Package: FishResp 1.1.1

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:Sergey Morozov [aut, cre], Scott McCairns [aut, ths], Juha Merila [ths], Federico Calboli [ctb], Jenni Prokkola [dtc], Stephen White [dtc], Daniel Montgomery [dtc], Laura Almodovar-Acevedo [dtc], Niclas Kolm [dtc], Alexander Kotrschal [dtc], Erik Gill [dtc]

FishResp_1.1.1.tar.gz
FishResp_1.1.1.tar.gz(r-4.5-noble)FishResp_1.1.1.tar.gz(r-4.4-noble)
FishResp_1.1.1.tgz(r-4.4-emscripten)FishResp_1.1.1.tgz(r-4.3-emscripten)
FishResp.pdf |FishResp.html✨
FishResp/json (API)
NEWS

# Install 'FishResp' in R:
install.packages('FishResp', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • 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.

17 exports 2 stars 1.08 score 40 dependencies 3 mentions 32 scripts 440 downloads

Last updated 2 years agofrom:41900fc6ea. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 15 2024
R-4.5-linuxNOTESep 15 2024

Exports:calculate.MRconvert.respirometryconvert.rMRcorrect.measexport.MRextract.slopeimport.measimport.testinput.infoprepare.datapresens.aquaresppyroscience.aquaresppyroscience.pumprespQC.activityQC.measQC.sloperm.data

Dependencies:biglmbirkchronclicpp11DBIdplyrfansigenericsgluegswlatticelifecyclelubridatemagrittrmarelacMASSmclustmeasurementsminpack.lmnlmeocepillarpkgconfigplyrR6RcpprespirometryrlangrMRseacarbsegmentedshapeSolveSAPHEtibbletidyselecttimechangeutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Active Metabolic Rate: Final DataAMR
Active Metabolic Rate: Corrected Raw DataAMR.clean
Active Metabolic Rate: Raw DataAMR.raw
Active Metabolic Rate: Extracted Slope(s)AMR.slope
Calculation of Metabolic Ratecalculate.MR
Convert Raw Respirometry Data (respirometry)convert.respirometry
Convert Raw Respirometry Data (rMR)convert.rMR
Correction of Metabolic Rate Measurementscorrect.meas
Export Metabolic Rateexport.MR
Extraction of Slope(s)extract.slope
FishResp: Analytical Tool for Aquatic RespirometryFishResp
Import Raw Data of Metabolic Rate Measurementsimport.meas
Import Background Respiration Dataimport.test
Info about Individuals and Chambersinfo
Input the Information about Individuals and Chambersinput.info
Post Raw Datapost
Pre Raw Datapre
Prepare Raw Respirometry Dataprepare.data
Convert Respirometry Data from PreSens and AquaResp Software to the FishResp Formatpresens.aquaresp
Convert Respirometry Data from PyroScience and AquaResp Software to the FishResp Formatpyroscience.aquaresp
Convert Respirometry Data from PyroScience and the pump controller PumpResp to the FishResp Formatpyroscience.pumpresp
Quality Control of Animal ActivityQC.activity
Quality Control of Raw DataQC.meas
Quality Control of Slope(s)QC.slope
Results of Analysis: SMR, AMR and MSresults
Remove Poor Quality Datarm.data
Standard Metabolic Rate: Final DataSMR
Standard Metabolic Rate: Corrected Raw DataSMR.clean
Standard Metabolic Rate: Raw DataSMR.raw
Standard Metabolic Rate: Extracted Slope(s)SMR.slope