing variables.
It can also modify (if the name is the same as an existing
column) and delete columns (by setting their value to NULL).
## S3 method for class 'DataFrame' mutate(.data, ...)## S3 method for class 'DataFrame' mutate(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< The value can be:
|
An object of the same type as .data. The output has the following
properties:
Columns from .data will be preserved according to the .keep argument.
Existing columns that are modified by ... will always be returned in
their original location.
New columns created through ... will be placed according to the
.before and .after arguments.
The number of rows is not affected.
Columns given the value NULL will be removed.
Groups will be recomputed if a grouping variable is mutated.
Data frame attributes are preserved.
Because mutating expressions are computed within groups, they may yield different results on grouped tibbles. This will be the case as soon as an aggregating, lagging, or ranking function is involved. Compare this ungrouped mutate:
starwars %>% select(name, mass, species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE))
With the grouped equivalent:
starwars %>% select(name, mass, species) %>% group_by(species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE))
The former normalises mass by the global average whereas the
latter normalises by the averages within species levels.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
Methods available in currently loaded packages: no methods found.
Other single table verbs:
arrange(),
filter(),
reframe(),
rename(),
select(),
slice(),
summarise()
# Newly created variables are available immediately starwars %>% select(name, mass) %>% mutate( mass2 = mass * 2, mass2_squared = mass2 * mass2 ) # As well as adding new variables, you can use mutate() to # remove variables and modify existing variables. starwars %>% select(name, height, mass, homeworld) %>% mutate( mass = NULL, height = height * 0.0328084 # convert to feet ) # Use across() with mutate() to apply a transformation # to multiple columns in a tibble. starwars %>% select(name, homeworld, species) %>% mutate(across(!name, as.factor)) # see more in ?across # Window functions are useful for grouped mutates: starwars %>% select(name, mass, homeworld) %>% group_by(homeworld) %>% mutate(rank = min_rank(desc(mass))) # see `vignette("window-functions")` for more details # By default, new columns are placed on the far right. df <- tibble(x = 1, y = 2) df %>% mutate(z = x + y) df %>% mutate(z = x + y, .before = 1) df %>% mutate(z = x + y, .after = x) # By default, mutate() keeps all columns from the input data. df <- tibble(x = 1, y = 2, a = "a", b = "b") df %>% mutate(z = x + y, .keep = "all") # the default df %>% mutate(z = x + y, .keep = "used") df %>% mutate(z = x + y, .keep = "unused") df %>% mutate(z = x + y, .keep = "none") # Grouping ---------------------------------------- # The mutate operation may yield different results on grouped # tibbles because the expressions are computed within groups. # The following normalises `mass` by the global average: starwars %>% select(name, mass, species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE)) # Whereas this normalises `mass` by the averages within species # levels: starwars %>% select(name, mass, species) %>% group_by(species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE)) # Indirection ---------------------------------------- # Refer to column names stored as strings with the `.data` pronoun: vars <- c("mass", "height") mutate(starwars, prod = .data[[vars[[1]]]] * .data[[vars[[2]]]]) # Learn more in ?rlang::args_data_masking# Newly created variables are available immediately starwars %>% select(name, mass) %>% mutate( mass2 = mass * 2, mass2_squared = mass2 * mass2 ) # As well as adding new variables, you can use mutate() to # remove variables and modify existing variables. starwars %>% select(name, height, mass, homeworld) %>% mutate( mass = NULL, height = height * 0.0328084 # convert to feet ) # Use across() with mutate() to apply a transformation # to multiple columns in a tibble. starwars %>% select(name, homeworld, species) %>% mutate(across(!name, as.factor)) # see more in ?across # Window functions are useful for grouped mutates: starwars %>% select(name, mass, homeworld) %>% group_by(homeworld) %>% mutate(rank = min_rank(desc(mass))) # see `vignette("window-functions")` for more details # By default, new columns are placed on the far right. df <- tibble(x = 1, y = 2) df %>% mutate(z = x + y) df %>% mutate(z = x + y, .before = 1) df %>% mutate(z = x + y, .after = x) # By default, mutate() keeps all columns from the input data. df <- tibble(x = 1, y = 2, a = "a", b = "b") df %>% mutate(z = x + y, .keep = "all") # the default df %>% mutate(z = x + y, .keep = "used") df %>% mutate(z = x + y, .keep = "unused") df %>% mutate(z = x + y, .keep = "none") # Grouping ---------------------------------------- # The mutate operation may yield different results on grouped # tibbles because the expressions are computed within groups. # The following normalises `mass` by the global average: starwars %>% select(name, mass, species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE)) # Whereas this normalises `mass` by the averages within species # levels: starwars %>% select(name, mass, species) %>% group_by(species) %>% mutate(mass_norm = mass / mean(mass, na.rm = TRUE)) # Indirection ---------------------------------------- # Refer to column names stored as strings with the `.data` pronoun: vars <- c("mass", "height") mutate(starwars, prod = .data[[vars[[1]]]] * .data[[vars[[2]]]]) # Learn more in ?rlang::args_data_masking
pull() is similar to $. It's mostly useful because it looks a little
nicer in pipes, it also works with remote data frames, and it can optionally
name the output.
## S3 method for class 'DataFrame' pull(.data, var = -1, name = NULL, ...)## S3 method for class 'DataFrame' pull(.data, var = -1, name = NULL, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
var |
A variable specified as:
The default returns the last column (on the assumption that's the column you've created most recently). This argument is taken by expression and supports quasiquotation (you can unquote column names and column locations). |
name |
An optional parameter that specifies the column to be used
as names for a named vector. Specified in a similar manner as |
... |
For use by methods. |
A vector the same size as .data.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
d <- S4Vectors::DataFrame(mtcars) pull(d, cyl)d <- S4Vectors::DataFrame(mtcars) pull(d, cyl)
rename() changes the names of individual variables using
new_name = old_name syntax; rename_with() renames columns using a
function.
rename2(.data, ...)rename2(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
For For |
An object of the same type as .data. The output has the following
properties:
Rows are not affected.
Column names are changed; column order is preserved.
Data frame attributes are preserved.
Groups are updated to reflect new names.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Other single table verbs:
arrange(),
filter(),
mutate(),
reframe(),
select(),
slice(),
summarise()
iris <- as_tibble(iris) # so it prints a little nicer rename(iris, petal_length = Petal.Length) # Rename using a named vector and `all_of()` lookup <- c(pl = "Petal.Length", sl = "Sepal.Length") rename(iris, all_of(lookup)) # If your named vector might contain names that don't exist in the data, # use `any_of()` instead lookup <- c(lookup, new = "unknown") try(rename(iris, all_of(lookup))) rename(iris, any_of(lookup)) rename_with(iris, toupper) rename_with(iris, toupper, starts_with("Petal")) rename_with(iris, ~ tolower(gsub(".", "_", .x, fixed = TRUE))) # If your renaming function uses `paste0()`, make sure to set # `recycle0 = TRUE` to ensure that empty selections are recycled correctly try(rename_with( iris, ~ paste0("prefix_", .x), starts_with("nonexistent") )) rename_with( iris, ~ paste0("prefix_", .x, recycle0 = TRUE), starts_with("nonexistent") )iris <- as_tibble(iris) # so it prints a little nicer rename(iris, petal_length = Petal.Length) # Rename using a named vector and `all_of()` lookup <- c(pl = "Petal.Length", sl = "Sepal.Length") rename(iris, all_of(lookup)) # If your named vector might contain names that don't exist in the data, # use `any_of()` instead lookup <- c(lookup, new = "unknown") try(rename(iris, all_of(lookup))) rename(iris, any_of(lookup)) rename_with(iris, toupper) rename_with(iris, toupper, starts_with("Petal")) rename_with(iris, ~ tolower(gsub(".", "_", .x, fixed = TRUE))) # If your renaming function uses `paste0()`, make sure to set # `recycle0 = TRUE` to ensure that empty selections are recycled correctly try(rename_with( iris, ~ paste0("prefix_", .x), starts_with("nonexistent") )) rename_with( iris, ~ paste0("prefix_", .x, recycle0 = TRUE), starts_with("nonexistent") )
Select (and optionally rename) variables in a data frame, using a concise
mini-language that makes it easy to refer to variables based on their name
(e.g. a:f selects all columns from a on the left to f on the
right) or type (e.g. where(is.numeric) selects all numeric columns).
Tidyverse selections implement a dialect of R where operators make it easy to select variables:
: for selecting a range of consecutive variables.
! for taking the complement of a set of variables.
& and | for selecting the intersection or the union of two
sets of variables.
c() for combining selections.
In addition, you can use selection helpers. Some helpers select specific columns:
everything(): Matches all variables.
last_col(): Select last variable, possibly with an offset.
group_cols(): Select all grouping columns.
Other helpers select variables by matching patterns in their names:
starts_with(): Starts with a prefix.
ends_with(): Ends with a suffix.
contains(): Contains a literal string.
matches(): Matches a regular expression.
num_range(): Matches a numerical range like x01, x02, x03.
Or from variables stored in a character vector:
all_of(): Matches variable names in a character vector. All
names must be present, otherwise an out-of-bounds error is
thrown.
any_of(): Same as all_of(), except that no error is thrown
for names that don't exist.
Or using a predicate function:
where(): Applies a function to all variables and selects those
for which the function returns TRUE.
## S3 method for class 'DataFrame' select(.data, ...)## S3 method for class 'DataFrame' select(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< |
An object of the same type as .data. The output has the following
properties:
Rows are not affected.
Output columns are a subset of input columns, potentially with a different
order. Columns will be renamed if new_name = old_name form is used.
Data frame attributes are preserved.
Groups are maintained; you can't select off grouping variables.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Here we show the usage for the basic selection operators. See the
specific help pages to learn about helpers like starts_with().
The selection language can be used in functions like
dplyr::select() or tidyr::pivot_longer(). Let's first attach
the tidyverse:
library(tidyverse) # For better printing iris <- as_tibble(iris)
Select variables by name:
starwars %>% select(height) #> # A tibble: 87 x 1 #> height #> <int> #> 1 172 #> 2 167 #> 3 96 #> 4 202 #> # i 83 more rows iris %>% pivot_longer(Sepal.Length) #> # A tibble: 150 x 6 #> Sepal.Width Petal.Length Petal.Width Species name value #> <dbl> <dbl> <dbl> <fct> <chr> <dbl> #> 1 3.5 1.4 0.2 setosa Sepal.Length 5.1 #> 2 3 1.4 0.2 setosa Sepal.Length 4.9 #> 3 3.2 1.3 0.2 setosa Sepal.Length 4.7 #> 4 3.1 1.5 0.2 setosa Sepal.Length 4.6 #> # i 146 more rows
Select multiple variables by separating them with commas. Note how the order of columns is determined by the order of inputs:
starwars %>% select(homeworld, height, mass) #> # A tibble: 87 x 3 #> homeworld height mass #> <chr> <int> <dbl> #> 1 Tatooine 172 77 #> 2 Tatooine 167 75 #> 3 Naboo 96 32 #> 4 Tatooine 202 136 #> # i 83 more rows
Functions like tidyr::pivot_longer() don't take variables with
dots. In this case use c() to select multiple variables:
iris %>% pivot_longer(c(Sepal.Length, Petal.Length)) #> # A tibble: 300 x 5 #> Sepal.Width Petal.Width Species name value #> <dbl> <dbl> <fct> <chr> <dbl> #> 1 3.5 0.2 setosa Sepal.Length 5.1 #> 2 3.5 0.2 setosa Petal.Length 1.4 #> 3 3 0.2 setosa Sepal.Length 4.9 #> 4 3 0.2 setosa Petal.Length 1.4 #> # i 296 more rows
The : operator selects a range of consecutive variables:
starwars %>% select(name:mass) #> # A tibble: 87 x 3 #> name height mass #> <chr> <int> <dbl> #> 1 Luke Skywalker 172 77 #> 2 C-3PO 167 75 #> 3 R2-D2 96 32 #> 4 Darth Vader 202 136 #> # i 83 more rows
The ! operator negates a selection:
![[Deprecated]](../help/figures/lifecycle-deprecated.svg)
starwars %>% select(!(name:mass))
#> # A tibble: 87 x 11
#> hair_color skin_color eye_color birth_year sex gender homeworld species
#> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 blond fair blue 19 male masculine Tatooine Human
#> 2 <NA> gold yellow 112 none masculine Tatooine Droid
#> 3 <NA> white, blue red 33 none masculine Naboo Droid
#> 4 none white yellow 41.9 male masculine Tatooine Human
#> # i 83 more rows
#> # i 3 more variables: films <list>, vehicles <list>, starships <list>
iris %>% select(!c(Sepal.Length, Petal.Length))
#> # A tibble: 150 x 3
#> Sepal.Width Petal.Width Species
#> <dbl> <dbl> <fct>
#> 1 3.5 0.2 setosa
#> 2 3 0.2 setosa
#> 3 3.2 0.2 setosa
#> 4 3.1 0.2 setosa
#> # i 146 more rows
iris %>% select(!ends_with("Width"))
#> # A tibble: 150 x 3
#> Sepal.Length Petal.Length Species
#> <dbl> <dbl> <fct>
#> 1 5.1 1.4 setosa
#> 2 4.9 1.4 setosa
#> 3 4.7 1.3 setosa
#> 4 4.6 1.5 setosa
#> # i 146 more rows
& and | take the intersection or the union of two selections:
iris %>% select(starts_with("Petal") & ends_with("Width"))
#> # A tibble: 150 x 1
#> Petal.Width
#> <dbl>
#> 1 0.2
#> 2 0.2
#> 3 0.2
#> 4 0.2
#> # i 146 more rows
iris %>% select(starts_with("Petal") | ends_with("Width"))
#> # A tibble: 150 x 3
#> Petal.Length Petal.Width Sepal.Width
#> <dbl> <dbl> <dbl>
#> 1 1.4 0.2 3.5
#> 2 1.4 0.2 3
#> 3 1.3 0.2 3.2
#> 4 1.5 0.2 3.1
#> # i 146 more rows
To take the difference between two selections, combine the & and
! operators:
iris %>% select(starts_with("Petal") & !ends_with("Width"))
#> # A tibble: 150 x 1
#> Petal.Length
#> <dbl>
#> 1 1.4
#> 2 1.4
#> 3 1.3
#> 4 1.5
#> # i 146 more rows
Other single table verbs:
arrange(),
filter(),
mutate(),
reframe(),
rename(),
slice(),
summarise()
slice() lets you index rows by their (integer) locations. It allows you
to select, remove, and duplicate rows. It is accompanied by a number of
helpers for common use cases:
slice_head() and slice_tail() select the first or last rows.
slice_sample() randomly selects rows.
slice_min() and slice_max() select rows with the smallest or largest
values of a variable.
If .data is a grouped_df, the operation will be performed on each group,
so that (e.g.) slice_head(df, n = 5) will select the first five rows in
each group.
## S3 method for class 'DataFrame' slice(.data, ..., .preserve = FALSE)## S3 method for class 'DataFrame' slice(.data, ..., .preserve = FALSE)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
For Provide either positive values to keep, or negative values to drop. The values provided must be either all positive or all negative. Indices beyond the number of rows in the input are silently ignored. For |
.preserve |
Relevant when the |
Slice does not work with relational databases because they have no
intrinsic notion of row order. If you want to perform the equivalent
operation, use filter() and row_number().
An object of the same type as .data. The output has the following
properties:
Each row may appear 0, 1, or many times in the output.
Columns are not modified.
Groups are not modified.
Data frame attributes are preserved.
These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
Methods available in currently loaded packages:
slice(): no methods found.
slice_head(): no methods found.
slice_tail(): no methods found.
slice_min(): no methods found.
slice_max(): no methods found.
slice_sample(): no methods found.
Other single table verbs:
arrange(),
filter(),
mutate(),
reframe(),
rename(),
select(),
summarise()
# Similar to head(mtcars, 1): mtcars %>% slice(1L) # Similar to tail(mtcars, 1): mtcars %>% slice(n()) mtcars %>% slice(5:n()) # Rows can be dropped with negative indices: slice(mtcars, -(1:4)) # First and last rows based on existing order mtcars %>% slice_head(n = 5) mtcars %>% slice_tail(n = 5) # Rows with minimum and maximum values of a variable mtcars %>% slice_min(mpg, n = 5) mtcars %>% slice_max(mpg, n = 5) # slice_min() and slice_max() may return more rows than requested # in the presence of ties. mtcars %>% slice_min(cyl, n = 1) # Use with_ties = FALSE to return exactly n matches mtcars %>% slice_min(cyl, n = 1, with_ties = FALSE) # Or use additional variables to break the tie: mtcars %>% slice_min(tibble(cyl, mpg), n = 1) # slice_sample() allows you to random select with or without replacement mtcars %>% slice_sample(n = 5) mtcars %>% slice_sample(n = 5, replace = TRUE) # you can optionally weight by a variable - this code weights by the # physical weight of the cars, so heavy cars are more likely to get # selected mtcars %>% slice_sample(weight_by = wt, n = 5) # Group wise operation ---------------------------------------- df <- tibble( group = rep(c("a", "b", "c"), c(1, 2, 4)), x = runif(7) ) # All slice helpers operate per group, silently truncating to the group # size, so the following code works without error df %>% group_by(group) %>% slice_head(n = 2) # When specifying the proportion of rows to include non-integer sizes # are rounded down, so group a gets 0 rows df %>% group_by(group) %>% slice_head(prop = 0.5) # Filter equivalents -------------------------------------------- # slice() expressions can often be written to use `filter()` and # `row_number()`, which can also be translated to SQL. For many databases, # you'll need to supply an explicit variable to use to compute the row number. filter(mtcars, row_number() == 1L) filter(mtcars, row_number() == n()) filter(mtcars, between(row_number(), 5, n()))# Similar to head(mtcars, 1): mtcars %>% slice(1L) # Similar to tail(mtcars, 1): mtcars %>% slice(n()) mtcars %>% slice(5:n()) # Rows can be dropped with negative indices: slice(mtcars, -(1:4)) # First and last rows based on existing order mtcars %>% slice_head(n = 5) mtcars %>% slice_tail(n = 5) # Rows with minimum and maximum values of a variable mtcars %>% slice_min(mpg, n = 5) mtcars %>% slice_max(mpg, n = 5) # slice_min() and slice_max() may return more rows than requested # in the presence of ties. mtcars %>% slice_min(cyl, n = 1) # Use with_ties = FALSE to return exactly n matches mtcars %>% slice_min(cyl, n = 1, with_ties = FALSE) # Or use additional variables to break the tie: mtcars %>% slice_min(tibble(cyl, mpg), n = 1) # slice_sample() allows you to random select with or without replacement mtcars %>% slice_sample(n = 5) mtcars %>% slice_sample(n = 5, replace = TRUE) # you can optionally weight by a variable - this code weights by the # physical weight of the cars, so heavy cars are more likely to get # selected mtcars %>% slice_sample(weight_by = wt, n = 5) # Group wise operation ---------------------------------------- df <- tibble( group = rep(c("a", "b", "c"), c(1, 2, 4)), x = runif(7) ) # All slice helpers operate per group, silently truncating to the group # size, so the following code works without error df %>% group_by(group) %>% slice_head(n = 2) # When specifying the proportion of rows to include non-integer sizes # are rounded down, so group a gets 0 rows df %>% group_by(group) %>% slice_head(prop = 0.5) # Filter equivalents -------------------------------------------- # slice() expressions can often be written to use `filter()` and # `row_number()`, which can also be translated to SQL. For many databases, # you'll need to supply an explicit variable to use to compute the row number. filter(mtcars, row_number() == 1L) filter(mtcars, row_number() == n()) filter(mtcars, between(row_number(), 5, n()))
summarise() creates a new data frame. It returns one row for each
combination of grouping variables; if there are no grouping variables, the
output will have a single row summarising all observations in the input. It
will contain one column for each grouping variable and one column for each of
the summary statistics that you have specified.
summarise() and summarize() are synonyms.
## S3 method for class 'DataFrame' summarise(.data, ...)## S3 method for class 'DataFrame' summarise(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< The value can be:
|
An object usually of the same type as .data.
The rows come from the underlying group_keys().
The columns are a combination of the grouping keys and the summary expressions that you provide.
The grouping structure is controlled by the .groups= argument, the
output may be another grouped_df, a tibble or a rowwise data frame.
Data frame attributes are not preserved, because summarise()
fundamentally creates a new data frame.
Count: n(), n_distinct()
The data frame backend supports creating a variable and using it in the
same summary. This means that previously created summary variables can be
further transformed or combined within the summary, as in mutate().
However, it also means that summary variables with the same names as previous
variables overwrite them, making those variables unavailable to later summary
variables.
This behaviour may not be supported in other backends. To avoid unexpected results, consider using new names for your summary variables, especially when creating multiple summaries.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Other single table verbs:
arrange(),
filter(),
mutate(),
reframe(),
rename(),
select(),
slice()
# A summary applied to ungrouped tbl returns a single row mtcars %>% summarise(mean = mean(disp), n = n()) # Usually, you'll want to group first mtcars %>% group_by(cyl) %>% summarise(mean = mean(disp), n = n()) # Each summary call removes one grouping level (since that group # is now just a single row) mtcars %>% group_by(cyl, vs) %>% summarise(cyl_n = n()) %>% group_vars() # BEWARE: reusing variables may lead to unexpected results mtcars %>% group_by(cyl) %>% summarise(disp = mean(disp), sd = sd(disp)) # Refer to column names stored as strings with the `.data` pronoun: var <- "mass" summarise(starwars, avg = mean(.data[[var]], na.rm = TRUE)) # Learn more in ?rlang::args_data_masking # In dplyr 1.1.0, returning multiple rows per group was deprecated in favor # of `reframe()`, which never messages and always returns an ungrouped # result: mtcars %>% group_by(cyl) %>% summarise(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75)) # -> mtcars %>% group_by(cyl) %>% reframe(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))# A summary applied to ungrouped tbl returns a single row mtcars %>% summarise(mean = mean(disp), n = n()) # Usually, you'll want to group first mtcars %>% group_by(cyl) %>% summarise(mean = mean(disp), n = n()) # Each summary call removes one grouping level (since that group # is now just a single row) mtcars %>% group_by(cyl, vs) %>% summarise(cyl_n = n()) %>% group_vars() # BEWARE: reusing variables may lead to unexpected results mtcars %>% group_by(cyl) %>% summarise(disp = mean(disp), sd = sd(disp)) # Refer to column names stored as strings with the `.data` pronoun: var <- "mass" summarise(starwars, avg = mean(.data[[var]], na.rm = TRUE)) # Learn more in ?rlang::args_data_masking # In dplyr 1.1.0, returning multiple rows per group was deprecated in favor # of `reframe()`, which never messages and always returns an ungrouped # result: mtcars %>% group_by(cyl) %>% summarise(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75)) # -> mtcars %>% group_by(cyl) %>% reframe(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))
summarise() creates a new data frame. It returns one row for each
combination of grouping variables; if there are no grouping variables, the
output will have a single row summarising all observations in the input. It
will contain one column for each grouping variable and one column for each of
the summary statistics that you have specified.
summarise() and summarize() are synonyms.
## S3 method for class 'DataFrame' summarize(.data, ...)## S3 method for class 'DataFrame' summarize(.data, ...)
.data |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details. |
... |
< The value can be:
|
An object usually of the same type as .data.
The rows come from the underlying group_keys().
The columns are a combination of the grouping keys and the summary expressions that you provide.
The grouping structure is controlled by the .groups= argument, the
output may be another grouped_df, a tibble or a rowwise data frame.
Data frame attributes are not preserved, because summarise()
fundamentally creates a new data frame.
Count: n(), n_distinct()
The data frame backend supports creating a variable and using it in the
same summary. This means that previously created summary variables can be
further transformed or combined within the summary, as in mutate().
However, it also means that summary variables with the same names as previous
variables overwrite them, making those variables unavailable to later summary
variables.
This behaviour may not be supported in other backends. To avoid unexpected results, consider using new names for your summary variables, especially when creating multiple summaries.
This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
The following methods are currently available in loaded packages: no methods found.
Other single table verbs:
arrange(),
filter(),
mutate(),
reframe(),
rename(),
select(),
slice()
# A summary applied to ungrouped tbl returns a single row mtcars %>% summarise(mean = mean(disp), n = n()) # Usually, you'll want to group first mtcars %>% group_by(cyl) %>% summarise(mean = mean(disp), n = n()) # Each summary call removes one grouping level (since that group # is now just a single row) mtcars %>% group_by(cyl, vs) %>% summarise(cyl_n = n()) %>% group_vars() # BEWARE: reusing variables may lead to unexpected results mtcars %>% group_by(cyl) %>% summarise(disp = mean(disp), sd = sd(disp)) # Refer to column names stored as strings with the `.data` pronoun: var <- "mass" summarise(starwars, avg = mean(.data[[var]], na.rm = TRUE)) # Learn more in ?rlang::args_data_masking # In dplyr 1.1.0, returning multiple rows per group was deprecated in favor # of `reframe()`, which never messages and always returns an ungrouped # result: mtcars %>% group_by(cyl) %>% summarise(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75)) # -> mtcars %>% group_by(cyl) %>% reframe(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))# A summary applied to ungrouped tbl returns a single row mtcars %>% summarise(mean = mean(disp), n = n()) # Usually, you'll want to group first mtcars %>% group_by(cyl) %>% summarise(mean = mean(disp), n = n()) # Each summary call removes one grouping level (since that group # is now just a single row) mtcars %>% group_by(cyl, vs) %>% summarise(cyl_n = n()) %>% group_vars() # BEWARE: reusing variables may lead to unexpected results mtcars %>% group_by(cyl) %>% summarise(disp = mean(disp), sd = sd(disp)) # Refer to column names stored as strings with the `.data` pronoun: var <- "mass" summarise(starwars, avg = mean(.data[[var]], na.rm = TRUE)) # Learn more in ?rlang::args_data_masking # In dplyr 1.1.0, returning multiple rows per group was deprecated in favor # of `reframe()`, which never messages and always returns an ungrouped # result: mtcars %>% group_by(cyl) %>% summarise(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75)) # -> mtcars %>% group_by(cyl) %>% reframe(qs = quantile(disp, c(0.25, 0.75)), prob = c(0.25, 0.75))
count() lets you quickly count the unique values of one or more variables:
df %>% count(a, b) is roughly equivalent to
df %>% group_by(a, b) %>% summarise(n = n()).
count() is paired with tally(), a lower-level helper that is equivalent
to df %>% summarise(n = n()). Supply wt to perform weighted counts,
switching the summary from n = n() to n = sum(wt).
add_count() and add_tally() are equivalents to count() and tally()
but use mutate() instead of summarise() so that they add a new column
with group-wise counts.
## S3 method for class 'DataFrame' tally(x, wt = NULL, sort = FALSE, name = NULL)## S3 method for class 'DataFrame' tally(x, wt = NULL, sort = FALSE, name = NULL)
x |
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). |
wt |
<
|
sort |
If |
name |
The name of the new column in the output. If omitted, it will default to |
An object of the same type as .data. count() and add_count()
group transiently, so the output has the same groups as the input.
# count() is a convenient way to get a sense of the distribution of # values in a dataset starwars %>% count(species) starwars %>% count(species, sort = TRUE) starwars %>% count(sex, gender, sort = TRUE) starwars %>% count(birth_decade = round(birth_year, -1)) # use the `wt` argument to perform a weighted count. This is useful # when the data has already been aggregated once df <- tribble( ~name, ~gender, ~runs, "Max", "male", 10, "Sandra", "female", 1, "Susan", "female", 4 ) # counts rows: df %>% count(gender) # counts runs: df %>% count(gender, wt = runs) # When factors are involved, `.drop = FALSE` can be used to retain factor # levels that don't appear in the data df2 <- tibble( id = 1:5, type = factor(c("a", "c", "a", NA, "a"), levels = c("a", "b", "c")) ) df2 %>% count(type) df2 %>% count(type, .drop = FALSE) # Or, using `group_by()`: df2 %>% group_by(type, .drop = FALSE) %>% count() # tally() is a lower-level function that assumes you've done the grouping starwars %>% tally() starwars %>% group_by(species) %>% tally() # both count() and tally() have add_ variants that work like # mutate() instead of summarise df %>% add_count(gender, wt = runs) df %>% add_tally(wt = runs)# count() is a convenient way to get a sense of the distribution of # values in a dataset starwars %>% count(species) starwars %>% count(species, sort = TRUE) starwars %>% count(sex, gender, sort = TRUE) starwars %>% count(birth_decade = round(birth_year, -1)) # use the `wt` argument to perform a weighted count. This is useful # when the data has already been aggregated once df <- tribble( ~name, ~gender, ~runs, "Max", "male", 10, "Sandra", "female", 1, "Susan", "female", 4 ) # counts rows: df %>% count(gender) # counts runs: df %>% count(gender, wt = runs) # When factors are involved, `.drop = FALSE` can be used to retain factor # levels that don't appear in the data df2 <- tibble( id = 1:5, type = factor(c("a", "c", "a", NA, "a"), levels = c("a", "b", "c")) ) df2 %>% count(type) df2 %>% count(type, .drop = FALSE) # Or, using `group_by()`: df2 %>% group_by(type, .drop = FALSE) %>% count() # tally() is a lower-level function that assumes you've done the grouping starwars %>% tally() starwars %>% group_by(species) %>% tally() # both count() and tally() have add_ variants that work like # mutate() instead of summarise df %>% add_count(gender, wt = runs) df %>% add_tally(wt = runs)
tbl_vars() returns all variables while tbl_nongroup_vars()
returns only non-grouping variables. The groups attribute
of the object returned by tbl_vars() is a character vector of the
grouping columns.
## S3 method for class 'DataFrame' tbl_vars(x)## S3 method for class 'DataFrame' tbl_vars(x)
x |
A tbl object |
all variables, with a groups attribute when grouped.
group_vars() for a function that returns grouping
variables.
Most data operations are done on groups defined by variables.
group_by() takes an existing tbl and converts it into a grouped tbl
where operations are performed "by group". ungroup() removes grouping.
## S3 method for class 'DataFrame' ungroup(x, ...)## S3 method for class 'DataFrame' ungroup(x, ...)
x |
A |
... |
In |
A grouped data frame with class grouped_df,
unless the combination of ... and add yields a empty set of
grouping columns, in which case a tibble will be returned.
These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.
Methods available in currently loaded packages:
group_by(): no methods found.
ungroup(): no methods found.
Currently, group_by() internally orders the groups in ascending order. This
results in ordered output from functions that aggregate groups, such as
summarise().
When used as grouping columns, character vectors are ordered in the C locale
for performance and reproducibility across R sessions. If the resulting
ordering of your grouped operation matters and is dependent on the locale,
you should follow up the grouped operation with an explicit call to
arrange() and set the .locale argument. For example:
data %>% group_by(chr) %>% summarise(avg = mean(x)) %>% arrange(chr, .locale = "en")
This is often useful as a preliminary step before generating content intended for humans, such as an HTML table.
Prior to dplyr 1.1.0, character vector grouping columns were ordered in the
system locale. If you need to temporarily revert to this behavior, you can
set the global option dplyr.legacy_locale to TRUE, but this should be
used sparingly and you should expect this option to be removed in a future
version of dplyr. It is better to update existing code to explicitly call
arrange(.locale = ) instead. Note that setting dplyr.legacy_locale will
also force calls to arrange() to use the system locale.
Other grouping functions:
group_map(),
group_nest(),
group_split(),
group_trim()
by_cyl <- mtcars %>% group_by(cyl) # grouping doesn't change how the data looks (apart from listing # how it's grouped): by_cyl # It changes how it acts with the other dplyr verbs: by_cyl %>% summarise( disp = mean(disp), hp = mean(hp) ) by_cyl %>% filter(disp == max(disp)) # Each call to summarise() removes a layer of grouping by_vs_am <- mtcars %>% group_by(vs, am) by_vs <- by_vs_am %>% summarise(n = n()) by_vs by_vs %>% summarise(n = sum(n)) # To removing grouping, use ungroup by_vs %>% ungroup() %>% summarise(n = sum(n)) # By default, group_by() overrides existing grouping by_cyl %>% group_by(vs, am) %>% group_vars() # Use add = TRUE to instead append by_cyl %>% group_by(vs, am, .add = TRUE) %>% group_vars() # You can group by expressions: this is a short-hand # for a mutate() followed by a group_by() mtcars %>% group_by(vsam = vs + am) # The implicit mutate() step is always performed on the # ungrouped data. Here we get 3 groups: mtcars %>% group_by(vs) %>% group_by(hp_cut = cut(hp, 3)) # If you want it to be performed by groups, # you have to use an explicit mutate() call. # Here we get 3 groups per value of vs mtcars %>% group_by(vs) %>% mutate(hp_cut = cut(hp, 3)) %>% group_by(hp_cut) # when factors are involved and .drop = FALSE, groups can be empty tbl <- tibble( x = 1:10, y = factor(rep(c("a", "c"), each = 5), levels = c("a", "b", "c")) ) tbl %>% group_by(y, .drop = FALSE) %>% group_rows()by_cyl <- mtcars %>% group_by(cyl) # grouping doesn't change how the data looks (apart from listing # how it's grouped): by_cyl # It changes how it acts with the other dplyr verbs: by_cyl %>% summarise( disp = mean(disp), hp = mean(hp) ) by_cyl %>% filter(disp == max(disp)) # Each call to summarise() removes a layer of grouping by_vs_am <- mtcars %>% group_by(vs, am) by_vs <- by_vs_am %>% summarise(n = n()) by_vs by_vs %>% summarise(n = sum(n)) # To removing grouping, use ungroup by_vs %>% ungroup() %>% summarise(n = sum(n)) # By default, group_by() overrides existing grouping by_cyl %>% group_by(vs, am) %>% group_vars() # Use add = TRUE to instead append by_cyl %>% group_by(vs, am, .add = TRUE) %>% group_vars() # You can group by expressions: this is a short-hand # for a mutate() followed by a group_by() mtcars %>% group_by(vsam = vs + am) # The implicit mutate() step is always performed on the # ungrouped data. Here we get 3 groups: mtcars %>% group_by(vs) %>% group_by(hp_cut = cut(hp, 3)) # If you want it to be performed by groups, # you have to use an explicit mutate() call. # Here we get 3 groups per value of vs mtcars %>% group_by(vs) %>% mutate(hp_cut = cut(hp, 3)) %>% group_by(hp_cut) # when factors are involved and .drop = FALSE, groups can be empty tbl <- tibble( x = 1:10, y = factor(rep(c("a", "c"), each = 5), levels = c("a", "b", "c")) ) tbl %>% group_by(y, .drop = FALSE) %>% group_rows()