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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.

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R package for aquatic respirometry [FishResp project]

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