oxy_crit: Calculate critical oxygen values, such as PCrit

In januarharianto/respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data

Calculate critical oxygen values, such as PCrit

Description

Identifies critical oxygen values, the oxygen tension or concentration below which an uptake rate transitions from independent to dependent on the oxygen supply, typically known as PCrit.

Usage

oxy_crit(
  x,
  method = "bsr",
  time = NULL,
  oxygen = NULL,
  rate = NULL,
  width = 0.1,
  parallel = FALSE,
  thin = 5000,
  plot = TRUE,
  ...
)

Arguments

x	object of class inspect or a data.frame containing either paired oxygen~time values, or paired rate~oxygen values. See Details.
method	string. Defaults to "bsr". Critical oxygen value analysis method. Either "bsr" or "segmented". See Details.
time	integer or string. Defaults to 1. Specifies column number or column name of the time data.
oxygen	integer or string. Defaults to 2. Specifies column number or column name of the oxygen data.
rate	integer or string. Defaults to NULL. Specifies column number or column name of the rate data.
width	numeric value between 0 and 1 representing proportion of the total data length. Determines the width of the rolling regression used to determine the rolling rate and the rolling mean of oxygen values the rate is paired with. Defaults to 0.1, representing 10% of total rows.
parallel	logical. Defaults to FALSE. Enables parallel processing for computationally intensive analyses of large datasets.
thin	integer. Defaults to 5000. Number of rows to subsample x data to before running "bsr" analysis. No effect on datasets smaller than this value or with "segmented" method. To perform no subsampling enter as NULL. See Details.
plot	logical. Defaults to TRUE.
...	Allows additional plotting controls to be passed, such as legend = FALSE, quiet = TRUE, rate.rev = FALSE, and panel. See Plotting section.

Details

In earlier versions of respR, this function was known as pcrit or calc_pcrit. It was renamed to avoid conflicts with functions of the same name in another package, and also because technically the P in PCrit stands for the partial pressure of oxygen. Since the function returns the value in the units of the data as entered, whether they are concentration or pressure units, this terminology can be technically in error. Instead, for the purposes of the documentation we refer to this as the Critical Oxygen Value, or "COV". If the units of oxygen are partial pressure units (e.g. kPa), this is equivalent to PCrit, otherwise they should be reported with this in mind.

Methods

The oxy_crit() function provides two methods (one of which outputs two results) to calculate the COV. These are selected using the method input.

Broken Stick Regression: method = "bsr"

This is the default method, adapted from the “Broken-Stick” regression (BSR) approach, of Yeager & Ultsch (1989), in which two segments of the data are iteratively fitted and the intersection with the smallest sum of the residual sum of squares between the two linear models is the estimated COV. Two slightly different ways of reporting this breakpoint are detailed by Yeager & Ultsch (1989); the intercept and midpoint. These are usually very close in value, and the function returns both.

The thin input influences the BSR analysis. The method is very computationally intensive, so to speed up analyses the thin input will subsample datasets longer than this input to this number or rows before analysis. The default value of 5000 has in testing provided a good balance between speed and results accuracy and repeatability. However, results may vary with different datasets, so users should experiment with varying the value. To perform no subsampling and use the entire dataset enter thin = NULL. It has no effect on datasets shorter than the thin input.

Segmented Regression: method = "segmented"

The second method is a wrapper for the "Segmented" regression approach, available as part of the segmented R package (Muggeo 2008), which estimates the COV by iteratively fitting two intersecting models and selecting the value that minimises the “gap” between the fitted lines.

Inputs

The data input x should be an inspect object or data.frame containing oxygen~time data, or a data.frame containing rate~oxygen data.

Oxygen ~ Time data

This is the typical input, where a timeseries of oxygen concentrations or partial pressures against time has been recorded, generally down to a very low value of oxygen. A column of time and a column of oxygen should be specified. The function defaults to time = 1 and oxygen = 2 if no other inputs are entered. These can also be specified using the column names.

If an inspect object is entered as the x input, the data frame is extracted automatically and column identifiers are not required since these were already entered in inspect. Note, if multiple oxygen columns were entered in inspect only the first entered one will be used in oxy_crit.

To calculate the COV, the function requires data in the form of oxygen uptake rate against oxygen value. Therefore, the function performs a rolling regression on the oxygen~time data to determine rates, and pairs these against a rolling mean of the oxygen data. The function then performs the selected analysis method on these data. The width of the rolling regression and rolling mean is determined by the width input. The default is 0.1, representing 10% of the length of the data. This performs well in testing, however performance may vary with data that has abrupt changes in rate, or is particularly noisy. Users should experiment with different width values to see how it affects results, and report this with their results and analysis parameters.

Rate ~ Oxygen data

Alternatively, if existing rolling oxygen uptake rates have been calculated, and have appropriate paired oxygen concentration or partial pressure values, these can be entered with the rate and oxygen inputs specifying the respective columns as either numbers or the column names. In this case the function performs the selected analysis method on these data directly without any processing. The width input in this case is not relevant and is ignored.

This option can only be used with data frame x inputs. Note, other columns such as time data may be present in the input, but are not required so need not be specified.

Plot

A plot is produced (provided plot = TRUE) of the input data and results. The top panel is the input data, either the oxygen~time timeseries, or the rate~oxygen series, depending on what was entered in x. If the former, the critical oxygen value is indicated by a horizontal line, or two lines in the case of the Broken-Stick analysis. Note, since the two BSR results are usually close in value these may overlay each other.

The bottom plot is the rate~oxygen series upon which the analysis was conducted, either as input or as calculated. Critical oxygen values are indicated by vertical lines, and regression fits upon which the analysis was based by black dashed lines.

Note, that in respR oxygen uptake rates are negative since they represent a negative slope of oxygen against time, therefore by default rates are plotted on a reverse y-axis so higher rates appear higher on the plot. If analysing already calculated rates which are positive values this behaviour can be reversed by passing rate.rev = FALSE in either the main function call or when calling plot() on the output object. There is no issue with using positive rate values; they will give identical critical value results in the analysis.

Additional plotting options

If the legend obscures parts of the plot they can be suppressed using legend = FALSE. Suppress console output messages with quiet = TRUE. Each panel can be plotted on its own using panel = 1 or panel = 2. If using already-calculated, positive rate values to identify critical oxygen values, the y-axis of the rolling rate plot can be plotted not reversed by passing rate.rev = FALSE These inputs can be passed in either the main oxy_crit call or when calling plot() on the output object. If axis labels (particularly y-axis) are difficult to read, las = 2 can be passed to make axis labels horizontal, and oma (outer margins, default oma = c(0.4, 1, 1.5, 0.4)), and mai (inner margins, default mai = c(0.3, 0.15, 0.35, 0.15)) used to adjust plot margins.

S3 Generic Functions

Saved output objects can be used in the generic S3 functions print() and summary().

• print(): prints the critical oxygen value for the particular method used.

• summary(): prints critical oxygen value, plus additional coefficients and metadata for the particular method used. See Yeager & Ultsch (1989) and Muggeo (2008) for what these represent. The summary can be exported as a separate data frame by passing export = TRUE.

More

For additional help, documentation, vignettes, and more visit the respR website at https://januarharianto.github.io/respR/

Value

Output is a list object of class oxy_crit containing input parameters and data, various summary data, metadata, and the primary output of interest ⁠$crit⁠, which is the critical oxygen value in the units of the oxygen data as entered. This can be converted to additional units using convert_DO(). Note, if the Broken-Stick analysis (method == "bsr") has been used, ⁠$crit⁠ will contain two results; ⁠$crit.intercept⁠ and ⁠$crit.midpoint⁠. For full explanation of the difference between these see Yeager & Ultsch (1989), however they are generally very close in value.

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

## Run on oxygen~time data.frame with default inputs
oxy_crit(squid.rd)

## Try a lower 'thin' input to speed up analysis
oxy_crit(squid.rd, thin = 1000)

## Use the Segmented method instead
oxy_crit(squid.rd, method = "segmented")

## Experiment with different 'width' input
# Higher widths tend to oversmooth data
oxy_crit(squid.rd, method = "segmented", width = 0.2)
# Lower width in this case gives very similar result to default 0.1
oxy_crit(squid.rd, method = "segmented", width = 0.05)

## Run on oxygen~time data in 'inspect' object
insp <- inspect(squid.rd, time = 1, oxygen = 2)
oxy_crit(insp)

## Run on already calculated rate~oxygen data
# Calculate a rolling rate
rate <- auto_rate(squid.rd,
                  method = "rolling",
                  width = 0.1,
                  plot = FALSE)$rate

## Calculate a rolling mean oxygen
oxy <- na.omit(roll::roll_mean(squid.rd[[2]],
                               width = 0.1 * nrow(squid.rd)))
## Combine to data.frame
squid_rate_oxy <- data.frame(oxy, rate)
## Perform COV analysis
oxy_crit(squid_rate_oxy, oxygen = 1, rate = 2)

januarharianto/respR documentation built on April 20, 2024, 4:34 p.m.