This S4 class represents a DGrowthR model. — DGrowthR-class • DGrowthR

It is used to store and validate data and parameters necessary for DGrowthR analysis.

Slots

od_data: A data.frame expected to contain the following columns: "timepoint", "od", and "curve_id". These represent the time points, and optical density (od), and an identifier for each curve respectively.
metadata: A data.frame that contains the "curve_id" column along with any metadata variables
raw_od: Optical density information before pre-processing or re-formatting.
verbose: A logical value indicating whether the output should be suppressed. Defaults to TRUE, i.e., output is not suppressed.
fpca: An fpca object as the output of FPCA from fdapace
umap_coord: Coordinates for UMAP embedding
cluster_assignment: A data.frame matching curve_ids to the cluster assigned by clustering() function.
gpfit_info: A list with the estimated mean gp process and the parameters used for fitting.
growth_comparison: The results of a growth comparison.
log_od: A logical indicating if the OD data has been logged.
preprocessed: A logical variable indicating if the od data has been preprocessed with the preprocess_data() function.
growth_parameters: A data.frame with the estimated growth parameters after gp modelling

For an object to be a valid DGrowthR, it must meet the following criteria:

The "od_data" slot must be a data frame containing the columns "timepoint", "timepoint_n", "curve_id", and "od".
The "metadata" slot must be a data frame with the "curve_id" column.
All of the "curve_id"s in the "od_data" data frame must be present in the "curve_id" column of the metadata.