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Grid Developer Notes

Source: R/Grid.R, R/GridEven.R, R/GridEvent.R, and 6 more
Grid-Dev.Rd

Developer details for implementing / extending Grid objects for defining generated quantities for SurvivalQuantities and LongitudinalQuantities.

Details

All grid classes must inherit from the abstract Grid class. All grid classes must provide as.QuantityGenerator(object, data) and as.QuantityCollapser(object, data) methods where data is a DataJoint object. These methods must return a QuantityGenerator and QuantityCollapser object respectively. The QuantityGenerator object specifies unique subject/timepoint combinations that samples should be generated at. The QuantityCollapser object specifies how to combine these generated samples to form the desired quantities. As an example say we want to generate grouped samples for the groups Group-1 and Group-2 which consist of the subjects sub-1, sub-2 and sub-3, sub-4 respectively at two time points 10 and 20. We can achieve this as follows:

QuantityGenerator(
    times = c(10, 10, 10, 10, 20, 20, 20, 20),
    subjects = c("sub-1" "sub-2", "sub-3", "sub-4", "sub-1" "sub-2", "sub-3", "sub-4")
  )
QuantityCollapser(
    times = c(10, 20, 10 , 20),
    groups = c("Group-1", "Group-1", "Group-2", "Group-2"),
    indexes = list(c(1, 2), c(5, 6), c(3, 4), c(7, 8))
  )

For population based quantities use the arms and studies arguments of QuantityGenerator instead of subjects.

Slots

subjects

(character or NULL)
vector of subjects to extract quantities for. If NULL will default to all subjects within the dataset.

times

(numeric or NULL)
vector of time points to extract quantities at. If NULL will default to 201 evenly spaced timepoints between 0 and either the max

groups

(list)
named list of subjects to extract quantities for. See details.

Group Specification

For GridGrouped(), groups must be a named list of character vectors. Each element of the list must be a character vector of the subjects that will form the group where the element name is the corresponding name of the group. For example if the goal was to create two groups named Group-1 and Group-2 which are composed of the subjects sub-1, sub-2 and sub-3, sub-4 respectively then this would be specified as:

GridGrouped(
    groups = list(
        "Group-1" = c("sub-1", "sub-2"),
        "Group-2" = c("sub-3", "sub-4")
    )
  )

See also

Quant-Dev