Package: respirometry 2.0.0

respirometry: Tools for Conducting and Analyzing Respirometry Experiments

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.

Authors:Matthew A. Birk

respirometry_2.0.0.tar.gz
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respirometry_2.0.0.tgz(r-4.4-any)respirometry_2.0.0.tgz(r-4.3-any)
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respirometry.pdf |respirometry.html✨
respirometry/json (API)
NEWS

# Install 'respirometry' in R:
install.packages('respirometry', repos = c('https://matthewabirk.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

40 exports 0.91 score 34 dependencies 1 dependents 1 mentions 67 scripts 478 downloads

Last updated 2 months agofrom:88fbf5e8d4. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winOKSep 17 2024
R-4.5-linuxOKSep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:adj_by_tempcalc_alphacalc_bcalc_Ecalc_mo2calc_MO2calc_pcritcalc_q10closedco2_addco2_flushco2_rateconv_nh4conv_o2conv_resp_unitcorrect_bubbleflush_carbflush_o2flush_watergoal_flush_pHguess_TAguess_whenimport_firestingimport_presensimport_pyroscience_workbenchimport_witroxmake_binsmax_mo2max_MO2mean_pHmin_flowperi_pumpplot_pcritpredict_nh3predict_pHq10Q10RQscale_mo2scale_MO2

Dependencies:birkclicpp11dplyrfansigenericsgluegswlatticelifecyclelubridatemagrittrmarelacMASSmeasurementsminpack.lmnlmeocepillarpkgconfigplyrR6RcpprlangseacarbsegmentedshapeSolveSAPHEtibbletidyselecttimechangeutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Predict biological parameters at a new temperatureadj_by_temp
Calculate the oxygen supply capacity (alpha)calc_alpha
Calculate the metabolic scaling coefficient, bcalc_b
Calculate E temperature coefficientcalc_E
Calculate metabolic ratecalc_MO2 calc_mo2
Calculate Pcritcalc_pcrit
Closed respirometryclosed
Calculate CO2 to add to waterco2_add
Calculate CO2 to add to flush reservoirco2_flush
Calculate CO2 to add to a respirometer intake flowco2_rate
Convert between units of ammonia (NH3) / ammonium (NH4+)conv_nh4
Convert between units of oxygen partial pressure and concentrationconv_o2
Convert units related to respirometryconv_resp_unit
Adjust respirometer volume for bubblescorrect_bubble
Estimate carbonate chemistry after a flushflush_carb
Estimate dissolved O2 after a flushflush_o2
Find percent of water exchanged after a flushflush_water
Calculate goal pH of a flush reservoir to achieve the post-flush goal pCO2goal_flush_pH
Estimate total alkalinity from salinityguess_TA
Estimate when the O2 level will reach a defined levelguess_when
Import data from Pyro Oxygen Loggerimport_firesting
Import data from a PreSens O2 transmitterimport_presens
Import data from Pyroscience Workbenchimport_pyroscience_workbench
Import data from a Loligo Systems Witrox O2 transmitterimport_witrox
Make time binning thresholds for MO2 calculationsmake_bins
Maximum MO2 supported by flow ratemax_MO2 max_mo2
Mean pH by [H+]mean_pH
Minimum flow rate to support MO2min_flow
Calculate peristaltic pump gaseous flow rateperi_pump
Plot Pcritplot_pcrit
Predict NH3 / NH4+ concentration post-respirationpredict_nh3
Predict pH post-respirationpredict_pH
Parameters of Q10 Temperature Coefficientcalc_q10 Q10 q10
Tools for Conducting Respirometry Experimentsrespirometry-package respirometry
Calculate respiratory quotientRQ
Mass-correct metabolic ratescale_MO2 scale_mo2