The intended use is to subset based on variables define in the dots list,
however some internal column data is also available to query.
ys_filter(x, expr, .default = NULL, .enclos = parent.frame())A yspec object.
An unquoted expression.
A named list or environment containing defaults for expr;
consider using ys_fill_dots() as an alternative to passing .default.
An enclosing environment for evaluating expr.
A yspec object
The following fields always exist in the spec and are available for querying in the filter expression:
col: column name <character>
type: data type <character>; either numeric, character, or integer
discrete: discrete data flag <logical>; yspec sets this to TRUE
when the values field is populated
continuous: continuous data flag <logical>; yspec sets this to TRUE
when the range field is populated
short: the short name <character>
do_lookup: lookup indicator; yspec sets this to TRUE when some or all
of the column data is defined by an external lookup file
The following fields will be provided defaults when the filter expression is evaluated:
unit: as specified by the user <character>; default value is ""
covariate: as specified by the user in dots <logical>; default value
is FALSE
In addition to these fields, you can build the filter expression using
items in the dots field.
In order to determine if any column should get selected, ys_filter(),
builds an environment and evaluates expr in that environment. Columns are
selected only if expr evaluates to TRUE (via isTRUE()).
The environment is comprised of pre-existing data items in the spec (e.g.
col or short; these items are always present), data items in the enclosing
environment (.enclos; this defaults to parent.frame()), the .defaults
list (passed by the user at run time) and the .dots list associated with
each column.
Users are encouraged to filter based on logical data items in dots that are
set through the flags field in SETUP__. When flags are set, every
column is given a logical data item that can always be evaluated for every
column. This is the safest and simplest way to go and should be the target
usage. In case more complicated applications are required, users can appeal
to data items in dots which may or may not be logical. Of course, the user
can enter data into dots for every column to ensure that data item is
available for evaluating expr but that might not be very convenient. In
that case, pass a list of .defaults that will be used when the filter
variable isn't available in dots. As an alternative to using .defaults,
the user can run the spec object through ys_dots_fill which will
fill in dots data items with default values only when they don't exist. This
is probably more convenient, but the user is warned that these data items
in dots stay with the yspec object for the life of the object.
spec <- ys_help$spec()
ys_filter(spec, is.character(decode))
#> name info unit short source
#> C cd- . comment character ysdb_internal
#> NUM --- . record number ysdb_internal
#> ID --- . subject identifier ysdb_internal
#> SUBJ c-- . subject identifier ysdb_internal
#> TIME --- hour TIME look
#> SEQ -d- . SEQ .
#> CMT --- . compartment number ysdb_internal
#> EVID -d- . event ID ysdb_internal
#> AMT --- mg dose amount ysdb_internal
#> DV --- micrograms/L dependent variable ysdb_internal
#> AGE --- years age ysdb_internal
#> WT --- kg weight ysdb_internal
#> CRCL --- ml/min CRCL .
#> ALB --- g/dL albumin ysdb_internal
#> BMI --- m2/kg BMI ysdb_internal
#> AAG --- mg/dL alpha-1-acid glycoprotein .
#> SCR --- mg/dL serum creatinine .
#> AST --- . aspartate aminotransferase .
#> ALT --- . alanine aminotransferase .
#> HT --- cm height ysdb_internal
#> CP -d- . Child-Pugh score look
#> TAFD --- hours time after first dose .
#> TAD --- hours time after dose .
#> LDOS --- mg last dose amount .
#> MDV -d- . MDV ysdb_internal
#> BLQ -d- . below limit of quantification .
#> PHASE --- . study phase indicator .
#> STUDY -d- . study number .
#> RF cd- . renal function stage .
ys_filter(spec, unit == "kg" | type == "character")
#> name info unit short source
#> C cd- . comment character ysdb_internal
#> SUBJ c-- . subject identifier ysdb_internal
#> WT --- kg weight ysdb_internal
#> RF cd- . renal function stage .
ys_filter(spec, covariate)
#> name info unit short source
#> AGE --- years age ysdb_internal
#> WT --- kg weight ysdb_internal
#> CRCL --- ml/min CRCL .
#> ALB --- g/dL albumin ysdb_internal
#> BMI --- m2/kg BMI ysdb_internal
#> AAG --- mg/dL alpha-1-acid glycoprotein .
#> SCR --- mg/dL serum creatinine .
#> AST --- . aspartate aminotransferase .
#> ALT --- . alanine aminotransferase .
#> HT --- cm height ysdb_internal
#> CP -d- . Child-Pugh score look