PP1step: Photosynthesis-irradiance models

In primprod: Modelling Primary production based on P-I curves

Description

Calculates the photosynthesis as a function of temperature, salinity, Si, and the relative contribution of diatoms.

• EP estimates the Eilers-Peeters model

• Platt implements the Platt formulation

• PEmod includes temperature dependency only on Pmax

• Pemod2 includes temperature dependency on Pmax and alpha

• PemodFlynn includes the model sensu Flynn

Used in the one-step fit approach

Usage

EP (E, a = 0.0005, b = 0.1, c = 50)

Platt (E, Pm = 5, alpha = 0.005)

PEmod (E, temp, Si, dia, S,
  Pmd = 5, Pma = 5, ad = 0.01, aa = 0.01,
  Q10d = 2,  Q10a = 2, kSi = 0.005, bS = 0.09)

PEmod2 <- function(E, temp, Si, dia, S,
  Pmd = 5, Pma = 5, ad = 0.01, aa = 0.01,
  Q10da = 2,  Q10dP = 2, Q10aa = 2, Q10aP = 2,
  kSia = 0.005, kSiP = 0.005, bS = 0.09)
  
PEmodFlynn (E, temp, Si, dia, S,
  Pmd = 5, Pma = 5, ad = 0.01, aa = 0.01,
  Q10d = 2, Q10a = 2, kSi = 0.005, bS = 0.09)

Arguments

E	the incident light intensity, (micromol photons/m2/s),
temp	the temperature, dgC,
Si	dissolved silicate concentration, mmol/m3,
dia	percentage diatoms,
S	salinity, -
a, b, c	fitting parameters,
Pm	maximal photosynthetic rate, Pmax, at reference temperature of 10 dgC, (gC/gChl/hr),
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),
alpha	photosynthetic efficiency, at reference temperature of 10 dgC, (gC/gChl/hr)/(micromol photons / m2 / s),
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, kSiP, kSia	half-saturation silicate concentration, used in Monod-limitation formula, (mmol Si/m3),
bS	linear factor expressing salinity dependence, f(S) = 1+bS*S, (-).

Details

The Eilers-Peeters model is given by:

P=E/(aE^2+bE+c)

The Webb model is:

P=F(E)

The PEmod is:

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

The PEmod2 is:

???

and where

F(E)=(1-exp((-alpha E)/Pm)

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

f(S)=1+bS*S

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

Value

The estimated photosynthesis rate, gC/gChl/hour.

Note

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

Author(s)

Tom Cox <[e-mail]>

Karline Soetaert <[e-mail]>

See Also

alfamod, Pmmod for two-step models

Examples

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

E <- seq(0,1500, by=10)

## PE-curves
pemod <- PEmod(E, temp=10, Si =1, dia = 50, S = 0)
plot(E,pemod, xlab="Incident light", main="photosynthesis", type="l")

platt <- Platt(E)
lines(E,platt, col="red")

eilers <- EP(E)
lines(E,eilers, col="blue")

flynn <- PEmodFlynn(E, temp=10, Si =1, dia = 50, S = 0)
lines(E,flynn, col="green")

## Function of temperature, Si, Salinity
P <- PEmod(E=100,temp=1:20, Si =1, dia = 50, S = 0)
plot(1:20, P, xlab="Temperature", main="photosynthesis", type="l")

Si <- seq(0,0.5,0.01)
P <- PEmod(E=100,temp=10, Si =Si, dia = 50, S = 0)
plot(Si, P, xlab="Silicate",  main="photosynthesis", type="l")

Sal <- seq(0,35,1)
P <- PEmod(E=100,temp=10, Si =1, dia = 50, S = Sal)
plot(Sal, P, xlab="Salinity",  main="photosynthesis", type="l")

par(mfrow=pr)

primprod documentation built on May 2, 2019, 6:04 p.m.