Table Hierarchy
Abinaya Yogasekaram
2023-12-07
Source:vignettes/dev-guide/dg_table_hierarchy.Rmd
dg_table_hierarchy.RmdDisclaimer
This article is intended for use by developers only and will contain
low-level explanations of the topics covered. For user-friendly
vignettes, please see the Articles
page on the rtables website.
Any code or prose which appears in the version of this article on the
main branch of the repository may reflect a specific state
of things that can be more or less recent. This guide describes very
important aspects of table hierarchy that are unlikely to change.
Regardless, we invite the reader to keep in mind that the current
repository code may have drifted from the following material in this
document, and it is always the best practice to read the code directly
on main.
Please keep in mind that rtables is still under active
development, and it has seen the efforts of multiple contributors across
different years. Therefore, there may be legacy mechanisms and ongoing
transformations that could look different in the future.
Introduction
The scope of this vignette is to understand the structure of rtable objects, class hierarchy with an exploration of tree structures as S4 objects. Exploring table structure enables a better understanding of rtables concepts such as split machinery, tabulation, pagination and export. More details from the user’s perspective of table structure can be found in the relevant vignettes.
isS4 getclass - for class structure
Process and Methods
We invite developers to use the provided examples to interactively explore the rtables hierarchy. The most helpful command is ‘getClass’ for a list of the slots associated with a class, in addition to related classes and their relative distances.
Table Representation
“PredataAxisLayout” class is used to define the data subset instructions for tabulation. 2 subclasses (one for each axis): PredataColLayout, PredataRowLayout
Content (summary row groups)
Splits are core functionality for rtables as tabulation and calculations are often required on subsets of the data.
Split Machinery
## Class "TreePos" [package "rtables"]
##
## Slots:
##
## Name: splits s_values sval_labels subset
## Class: list list character SubsetDef“TreePos” class contains split information as a list of the splits, split label values, and the subsets of the data that are generated by the split.
AllSplit RootSplit MultiVarSplit VarStaticCutSplit CumulativeCutSplit VarDynCutSplit CompoundSplit VarLevWBaselineSplit
The highest level of the table hierarchy belong to “TableTree”. The code below identifies the slots associated with with this class.
getClass("TableTree")## Class "TableTree" [package "rtables"]
##
## Slots:
##
## Name: content page_title_prefix children
## Class: ElementaryTable character list
##
## Name: rowspans labelrow page_titles
## Class: data.frame LabelRow character
##
## Name: horizontal_sep header_section_div trailing_section_div
## Class: character character character
##
## Name: col_info format na_str
## Class: InstantiatedColumnInfo FormatSpec character
##
## Name: indent_modifier table_inset level
## Class: integer integer integer
##
## Name: name main_title subtitles
## Class: character character character
##
## Name: main_footer provenance_footer
## Class: character character
##
## Extends:
## Class "VTableTree", directly
## Class "VTableNodeInfo", by class "VTableTree", distance 2
## Class "VTree", by class "VTableTree", distance 2
## Class "VTitleFooter", by class "VTableTree", distance 2
## Class "VNodeInfo", by class "VTableTree", distance 3As an S4 object, the slots can be accessed using “@” (similar to the use of “$” for list objects). You’ll notice there are classes that fall under “Extends”. The classes contained here have a relationship to the TableTree object and are “virtual” classes. To avoid the repetition of slots and carrying the same data (set of slots for example) that multiple classes may need, rtables extensively uses virtual classes. A virtual class cannot be instantiated, the purpose is for other classes to inherit information from it.
lyt <- basic_table(title = "big title") %>%
split_rows_by("SEX", page_by = TRUE) %>%
analyze("AGE")
tt <- build_table(lyt, DM)
# Though we don't recommend using str for studying rtable objects,
# we do find it useful in this instance to visualize the parent/child relationships.
str(tt, max.level=2)## Formal class 'TableTree' [package "rtables"] with 20 slots
## ..@ content :Formal class 'ElementaryTable' [package "rtables"] with 19 slots
## ..@ page_title_prefix : chr "SEX"
## ..@ children :List of 4
## ..@ rowspans :'data.frame': 0 obs. of 0 variables
## ..@ labelrow :Formal class 'LabelRow' [package "rtables"] with 13 slots
## ..@ page_titles : chr(0)
## ..@ horizontal_sep : chr "—"
## ..@ header_section_div : chr NA
## ..@ trailing_section_div: chr NA
## ..@ col_info :Formal class 'InstantiatedColumnInfo' [package "rtables"] with 9 slots
## ..@ format : NULL
## ..@ na_str : chr NA
## ..@ indent_modifier : int 0
## ..@ table_inset : int 0
## ..@ level : int 1
## ..@ name : chr "SEX"
## ..@ main_title : chr "big title"
## ..@ subtitles : chr(0)
## ..@ main_footer : chr(0)
## ..@ provenance_footer : chr(0)## Warning: str provides a low level, implementation-detail-specific description
## of the TableTree object structure. See table_structure(.) for a summary of
## table struture intended for end users.Tree Paths
Root to Leaves, are vectors of vectors Tables are tree, nodes in the tree can have summaries associated with them. Tables are trees because of the nested structure. There is also the benefit of keeping and repeating necessary information when trying to paginate a table.
Children of ElementaryTables are row objects. TableTree can have children that are either row objects or other table objects.