20 Glossary

This glossary contains definitions of terms used in when describing evidence synthesis (e.g., systematic reviews) as well as terms introduced by {metabefor}.

Block core: The block core is is a part of an Rxs file: it is the part of an entity block where the extracted value for an entity is specified during extraction. This is explained in detail in the Execution: Extraction chapter (Chapter 12 in this version of the book).
Block end marker: The block end marker is a part of an Rxs file: it is a sequence of characters that denote that en entity block ends (which was started by a block start marker). This is explained in detail in the Execution: Extraction chapter (Chapter 12 in this version of the book).
Block start marker: The block start marker is a part of an Rxs file: it is a sequence of characters that denote that en entity block starts (which is then ended by a block end marker). This is explained in detail in the Execution: Extraction chapter (Chapter 12 in this version of the book).
Container entity: An entity that does not store a value (i.e. cannot itself be extracted) but serves to organise other entities in a hierarchy. For example, a container entity could be “Provenance”, containing “regular” entities “Authors”, “Region”, and “Date”. For the latter three, values are extracted, and though those three together can form a source’s provenance, the entity provenance itself has no value: it just contains the other three entities.
Cluster: A set of entities specified in a list in a parent entity: see clustering entity and clustered entity.
Clustered entity: An entity that is specified in a list within a clustering entity. To specify that an entity is a value list entity, specify as its parent entity a clustering entity. Clustering entities are presented in a list in the Rxs template (within the parent entity). The coding guides that are normally presented above and below every entity are then concatenated and shows after it. This has two drawbacks. First, if word wrapping is active, it makes the Rxs file look quite messy and potentially intimidating. Second, since the descriptions and examples are less salient, this is a bit less straightforward for extractors, so may require more intensive training.
Clustering entity: An entity that as its value contains a list of clustered entities. To specify that an entity is a clustering entity, set the list column in the Rxs specification spreadsheet to TRUE. All entities that specify that clustering entity as parent will then be presented in a list within that entity in the Rxs template. They are useful to efficiently extract closely related information. For example, characteristics of a variable that is reported on in a source; various possible effect size measures that could be reported to describe an association; or closely related characteristics of a procedure that is described in a source.
Entity: Something that can be extracted from a source: examples are effect sizes, sample sizes, study design characteristics, author names, publication dates, journal names, whether sampling strategies were justified, or the literal text used to phrase the main conclusion. Once an extraction script has been parsed, entities are also commonly referred to as fields that hold values. However, note that entities can be repeating: they refer to a type of thing that can be extracted, not to any specific thing that has been extracted, whereas a field always holds a specific extracted value. For example, it is possible to specify a clustering entity called result_association used to extract various effect sizes or other statistics that may be specified to describe an association between two variables, each as a clustered entity, e.g. entities called pearson_r and cohen_d. In any given extraction script, multiple instances of that result_association entity can be extracted, each being represented by a different entity node, and each of those clustering entities holding multiple clustered entities or fields. Each entity node holds a pearson_r field and a cohen_d field, but in the extraction script specification, only one entity is specified for each of result_association, pearson_r, and cohen_d. To refer explicitly to the entity as a “thing that can be extracted”, you can use the terms entity specification or extractable entity. To refer explicitly to an entity that has been extracted, use field or extracted entity.
Entity block: An entity block is a part of an Rxs file: it is a block in that plain text file with the information about an entity to extract. It starts with a block start marker and ends with a block end marker. This is explained in detail in the Execution: Extraction chapter (Chapter 12 in this version of the book).
Entity container: See container entity.
Entity description sub-block: An entity description sub-block is a part of an Rxs file: it specified the label and the description of the entity to extract in the entity block it is a part of. This is explained in detail in the Execution: Extraction chapter (Chapter 12 in this version of the book).
Entity identifier: The unique identifier of an entity as specified in the identifier column of the extraction script specification.
Entity node: In the data.tree object representing each extracted source, entities are stored as nodes in a hierarchical tree. In this tree, each entity correponds to one or more entity nodes, except for clustered entities, which are stored as values in a list in the entity node representing their clustering entity (i.e. their parent entity).
Entity node identifier: The unique identifier of an extracted entity (i.e. an instance of an entity specification)
Entity specification: A way to explicitly refer to an entity in its generic definition, as a class of things that can be extracted, as opposed to as a field or entity node, which represents an extracted entity. This distinction is important because entities can be repeated (see entity).
Extractable entity: See entity specification.
Extracted entity: A way to explicitly refer to an entity that has been extracted, as an instance of the entity specification or extractable entity (a generic description of a class of things that can be extracted). Extracted entities are entity nodes unless they are clustered entities, in which case they are stored as fields holding values in a list in their parent entity (i.e. their clustering entity). Extracted entities that are entity nodes are either container entities (if they don’t store a value themselves, but instead are used to organise other entities), fields (if they hold a single value), or clustering entities (if they hold a list specifying the values for multiple clustered entities).
Extraction: The act of registering an entity in an extraction script (or extraction form, if metabefor isn’t used) in the form of a text string or an entity conform the coding instructions (as specified in the Rxs specification if metabefor is used).
Extraction script (.Rxs file): An R Markdown file with the extension .Rxs.Rmd that is a completed Rxs template, and as such, set up such that it can be parsed by metabefor.
Extraction script specification: A spreadsheet specifying which entities to extract, how they are hierarchically structured, which value templates they use, and their extraction instructions (or coding instructions).
Field: A synonym of entity that is used when it is referred to as a specific value holder in the context of a completed extraction script. For example, when in an extraction script specification an entity is specified to extract the source’s publication date with entity identifier pub_date, in the parsed extraction script, the value of that date can be referred to as being stored in the pub_date field. A field represents an instance of an entity: see that definition for more details.
List: A list of multiple clustered entities. Lists are an efficient way to extract closely related entities, such as measurement details about a given variable, descriptives for an outcome, or various effect size metrics that may be reported.
Rxs file: A file with an R extraction script. One example is an Rxs template as produced by [metabefor::rxs_fromSpecifications()], but usually these Rxs files will be completed versions of that template, each containing one or more extracted entities from a source. Rxs files have the extension .Rxs.Rmd.
Rxs specification: See extraction script specification.
Rxs template: The structured R Markdown file produced by metabefor after it parsed the Rxs specification spreadsheet.
Source: Something that entities can be extracted from, such as an article, book, case law, report, webpage, or other source.
Value: A value; usually a single number or character string, but values can be more complex, too, e.g. vectors of numbers of strings, or even tables (matrices or arrays).
Value description sub-block: A value description sub-block is a part of an Rxs file: it specified the value to extract for the entity in the entity block it is a part of. This is explained in detail in the Execution: Extraction chapter (chapter @ref(execution-extraction) in this version of the book).
Value list: A list of values; a synonym for all extracted clustered entities stored in an extracted clustering entity.
Value templates: In an Rxs specification, a template for a data type that can be extracted, specifying the values that are allowed, the default value, instructions, and validation rules.