ADaM specifications

mighty.metadata uses YAML files to specify Analysis Data Model (ADaM) datasets. Each YAML file follows a fixed structure with defines properties and entries.

This structure is defined in a JSON-schema that you can access with:

system.file("schema", "adam.json", package = "mighty.metadata")

Below you can find a detailed description of the structure.

Mighty Metadata ADaM Domain Specification

Common schema for ADaM dataset specification in the mightyverse

Type Required Additional Properties
object id
label
class
structure
keys
columns		 No

Properties

Name Description Type Required
id Name of the ADaM dataset cdisc/name Yes
label Label of the ADaM dataset string Yes
include Conditional expression to include the domain mighty/include No
class CDISC class of the dataset cdisc/class Yes
subclass CDISC subclass of the dataset cdisc/subclass No
structure Text description of the structure of the dataset string Yes
keys Key variables for the dataset keys Yes
comment Comment to the dataset string No
usecore Flag to populate with core variables from ADSL boolean No
population Population and base domain used to create the dataset mighty/population No
columns Columns in the dataset columns Yes
rows Row derivations for mighty rows No
parameters Parameters in a BDS dataset parameters No

Definitions

keys

Keys are always unique and of minimum length 1

Type Items Min Items Unique Items
array cdisc/name 1 Yes
cdisc/name

columns

List of column specifications

Type Items Min Items Unique Items
array column 1 Yes

column

Specification of a single column

Type Required Additional Properties
object id No

Properties

Name Description Type Required
id Name of the column cdisc/name Yes
include Conditional expression to include the column mighty/include No
label Label of the column string No
method How to derive the column (free text) string No
origin Origin type of the column cdisc/origin No
codelist Codelist of possible values of the column string No
is_core Flag for designating a core variables in subject level datasets boolean No
format Data format of the column standard/dataformat No
component Mighty component to create the column mighty/component No
depends dependencies required to create the column mighty/depends No
core Describes whether a variable is required (Req), conditionally required (Cond) or permissible (Perm) cdisc/core No
comment Comment to the column (free text) string No

rows

List of row action specifications. Typically used when adding additional rows to the data.

Type Items Min Items Unique Items
array row 1 Yes

row

Specification of a single row action

Type Required Additional Properties
object id No

Properties

Name Description Type Required
id Unique identifier of the action. Used to reference in other places, e.g. as a dependency. cdisc/name Yes
include Conditional expression to include the row mighty/include No
method How to derive the row action (free text) string No
component Mighty component to do the row action mighty/component No
depends Dependencies needed before the action can be carried out mighty/depends No

parameters

Specification of parameters in a BDS dataset

Type Items Min Items Unique Items
array parameter 1 Yes

parameter

Specification of a single BDS parameter

Type Required Additional Properties
object id No

Properties

Name Description Type Required
id Parameter id (PARAMCD) cdisc/name Yes
include Conditional expression to include the parameter mighty/include No
label Parameter label (PARAM) string No
columns Additional columns to derive for the parameter, e.g. AVAL and AVALC columns No
component Mighty component used to derive the parameter and all relevant columns mighty/component No
depends Dependencies required to create the parameter mighty/depends No

standard

Additional definitions used for e.g. define.xml

dataformat

Format used to display the data

Type Required
object type
length

Properties

Name Description Type Enum Minimum Pattern Required
type Data type string text , integer , float , datetime , date , time , partialDate , partialTime , partialDatetime , incompleteDatetime, durationDatetime , intervalDatetime Yes
length Maximum length of content integer NULL 1 Yes
display SAS display format string NULL . No

cdisc

Definitions from CDISC standards

name

Uppercase identifier

Type Pattern
string ^[A-Z][A-Z0-9_]*$

class

Subset of CDISC controlled terminology C103329

Type Enum
string SUBJECT LEVEL ANALYSIS DATASET
BASIC DATA STRUCTURE
OCCURRENCE DATA STRUCTURE
ADAM OTHER

subclass

Union of CDISC controlled terminology C165635 and C176227

Type Enum
string TIME-TO-EVENT
NON-COMPARTMENTAL ANALYSIS
POPULATION PHARMACOKINETIC ANALYSIS
ADVERSE EVENT

origin

Controlled terminology C170449

Type Enum
string Assigned
Collected
Derived
Not Available
Other
Predecessor
Protocol

core

Indicator of whether a variable is required (Req), conditionally required (Cond), or permissible (Perm) in the dataset

Type Enum
string Cond
Perm
Req

mighty

Definitions only relevant when using mighty to generate code

population

mighty - specification of the base domain(s) and any global filters to apply

Type Required
object base

Properties

Name Description Required Type
base mighty - domains to filter and combine to create initial dataset Yes mighty/base_input_list
global mighty - global filters to apply after combining base datasets No mighty/global_input_list

base_input_list

mighty - list of base input datasets

Type Items Min Items Unique Items
array mighty/base_input 1 Yes

base_input

mighty - single base input dataset with filters

Type Required Additional Properties
object domain
depends
filter		 No

Properties

Name Description Required Type
domain Name of the dataset to use Yes cdisc/name
depends Which columns in the dataset the filter depends on Yes mighty/depends
filter Yes mighty/filter

global_input_list

mighty - list of global filters

Type Items Min Items Unique Items
array mighty/global_input 1 Yes

global_input

mighty - single global filter

Type Required Additional Properties
object filter
depends		 No

Properties

Name Description Required Type
filter Yes mighty/filter
depends Which columns the filter depends on Yes mighty/depends

depends_string

A single dependency: COLUMN, DOMAIN.COLUMN, rows.ID, or parameters.ID

Type Pattern
string ([A-Z][A-Z0-9_](.[A-Z][A-Z0-9_])?)$|(rows|parameters).[A-Z][A-Z0-9_]*$

depends

List of dependencies needed before the component code can be evaluated

Type Items Min Items Unique Items
array mighty/depends_string 1 Yes
mighty/depends_string

include

Glue expression that evaluates to TRUE or FALSE

Type Pattern
string ^{.*}$
boolean

filter

Filter specification. Must be an R expression that can be evaluated.

Type
string

component

mighty component used to carry out the desired derivation

Type Required Additional Properties
object id No

Properties

Name Description Type Required
id ID of the component. Either name of standard or file path to local component. string Yes
with named list of input arguments needed to render component object No