Bug reports for 'FishResp'
Quote from Sergey Morozov on August 16, 2017, 8:08 amFill free to leave your bug reports here.
If it is possible, please, supply a bug description with R-code and/or screenshots.Current version of the R package: 0.4.0
Fill free to leave your bug reports here.
If it is possible, please, supply a bug description with R-code and/or screenshots.
Current version of the R package: 0.4.0
Quote from StefanM on September 3, 2018, 12:02 pmHi, I have a dataset of raw respirometry data that includes 4 measurement phases with flush phases in between (i.e. 3 measurement loops of ca. 45 min for metabolic rate measurements plus a long phase of closed loop measurement until the Pcrit was hit).
The import.meas function only picks up the first three phases. Is the last phase (ca. 8h 25min) too long?
You can find my dataset here: https://box.hu-berlin.de/f/36448e70e49d4ba6bd7d/
The DO unit is mmol/L, the chamber of interest is chamber 2
Best,
Stefan
Hi, I have a dataset of raw respirometry data that includes 4 measurement phases with flush phases in between (i.e. 3 measurement loops of ca. 45 min for metabolic rate measurements plus a long phase of closed loop measurement until the Pcrit was hit).
The import.meas function only picks up the first three phases. Is the last phase (ca. 8h 25min) too long?
You can find my dataset here: https://box.hu-berlin.de/f/36448e70e49d4ba6bd7d/
The DO unit is mmol/L, the chamber of interest is chamber 2
Best,
Stefan
Quote from Sergey Morozov on September 3, 2018, 1:41 pmHi Stefan,
As FishResp is designed for intermittent-flow respirometry approach with a priori defined length of phases (e.g. flush phase - 300s, wait phase - 100s, measurement phase - 600s), the software expects the same length of measurement phases in raw data. At this moment, we have tested FishResp with AutoResp (LoligoSystems), Q-box AQUA (QubitSystem), and AquaResp (free software) used in combination with PreSens and PyroScience logger software. What kind of logger software did you use? Did you use intermittent-flow or closed respirometry approach?
If measurement phases have different length, FishResp may not be able to work correctly with such data. Then, there are two options: (1) standardize the length of all measurement phases in raw data, (2) load them as separate datasets and analyze them independently.
In your situation, I would split the dataset in two files, where the first has M1, M2,M3; and second - only M4. Actually, when I played with your data, both above-mentioned options worked well.
Best wishes,
Sergey
Hi Stefan,
As FishResp is designed for intermittent-flow respirometry approach with a priori defined length of phases (e.g. flush phase - 300s, wait phase - 100s, measurement phase - 600s), the software expects the same length of measurement phases in raw data. At this moment, we have tested FishResp with AutoResp (LoligoSystems), Q-box AQUA (QubitSystem), and AquaResp (free software) used in combination with PreSens and PyroScience logger software. What kind of logger software did you use? Did you use intermittent-flow or closed respirometry approach?
If measurement phases have different length, FishResp may not be able to work correctly with such data. Then, there are two options: (1) standardize the length of all measurement phases in raw data, (2) load them as separate datasets and analyze them independently.
In your situation, I would split the dataset in two files, where the first has M1, M2,M3; and second - only M4. Actually, when I played with your data, both above-mentioned options worked well.
Best wishes,
Sergey
Quote from StefanM on September 3, 2018, 1:51 pmHi, thanks for the answer. I didn't know that FishResp expects identic phase lengths.
I used WitroxView (LoligoSystems) for my measurements. I imported the raw data with the import.witrox function from Matthew A. Birk's respirometry package and modified it according to the FishResp standardized format rules. The experiments were conducted in the field and thus limited in some technical aspects. I mixed both methods and first conducted intermitent-flow respirometry for 3 cycles at normoxia with a subsequent phase of closed respirometry to estimate the Pcrit.
Best,
Stefan
P.S.: I'm currently writing a small step-by-step guide on how to use the FishResp package for MR analysis. As I do not have access to logfiles from other software than WitroxView, I was wondering how the import from the above mentioned software works when you can only input "AutoResp" or "FishResp" as argument for the logger variable?
Hi, thanks for the answer. I didn't know that FishResp expects identic phase lengths.
I used WitroxView (LoligoSystems) for my measurements. I imported the raw data with the import.witrox function from Matthew A. Birk's respirometry package and modified it according to the FishResp standardized format rules. The experiments were conducted in the field and thus limited in some technical aspects. I mixed both methods and first conducted intermitent-flow respirometry for 3 cycles at normoxia with a subsequent phase of closed respirometry to estimate the Pcrit.
Best,
Stefan
P.S.: I'm currently writing a small step-by-step guide on how to use the FishResp package for MR analysis. As I do not have access to logfiles from other software than WitroxView, I was wondering how the import from the above mentioned software works when you can only input "AutoResp" or "FishResp" as argument for the logger variable?
Quote from Sergey Morozov on September 3, 2018, 2:40 pmHi Stefan,
OK, I see. Sounds very promising and looking forward to see your research published in near future! I am your subscriber on ResearchGate;-)
Concerning the question, we published a new version of FishResp (0.4.0), but have not yet announced it on the website/Twitter, as the GUI application is still under development. Briefly, there are two major upgrades: (1) ability to import data from above mentioned software, (2) implementation of regression diagnostics (residuals, QQ plot, etc) for extracted slopes with raw data. There are also several minor upgrades, such as increasing wait phase (if it is absent or not long enough to avoid non-linear change at the first stage of a measurement phase), etc. I guess we will 'officially' announce next week, when the GUI application will be uploaded on the website.
Raw data from Q-box AQUA should be imported directly, as AutoResp or FishResp in the version 0.3.0. Raw data from OxyView (or WitroxView) and Pyro Oxygen Logger (PyroScience) should be converted automatically using new functions presens.aquaresp or pyroscience.aquaresp (if AquaResp was used), or manually (as you did) and then imported in the FishResp format.
Sorry for providing only technical documentation here and on CRAN. We are currently trying to publish a paper, where we describe FishResp software in detail, its aim and typical pipeline for MR analysis.
If you have other questions, please feel free to contact me.
Best wishes,
Sergey
Hi Stefan,
OK, I see. Sounds very promising and looking forward to see your research published in near future! I am your subscriber on ResearchGate;-)
Concerning the question, we published a new version of FishResp (0.4.0), but have not yet announced it on the website/Twitter, as the GUI application is still under development. Briefly, there are two major upgrades: (1) ability to import data from above mentioned software, (2) implementation of regression diagnostics (residuals, QQ plot, etc) for extracted slopes with raw data. There are also several minor upgrades, such as increasing wait phase (if it is absent or not long enough to avoid non-linear change at the first stage of a measurement phase), etc. I guess we will 'officially' announce next week, when the GUI application will be uploaded on the website.
Raw data from Q-box AQUA should be imported directly, as AutoResp or FishResp in the version 0.3.0. Raw data from OxyView (or WitroxView) and Pyro Oxygen Logger (PyroScience) should be converted automatically using new functions presens.aquaresp or pyroscience.aquaresp (if AquaResp was used), or manually (as you did) and then imported in the FishResp format.
Sorry for providing only technical documentation here and on CRAN. We are currently trying to publish a paper, where we describe FishResp software in detail, its aim and typical pipeline for MR analysis.
If you have other questions, please feel free to contact me.
Best wishes,
Sergey
