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Quantity Grid Specification

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

These functions are used to specify which subjects and timepoints should be generated when calculating quantities via SurvivalQuantities and LongitudinalQuantities.

Usage

GridEven(subjects = NULL, length.out = 30)

GridEvent(subjects = NULL)

GridFixed(subjects = NULL, times = NULL)

GridGrouped(groups, times = NULL)

GridManual(spec)

GridObserved(subjects = NULL)

GridPopulation(times = NULL)

GridPrediction(times = NULL, newdata, params = list())

Arguments

subjects

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

length.out

(numeric)
number of evenly spaced timepoints to generate quantities at.

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 observation time (for LongitudinalQuantities) or max event time (for SurvivalQuantities).

groups

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

spec

(list)
named list of subjects to extract quantities for. The names of each element should be the required subjects with the element itself being a numeric vector of timepoints to generate the quantity at.

newdata

(data.frame)
new data to generate quantities for. Must contain the same columns and factor levels of the original data used in the DataSurvival object.

params

(list)
named list of parameters to fix the longitudinal model parameters at when predicting survival quantities. See getPredictionNames() for the required parameters.

Details

  • GridFixed() is used to specify a fixed set of timepoints to generate quantities at for all the specified subjects.

  • GridGrouped() is similar to GridFixed() but allows for groupwise averaging (see Group Specification).

  • GridObserved() generates quantities at the observed longitudinal timepoints for each subject.

  • GridManual() allows for individual timepoint specification for each subject.

  • GridEven() generates quantities for each subject at N evenly spaced timepoints between each subjects first and last longitudinal observations.

  • GridEvent() generates one quantity for each subject at their event/censor time as indicated by the time variable in the survival dataset.

  • GridPopulation() generates longitudinal model quantities based on the population parameters at the specified time points. Generates 1 set of quantities for each distinct combination of arm and study within the DataSubject object provided to the JointModel.

  • GridPrediction() generates survival quantities based on any user-defined values at the specified time points. This is useful for generating quantities for a new dataset on specific longitudinal model parameters. See getPredictionNames() to determine which longitudinal model parameters need to be defined for a given longitudinal model.

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

SurvivalQuantities, LongitudinalQuantities