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Description

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>.

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.

Notes

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".

To see the list of changes made in various versions of the R package, open the file 'NEWS.md'.

If you find a bug, please report about it on the FishResp forum or the GitHub repository.

People and organisations who developed, contributed or financed the ‘FishResp’ project are listed here.

Metadata

Version

1.1.1

License

Unknown

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