new_src_cfg {ricu} | R Documentation |
Internal utilities for working with data source configurations
Description
Data source configuration objects store information on data sources used
throughout ricu
. This includes URLs for data set downloading, Column
specifications used for data set importing, default values per table for
important columns such as index columns when loading data and how different
patient identifiers used throughout a dataset relate to another. Per
dataset, a src_cfg
object is created from a JSON file (see
load_src_cfg()
), consisting of several helper-classes compartmentalizing
the pieces of information outlined above. Alongside constructors for the
various classes, several utilities, such as inheritance checks, coercion
functions, as well as functions to extract pieces of information from these
objects are provided.
Usage
new_src_cfg(name, id_cfg, col_cfg, tbl_cfg, ..., class_prefix = name)
new_id_cfg(
src,
name,
id,
pos = seq_along(name),
start = NULL,
end = NULL,
table = NULL,
class_prefix = src
)
new_col_cfg(src, table, ..., class_prefix = src)
new_tbl_cfg(
src,
table,
files = NULL,
cols = NULL,
num_rows = NULL,
partitioning = NULL,
...,
class_prefix = src
)
is_src_cfg(x)
as_src_cfg(x)
is_id_cfg(x)
as_id_cfg(x)
is_col_cfg(x)
as_col_cfg(x)
is_tbl_cfg(x)
as_tbl_cfg(x)
src_name(x)
tbl_name(x)
src_extra_cfg(x)
src_prefix(x)
src_url(x)
id_var_opts(x)
default_vars(x, type)
Arguments
name |
Name of the data source |
id_cfg |
An |
col_cfg |
A list of |
tbl_cfg |
A list of |
... |
Further objects to add (such as an URL specification) |
class_prefix |
A character vector of class prefixes that are added to the instantiated classes |
src |
Data source name |
id , start , end |
Name(s) of ID column(s), as well as respective start and end timestamps |
pos |
Integer valued position, ordering IDs by their cardinality |
table |
Table name |
cols |
List containing a list per column each holding string valued
entries |
num_rows |
A count indicating the expected number of rows |
partitioning |
A table partitioning is defined by a column name and a
vector of numeric values that are passed as |
x |
Object to coerce/query |
Details
The following classes are used to represent data source configuration objects:
-
src_cfg
: wraps objectsid_cfg
,col_cfg
and optionallytbl_cfg
-
id_cfg
: contains information in ID systems and is created fromid_cfg
entries in config files -
col_cfg
: contains column default settings represented bydefaults
entries in table configuration blocks -
tbl_cfg
: used when importing data and therefore encompasses information infiles
,num_rows
andcols
entries of table configuration blocks
Represented by a col_cfg
, a table can have some of its columns marked as
default columns for the following concepts and further column meanings can
be specified via ...
:
-
id_col
: column will be used for as id foricu_tbl
objects -
index_col
: column represents a timestamp variable and will be use as such forts_tbl
objects -
val_col
: column contains the measured variable of interest -
unit_col
: column specifies the unit of measurement in the correspondingval_col
Alongside constructors (new_*()
), inheritance checking functions
(is_*()
), as well as coercion functions (as_*(
), relevant utility
functions include:
-
src_url()
: retrieve the URL of a data source -
id_var_opts()
: column name(s) corresponding to ID systems -
src_name()
: name of the data source -
tbl_name()
: name of a table
Coercion between objects under some circumstances can yield list-of object
return types. For example when coercing src_cfg
to tbl_cfg
, this will
result in a list of tbl_cfg
objects, as multiple tables typically
correspond to a data source.
Value
Constructors new_*()
as well as coercion functions as_*()
return the respective objects, while inheritance tester functions is_*()
return a logical flag.
-
src_url()
: string valued data source URL -
id_var_opts()
: character vector of ID variable options -
src_name()
: string valued data source name -
tbl_name()
: string valued table name