a-Glossary-and-templates.RmdThe glossary describes the main objects used in Rmonize functions. The main components of each object are listed and must have the names as presented to be used in functions, except where indicated in square brackets ([…]). An asterisk (*) indicates a required object or component. You can download templates or find additional documentation where available using the links provided.
List of core variables to generate across datasets and related metadata.
Metadata table containing the list of core variables to generate across datasets and related metadata about the variables. This table is required and uses the following columns.
| Name | Description |
|---|---|
| index | Index to order variables in the table. |
| name * | Name of the DataSchema variable. Each entry must be unique. The first entry must be the primary identifier variable (e.g., participant unique ID). |
| label | Short description of the DataSchema variable. A language can be specified using a language code, such as ‘label:en’ for english or ‘label:fr’ for french. |
| valueType | Value type of the input dataset variable (e.g., text, integer, decimal, boolean, date, datetime). See additional details. |
Metadata table containing the list of categories and related metadata (coding and description of the response options) defined for categorical variables (if any). If there are categorical variables defined, this table is required and uses the following columns.
| Name | Description |
|---|---|
| variable * | Name of the DataSchema variable to which the category belongs. This column is required if the Categories table is present. The value must also be present in the column ‘name’ in the Variables table. |
| name * | Category code value. This column is required if the table Categories is present. The combination of ‘variable’ and ‘name’ within the Categories table (i.e., the combination of DataSchema variable and category code value) must be unique. |
| label | Short description of the category code value. A language can be specified using a language code, such as ‘label:en’ for english or ‘label:fr’ for french. |
| missing | Boolean value (TRUE/FALSE or 1/0) indicating if the value in ‘name’ is interpreted as a missing value (e.g., question skipped by design in a questionnaire or a response option “Prefer not to answer”). |
Data table containing a collection of variables to process under the DataSchema format.
| Name | Description |
|---|---|
| [col_1] * | First variable in the input dataset, typically the identifier or index. A dataset must have at least one variable. |
| [col_2] … | Additional variable(s) in the input dataset. |
List of variables in an input dataset and related metadata.
Metadata table containing the list of variables in an input dataset and metadata about the input variables. If a data dictionary is defined for an input dataset, this table is required and uses the following columns.
| Name | Description |
|---|---|
| index | Index to order variables in the table. |
| name * | Name of the input dataset variable. Each entry must be unique. The first entry is typically the primary identifier variable (e.g., participant unique ID). |
| label | Short description of the input dataset variable. A language can be specified using a language code, such as ‘label:en’ for english or ‘label:fr’ for french. |
| valueType | Value type of the input dataset variable (e.g., text, integer, decimal, boolean, date, datetime). See additional details. |
Metadata table containing the list of categories and related metadata (coding and description of the response options) defined for categorical variables (if any). If there are categorical variables defined, this table is required and uses the following columns.
| Name | Description |
|---|---|
| variable * | Name of the input dataset variable to which the category belongs. This column is required if the Categories table is present. The value must also be present in the column ‘name’ in the Variables table. |
| name * | Category code value. This column is required if the table Categories is present. The combination of ‘variable’ and ‘name’ within the Categories table (i.e., the combination of DataSchema variable and category code value) must be unique. |
| label | Short description of the category code value. A language can be specified using a language code, such as ‘label:en’ for english or ‘label:fr’ for french. |
| missing | Boolean value (TRUE/FALSE or 1/0) indicating if the value in ‘name’ is interpreted as a missing value (e.g., question skipped by design in a questionnaire or a response option “Prefer not to answer”). |
Metadata table containing the elements defining the possibility for each input dataset to generate each DataSchema variable and, where applicable, the algorithms to generate harmonized variables in the DataSchema formats.
See additional documentation for Data Processing Elements.
| Name | Description |
|---|---|
| index | Index to order algorithms in the table. |
| dataschema_variable * | Name of the DataSchema variable being generated (must match a variable in the DataSchema).The first entry must be the primary identifier variable (e.g., participant unique ID). |
| label | Short description of the DataSchema variable (as in the DataSchema). |
| valueType | Value type of the DataSchema variable (as in the DataSchema). |
| input_dataset * | Name of the Input Dataset used to generate the DataSchema variable (as named in the Dossier). |
| input_variables * | Name of the variable(s) in the ‘input_dataset’ used to generate the DataSchema variable. |
| Mlstr_harmo:rule_category * | Type of algorithm used to generate the DataSchema variable from the input variables. The first entry must be the creation of a harmonized primary identifier variable (e.g., participant unique ID). |
| Mlstr_harmo:algorithm * | Algorithm used to generate the DataSchema variable from the input variables. |
| Mlstr_harmo:status | Possibility to generate the DataSchema variable from the input dataset. This is considered “complete” if the DataSchema variable can be generated from the input dataset or “impossible” if not. |
| Mlstr_harmo:status_detail | Additional information about the possibility to generate the DataSchema variable from the input dataset. If ‘Mlstr_harmo:status’ is “complete”, the information could be considered “identical” or “compatible” with the DataSchema variable. If ‘Mlstr_harmo:status’ is “impossible”, the information could be considered “incompatible” or “unavailable” for harmonization. |
| Mlstr_harmo:comment | Additional information about the inputs or algorithms to document with the harmonized variable. |
Set of one or more input dataset(s) and their associated input data dictionary(ies).
| Name | Description |
|---|---|
| [input_dataset_1] * | Data table containing a collection of variables to process under the DataSchema formats and its associated input data dictionary. At least one input dataset is required. The input dataset name is defined by the user and is indicated in the Data Processing Elements column ‘input_dataset’. This name identifies the source of input variables for data processing. |
| [input_dataset_2] … | Additional input dataset and associated data dictionary. |
Data table containing a collection of harmonized variables processed under the DataSchema formats.
| Name | Description |
|---|---|
| [harmonized_variable_1] * | First harmonized variable. This is the primary identifier variable (e.g., participant unique ID). Variables in the harmonized dataset are generated in the order defined in the DataSchema. |
| [harmonized_variable_2] … | Additional harmonized variable. |
List of variables in a harmonized dataset and related metadata.
Metadata table containing the list of variables in a harmonized dataset and metadata about the harmonized variables (taken from the DataSchema and Data Processing Elements).
| Name | Description |
|---|---|
| index | Index to order variables in the table (taken from the DataSchema). |
| name * | Name of the harmonized variable (taken from the DataSchema). |
| label | Short description of the harmonized variable (taken from the DataSchema). |
| valueType | Value type of the harmonized variable (taken from the DataSchema). |
| Mlstr_harmo:rule_category | Type of algorithm used to generate the DataSchema variable from the input variables (taken from the Data Processing Elements). |
| Mlstr_harmo:algorithm | Algorithm used to generate the harmonized variable from the input variables (taken from the Data Processing Elements). |
| Mlstr_harmo:status | Possibility to generate the DataSchema variable from the input dataset (taken from the Data Processing Elements). |
| Mlstr_harmo:status_detail | Additional information about the possibility to generate the DataSchema variable from the input dataset (taken from the Data Processing Elements). |
| Mlstr_harmo:comment | Additional information about the inputs or algorithms to document with the harmonized variable (taken from the Data Processing Elements). |
Metadata table containing the list of categories and related metadata (taken from the DataSchema).
| Name | Description |
|---|---|
| variable * | Name of the harmonized variable to which the category belong (taken from the DataSchema). |
| name * | Category code value (taken from the DataSchema). |
| label | Short description of the category code value (taken from the DataSchema). |
| missing | Boolean value (TRUE/FALSE or 1/0) indicating if the value in ‘name’ is interpreted as a missing value (taken from the DataSchema). |
Set of one or more harmonized dataset(s) and their associated data dictionary(ies).
| Name | Description |
|---|---|
| [harmonized_dataset_1] * | Data table containing a collection of harmonized variables processed under the DataSchema format and its associated data dictionary. There is one harmonized dataset per input dataset. |
| [harmonized_dataset_2] … | Additional harmonized dataset and its associated data dictionary. |
Combined data table containing multiple harmonized datasets processed under the same DataSchema formats.
| Name | Description |
|---|---|
| [harmonized_dataset_1] * | First harmonized variable. This is the primary unique identifier variable. Variables in the harmonized dataset are generated in the order defined in the DataSchema. |
| [harmonized_dataset_2] … | Additional harmonized variable. |
List of variables in a pooled harmonized dataset and related metadata.
Metadata table containing the list of variables in a pooled harmonized dataset and metadata about the harmonized variables (taken from the DataSchema).
| Name | Description |
|---|---|
| index | Index to order variables in the table (taken from the DataSchema). |
| name * | Name of the harmonized variable (taken from the DataSchema). |
| label | Short description of the harmonized variable (taken from the DataSchema). |
| valueType | Value type of the harmonized variable (taken from the DataSchema). |
Metadata table containing the list of categories and related metadata (taken from the DataSchema).
| Name | Description |
|---|---|
| variable * | Name of the harmonized variable to which the category belong (taken from the DataSchema). |
| name * | Category code value (taken from the DataSchema). |
| label | Short description of the category code value (taken from the DataSchema). |
| missing | Boolean value (TRUE/FALSE or 1/0) indicating if the value in ‘name’ is interpreted as a missing value (taken from the DataSchema). |