#Searcarb training #---------------------------------------------------------------------- # Simple calculations #---------------------------------------------------------------------- # Using up-arrow to repeat or edit previous commands (try) #---------------------------------------------------------------------- # Create vectors of data c(1,2,3,4,5) 1:5 seq(1,5,by=1) #---------------------------------------------------------------------- # Variable assignment test1 <- 1:5 test1 #---------------------------------------------------------------------- # computation with vectors test1*10 test2 <- 1:5 test1-test2 #---------------------------------------------------------------------- # How to get help? help(c) help(log) ?log #---------------------------------------------------------------------- # Other functions useful for beginners example(log) demo() demo(graphics) #---------------------------------------------------------------------- # Additional help in the help menu of R #---------------------------------------------------------------------- # Go to CRAN to show packages # get seacarb.pdf # CRITICAL step to do: load seacarb! library(seacarb) # List of functions help(package="seacarb") # example of a function ?buffer # look through the functions: example(Kspc) # look through the functions example(bjerrum) # look through the functions example(rho) # explore carb ?carb # note syntax at the bottom of the R Console # note units #---------------------------------------------------------------------- # AT and DIC are known: carb(flag=15, var1=2400e-6, var2=2000e-6, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") # AT and DIC are known but one uses the Roy et al. constants and the free scale: carb(flag=15, var1=2400e-6, var2=2000e-6, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="r", kf="dg", pHscale="F") # pH and AT are known: carb(flag=8, var1=8.2, var2=0.00234, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") # pCO2 and AT are known: carb(flag=24, var1=370, var2=2400e-6, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") # AT is known and one wants to know pCO2 at various pHs: seq(7.9, 8.2, 0.05) pH <- seq(7.9, 8.2, 0.05) carb(flag=8, var1=pH, var2=2400e-6, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") #---------------------------------------------------------------------- # Other examples using multiple input lines data(seacarb_test_P0) data <- seacarb_test_P0 data carb(flag=data\$flag, var1=data\$var1, var2=data\$var2, S=data\$S, T=data\$T, P=data\$P, Sit=data\$Sit, Pt=data\$Pt) #---------------------------------------------------------------------- # Store, extract and re-use data (pH and at known) carb <- carb(flag=8, var1=pH, var2=2400e-6, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") carb\$pCO2 carb\$OmegaCalcite #---------------------------------------------------------------------- # Simple xy plot plot(carb\$pH,carb\$pCO2) #---------------------------------------------------------------------- # Customize simple xy plot plot(carb\$pH,carb\$pCO2,col="red") plot(carb\$pH,carb\$pCO2,col="red", xlab="pH (total scale)", ylab="pCO2 (uatm)") #---------------------------------------------------------------------- # One wants to know pCO2 at various pHs and ATs: pH <- seq(7.9, 8.2, length.out=10) AT <- seq(2200e-6, 2600e-6, length.out=10) dat <- expand.grid(pH, AT) dat carb <- carb(flag=8, var1=dat\$Var1, var2=dat\$Var2, S=35, T=25, P=0, Pt=0, Sit=0, k1k2="l", kf="pf", pHscale="T") carb # Do a simple contour plot pCO2 <- carb\$pCO2 dim(pCO2) <- c(length(pH), length(AT)) # contour(pH, AT, pCO2) # Do a more elaborated contour plot contour(pH, AT*1e6, pCO2, xlab="pH (total scale)", ylab="Total alkalinity (umol/kg)", levels=seq(200, 700, by=100), labcex=1.5, method="edge", col="red", lwd=2, lty="solid", ) #---------------------------------------------------------------------- # Convert pH to a different scale # SWS to total scale pHconv(flag=1, pH=8.10, S=35, T=25, P=0) # One can convert many values in one go pHsws <- seq(7.7, 8.3, by=0.01) pHsws pHtotal <- pHconv(flag=1, pH=pHsws, S=35, T=25, P=0) pHtotal #---------------------------------------------------------------------- # Read data from a file # IMPORTANT: path is needed. In R: menu "Misc:Change directory" # Or one can use the "setwd" function: setwd("/Users/gattuso/Documents/...") # look at the file cc <- c(rep("numeric", 8), rep("character",3)) inp <- read.table("comparison_of_software_inp.csv", header=T, sep=",", colClasses=cc) inp out <- carb(flag=inp\$flag, var1=inp\$pCO2, var2=inp\$AT, S=inp\$S, T=inp\$T, P=inp\$Pressure, Sit=inp\$Sil, Pt=inp\$PO4, k1k2=inp\$k1k2, kf=inp\$kf, pHscale=inp\$scale) out #---------------------------------------------------------------------- # Save data to a file write.table(out, file="comparison_of_software_out.csv", sep=",")