GPPFourier_t: Calculate GPP(t) from by complex demodulation of O2 time...

In tomjscox/GPPFourier: Calculate Gross Primary Production (GPP) from O2 Time Series

Description

Calculate GPP(t) from by complex demodulation of O2 time series

Usage

GPPFourier_t(x, dt = NULL, units = c("days", "hours", "mins", "secs"),
  Nfilt = NULL, nf = 1, NLowPass = NULL, fDL = NULL,
  MAcorrect = FALSE, phi = 51.176, lambda = 4.326, ...)

Arguments

x	Regularly sampled O2 time series. x can be a dataframe with time (POSIXt) in first column and O2 concentrations in second column or a vector of concentrations sampled with time step = dt
dt	Sampling time step. Either a difftime object or a numerical value. When dt is given as a numerical value, the unit is assumed to be days, unless units is provided. Can be omitted when x is a data frame, then dt is calculated from the time spacing between the first two samples.
units	Unit of sampling time step.
Nfilt	Moving average filter width for detrending time series. See GPPFourierPreprocess
nf	Number of iterative applications of moving average filter, to reduce filter width
NLowPass	Moving average filter width for low pass filtering demodulated O2 series. See demod
fDL	Optional. Relative fraction of light hours during the day. When x is a data frame, and no value for fDL is provided, fDL is calculated with fDLfun
MAcorrect	correction factor for moving average filter
phi	Latitude
lambda	Longitude
...	Other parameters to be passed to GPPFourierPreprocess

Value

Data frame with time and GPPt column.

References

Cox et al (2017). Tune in on 11.57 muHz and listen to primary production. Biogeosciences Discussions. doi:10.5194/bg-2017-81

See Also

GPPFourierPreprocess, GPPFourier, WindowGPPFourier.gts, SunRiseSet

Examples

# Calculate GPP(t) by complex demodulation of simulated water column time series
# More examples in vignette("GPPFourier").

dt <- as.numeric(difftime(watercolumn$time[2], watercolumn$time[1] , units="days"))
Nfilt <- 1/dt
GPPt <- GPPFourier_t(watercolumn[,c("time", "O2")], 
                        dt=dt, 
                        units="days", 
                        Detrend=TRUE, 
                        filter=TRUE, 
                        Nfilt=Nfilt, 
                        NLowPass=Nfilt, 
                        fDL=NULL, 
                        circular=FALSE, 
                        sides=2, 
                        nf=1)


par(mfrow=c(2,1), cex=1.2)
plot(watercolumn[,c("time", "O2")], type="l", xlab="", ylab=expression(paste(O[2], " [", mu, "M]")))
title(main="Water column")
plot(GPPt, type="l", lwd=3, ylim=c(0,30), xlab="", ylab="GPP")
lines(watercolumn[,c("time","GPP")], col="red")
legend("topleft", 
         lty=1, 
         col=c("red", "black"), 
         legend=c( "Simulated GPP", expression(paste("Complex demodulated ", O[2], " series"))), 
         bty="n")

tomjscox/GPPFourier documentation built on May 3, 2019, 2:57 p.m.