GPPFourier_t: Calculate GPP(t) from by complex demodulation of O2 time...
In GPPFourier: Calculate Gross Primary Production (GPP) from O2 Time Series

Description Usage Arguments Value References See Also Examples

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

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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, ...)

`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

Data frame with time and GPPt column.

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

GPPFourierPreprocess, GPPFourier, WindowGPPFourier.gts, SunRiseSet

# 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")