Package: respR 2.3.3

Nicholas Carey

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

Provides a structural, reproducible workflow for the processing and analysis of respirometry data. It contains analytical functions and utilities for working with oxygen time-series to determine respiration or oxygen production rates, and to make it easier to report and share analyses. See Harianto et al. 2019 <doi:10.1111/2041-210X.13162>.

Authors:Nicholas Carey [aut, cre], Januar Harianto [aut]

respR_2.3.3.tar.gz
respR_2.3.3.zip(r-4.5)respR_2.3.3.zip(r-4.4)respR_2.3.3.zip(r-4.3)
respR_2.3.3.tgz(r-4.4-any)respR_2.3.3.tgz(r-4.3-any)
respR_2.3.3.tar.gz(r-4.5-noble)respR_2.3.3.tar.gz(r-4.4-noble)
respR_2.3.3.tgz(r-4.4-emscripten)respR_2.3.3.tgz(r-4.3-emscripten)
respR.pdf |respR.html✨
respR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/januarharianto/respr/issues

Datasets:

On CRAN:

respirometryrstudio

27 exports 11 stars 1.92 score 38 dependencies 109 scripts 352 downloads

Last updated 4 months agofrom:14d8c7108a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winNOTESep 11 2024
R-4.5-linuxNOTESep 11 2024
R-4.4-winOKSep 11 2024
R-4.4-macOKSep 11 2024
R-4.3-winOKSep 11 2024
R-4.3-macOKSep 11 2024

Exports:%>%adjust_rateadjust_rate.ftauto_rateauto_rate.intcalc_ratecalc_rate.bgcalc_rate.ftcalc_rate.intconvert_DOconvert_MRconvert_rateconvert_rate.ftconvert_valformat_timeimport_fileinspectinspect.ftoxy_critselectselect_rateselect_rate.ftsim_datasubsamplesubset_datatest_linunit_args

Dependencies:clicpp11data.tabledplyrfansigenericsgluegswlatticelifecyclelubridatemagrittrmarelacMASSnlmeocepillarpkgconfigpurrrR6RcppRcppArmadilloRcppParallelrlangrollseacarbsegmentedshapeSolveSAPHEstringistringrtibbletidyselecttimechangeutf8vctrswithrxml2

Readme and manuals

Help Manual

Help pageTopics
Adjust rates to account for background respiration or oxygen flux.adjust_rate
Adjust rates in flowthrough respirometry to account for background respiration or oxygen flux.adjust_rate.ft
Oxygen production respirometry dataalgae.rd
Automatically determine most linear, highest, lowest and rolling oxygen uptake or production ratesauto_rate
Run auto_rate on multiple replicates in intermittent-flow respirometry dataauto_rate.int
Background respirometry data (constant)background_con.rd
Background respirometry data (exponential)background_exp.rd
Background respirometry data (linear)background_lin.rd
Calculate rate of change in oxygen over timecalc_rate
Calculate background oxygen uptake or input ratescalc_rate.bg
Calculate rate of change in oxygen from flowthrough respirometry datacalc_rate.ft
Extract rates from multiple replicates in intermittent-flow respirometry datacalc_rate.int
Convert between units of dissolved oxygenconvert_DO
Convert between units of absolute, mass-specific, or area-specific metabolic ratesconvert_MR
Convert a unitless oxygen rate value to absolute, mass-specific or area-specific rateconvert_rate
Convert a unitless oxygen rate value from flowthrough respirometry to absolute, mass-specific or area-specific ratesconvert_rate.ft
Convert values of temperature, volume, mass, area, and atmospheric pressure to different unitsconvert_val
Multi-column flowthrough respirometry dataflowthrough_mult.rd
Flowthrough respirometry data with increasing background rateflowthrough_sim.rd
Flowthrough respirometry data on the chiton, _Mopalia lignosa_flowthrough.rd
Parse date-time data to numeric time for use in respR functionsformat_time
Import respirometry system raw data files (DEPRECATED)import_file
Explore and visualise respirometry data and check for common errorsinspect
Explore and visualise flowthrough respirometry data and check for errorsinspect.ft
Respirometry data of the sea urchin, _Heliocidaris Erythrogramma_intermittent.rd
Calculate critical oxygen values, such as PCritoxy_crit
Respirometry data of the sardine, _Sardinops sagax_sardine.rd
Select rate results based on a range of criteriaselect_rate select_rate.ft
Respirometry data of the squid, _Doryteuthis opalescens_squid.rd
Subsample a data frame objectsubsample
Subset a 'data.frame', 'inspect', or 'inspect.ft' objectsubset_data
Print examples of unit inputsunit_args
Multi-column respirometry data of the sea urchin, _Heliocidaris Erythrogramma_, including background respirationurchins.rd
Respirometry data of a zebrafish, _Danio rerio_zeb_intermittent.rd