jeffpowell2
commented
6 years ago The two problematic codeStems in seqSamples and traits.stem are 'acpa2' and 'lepa4'.
I suspect that 'lepa4' should be 'lepa1' but I can't confirm this from Jess' notes. @marissalee or @wcornwell , whichever one of you currently has the shavings from the T0 small samples (I'm pretty sure that I handed these over with the large ones), could you check the writing on the bags? If you find 'lepa1', Jess made a mistake reading it but it should be fine to just change the label. If you find 'lepa4', then either Brad made a mistake writing on the bag (possibly) or we harvested a fourth stem and cut it up but only analysed the shavings and didn't use the cut up pieces (unlikely, but see below).
'acpa2' looks like an extra sample that was analysed for fungi and chemistry since we have four 'acpa' samples in those data. Three of the 'acpa' stems (1, 3, 4) have massloss data - I have no idea why we have shavings but didn't use the cut up pieces for anything else. In any case, I suggest just leave 'acpa2' out.
See lines 118-132 in the readme.Rmd...
There are 2 unique codeStem ids that are found in the trait data (xrf sample names) and the sequence data, but not in the stemSamples data (deployment sample names). These codeStem ids are not found in the percent mass loss data. Because the main goal is to analyze decay responses, I'm going to continue to leave these codeStems out of the stemSamples dataframe. Is it possible that stem id numbers got switched? Something to follow-up on.