Aggregate Observed Data Groups

This function aggregates observed data based on specified groups and an aggregation method. It allows for different aggregation techniques, including geometric and arithmetic standard deviations, percentiles, or a user-defined custom function.

Usage

aggregateObservedDataGroups(
  dataObserved,
  groups = NULL,
  aggregationFlag = c("GeometricStdDev", "ArithmeticStdDev", "Percentiles", "Custom"),
  percentiles = getOspsuite.plots.option(optionKey = OptionKeys$Percentiles)[c(1, 3, 5)],
  groupSuffix = "aggregated",
  customFunction = NULL,
  lloqCheckColumns2of3 = NULL,
  lloqCheckColumns1of2 = NULL
)

Arguments

dataObserved

A `data.table` containing observed data.

groups

A character vector specifying the groups to aggregate. If NULL, all available groups are used.

aggregationFlag

A character string indicating the aggregation method. Options include "GeometricStdDev", "ArithmeticStdDev", "Percentiles", or "Custom".

percentiles

A numeric vector of percentiles to calculate if `aggregationFlag` is "Percentiles". Default is c(5, 50, 95).

groupSuffix

A character string to append to group names in the aggregated output. Default is 'aggregated'.

customFunction

A custom function for aggregation if `aggregationFlag` is "Custom". Default is NULL.

lloqCheckColumns2of3

A character vector specifying columns to check for LLOQ (Lower Limit of Quantification) for 1/3 data points. Default is NULL, is used only for `aggregationFlag` "Custom".

lloqCheckColumns1of2

A character vector specifying columns to check for LLOQ for 2/3 data points. Default is NULL, is used only for `aggregationFlag` "Custom".

Value

A `data.table` containing aggregated observed data.

Details

The function also checks for values below the Lower Limit of Quantification (LLOQ) and adjusts the aggregated results accordingly. For aggregationFlag 'GeometricStdDev' and 'GeometricStdDev', the statistics at any time point will only be calculated if at least 2/3 of the individual data were measured and were above the lower limit of quantification (lloq). For aggregationFlag 'Percentile', the statistics will only be calculated if less than or equal to 1/2 of the data is above LLOQ. If you use aggregationFlag 'Custom', please set parameters lloqCheckColumns2of3 and lloqCheckColumns1of2 accordingly.

A custom function should take a numeric vector `y` as input and return a list containing: - `yValues`: The aggregated value (e.g., mean). - `yMin`: The lower value of the aggregated data (e.g., mean - sd). - `yMax`: The upper value of the aggregated data (e.g., mean + sd). - `yErrorType`: A string indicating the type of error associated with the aggregation, it is used in plot legends and captions. It must be a concatenation of the descriptor of yValues and the descriptor of yMin - yMax range separated by "|" (e.g., "mean | standard deviation" or "median | 5th - 95th percentile").

See also

Other observed data processing: addBiometricsToConfig(), convertDataCombinedToDataTable(), convertDataTableToDataCombined(), readObservedDataByDictionary(), updateDataGroupId(), updateOutputPathId(), validateObservedData()