Two step fitting models for alfa, Pm

Description

Estimates the values of alfa and Pmax, as a function of temperature, salinity, Si and the relative contribution of diatoms.

  • alfamod estimates the photosynthetic efficiency

  • Pmmod estimates the maximal photosynthetic rate

Used in the two-step fit approach

Usage

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alfamod (temp, Si, dia, S,
  ad = 0.01, aa = 0.01, Q10d = 2, Q10a = 2,
  kSi = 0.005, bS = 0.09)

Pmmod (temp, Si, dia, S,
  Pmd = 5, Pma = 5, Q10d = 2, Q10a = 2,
  kSi = 0.005, bS = 0.09)

Arguments

temp

the temperature, dgC,

Si

dissolved silicate concentration, mmol/m3,

dia

percentage diatoms,

S

salinity, -

Pmd

diatom maximal photosynthetic rate, Pmax, at reference temperature of 10 dgC, (gC/gChl/hr),

Pma

non-diatom maximal photosynthetic rate, Pmax, at reference temperature of 10 dgC, (gC/gChl/hr),

ad

diatom photosynthetic efficiency, alpha, at reference temperature of 10 dgC, (gC/gChl/hr)/(micromol photons / m2 / s),

aa

non-diatom photosynthetic efficiency, alpha, at reference temperature of 10 dgC, (gC/gChl/hr)/(micromol photons / m2 / s),

Q10d

diatom Q10, parameter determining the temperature dependence, the multiplication factor for a 10 dgC temperature increase, (-),

Q10a

non-diatom Q10, parameter determining the temperature dependence, the multiplication factor for a 10 dgC temperature increase, (-),

kSi

half-saturation silicate concentration, used in Monod-limitation formula, (mmol Si/m3),

bS

linear factor expressing salinity dependence, f(S) = 1+bS*S, (-).

Details

Alfa is estimated as:

(ad*fd(T)*M(si)*dia/100+aa*fa(T)*(1-dia/100))*g(S)

Pmax is estimated as:

(Pmd*fd(T)*M(si)*dia/100+Pma*fa(T)*(1-dia/100))*g(S)

where:

f(T)=Q10^((T-10)/10)

f(S)=1+bS*S

M(Si)=Si/(Si+kSi)

Value

The estimated value of alpha, community photosynthetic efficiency (alfamod) or Pmax, community maximal photosynthetic rate (Pmmod).

Note

This implements the models required for the two-step fitting approach.

Author(s)

Tom Cox <t.cox@nioo.knaw.nl>

Karline Soetaert <k.soetaert@nioo.knaw.nl>

See Also

Platt for the Platt model, etc

Examples

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pr <- par(mfrow=c(2,2))

## Alfa
alfaT <- alfamod(temp=1:20, Si =1, dia = 50, S = 0)
plot(1:20,alfaT, xlab="Temperature", main="alpha")

Si <- seq(0,0.5,0.01)
alfaSi <- alfamod(temp=10, Si =Si, dia = 50, S = 0)
plot(Si, alfaSi, xlab="Silicate", main="alpha")

Dia <- seq(0,100,1)
alfaDia <- alfamod(temp=10, Si =1, dia = Dia, S = 0)
plot(Dia, alfaDia, xlab="% diatoms", main="alpha")

Sal <- seq(0,35,1)
alfaSal <- alfamod(temp=10, Si =1, dia = 50, S = Sal)
plot(Sal, alfaSal, xlab="Salinity", main="alpha")


## Pmax
PmaxT <- Pmmod(temp=1:20, Si =1, dia = 50, S = 0)
plot(1:20, PmaxT, xlab="Temperature", main="Pmax")

Si <- seq(0,0.5,0.01)
PmaxSi <- Pmmod(temp=10, Si =Si, dia = 50, S = 0)
plot(Si, PmaxSi, xlab="Silicate", main="Pmax")

Dia <- seq(0,100,1)
PmaxDia <- Pmmod(temp=10, Si =1, dia = Dia, S = 0)
plot(Dia, PmaxDia, xlab="% diatoms", main="Pmax")

Sal <- seq(0,35,1)
PmaxSal <- Pmmod(temp=10, Si =1, dia = 50, S = Sal)
plot(Sal, PmaxSal, xlab="Salinity", main="Pmax")

par(mfrow=pr)