load_id {ricu}

Load data as id_tbl or ts_tbl objects

Description

Building on functionality provided by load_src() and load_difftime(), load_id() and load_ts() load data from disk as id_tbl and ts_tbl objects respectively. Over load_difftime() both load_id() and load_ts() provide a way to specify meta_vars() (as id_var and index_var arguments), as well as an interval size (as interval argument) for time series data.

Usage

load_id(x, ...)

## S3 method for class 'src_tbl'
load_id(
  x,
  rows,
  cols = colnames(x),
  id_var = id_vars(x),
  interval = hours(1L),
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'character'
load_id(x, src, ...)

## S3 method for class 'itm'
load_id(
  x,
  cols = colnames(x),
  id_var = id_vars(x),
  interval = hours(1L),
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'fun_itm'
load_id(x, ...)

## Default S3 method:
load_id(x, ...)

load_ts(x, ...)

## S3 method for class 'src_tbl'
load_ts(
  x,
  rows,
  cols = colnames(x),
  id_var = id_vars(x),
  index_var = ricu::index_var(x),
  interval = hours(1L),
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'character'
load_ts(x, src, ...)

## S3 method for class 'itm'
load_ts(
  x,
  cols = colnames(x),
  id_var = id_vars(x),
  index_var = ricu::index_var(x),
  interval = hours(1L),
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'fun_itm'
load_ts(x, ...)

## Default S3 method:
load_ts(x, ...)

load_win(x, ...)

## S3 method for class 'src_tbl'
load_win(
  x,
  rows,
  cols = colnames(x),
  id_var = id_vars(x),
  index_var = ricu::index_var(x),
  interval = hours(1L),
  dur_var = ricu::dur_var(x),
  dur_is_end = TRUE,
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'character'
load_win(x, src, ...)

## S3 method for class 'itm'
load_win(
  x,
  cols = colnames(x),
  id_var = id_vars(x),
  index_var = ricu::index_var(x),
  interval = hours(1L),
  dur_var = ricu::dur_var(x),
  dur_is_end = TRUE,
  time_vars = ricu::time_vars(x),
  ...
)

## S3 method for class 'fun_itm'
load_win(x, ...)

## Default S3 method:
load_win(x, ...)

Arguments

x

Object for which to load data

...

Generic consistency

rows

Expression used for row subsetting (NSE)

cols

Character vector of column names

id_var

The column defining the id of ts_tbl and id_tbl objects

interval

The time interval used to discretize time stamps with, specified as base::difftime() object

time_vars

Character vector enumerating the columns to be treated as timestamps and thus returned as base::difftime() vectors

src

Passed to as_src_tbl() in order to determine the data source

index_var

The column defining the index of ts_tbl objects

dur_var

The column used for determining durations

dur_is_end

Logical flag indicating whether to use durations as-is or to calculated them by subtracting the index_var column

Details

While for load_difftime() the ID variable can be suggested, the function only returns a best effort at fulfilling this request. In some cases, where the data does not allow for the desired ID type, data is returned using the ID system (among all available ones for the given table) with highest cardinality. Both load_id() and load_ts() are guaranteed to return an object with id_vars() set as requested by the id_var argument. Internally, the change of ID system is performed by change_id().

Additionally, while times returned by load_difftime() are in 1 minute resolution, the time series step size can be specified by the interval argument when calling load_id() or load_ts(). This rounding and potential change of time unit is performed by change_interval() on all columns specified by the time_vars argument. All time stamps are relative to the origin provided by the ID system. This means that for an id_var corresponding to hospital IDs, times are relative to hospital admission.

When load_id() (or load_ts()) is called on itm objects instead of src_tbl (or objects that can be coerced to src_tbl), The row-subsetting is performed according the the specification as provided by the itm object. Furthermore, at default settings, columns are returned as required by the itm object and id_var (as well as index_var) are set accordingly if specified by the itm or set to default values for the given src_tbl object if not explicitly specified.

Value

An id_tbl or a ts_tbl object.

Examples

if (require(mimic.demo)) {
load_id("admissions", "mimic_demo", cols = "admission_type")

dat <- load_ts(mimic_demo$labevents, itemid %in% c(50809L, 50931L),
               cols = c("itemid", "valuenum"))

glu <- new_itm(src = "mimic_demo", table = "labevents",
               sub_var = "itemid", ids = c(50809L, 50931L))

identical(load_ts(glu), dat)
}