compute.Aph: Compute phytoplankton absorption spectrum (Aph) from total...
In belasi01/RspectroAbs: Processing absorbance spectra from spectrophotometer

Description Usage Arguments Value Author(s)

Compute phytoplankton absorption spectrum (Aph) from total particulate absorption (Ap) and, if available, the non-algal particles absorption (Anap) spectra

1	compute.Aph(waves, Ap, Anap)

`waves`	is a vector of wavelengths
`Ap`	is the total particulate absorption vector (mandatory)
`Anap`	is the non-algal particles absorption vector. If Anap=NA only the spectral deconvolution method of Bricaud and Stramski (1990) is applied.

It returns a list with all the cumputed spectra of Aph and Anap as well as the NAP spectral slopes for the different method. The program computes the Aph using three approaches:

1. The Anap is subtracted from Ap after adjusting the NIR of Anap such as Ap(NIR)==Anap(NIR) to obtain Aph.offset;
2. An exponential fit is applied to the Anap spectrum (Anap.fitted) avoiding the blue and red portions of the spectrum where some remaining pigments on the filter after methanol extraction may be present.
3. A spectral deconvolution following the method of Bricaud and Stramski (1990) is performed. Two equations are applied to Ap spectra (their eq. 5 and eq 6) yielding Aph.BS90, Anap.BS90 and Aph.BS90.v2, Anap.BS90.v2.

Simon Belanger

belasi01/RspectroAbs documentation built on July 27, 2020, 9:52 p.m.