Cannot Import Data
Quote from Cvenny on November 3, 2021, 7:42 pmHello,
When I try to import SMR data I keep receiving an error after a few seconds of loading in the bottom right of the interface. I think I know what the issue is but I just wanted to check anyway. When I was conducting my trials I didn't start and stop new tests for background measurements. Instead, I have one data file but made comments on what phases the pre and post background tests start. The same goes for SMR and MMR. Is there any way I can fix this?
Anything helps!
Hello,
When I try to import SMR data I keep receiving an error after a few seconds of loading in the bottom right of the interface. I think I know what the issue is but I just wanted to check anyway. When I was conducting my trials I didn't start and stop new tests for background measurements. Instead, I have one data file but made comments on what phases the pre and post background tests start. The same goes for SMR and MMR. Is there any way I can fix this?
Anything helps!
Quote from Cvenny on November 3, 2021, 7:54 pmI should also mention that my Dissolved oxygen units are in % saturation and that is not an option in the global settings.
I should also mention that my Dissolved oxygen units are in % saturation and that is not an option in the global settings.
Quote from Sergey Morozov on November 3, 2021, 8:37 pmDear Sir/Madam,
Could you please send the sample of your data to fishresp[at]gmail.com or attach to your answer here? The problem seems to be with a data format, thus I need to check it manually.
Concerning the second issue: first, convert % saturation to one of the acceptable units by FishResp (e.g. mg O2/L) using one of the converters located in "Extensions module" on the 'General' page (see the attached screenshot below). Then, run a pipeline described in the publication (https://doi.org/10.1093/conphys/coz003).
Best wishes,
Sergey
Dear Sir/Madam,
Could you please send the sample of your data to fishresp[at]gmail.com or attach to your answer here? The problem seems to be with a data format, thus I need to check it manually.
Concerning the second issue: first, convert % saturation to one of the acceptable units by FishResp (e.g. mg O2/L) using one of the converters located in "Extensions module" on the 'General' page (see the attached screenshot below). Then, run a pipeline described in the publication (https://doi.org/10.1093/conphys/coz003).
Best wishes,
Sergey
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Quote from Cvenny on November 8, 2021, 5:22 pmHello Sergey,
Any luck with the file I sent you? If not, would I be able to use the R package instead of the GUI or will the same problem persist?
Thanks,
Cody
Hello Sergey,
Any luck with the file I sent you? If not, would I be able to use the R package instead of the GUI or will the same problem persist?
Thanks,
Cody
Quote from Sergey Morozov on November 9, 2021, 6:50 pmHello Cody,
I have finally found the sources of the loading error in raw data:
- First of all, replace all hyphens (-) in the 'Date & Time' column to slashes (/), so your YMD format would look like this: 11/2/2021/12:05:02 PM
- Second, find rows where the column 'Phase' contains 'Skipp' value. 'Skipp' means that the measurement was somehow interrapted by AutoResp or Loligo's hardware. Rows with interrupted measurement phases should be removed from raw data (in your case M36 and a lot of them in the end of your dataset). FishResp expects the same length for all measurement phases in a raw data file, otherwise the file won't be loaded.
The latter issue has been recently reported by another user on our forum (see here), seems to be that AutoResp has been updated and this interruptions occur from time to time since then. I will try to fix it next week. At present, only the above-mentioned manual correction of raw data will work well with in FishResp and FishRespGUI.
Concerning your question about SMR, MMR, pre- and post-tests, you should split your dataset manually into four different files. But, keep the header from LoligoSystem the same for all these files (i.e. copy first 38 rows). Then, follow to the pipeline explained in this publication, Case 2.
Please, do not hesitate to ask further questions if my instructions are unclear or new issues arise.
Best wishes,
Sergey
Hello Cody,
I have finally found the sources of the loading error in raw data:
- First of all, replace all hyphens (-) in the 'Date & Time' column to slashes (/), so your YMD format would look like this: 11/2/2021/12:05:02 PM
- Second, find rows where the column 'Phase' contains 'Skipp' value. 'Skipp' means that the measurement was somehow interrapted by AutoResp or Loligo's hardware. Rows with interrupted measurement phases should be removed from raw data (in your case M36 and a lot of them in the end of your dataset). FishResp expects the same length for all measurement phases in a raw data file, otherwise the file won't be loaded.
The latter issue has been recently reported by another user on our forum (see here), seems to be that AutoResp has been updated and this interruptions occur from time to time since then. I will try to fix it next week. At present, only the above-mentioned manual correction of raw data will work well with in FishResp and FishRespGUI.
Concerning your question about SMR, MMR, pre- and post-tests, you should split your dataset manually into four different files. But, keep the header from LoligoSystem the same for all these files (i.e. copy first 38 rows). Then, follow to the pipeline explained in this publication, Case 2.
Please, do not hesitate to ask further questions if my instructions are unclear or new issues arise.
Best wishes,
Sergey
