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davidjpmoore / B2Pop_Physiology

GITHUB for ecophysiology analysis at B2 Poplar plantation
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New workflow for Photosynthesis data for all years and times #16

Open davidjpmoore opened 9 years ago

davidjpmoore commented 9 years ago

Pecan.photosynthesis has utility to read Licor files ecophys package can be used to estimate A/ci and A/q responses

ianshiach commented 9 years ago

@davidjpmoore how does pecan distinguish between curves? How were different curves delineated in the fluxcourse data and how do the data frames look after passing through read.licor?

davidjpmoore commented 9 years ago

I think Pecan just guestimates which are different curves based on the timestamp and sequence of data collection. I haven’t gotten passed the licor.QC step – but the data are pushed to the QAQC procedure and you click on them.

Dave

David JP Moore Associate Professor School of Natural Resources and the Environment ENR2 Bldg. N407 1064 E. Lowell Street The University of Arizona Tucson, AZ 85721

Office: N225 Phone: 520 621 9998 https://snre.arizona.edu/people/david-moore http://djpmoore.tumblr.com https://twitter.com/DJPMoore

From: Ian Shiach [mailto:notifications@github.com] Sent: Wednesday, September 16, 2015 2:19 PM To: davidjpmoore/B2Pop_Physiology Cc: Moore, David Joseph - (davidjpmoore) Subject: Re: [B2Pop_Physiology] New workflow for Photosynthesis data for all years and times (#16)

@davidjpmoorehttps://github.com/davidjpmoore how does pecan distinguish between curves? How were different curves delineated in the fluxcourse data and how do the data frames look after passing through read.licor?

— Reply to this email directly or view it on GitHubhttps://github.com/davidjpmoore/B2Pop_Physiology/issues/16#issuecomment-140897875.

davidjpmoore commented 9 years ago

@ianshiach see d58194cc0358762e41d7a38e31175501dc26ff7c

YOu can extract the parameter estimates for a given fit using the function summary(fit$params)

It looks like the Vignette explains how to do this and how to run ANOVA's or estimate treatment effects

You could also just carry out fits independently on different genotypes or times etc

Take a read through the vignette to see if there's a more economical way to do this

https://github.com/PecanProject/pecan/blob/master/modules/photosynthesis/vignettes/ResponseCurves.Rmd

ParamEstimates= summary(fit$params) ## parameter estimates

  1. Empirical mean and standard deviation for each variable, plus standard error of the mean:
        Mean        SD  Naive SE Time-series SE

Jmax0 151.61553 15.831157 1.293e-01 2.294e+00 alpha0 0.25832 0.089659 7.321e-04 5.167e-03 cp0 67.65667 2.990009 2.441e-02 1.030e-01 r0 1.04778 0.559505 4.568e-03 2.152e-02 tau 0.02416 0.001174 9.583e-06 9.802e-06 vmax0 34.77225 1.859035 1.518e-02 4.853e-02

  1. Quantiles for each variable:

      2.5%       25%       50%       75%     97.5%

    Jmax0 138.6027 143.54607 147.22338 153.21021 190.56929 alpha0 0.1137 0.19196 0.25133 0.31701 0.44901 cp0 61.2252 65.73743 67.83537 69.71906 73.07700 r0 0.2724 0.62063 0.94420 1.37327 2.34800 tau 0.0219 0.02336 0.02414 0.02494 0.02649 vmax0 32.6062 33.55512 34.28942 35.44026 39.71543