respirometry (version 2.0.0)

calc_alpha: Calculate the oxygen supply capacity (alpha)

Description

The oxygen supply capacity (\(\alpha\)) is a species- and temperature-specific value quantifying an animal's ability to extract oxygen from the ambient medium to support its metabolism (e.g. umol O2 / g / hr / kPa). This function calculates \(\alpha\) based on the single highest \(\alpha0\) (MO2/PO2) value in the dataset. If there are outliers that make this prohibitive, consider setting a threshold MO2 value with mo2_threshold.

Usage

calc_alpha(po2, mo2, avg_top_n = 1, MR = NULL, mo2_threshold = Inf)

Value

Returns a list of 1) alpha, 2) a list of the PO2, MO2, and alpha0 value(s) where alpha was reached (the number of observations averaged is set by avg_top_n), and 3) the Pcrit at a metabolic rate of MR.

Arguments

po2

a vector of PO2 values.

mo2

a vector of metabolic rate values. Must be the same length and corresponding to po2.

avg_top_n

a numeric value representing the number of top \(\alpha0\) (MO2/PO2) values to average together to estimate \(\alpha\). Default is 1. When analyzing a trial where the animal was not at MMR the whole time, we recommend no more than 3 to avoid diminishing the \(\alpha\) value with sub-maximal observations. If all observations are believed to be at maximal O2 supply capacity, Inf can be used to average all observations.

MR

a vector of values for the metabolic rate at which pcrit_alpha should be returned. Default is NULL. If not specified, then pcrit_alpha is not returned and a message is added to the top of the return.

mo2_threshold

a single numeric value above which mo2 values are ignored. Useful to removing obviously erroneous values. Default is Inf.

Author

Matthew A. Birk,

References

Seibel, B. A., A. Andres, M. A. Birk, A. L. Burns, C. T. Shaw, A. W. Timpe, C. J. Welsh. 2021. “Oxygen supply capacity breathes new life into the critical oxygen partial pressure (Pcrit).” Journal of Experimental Biology.

See Also

calc_pcrit, plot_pcrit

Examples

mo2_data <- read.csv(system.file('extdata', 'mo2_v_po2.csv', package = 'respirometry'))
calc_alpha(po2 = mo2_data$po2, mo2 = mo2_data$mo2, MR = 1.5) # MR set to 1.5 to capture the 
# Pcrit corresponding to some of the lowest MO2 values recorded (something close to SMR).

# extract the alpha0 values that were averaged together
sapply(calc_alpha(po2 = mo2_data$po2, mo2 = mo2_data$mo2, 
  MR = 1.5, avg_top_n = 3)$alpha_obs, function(i) i[3])