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 = TRUE, 
               highlight = TRUE, 
               fig.width = 10, 
               fig.height = 5,
               fig.align = "center",
               R.options = list(
                 scipen = 999, 
                 digits = 3))

Future features

These features are in development, planned or being considered. We are happy to take any input as to which we should prioritise. Please feel free to chime in via any of the methods listed in vignette("contact").

Intermittent-flow respirometry

• ~~A function or workflow to automatically identify replicates, run calc_rate or auto_rate on each one, then summarise the result. See here and feel free to make suggestions.~~

This is now implemented! As part of v2.1 the calc_rate.int(), auto_rate.int() and select_rate() functions allow you to extract rates from every replicate in intermittent-flow respirometry data and summarise them according to a huge array of criteria. It's not quite automatic identification of replicates, but the process of specifying them is very straightforward, and leaves open the option to have some sort of automatic identification included in the future.

convert_MR

• ~~A function for converting between units of oxygen uptake or production rate. Could be useful for comparing outputs to results from the literature.~~

This is now added! As part of v2.3 the convert_MR() function allows you to convert between metabolic rates, including those from older publications. See vignette("convert_MR") for details.

oxy_crit

• Addition of further methods of determining critical oxygen values.
• Priorities would be the non-linear methods of Marshall et al. (2013) and α-method of Seibel et al. (2021).
• See here and feel free to make suggestions.

Shiny app

• We are in the early stages of thinking about creating a Shiny web-app version of respR. While we have made it easy to use, some people still cry out for a graphical user interface.

auto_rate.ft

• Flowthrough analysis workflow currently has no equivalent of auto_rate, that is some way of automatically and objectively identifying stable rates.

Air respirometry

We are still desperate to hear from users who have used (or tried to use) respR with data from air respirometry experiments so that we can get an idea of how we can update the package to directly support it.

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