Happy new year to you!
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Toby Marthews, Carbon dynamics of representative ecosystems in nortwestern Peruvian Amazon, Soil respiration
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Hear the fan is a good option, we did not realize it, but we will take this into account.
No, I do not have access to another one. In fact we have another “old/recycled one” which was used in Allpahuayo plots and stopped working in 2013. It would be great to send it to you in Oxford. Maybe people of PP Systems can do something with it. Is that possible? We bought the EGM we are using in at the end of 2013 and it had been working very well before this problem. The soda lime is still green so it is ok. I think the problem is solved, hence thank you for your help.
We have the problem of NV in partitioning respiration experiment data of Allpahuayo. If we ran the analysis (data collected in 2011) without the NV data some values are negative and we are bricking against the wall with that. We did not know that it was needed to collect the NV, so we will collect it and look what happens next.
Thanks for the analysis.
Best,
Jhon -
Hi Jhon - Happy New Year!
As far as I'm aware, the high pitched sound has no other purpose other than to indicate that the chamber is flushing, hold in air. More important is that you can here the fan in the SRC whirring, indicating that it is working and indeed mixing the air inside the SRC.
Do you have access to another EGM and SRC unit? If so, it would be nice to take repeat measurements and check for agreement. If not, do you know when the EGM was last serviced/re-calibrated? Have you troubleshooted everything else (p73 of manual) such as checking if the soda lime needs replacing? It should be replaced if 2/3's of it in the tube is turning brown. It's hard to know if what you are seeing is the machine or indeed real measurements, but if you suspect it to be faulty, you can send it back to Oxford and we can get it fully serviced by PP Systems for you.
For the control experiment in order to calculate NV or pre-existing spatial variation, I don't think it matters too much that you are measuring this at a later date - we can assume that the spatial variation is the same now as it was then - perhaps just try to carry out the measurements in a similar time of year so that soil moisture levels are similar.
As for the analysis, I will try to find out where this is described in detail and get back to you.
Cheers,
Sam -
Hi Sam,
Sorry for the slow feedback.
1. When I select the plot number, appears a message: “CHAMBER FLUSHING, HOLD IN AIR". At the same time, the chamber should sound for around 15 seconds but it had not been sounding. I just opened the SRC chamber and cleaned it inside and now it is sounding again. There was some dust in it. Something curious: this device is a “new one”. When I was working at Allpahuayo plots I had used a recycled one and never heard that sound, so I do not know if that is normal. The data looks a bit lower than usual but I am not sure if that is due to machine or it is a real measurement.
2. In the last manual, there is a proportion of ambient (NV) or pre-existing spatial variation. This is measured before collar installation, so what should I do if I do not have this data. Shall I do the procedure beside the already-installed tubes and consider them as initial measurements?
3. One last question is how to analyze the data of partitioning experiment using the protocol 2. The manual omits this chapter. I am going to set up these tubes and the protocol 2 looks interesting.
Thanks
Jhon -
Hi Jhon,
I'm sat next to Toby and he asked me to try and answer this for you as I've been using them far more recently than he has.
Firstly, when you say it sounds during pre-measurement, are you referring to the high pitched tone, or the sound of the fan flushing the chamber? I've never experienced not hearing the high pitched tone before, but I think so long as you can hear the fan flushing the chamber, that is the most important part of pre-measurement calibration and it should be OK and if the results look reasonable, then this is encouraging.
Secondly, it sounds as though you are implementing partitioning experiment protocol 1 (with 4 sets of 9 tubes)? I'm not absolutely clear what your question is, but essentially, if you have removed litter before taking an initial emission measurement, you can replace the litter that was removed (same amount) from the tube, wait for some time and take another measurement, which will include the flux from the litter. Then you can remove the litter again, wait some time, and take another measurement. The difference between these two measurements is attributable to the litter.
I hope this helps, but please tell me if it wasn't what you were asking for and I'll get back to you again.
All best from Oxford,
Sam
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Stem respiration, Soil respiration, Ingrowth cores, Comprehensive description of the carbon cycle of African forests
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Brill! Thanks a lot, Cécile!
That's right, we are just using flux data from the spreadsheets. You can find the code we use to convert from raw EGM data to flux data on github:
https://github.com/OxfordEcosystemsLab/GEMcarbon.R It is called "EGM_raw_to_flux_option1" (or option 2, depending on your experimental layout - see RAINFOR-GEM manual for descriptions of options).
Let me know if you need help, Cécile