Tips for selecting columns in step functions.
When selecting variables or model terms in step
functions, dplyr-like tools are used. The selector functions
can choose variables based on their name, current role, data
type, or any combination of these. The selectors are passed as
any other argument to the step. If the variables are explicitly
named in the step function, this might look like:
recipe( ~ ., data = USArrests) %>%
step_pca(Murder, Assault, UrbanPop, Rape, num_comp = 3)
The first four arguments indicate which variables should be
used in the PCA while the last argument is a specific argument
to step_pca() about the number of components.
Note that:
These arguments are not evaluated until the prep
function for the step is executed.
The dplyr-like syntax allows for negative signs to
exclude variables (e.g. -Murder) and the set of selectors will
processed in order.
A leading exclusion in these arguments (e.g. -Murder)
has the effect of adding all variables to the list except the
excluded variable(s), ignoring role information.
Select helpers from the tidyselect package can also be used:
tidyselect::starts_with(), tidyselect::ends_with(),
tidyselect::contains(), tidyselect::matches(),
tidyselect::num_range(), tidyselect::everything(),
tidyselect::one_of(), tidyselect::all_of(), and
tidyselect::any_of()
For example:
recipe(Species ~ ., data = iris) %>%
step_center(starts_with("Sepal"), -contains("Width"))
would only select Sepal.Length
Columns of the design matrix that may not exist when the step
is coded can also be selected. For example, when using
step_pca(), the number of columns created by feature extraction
may not be known when subsequent steps are defined. In this
case, using matches("^PC") will select all of the columns
whose names start with "PC" once those columns are created.
There are sets of recipes-specific functions that can be used to select
variables based on their role or type: has_role() and
has_type(). For convenience, there are also functions that are
more specific. The functions all_numeric() and all_nominal() select
based on type, with nominal variables including both character and factor;
the functions all_predictors() and all_outcomes() select based on role.
The functions all_numeric_predictors() and all_nominal_predictors()
select intersections of role and type. Any can be used in conjunction with
the previous functions described for selecting variables using their names.
A selection like this:
data(biomass)
recipe(HHV ~ ., data = biomass) %>%
step_center(all_numeric(), -all_outcomes())
is equivalent to:
data(biomass)
recipe(HHV ~ ., data = biomass) %>%
step_center(all_numeric_predictors())
Both result in all the numeric predictors: carbon, hydrogen, oxygen, nitrogen, and sulfur.
If a role for a variable has not been defined, it will never be selected using role-specific selectors.
Selectors can be used in step_interact() in similar ways but
must be embedded in a model formula (as opposed to a sequence
of selectors). For example, the interaction specification
could be ~ starts_with("Species"):Sepal.Width. This can be
useful if Species was converted to dummy variables
previously using step_dummy(). The implementation of
step_interact() is special, and is more restricted than
the other step functions. Only the selector functions from
recipes and tidyselect are allowed. User defined selector functions
will not be recognized. Additionally, the tidyselect domain specific
language is not recognized here, meaning that &, |, !, and -
will not work.
When creating variable selections:
If you are using column filtering steps, such as step_corr(), try
to avoid hardcoding specific variable names in downstream steps in
case those columns are removed by the filter. Instead, use
dplyr::any_of() and
dplyr::all_of().
dplyr::any_of() will be tolerant if a
column has been removed.
dplyr::all_of() will fail unless all of the
columns are present in the data.
For both of these functions, if you are going to save the recipe as a binary object to use in another R session, try to avoid referring to a vector in your workspace.
Preferred: any_of(!!var_names)
Avoid: any_of(var_names)
Some examples:
some_vars <- names(mtcars)[4:6]# No filter steps, OK for not saving the recipe
rec_1 <-
recipe(mpg ~ ., data = mtcars) %>%
step_log(all_of(some_vars)) %>%
prep()
# No filter steps, saving the recipe
rec_2 <-
recipe(mpg ~ ., data = mtcars) %>%
step_log(!!!some_vars) %>%
prep()
# This fails since `wt` is not in the data
recipe(mpg ~ ., data = mtcars) %>%
step_rm(wt) %>%
step_log(!!!some_vars) %>%
prep()
## Error in `chr_as_locations()`:
## ! Can't subset columns that don't exist.
## x Column `wt` doesn't exist.
# Best for filters (using any_of()) and when
# saving the recipe
rec_4 <-
recipe(mpg ~ ., data = mtcars) %>%
step_rm(wt) %>%
step_log(any_of(!!some_vars)) %>%
# equal to step_log(any_of(c("hp", "drat", "wt")))
prep()