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Extract Biovolumes from IFCB Data and Compute Carbon Content

Source: R/ifcb_extract_biovolumes.R
ifcb_extract_biovolumes.Rd

This function reads biovolume data from feature files generated by the ifcb-analysis repository (Sosik and Olson 2007) and matches them with corresponding classification results or manual annotations. It calculates biovolume in cubic micrometer and determines if each class is a diatom based World Register of Marine Species (WoRMS). Carbon content is computed for each roi using specific conversion functions depending on whether the class is identified as a diatom or not, according to Menden-Deuer and Lessard 2000.

Usage

ifcb_extract_biovolumes(
  feature_files,
  mat_folder,
  class2use_file = NULL,
  micron_factor = 1/3.4,
  diatom_class = "Bacillariophyceae",
  marine_only = FALSE,
  threshold = "opt",
  multiblob = FALSE,
  feature_recursive = TRUE,
  mat_recursive = TRUE,
  verbose = TRUE
)

Arguments

feature_files

A path to a folder containing feature files or a character vector of file paths.

mat_folder

Path to the folder containing class or manual files.

class2use_file

A character string specifying the path to the file containing the class2use variable (default NULL).

micron_factor

Conversion factor for biovolume to cubic microns. Default is 1 / 3.4.

diatom_class

A string vector of diatom class names in the World Register of Marine Species (WoRMS). Default is "Bacillariophyceae".

marine_only

Logical. If TRUE, restricts the WoRMS search to marine taxa only. Default is FALSE.

threshold

Threshold for selecting class information ("opt" or other, default is "opt").

multiblob

A logical indicating whether to include multiblob features. Default is FALSE.

feature_recursive

Logical. If TRUE, the function will search for feature files recursively within when feature_files is a folder. Default is TRUE.

mat_recursive

Logical. If TRUE, the function will search for MATLAB files recursively within the mat_folder. Default is TRUE.

verbose

A logical indicating whether to print progress messages. Default is TRUE.

Value

A data frame containing 'sample', 'classifier' 'roi_number', 'class', 'biovolume_um3', and computed 'carbon_pg'.

Details

The function combines biovolume data extracted from feature files with class information read from corresponding MATLAB files. It determines if each class is a diatom based on user-defined criteria and computes carbon content using conversion functions specific to diatoms and non-diatom protists.

References

Menden-Deuer Susanne, Lessard Evelyn J., (2000), Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton, Limnology and Oceanography, 3, doi: 10.4319/lo.2000.45.3.0569.

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

ifcb_read_features ifcb_is_diatom https://www.marinespecies.org/

Examples

if (FALSE) { # \dontrun{
# Example usage:
feature_files <- "data/features"
mat_folder <- "data/classified"
biovolume_df <- ifcb_extract_biovolumes(feature_files, mat_folder)
print(biovolume_df)
} # }