vol2C_diatom_auto: Convert Biovolume to Carbon for Diatoms, Choosing the...

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

Convert Biovolume to Carbon for Diatoms, Choosing the Equation by Volume

Description

This function converts biovolume in microns^3 to carbon in picograms for diatoms, selecting between the two Menden-Deuer and Lessard (2000) diatom relationships element-wise: volumes greater than 3000 micron^3 use the large-diatom equation (vol2C_lgdiatom), and the rest use the all-sizes equation (vol2C_diatom). It backs diatom_equation = "auto" in ifcb_extract_biovolumes() and ifcb_summarize_biovolumes(), and applies to whatever volume it is handed: the ROI biovolume under carbon_conversion = "roi", or the per-cell volume under carbon_conversion = "cell".

Usage

vol2C_diatom_auto(volume)

Arguments

volume

A numeric vector of biovolumes in microns^3.

Details

Be aware that the two relationships are not continuous at the 3000 micron^3 boundary: the all-sizes equation predicts about 190 pgC there and the large-diatom equation about 135 pgC. Selecting between them by volume therefore makes predicted carbon drop by roughly 41% as a cell grows across the boundary, which is why this is not the default. Use it when keeping each equation inside its calibrated size range matters more than a monotonic carbon-to-volume curve.

Value

A numeric vector of carbon content in picograms.

References

Menden-Deuer Susanne, Lessard Evelyn J., (2000), Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton, Limnology and Oceanography, 45(3), 569-579, doi: 10.4319/lo.2000.45.3.0569.

See Also

vol2C_diatom vol2C_lgdiatom

Examples

# Volumes in microns^3, spanning the 3000 micron^3 boundary
volume <- c(500, 2000, 5000, 20000)

# Small volumes use the all-sizes equation, large ones the large-diatom equation
vol2C_diatom_auto(volume)

iRfcb documentation built on Aug. 20, 2026, 1:06 a.m.