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

library(knitr) # load knitr to enable options
library(respR) # load respR

opts_chunk$set(collapse = TRUE, 
               comment = "#>", 
               cache = FALSE, 
               tidy = FALSE, 
               highlight = TRUE, 
               fig.width = 10, 
               fig.height = 5,
               fig.align = "center",
               R.options = list(
                 scipen = 999, 
                 digits = 3))

sard <- sardine.rd[,1:2]
sard[[1]] <- sard[[1]]/60

Introduction

calc_rate() is the general function in respR for manually determining rates across user-defined ranges of time, row or oxygen value. This contrasts with auto_rate() which uses a degree of automation to determine rates in the "linear" method, or allows rolling rates of a fixed width to be calculated across an entire dataset and then ordered in various ways.

Defaults

By default, if no other inputs are entered calc_rate will calculate a rate across an entire dataset as entered. The data used here is the sardine.rd dataset, but the time data has been converted to minutes to demonstrate the different x-axis values.

cr <- calc_rate(sard)

Time range

The default method by which a rate region can be specified is by = "time". The function finds the closest matching values if these exact values do not occur in the time data. If either of the values lie outside the actual time data range it will use the first or last value instead.

cr <- calc_rate(sard,
                from = 20, 
                to = 80,
                by = "time")

Row range

Similarly the rate region can be specified by = "row".

cr <- calc_rate(sard,
                from = 2000, 
                to = 6000,
                by = "row")

Oxygen range

Lastly, the rate region can be specified by = "oxygen". This option finds the first occurrence of the from value (or the closest matching value), and the last occurrence of the to value.

cr <- calc_rate(sard,
                from = 94, 
                to = 92,
                by = "oxygen")

Multiple rates

calc_rate can be used to extract multiple rates by entering vectors of paired values as from and to in any of these metrics.

cr <- calc_rate(sard,
                from = c(10, 20, 30, 40, 50, 60, 70), 
                to = c(20, 30, 40, 50, 60, 70, 80),
                by = "time")

summary(cr)

S3 generic methods

Saved calc_rate objects work with the generic S3 methods print, summary, plot, and mean

print

This simply prints the result to the console. If there are multiple rates it will print the first one. The pos input can be used to print others.

print(cr)
print(cr, pos = 2)

summary

This prints the summary table to the console which contains linear model coefficients and other metadata for each rate. If there are multiple rates the pos input can be used to select which to print. The export input can be used to export the pos selected rows as a dataframe, or the entire table if this is left NULL.

summary(cr)
summary(cr, pos = 1:4)

cr_exp <- summary(cr, pos = 1:4, export = TRUE)

cr_exp

mean

This averages all the values in the $rate column, or those selected using pos. The result can be saved as a value by using export = TRUE.

cr_mean <- mean(cr, pos = 1:4, export = TRUE)
cr_mean

plot

calc_rate objects can be plotted. pos can be used to select which result to plot, and panel to plot individual panels. legend can be used to suppress labels and legend, and quietto suppress console output. Additional plotting parameters can also be passed to adjust margins, axis label rotation, etc.

Here we plot result 2, panel 2, hide the equation legend, rotate the axis labels, give the left axis more space, and increase the space from axis labels to axis ticks.

plot(cr, pos = 2, panel = 2, legend = FALSE, quiet = TRUE, 
     las = 1, mai = c(0.3, 0.4, 0.35, 0.15), mgp = c(0, 0.5, 0))

Two-point rate

The output also includes a $rate.2pt. This is the rate determined by simple two-point calculation of difference in oxygen divided by difference in time. See vignette("twopoint") for an explanation of this output and when it might be useful.

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