pcrit: Calculate critical oxygen tension, P[crit]

Description Usage Arguments Details Value References Examples

View source: R/pcrit.R

Description

A function to calculate the critical oxygen tension, or the O2 concentration below which uptake rate becomes dependent upon oxygen concentration. It is calculated by both the "broken-stick" regression (BSR) approach, adopted from Yeager and Ultsch (1989), and the segmented regression approach, presented by Muggeo (2003).

Usage

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pcrit(df, width = floor(0.1 * nrow(df)), has.rate = FALSE, plot = TRUE,
  parallel = TRUE)

Arguments

df

data frame or object of class inspect_data. This is the data to analyse.

width

numeric. Number of rows over which to perform the rolling regression. Defaults to floor(0.1*nrow(df)), or 10% of total rows.

has.rate

logical. Defaults to FALSE. If you already possess a rate~DO dataset, change this to TRUE to process it without performing rolling regressions.

plot

logical. Defaults to TRUE.

parallel

logical. Defaults to TRUE. Should parallel processing be used?

Details

To calculate Pcrit, the function requires data in the form of the rate of oxygen uptake against dissolved oxygen (DO) concentration. The default data input is a data frame of DO against time (e.g. squid.rd). The function performs a rolling regression to determine rates, and matches these against a rolling mean of the DO data. The function then performs the two P[crit] analyses methods on these data. The width of the rolling regression is determined by the width argument. In most cases, the default width (10% of the data length) works well, but this may vary with data that has abrupt changes in rate, or is particularly noisy.

Alternatively, existing rate~DO data may be used, with the argument has.rate = "TRUE", in which case the function performs the two P[crit] analyses on these data directly without any processing.

Value

A list object of class pcrit.

References

Yeager DP, Ultsch GR (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

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

Examples

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# Intensive, and a large dataset, so may take some time.
## Not run: 
pcrit(squid.rd)

## End(Not run)

januarharianto/respR documentation built on July 30, 2018, 11:18 p.m.