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Closed respirometry techniques


Can I in any way use FishResp for closed respirometry

I wish to use the package for analyzes for four closed chambers. Three chambers have measured oxygen consumption in a crustacean exposed to different exposure solutions, while the last chamber has been empty and have measured the background consumption of oxygen.

Best regards

Hi Erik,

Yes, it can. There are a few things you need to do:

  1. prepare the data to the FishResp format, i.e. see "Details" of the function "import.meas" in the manual.
  2. make sure that the measurement (when the system was closed) is identified in the "Phase" column, i.e. "M1" (if you have several loops, "M1", "M2", ...).  When the system was open, fill in the column the parameter "F1" ("F2" and so on if you had several loops).
  3. do the same for all your files.

Please, let me know if you have further questions, I will be glad to help you.

Best wishes,


Hi Sergey and thanks for answering!

Unfortunately, I am fairly new to the use of R. So bear with me, there will probably be some follow-up questions.

So first, in connection with converting the data to the FishResp format it says in the import.meas; "use FishResp 'if you use free software' AquaResp 'in combination with equipment produced by' PreSens' or 'Pyroscience'.
I have not used Pyroscience in combination with AquaResp, only Pyroscience and the oxygen logger program that comes with it. Can I still convert the text file from Pyroscience directly to a FishResp file?
I have tried to convert the data, but I only received error messages from R, so I am probably doing something wrong with the coding.
I’m more than happy to send you my R script and a raw data file to have a look, if that's the easiest?


Best regards


Hi Erik!

You have to convert them manually then as FishResp does not know when the measurement phase began and ended. Do you have this information?

Sure, just send both your raw data and R script here (you can attach them) or via email: fishresp[at]

Best wishes,


Hello again

I understand. So I guess this is the format I should use / convert to?

Date&Time            Phase  Temp.1   Ox.1   Temp.2  Ox.2   Temp.3   Ox.3   Temp.4   Ox.4
19/08/2016/18:47:20   F1      24.49      7.78      24.56     7.73     24.49     7.78     24.56      7.73
19/08/2016/18:47:21    F1      24.49      7.78      24.56     7.73     24.49     7.78     24.56      7.73
19/08/2016/18:47:22   M1     24.49      7.77      24.56     7.72     24.49     7.78     24.56      7.73
19/08/2016/18:47:23   M1     24.49      7.76      24.56     7.72     24.49     7.78     24.56      7.73


Since I did not use a flush phase or loops, as I was wishing to find the critical oxygen concentration. I guess I Should let the first value be "F1" and all the next "M1"?

I will send the script if it does not work with the new conversion method.

Thank you!

Best regards



Hi Erik,

That is right.

When the measurement phase is over, fill the "Phase" column with "F2". If you have several measurements in one experiment, continue filling it as "M2", "F3", "M3", "F4", and so on.

BTW, you may also check up the GUI app if R is not comfortable for you.

Best wishes,