fhircrackr (version 1.0.0)

fhir_design: Create a '>fhir_design object

Description

A fhir_design is a named list of fhir_table_description objects (See fhir_table_description()) and should be created using the function described here. The design is used in fhir_crack() to tell the function how to flatten each resource type.

Usage

fhir_design(...)
# S4 method for fhir_table_description
fhir_design(...)
# S4 method for list
fhir_design(...)
# S4 method for fhir_table_list
fhir_design(...)

Arguments

...

One ore more fhir_table_description objects or a named list containing fhir_table_description objects, or an object of class '>fhir_df_list/'>fhir_dt_list. See fhir_table_description().

Details

A fhir_design looks for example like this:

A fhir_design with 2 table_descriptions:
=====================================================
Name: Patients
Resource type: Patient
Columns:
column name | xpath expression
------------------------
name        | name/family
gender      | gender
id          | id
Style:
sep: ||
brackets: '[' ']'
rm_empty_cols: FALSE
=====================================================
Name: MedicationAdministrations
Resource type: MedicationAdministration
Columns:
An empty fhir_columns object
Style:
sep: ' '
brackets: character(0)
rm_empty_cols: TRUE

The names of the table_descriptions are taken from the names of the arguments. If the table_descriptions are created within the call to fhir_design and therefore have no names, the names will be created from the respective resource type. See examples.

For backwards compatibility it is for the moment also possible to build it from an old-style design as used in fhircrackr (< 1.0.0). See examples.

If this function is given an object of class '>fhir_df_list or '>fhir_dt_list, it will extract the design that was used to create the respective list.

See Also

fhir_table_description(), fhir_crack()

Examples

# NOT RUN {
####Example 1####

###create fhir_table_descriptions first
#see ?fhir_table_description for explanation

pat <- fhir_table_description(resource = "Patient",
                    cols = c(name = "name/family",
                             gender = "gender",
                             id = "id"),
                    style = fhir_style(sep = "||",
                                       brackets = c("[", "]"),
                                       rm_empty_cols = FALSE
                            )
             )

meds <- fhir_table_description(resource = "MedicationAdministration")

###create design
#First option: Explicitly define names

design1 <- fhir_design(Pats = pat, Medics = meds)
print(design1)


#Second option: Names are taken from the object names

design2 <- fhir_design(pat, meds)
print(design2)


#Third option: Create table_description within fhir_design

design3 <- fhir_design(fhir_table_description(resource = "MedicationAdministration"))
print(design3)


#Fourth option: Names are taken from named list

design3 <- fhir_design(list(Patients = pat, Medications = meds))
print(design3)


####Example 2####
#This option will be deprecated at some point

#old style design
old_design <- list(
                 Patients = list(
                    resource = "//Patient",
                    cols = list(
                       name = "name/family",
                       gender = "gender",
                       id = "id"),
                    style = list(
                       sep = "||",
                       brackets = c("[", "]"),
                       rm_empty_cols = FALSE
                    )
                 ),
                 Medications = list(
                    resource = "//Medication"
                 )
              )

new_design <- fhir_design(old_design)
print(new_design)

###Example 3###
###Extract design from fhir_df_list/fhir_dt_list

#unserialize and crack example bundles
med_bundles <- fhir_unserialize(bundles = medication_bundles)
dfs <- fhir_crack(bundles = med_bundles, design = design1)

#extract design

fhir_design(dfs)

# }