extract.slope: Extraction of Slope(s)

In FishResp: Analytical Tool for Aquatic Respirometry

Extraction of Slope(s)

Description

The function extracts the slopes of the linear regression of corrected O_{2} concentration over time with defined parameters (see Arguments).

Usage

extract.slope(clean.data,
              method = c("all", "min", "max",
                         "lower.tail", "upper.tail",
                         "calcSMR.mlnd", "calcSMR.quant",
                         "calcSMR.low10", "calcSMR.low10pc"),
              r2=0.95, length = 999999, n.slope = 1000,
              percent = 10, p = 0.25, G = 1:4)

Arguments

clean.data	a data frame obtained by using the function correct.meas
method	string: the method of extracting slopes: 'all' all slopes 'min' extracts lowest absolute slopes, specify the number of extracted slopes (parameter: n.slope) 'max' extracts highest absolute slopes, specify the number of extracted slopes (parameter: n.slope) 'lower.tail' extracts slopes from a lower tail of absolute slope distribution, specify percentage of a lower tail (parameter: percent) 'upper.tail' extracts slopes from an upper tail of absolute slope distribution, specify percentage of an upper tail (parameter: percent) 'calcSMR.mlnd' calculates the mean of the lowest normal distribution (MLND) using the parameter G (see Appendix S1 in Chabot et al, 2016) 'calcSMR.quant' calculates quantile value of slope distribution using the parameter p (see Appendix S1 in Chabot et al, 2016) 'calcSMR.low10' calculates the mean of the 10 lowest absolute slopes (see Appendix S1 in Chabot et al, 2016) 'calcSMR.low10pc' calculates the mean of the lowest 10
r2	numeric: minimal coefficient of determination (r^{2}) for extracted slopes. Coefficient of determination is used as a threshold of quality to be determined by the user (by default r^{2} = 0.95)
length	integer: length of a measurement period for slope calculations (in seconds; by default - full length)
n.slope	integer: the number of extracted slopes, only one slope is calculated for each measurement phase (used in the methods "min" and "max"; by default - all slopes)
percent	integer: percentage of lower or upper tail (used in the methods "lower.tail" and "upper.tail", respectively; by default percent = 10)
p	integer: p-value of quantile used in the method "calcSMR.quant" (by default p = 0.25)
G	integer: G value is used in the method "calcSMR.mlnd" (by default G = 1:4)

Value

The function returns a data frame with the information about extracted slopes. The data frame is used in the functions QC.slope and calculate.MR.

References

1. Chabot, D., Steffensen, J. F., & Farrell, A. P. (2016). The determination of standard metabolic rate in fishes. Journal of Fish Biology, 88(1), 81-121.

2. Herrmann, J. P., & Enders, E. C. (2000). Effect of body size on the standard metabolism of horse mackerel. Journal of Fish Biology, 57(3), 746-760.

Examples

# if the data have been already loaded to R,
# skip the first two lines of the code:
data(SMR.clean)
data(AMR.clean)

SMR.slope <- extract.slope(SMR.clean,
                           method = "min",
                           n.slope = 3,
                           r2=0.95,
                           length = 1200)

AMR.slope <- extract.slope(AMR.clean,
                           method = "all",
                           r2=0.95,
                           length = 300)

FishResp documentation built on Sept. 18, 2022, 5:06 p.m.