Import, Process, Analyse, and Calculate Rates from Respirometry Data


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Documentation for package ‘respR’ version 2.0.2

Help Pages

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.
algae.rd Oxygen production respirometry data
auto_rate Automatically determine most linear, highest, lowest and rolling oxygen uptake or production rates
background_con.rd Background respirometry data (constant)
background_exp.rd Background respirometry data (exponential)
background_lin.rd Background respirometry data (linear)
calc_rate Calculate rate of change in oxygen over time
calc_rate.bg Calculate background oxygen uptake or input rates
calc_rate.ft Calculate rate of change in oxygen from flowthrough respirometry data
convert_DO Convert between units of dissolved oxygen
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_val Convert values of temperature, volume, mass, area, and atmospheric pressure to different units
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
format_time Parse date-time data to numeric time for use in respR functions
import_file Import respirometry system raw data files
inspect Explore and visualise respirometry data and check for common errors
inspect.ft Explore and visualise flowthrough respirometry data and check for errors
intermittent.rd Respirometry data of the sea urchin, _Heliocidaris Erythrogramma_
mean.adjust_rate Average adjust_rate object rates
mean.adjust_rate.ft Average adjust_rate.ft rates
mean.auto_rate Average auto_rate object rates
mean.calc_rate Average calc_rate object rates
mean.calc_rate.bg Average calc_rate.bg object rates
mean.calc_rate.ft Average calc_rate.ft object rates
mean.convert_DO Average convert_DO object values
mean.convert_rate Average convert_rate object rates
mean.convert_rate.ft Average convert_rate.ft object rates
mean.inspect Average inspect object rates
mean.inspect.ft Average inspect.ft object rates
mean.oxy_crit Average oxy_crit object rates
oxy_crit Calculate critical oxygen values, such as PCrit
plot.adjust_rate Plot adjust_rate objects
plot.adjust_rate.ft Plot adjust_rate.ft objects
plot.auto_rate Plot auto_rate objects
plot.calc_rate Plot calc_rate objects
plot.calc_rate.bg Plot calc_rate.bg objects
plot.calc_rate.ft Plot calc_rate.ft objects
plot.convert_DO Plot convert_DO objects
plot.convert_rate Plot convert_rate objects
plot.convert_rate.ft Plot convert_rate.ft objects
plot.inspect Plot inspect objects
plot.inspect.ft Plot inspect.ft objects
plot.oxy_crit Plot oxy_crit objects
plot_ar Plot auto_rate summary tables
print.adjust_rate Print adjust_rate objects
print.adjust_rate.ft Print adjust_rate.ft objects
print.auto_rate Print auto_rate objects
print.calc_rate Print calc_rate objects
print.calc_rate.bg Print calc_rate.bg objects
print.calc_rate.ft Print calc_rate.ft objects
print.convert_DO Print convert_DO objects
print.convert_rate Print convert_rate objects
print.convert_rate.ft Print convert_rate.ft objects
print.inspect Print inspect objects
print.inspect.ft Print inspect.ft objects
print.oxy_crit Print oxy_crit objects
sardine.rd Respirometry data of the sardine, _Sardinops sagax_
squid.rd Respirometry data of the squid, _Doryteuthis opalescens_
subsample Subsample a data frame object
subset_data Subset a 'data.frame', 'inspect', or 'inspect.ft' object
subset_rate Subset auto_rate results based on a range of criteria
summary.adjust_rate Summarise adjust_rate objects
summary.adjust_rate.ft Summarise adjust_rate.ft objects
summary.auto_rate Summarise auto_rate objects
summary.calc_rate Summarise calc_rate objects
summary.calc_rate.bg Summarise calc_rate.bg objects
summary.calc_rate.ft Summarise calc_rate.ft objects
summary.convert_DO Summarise convert_DO objects
summary.convert_rate Summarise convert_rate objects
summary.convert_rate.ft Summarise convert_rate.ft objects
summary.inspect Summarise inspect objects
summary.inspect.ft Summarise inspect.ft objects
summary.oxy_crit Summarise oxy_crit objects
test_lin_data Output objects for the function 'test_lin'
unit_args Print examples of unit inputs for use in convert_DO, convert_rate, and convert_rate.ft
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_