plotO2crit: Plot oxygen uptake values as a function of dissolved oxygen...
In denis-chabot/fishMO2: Calculate and Plot SMR, O2crit and SDA, and convert between oxygen units

Description Usage Arguments Details Value Warning Author(s) References See Also Examples

Takes an object created by calcO2crit. This object is self-contained and includes the original data, SMR and O2crit. This functions produces a plot showing the original values of oxygen uptake as a function of dissolved oxygen, along with an horizontal line representing SMR and a regression line fitted to those oxygen uptake values deemed to be conforming (related to dissolved oxygen). The O2crit is shown as the intersection of the two lines.

plotO2crit(
  o2critobj,
  plotID = "",
  o2lab = "Dissolved oxygen (% sat.)",
  mo2lab = expression(M[O[2]]),
  smr.cex = 0.9,
  o2crit.cex = 0.9,
  plotID.cex = 1.2,
  Transparency = T,
  ...
)

`o2critobj`	Object created by `calcO2crit`. It is a list that contains the original data, in addition to the SMR and O2crit.
`plotID`	Can be used to add a label (e.g., A, B, C, a, b, c) to the upper-left corner of a plot. For a finer control, produce the plot without plotID and add it manually afterward.
`o2lab`	Character string to be used to label the X-axis.
`mo2lab`	Character string to be used to label the Y-axis. The user can create an object with `makeO2lab` and use it here for a more sophisticated result than the default.
`smr.cex`	The size (cex) of the SMR value, shown on the plot.
`o2crit.cex`	The size (cex) of the O2crit value, shown on the plot.
`plotID.cex`	The size (cex) of the plot label, if shown on the plot.
`Transparency`	Some of the colours are transparent, which is not supported by all graphics devices. For `postscript` and other such devices, set `Transparency` to FALSE and similar but not transparent colours will be used instead.
`...`	Additional graphics parameters accepted by `plot`.

Produces a plot illustrating how O2crit was calculated for a given animal, based on data obtained by intermittent-flow respirometry. Typically the data set includes multiple measurements of oxygen uptake in conditions that are compatible with the determination of the Standard Metabolic Rate (SMR). Then the ambient level of dissolved oxygen is slowly decreased until the animal can no longer sustain its SMR. The only data required are contained in an object created by calcO2crit. Depending on the number of values of oxygen uptake identified as conforming (proportional) to dissolved oxygen level and below SMR, on the necessity (or not) to include a value of oxygen uptake far above SMR to increase the slope and on the type of regression fitted to these values the color and type of regression line changes. For ordinary LS regression, without added points: blue line, red symbols; ordinary LS regression, with an added point: blue line, red symbols, except orange for the added value; regression through origin, green dotted line, red symbols.

Produces a plot.

For R plotting devices that do not support transparency, set Transparency to FALSE.

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

Chabot, Denis, Steffensen, John F. and Farrell, Anthony P. (2016) The determination of the standard metabolic rate in fishes. Journal of Fish Biology 88, 81-121.

Claireaux, Guy and Chabot, Denis (2016) Responses by fishes to environmental hypoxia: integration through Fry's concept of aerobic metabolic scope. Journal of Fish Biology 88, 232-251. doi:doi:10.1111/jfb.1283

calcO2crit, calcSMR

data("GrHalO2crit")
# remove a 10-h acclimation period; also remove the last 11 h, when DO was decreasing to calculate O2crit. There were no low R^2s that required removal
smrData = subset(GrHalO2crit, DateTime >= DateTime[1] + 10*60*60 & DateTime <= DateTime[nrow(GrHalO2crit)] - 11*60*60)
smr = calcSMR(smrData$MO2)  # contains several estimations of SMR, need to chose one
SMR = as.numeric(ifelse(smr$CVmlnd > 5.4, smr$quant[4], smr$mlnd)); SMR # as recommended in Chabot et al. 2016
MyO2crit = calcO2crit(GrHalO2crit, SMR)
plotO2crit(MyO2crit)
plotO2crit(MyO2crit, plotID="A")