temp.R

In gholtgrieve/gassyPants: Functions Useful for Working With Gasses Dissolved in Water

library(gassyPants)
library(HEEL)

x.lt <- as.POSIXlt(FishtrapCr$dateTime)

temperature <- FishtrapCr$Temp_C
PAR <- FishtrapCr$PAR_uE
localHour <- x.lt$hour + x.lt$min/60 + x.lt$sec/3600
depth <- 0.32
DOY <- x.lt$yday
TAlk <- 1068.6
TCO2_init <- 1200     # Units of umol/L
pCO2_init <- 3000     # Units of uatm
O2init <- mg.to.umol(9, "O2")  #From the HEEL package
alphaPI_hr <- 1.7    # Units are umol/m2/hr/uE
Rstd_day <- 0.41        # Units are mol/m2/day
kstd_hr <- 0.01      # Units are m/hr
lat <- 48.93861111
long <- -122.47861111
tz <- -8
masl <- 1
salinity <- 0
referenceT <- 20
pCO2air = 410        # Units of uatm


out <- main(temperature = temperature, localHour = localHour, DOY = DOY, PAR = PAR,
            TALk = TAlk, pCO2_init = pCO2_init, O2_init = O2conc_init,
            alphaPI = alphaPI_hr, Rstd = Rstd_day, kstd = kstd_hr, lat = lat,
            long = long, depth = depth)

timeSeries <- out$timeSeries


plot(FishtrapCr$dateTime, FishtrapCr$pCO2_uatm, col="red", ylim=c(0, 5000))
lines(FishtrapCr$dateTime, timeSeries$pCO2, col="red", lwd=2)

O2_uM <- mg.to.umol(FishtrapCr$ODO_mgL, mol = "O2")

plot(FishtrapCr$dateTime, O2_uM, col="red", ylim=c(200, 300))
lines(FishtrapCr$dateTime, timeSeries$O2conc, col="red", lwd=2)