Tools for Conducting and Analyzing Respirometry Experiments

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Documentation for package ‘respirometry’ version 2.0.0

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respirometry-package Tools for Conducting Respirometry Experiments
adj_by_temp Predict biological parameters at a new temperature
calc_alpha Calculate the oxygen supply capacity (alpha)
calc_b Calculate the metabolic scaling coefficient, b
calc_E Calculate E temperature coefficient
calc_MO2 Calculate metabolic rate
calc_mo2 Calculate metabolic rate
calc_pcrit Calculate Pcrit
calc_q10 Parameters of Q10 Temperature Coefficient
closed Closed respirometry
co2_add Calculate CO2 to add to water
co2_flush Calculate CO2 to add to flush reservoir
co2_rate Calculate CO2 to add to a respirometer intake flow
conv_nh4 Convert between units of ammonia (NH3) / ammonium (NH4+)
conv_o2 Convert between units of oxygen partial pressure and concentration
conv_resp_unit Convert units related to respirometry
correct_bubble Adjust respirometer volume for bubbles
flush_carb Estimate carbonate chemistry after a flush
flush_o2 Estimate dissolved O2 after a flush
flush_water Find percent of water exchanged after a flush
goal_flush_pH Calculate goal pH of a flush reservoir to achieve the post-flush goal pCO2
guess_TA Estimate total alkalinity from salinity
guess_when Estimate when the O2 level will reach a defined level
import_firesting Import data from Pyro Oxygen Logger
import_presens Import data from a PreSens O2 transmitter
import_pyroscience_workbench Import data from Pyroscience Workbench
import_witrox Import data from a Loligo Systems Witrox O2 transmitter
make_bins Make time binning thresholds for MO2 calculations
max_MO2 Maximum MO2 supported by flow rate
max_mo2 Maximum MO2 supported by flow rate
mean_pH Mean pH by [H+]
min_flow Minimum flow rate to support MO2
peri_pump Calculate peristaltic pump gaseous flow rate
plot_pcrit Plot Pcrit
predict_nh3 Predict NH3 / NH4+ concentration post-respiration
predict_pH Predict pH post-respiration
Q10 Parameters of Q10 Temperature Coefficient
q10 Parameters of Q10 Temperature Coefficient
respirometry Tools for Conducting Respirometry Experiments
RQ Calculate respiratory quotient
scale_MO2 Mass-correct metabolic rate
scale_mo2 Mass-correct metabolic rate