plotR2: Make 3 plots involving the $"R"^2$ for each MO2 measurement...

In denis-chabot/fishMO2: Calculate and Plot SMR, O2crit and SDA, and convert between oxygen units

Description

Make 3 plots (R2 vs time, frequency distribution of R2s, R2s vs MO2) to help selecting the minimum R2 used in selecting valid oxygen uptake measurements for a single individual.

Usage

plotR2(
  r2,
  time,
  mo2,
  r2lab = expression(r^2),
  Timelab = "Time",
  mo2lab = expression(M[O[2]]),
  minR2 = NULL,
  cex = 0.7,
  ...
)

Arguments

r2	Vector or data frame column holding the R2 for each measurement of oxygen uptake.
time	Vector or data frame column holding the time, in POSIXct or numeric (hours) for each measurement of oxygen uptake.
mo2	Vector or data frame column holding the oxygen uptake measurements.
r2lab	Character string to label a plot axis involving R2.
Timelab	Character string to label a plot axis involving time.
mo2lab	Character string to label a plot axis involving oxygen uptake. The user can create a more sophisticated lable with makeO2lab and use it here.
minR2	If an estimate of what minR2, the minimum acceptable R2 for an oxygen uptake measurement, already exists, it can be entered here and it will be shown on the plots.
cex	cex, as in other plot functions in R.
...	Other parameters understood by the plot function.

Details

This function draws 3 plots to assess the quality of the oxygen uptake measurements during an intermittent-flow respirometry experiment. R2 is used here as a proxy for linearity, itself used as a demonstration of good mixing and absence of leaks in the respirometer. Typically a minimum acceptable value of R2 is selected, called minR2 here. Measurements of oxygen uptake (MO2) with a R2 greater or equal to minR2 are deemed acceptable, the others are rejected. These plots can be used to assess minR2, useful to calculate SMR and other variables, or to assess the validity and usefulness of an existing minR2 and modify it if required.

Value

Three plots are produced.

Author(s)

Denis Chabot, Institut Maurice-Lamontagne, Department of Fisheries and Oceans.

See Also

plot

Examples

data(codSDA)
plotR2(codSDA$r2, codSDA$DateTime, codSDA$MO2cor, minR2=0.95) 
# this produced 3 plots, you likely see only the last one

# to see all plots at once
def.par <- par(no.readonly = TRUE) # save default, for resetting...
layout(matrix(c(1,2,3,4), 2, 2, byrow = TRUE))
plotR2(codSDA$r2, codSDA$DateTime, codSDA$MO2cor, minR2=0.95) 
par(def.par)  #- reset to default

denis-chabot/fishMO2 documentation built on July 16, 2020, 1:53 a.m.