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Last data update: 2014.03.03

R: Calculates phytoplantkon production.

phytoprod

R Documentation

Calculates phytoplantkon production.

Description

Calculates phytoplankton production as a function of incident irradiance, an attenuation coefficient (kpar), photosynthetic-irradiance (PE) parameters, and an optional biomass profile.

Usage

phytoprod(PE, Ein, kpar, cz = matrix( data=c(1,1), ncol = 2), zmax = NA)

Arguments

`PE`	A list returned by either `fitEP`, `fitJP`, `fitPGH`, or `fitWebb`.
`Ein`	A two column matrix specifying the decimal day of year and PAR. The same format as returned by `incident`.
`kpar`	The attenuation coefficient of PAR. Units are m-1.
`cz`	Optional. A two column matrix specifying depth in column 1 and biomass in column 2. See Examples.
`zmax`	Optional. The maximum depth of integration. See Details.

Details

Units are dependent on the PE input.

If a zmax value is passed to the function and is shallower than the computed euphotic depth (defined here as 0.5 If a zmax value is not passed to the function or the specified value is deeper than the computed euphotic depth, then vertical integration is constrained to the euphotic depth.

If PE has noramalize=FALSE, then P has units of x m-3 hr-1 and PP has units of x m-2 day-1, where x is the original units of P passed to the fitPE function.

If PE has noramalize=TRUE, then P has units of mmol photons m-3 hr-1 and PP has units of mmol photons m-2 day-1.

Value

`PP`	A matrix specifying day of year and areal phytoplankton production
`z`	A vector specifying the depths over which photosynthetic rates are calculated
`t`	A vector specifying the times over which photosynthetic rates are calculated
`P`	A matrix of dimension [t,z] containing photosynthetic rates

Author(s)

Greg M. Silsbe

Sairah Y. Malkin

Examples


#Model incident irradiance for Lake Superior on July 31, 2007
date <- seq(ISOdatetime(2013,7,31,0,0,0,tz="UTC"),
            ISOdatetime(2013,8,1,0,0,0,tz="UTC"),
            by="10 min")

E0 <- incident(date, 47.33, -89.8, 180, -6, meanPAR=480, reflectance=TRUE)

plot(E0[,1],E0[,2],type="l")

#Model PE data 
P <- c(0.64,1.32,1.09,0.53,0.37,0.17,0.02)/24   #(umol C ug chla-1 hr-1)
E <- c(373,255,136,38.6,10.95,3.1,0.25)         #(umol m-2 s-1) 

#Fit data to Eilers and Peeters
myfit1 <- fitEP(E,P)

#Fit data to Jasbby and Platt
myfit2 <- fitJP(E,P)

#Plot PE curve
plot(E,P)
E <- c(0:400)
#Eilers and Peeters
P.EP <- E/((1/(myfit1$alpha[1]*myfit1$eopt[1]^2))*E^2+
           (1/myfit1$ps[1]-2/(myfit1$alpha[1]*myfit1$eopt[1]))*E+
           (1/myfit1$alpha[1]))
lines(E,P.EP,col="red")
#Jassby and Platt
P.JP <- myfit2$alpha[1]*myfit2$ek[1]*tanh(E/myfit2$ek[1])
lines(E,P.JP,col="blue")

#Compare Areal Primary production between two fits
#Assume constant chlorophyll through depth of 0.894 ug/L

#Eilers and Peeters
phytoprod(myfit1,
          E0,
          kpar=0.126,
          cz=matrix(data=c(1,0.894),ncol=2))$PP
#Units of umol C m-2 day-1

#Jassby and Platt
phytoprod(myfit2,
          E0,
          kpar=0.126,
          cz=matrix(data=c(1,0.894),ncol=2))$PP
#Units of umol C m-2 day-1

#Now let chlorophyll change with depth
cz <- matrix(data=c(0.462,0.699,1.065,1.332,1.245,1.156,0.636,0.558,
                    2,5,10,20,30,40,60,80),ncol=2)

myPP <- phytoprod(myfit1,
                  E0,
                  kpar=0.126,
                  cz,
                  zmax=80)

myPP$PP #Units of umol C m-2 day-1

#Plot photosynthetic rate through depth
#Units of umol C m-3 hr-1

image(x=myPP$t,
      y=myPP$z,
      z=myPP$P,
      col=rev(heat.colors(20)),
      ylim=c(80,0),
      zlim=c(1e-5,0.1),
      xlab="Decimal Day",
      ylab="Depth (m)")