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Read and Summarize Classified IFCB Data

Source: R/ifcb_read_summary.R
ifcb_read_summary.Rd

This function reads a MATLAB .mat file containing aggregated and classified IFCB (Imaging FlowCytobot) data generated by the countcells_allTBnew_user_training function from the ifcb-analysis repository (Sosik and Olson 2007), or a list of classified data generated by ifcb_summarize_class_counts. It returns a data frame with species counts and optionally biovolume information based on specified thresholds.

Usage

ifcb_read_summary(
  summary,
  hdr_directory = NULL,
  biovolume = FALSE,
  threshold = "opt"
)

Arguments

summary

A character string specifying the path to the .mat summary file or a list generated by ifcb_summarize_class_counts.

hdr_directory

A character string specifying the path to the directory containing header (.hdr) files. Default is NULL.

biovolume

A logical indicating whether the file contains biovolume data. Default is FALSE.

threshold

A character string specifying the threshold type for counts and biovolume. Options are "opt" (default), "adhoc", and "none".

Value

A data frame containing the summary information including file list, volume analyzed, species counts, optionally biovolume, and other metadata.

References

Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.

See also

https://github.com/hsosik/ifcb-analysis

Examples

if (FALSE) { # \dontrun{
summary_data <- ifcb_read_summary("path/to/summary_file.mat", biovolume = TRUE, threshold = "opt")
print(summary_data)
} # }