Package: FishResp 1.1.2
Sergey Morozov
FishResp: Analytical Tool for Aquatic Respirometry
Calculates metabolic rate of fish and other aquatic organisms measured using an intermittent-flow respirometry approach. The tool is used to run a set of graphical QC tests of raw respirometry data, correct it for background respiration and chamber effect, filter and extract target values of absolute and mass-specific metabolic rate. Experimental design should include background respiration tests and measuring of one or more metabolic rate traits. The R package is ideally integrated with the pump controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp). Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp' ('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and 'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
Authors:
FishResp_1.1.2.tar.gz
FishResp_1.1.2.tar.gz(r-4.5-noble)FishResp_1.1.2.tar.gz(r-4.4-noble)
FishResp_1.1.2.tgz(r-4.4-emscripten)FishResp_1.1.2.tgz(r-4.3-emscripten)
FishResp.pdf |FishResp.html✨
FishResp/json (API)
NEWS
| # Install 'FishResp' in R: |
| install.packages('FishResp', repos = 'https://cloud.r-project.org') |
- AMR - Active Metabolic Rate: Final Data
- AMR.clean - Active Metabolic Rate: Corrected Raw Data
- AMR.raw - Active Metabolic Rate: Raw Data
- AMR.slope - Active Metabolic Rate: Extracted Slope
- SMR - Standard Metabolic Rate: Final Data
- SMR.clean - Standard Metabolic Rate: Corrected Raw Data
- SMR.raw - Standard Metabolic Rate: Raw Data
- SMR.slope - Standard Metabolic Rate: Extracted Slope
- info - Info about Individuals and Chambers
- post - Post Raw Data
- pre - Pre Raw Data
- results - Results of Analysis: SMR, AMR and MS
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 months agofrom:e39846bd37. Checks:3 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 13 2025 |
| R-4.5-linux | OK | Mar 13 2025 |
| R-4.4-linux | OK | Mar 13 2025 |
Exports:calculate.MRconvert.respirometryconvert.rMRcorrect.measexport.MRextract.slopeimport.measimport.testinput.infoprepare.datapresens.aquaresppyroscience.aquaresppyroscience.pumprespQC.activityQC.measQC.sloperm.data
Dependencies:biglmbirkchronclicpp11DBIdplyrfansigenericsgluegswlatticelifecyclelubridatemagrittrmarelacMASSmclustmeasurementsminpack.lmnlmeocepillarpkgconfigplyrR6RcpprespirometryrlangrMRseacarbsegmentedshapeSolveSAPHEtibbletidyselecttimechangeutf8vctrswithr
Citation
To cite FishResp in publications use:
Morozov, S., McCairns, R.J.S., Merila, J. (2019). FishResp: R package and GUI application for analysis of aquatic respirometry data. Conservation Physiology, 7(1), coz003. URL https://doi.org/10.1093/conphys/coz003.
Corresponding BibTeX entry:
@Article{,
title = {FishResp: R package and GUI application for analysis of
aquatic respirometry data.},
author = {Sergey Morozov and R.J. Scott McCairns and Juha Merila},
journal = {Conservation Physiology},
year = {2019},
volume = {7},
number = {1},
pages = {coz003},
url = {https://doi.org/10.1093/conphys/coz003},
}
Readme and manuals
FishResp: R package for Aquatic Respirometry
Description
The R package 'FishResp' is designed to calculate metabolic rate of aquatic organisms measured using an intermittent-flow respirometry approach. Raw respirometry data can be imported from:
- PumpResp (open-source pump controller by FishResp)
- SensResp (open-source DO meter by FishResp).
- AutoResp (by LoligoSystems)
- Pyro Oxygen Logger (by PyroScience)
- OxyView (by PreSens)
- AquaResp (free software)
- Q-box Aqua (by QubitSystems)
The idea behind FishResp, an analysis pipeline and case studies are described in the academic publication by Morozov et al. (2019). Technical information about R functions and demo data can be found in Reference Manual. Brief descriptions of the R package 'FishResp' and other open-source tools for aquatic respirometry are located at the website fishresp.org.
Installation
The stable version of the ‘FishResp’ package can be installed from CRAN:install.packages("FishResp").
Alternativelly, download the latest release from GitHub and install using the following command:devtools::install_github("embedded-sergey/FishResp-Rpackage@*release").
If you are not familiar with the R language, please check out the graphical implementation of the R package: FishRespGUI.
Citation
To cite FishResp please refer to: "Morozov, S., McCairns, R.J.S., Merila, J. (2019) FishResp: R package and GUI application for analysis of aquatic respirometry data. Conserv Physiol 7(1): coz003; https://doi.org/10.1093/conphys/coz003".
Changelog
To see the list of changes made in various versions of the R package, read the file 'NEWS.md'.
Bug Reporting
If you find a bug, please report about it on the FishResp forum or through the GitHub repository.
Acknowledgements
The individuals and organizations who developed, contributed to, or funded the FishResp project are acknowledged here.