Package index • respR

Pre-processing

Functions for importing, processing, visualising and inspecting data:

import_file(): Import respirometry system raw data files (DEPRECATED)
format_time(): Parse date-time data to numeric time for use in respR functions
inspect(): Explore and visualise respirometry data and check for common errors
inspect.ft(): Explore and visualise flowthrough respirometry data and check for errors
subsample(): Subsample a data frame object
subset_data(): Subset a data.frame, inspect, or inspect.ft object

Functions for calculating rates of oxygen consumption or production:

auto_rate(): Automatically determine most linear, highest, lowest and rolling oxygen uptake or production rates
auto_rate.int(): Run auto_rate on multiple replicates in intermittent-flow respirometry data
calc_rate(): Calculate rate of change in oxygen over time
calc_rate.int(): Extract rates from multiple replicates in intermittent-flow respirometry data
calc_rate.bg(): Calculate background oxygen uptake or input rates
calc_rate.ft(): Calculate rate of change in oxygen from flowthrough respirometry data
oxy_crit(): Calculate critical oxygen values, such as PCrit

Functions for rate adjustments:

adjust_rate(): Adjust rates to account for background respiration or oxygen flux.
adjust_rate.ft(): Adjust rates in flowthrough respirometry to account for background respiration or oxygen flux.

Functions for rate and unit conversions:

convert_rate(): Convert a unitless oxygen rate value to absolute, mass-specific or area-specific rate
convert_rate.ft(): Convert a unitless oxygen rate value from flowthrough respirometry to absolute, mass-specific or area-specific rates
convert_DO(): Convert between units of dissolved oxygen
convert_MR(): Convert between units of absolute, mass-specific, or area-specific metabolic rates
convert_val(): Convert values of temperature, volume, mass, area, and atmospheric pressure to different units
unit_args(): Print examples of unit inputs

Functions for rate filtering and summarising:

select_rate() select_rate.ft(): Select rate results based on a range of criteria

Example data files:

algae.rd: Oxygen production respirometry data
background_con.rd: Background respirometry data (constant)
background_exp.rd: Background respirometry data (exponential)
background_lin.rd: Background respirometry data (linear)
flowthrough.rd: Flowthrough respirometry data on the chiton, Mopalia lignosa
flowthrough_mult.rd: Multi-column flowthrough respirometry data
flowthrough_sim.rd: Flowthrough respirometry data with increasing background rate
intermittent.rd: Respirometry data of the sea urchin, Heliocidaris Erythrogramma
sardine.rd: Respirometry data of the sardine, Sardinops sagax
squid.rd: Respirometry data of the squid, Doryteuthis opalescens
urchins.rd: Multi-column respirometry data of the sea urchin, Heliocidaris Erythrogramma, including background respiration
zeb_intermittent.rd: Respirometry data of a zebrafish, Danio rerio