README.md

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Welcome

This package is under active development, but is currently stable.

respR is an R package that provides a structural, reproducible workflow for the processing and analysis of respirometry data. While the focus of our package is on aquatic respirometry, respR is largely unitless and so can process linear relationships in any time-series data, such as oxygen flux or photosynthesis.

Here is how to get started.

Installation

respR is not yet published in CRAN. For now, use the devtools package to grab the stable version:

install.packages("devtools")
devtools::install_github("januarharianto/respR")

Usage

For a quick evaluation of the package, try out the following code:

library(respR) # load the library

# As lazy loading is in place, we do not need to call example data explicitly.
# This example will use the `urchins.rd` example data.

# 1. check data for errors, select cols 1 and 15:
urch <- inspect(urchins.rd, 1, 15) 
# 2. automatically determine linear segment:
rate <- auto_rate(urch)
# 3. convert units
out <- convert_rate(rate, "mg/l", "s", "mg/h/kg", 0.6, 0.4)

## Alternatively, use dplyr pipes:
urchins.rd %>%        # using the urchins dataset,
  select(1, 15) %>%   # select columns 1 and 15
  inspect()     %>%   # inspect the data, then
  auto_rate()   %>%   # automatically determine most linear segment
  print()       %>%   # just a quick preview
  convert_rate("mg/l", "s", "mg/h/kg", 0.6, 0.4) # convert units

Feedback and contributions

respR is under continuous development. If you have any bugs or feedback, you can contact us easily by opening an issue. Alternatively, you can fork this project and create a pull request.

Please also feel free to email with any feedback or problems you may encounter.

Collaborators

Acknowledgements

The design of this package would not have been possible without inspiration from the following authors and their packages:

References

Clark, T. D., Sandblom, E., & Jutfelt, F. (2013). Aerobic scope measurements of fishes in an era of climate change: respirometry, relevance and recommendations. Journal of Experimental Biology, 216(15), 2771–2782. doi: 10.1242/Jeb.084251

Gamble, S., Carton, A. G., & Pirozzi, I. (2014). Open-top static respirometry is a reliable method to determine the routine metabolic rate of barramundi, Lates calcarifer. Marine and Freshwater Behaviour and Physiology, 47(1), 19–28. doi: 10.1080/10236244.2013.874119

Leclercq, N., Gattuso, J.-P. & Jaubert, J. (1999). Measurement of oxygen metabolism in open-top aquatic mesocosms: Application to a coral reef community. Marine Ecology Progress Series, 177, 299–304. doi: 10.3354/meps177299

Lighton, J.R.B. (2008). Measuring Metabolic Rates: A Manual for Scientists. Oxford University Press, USA.

Muggeo, V.M.R. (2003). Estimating regression models with unknown break-points. Statistics in Medicine, 22, 3055–3071. doi: 10.1002/sim.1545

Muggeo, V. (2008). Segmented: An R package to fit regression models with broken-line relationships. R News, 8, 20–25.

Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman; Hall/CRC Press.

Steffensen, J. F. (1989). Some errors in respirometry of aquatic breathers: How to avoid and correct for them. Fish Physiology and Biochemistry, 6(1), 49–59. doi: 10.1007/BF02995809

Svendsen, M.B.S., Bushnell, P.G. & Steffensen, J.F. (2016). Design and setup of intermittent-flow respirometry system for aquatic organisms. Journal of Fish Biology, 88, 26–50. doi: 10.1111/jfb.12797

White, C.R. & Kearney, M.R. (2013). Determinants of inter-specific variation in basal metabolic rate. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, 183, 1–26. doi: 10.1007/s00360-012-0676-5

Yeager, D.P. & Ultsch, G.R. (1989). Physiological regulation and conformation: A BASIC program for the determination of critical points. Physiological Zoology, 62, 888–907. doi: 10.1086/physzool.62.4.30157935



januarharianto/respR documentation built on Nov. 19, 2018, 8:17 p.m.