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respirometry (version 2.0.0)

Tools for Conducting and Analyzing Respirometry Experiments

Description

Provides tools to enable the researcher to more precisely conduct respirometry experiments. Strong emphasis is on aquatic respirometry. Tools focus on helping the researcher setup and conduct experiments. Functions for analysis of resulting respirometry data are also provided. This package provides tools for intermittent, flow-through, and closed respirometry techniques.

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Version

Install

install.packages('respirometry')

Monthly Downloads

521

Version

2.0.0

License

GPL-3

Maintainer

Matthew Birk

Last Published

July 18th, 2024

Functions in respirometry (2.0.0)

calc_pcrit

Calculate Pcrit
flush_carb

Estimate carbonate chemistry after a flush
conv_nh4

Convert between units of ammonia (NH3) / ammonium (NH4+)
co2_flush

Calculate CO2 to add to flush reservoir
correct_bubble

Adjust respirometer volume for bubbles
conv_o2

Convert between units of oxygen partial pressure and concentration
make_bins

Make time binning thresholds for MO2 calculations
guess_TA

Estimate total alkalinity from salinity
import_presens

Import data from a PreSens O2 transmitter
max_MO2

Maximum MO2 supported by flow rate
import_firesting

Import data from Pyro Oxygen Logger
import_witrox

Import data from a Loligo Systems Witrox O2 transmitter
guess_when

Estimate when the O2 level will reach a defined level
import_pyroscience_workbench

Import data from Pyroscience Workbench
flush_o2

Estimate dissolved O2 after a flush
predict_pH

Predict pH post-respiration
predict_nh3

Predict NH3 / NH4+ concentration post-respiration
min_flow

Minimum flow rate to support MO2
plot_pcrit

Plot Pcrit
mean_pH

Mean pH by [H+]
peri_pump

Calculate peristaltic pump gaseous flow rate
scale_MO2

Mass-correct metabolic rate
respirometry

Tools for Conducting Respirometry Experiments
closed

Closed respirometry
adj_by_temp

Predict biological parameters at a new temperature
co2_add

Calculate CO2 to add to water
calc_E

Calculate E temperature coefficient
conv_resp_unit

Convert units related to respirometry
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
calc_MO2

Calculate metabolic rate
calc_alpha

Calculate the oxygen supply capacity (alpha)
co2_rate

Calculate CO2 to add to a respirometer intake flow
Q10

Parameters of Q10 Temperature Coefficient
RQ

Calculate respiratory quotient
calc_b

Calculate the metabolic scaling coefficient, b