Yumi's data analysis in R

Redox.r

# bring in the data
Redox = read.csv('Redox.csv', header=TRUE)

print(names(Redox))

# make an example plot for iron, PH average
ironsub = subset(Redox, trt == "High Fe(II)" | trt == "Low Fe(II)")

xlim = range(Redox$day, na.rm=TRUE)
ylim = range(Redox$pH, na.rm=TRUE)

ylim = c(floor(ylim[1]), ceiling(ylim[2]))

plot(0, 0, type="n", xlim=xlim, ylim=ylim, axes=FALSE, frame.plot=TRUE,
     xlab="Time(d)", ylab="pH")

lowFe100 = subset(Redox, trt == "Low Fe(II)" & per.dose == 100,
                  select=c(day, pH))

# setup a dummy avgpH vector that gives a place for the avg values to go
#avgpH = 1:length(unique(lowFe100$day))
#stdpH = avgpH
#
#for (i in avgpH)
    #{
    #phforthatday = subset(lowFe100, day == unique(lowFe100$day)[i], select = pH)
    #avgpH[i] = mean(phforthatday, na.rm=TRUE)
    #stdpH[i] = sd(phforthatday, na.rm=TRUE)
    #}
#points(unique(lowFe100$day), avgpH)

avgperday = aggregate(lowFe100, by=list(lowFe100$day), mean, na.rm=TRUE)
points(avgperday$day, avgperday$pH)