Package: LakeMetabolizer 1.5.5

Jake Zwart

LakeMetabolizer: Tools for the Analysis of Ecosystem Metabolism

A collection of tools for the calculation of freewater metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models).

Authors:Luke Winslow [aut], Jake Zwart [cre, aut], Ryan Batt [aut], Jessica Corman [aut], Hilary Dugan [aut], Paul Hanson [aut], Aline Jaimes [aut], Jordan Read [aut], Richard Woolway [aut]

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LakeMetabolizer.pdf |LakeMetabolizer.html✨
LakeMetabolizer/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/gleon/lakemetabolizer/issues

On CRAN:

46 exports 16 stars 2.20 score 3 dependencies 123 scripts 320 downloads

Last updated 2 years agofrom:3bed3c5fc3. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-win-x86_64NOTESep 12 2024
R-4.5-linux-x86_64NOTESep 12 2024
R-4.4-win-x86_64OKSep 12 2024
R-4.4-mac-x86_64OKSep 12 2024
R-4.4-mac-aarch64OKSep 12 2024
R-4.3-win-x86_64OKSep 12 2024
R-4.3-mac-x86_64OKSep 12 2024
R-4.3-mac-aarch64OKSep 12 2024

Exports:calc.lw.netcalc.lw.net.basecalc.zengget.Tsget.varsgetSchmidthas.varsis.dayis.nightk.colek.cole.basek.crusiusk.crusius.basek.heiskanenk.heiskanen.basek.macIntyrek.macIntyre.basek.readk.read.basek.read.solovievk.read.soloviev.basek.vachonk.vachon.basek600.2.kGASk600.2.kGAS.baseload.all.dataload.metametabmetab.bayesianmetab.bookkeepmetab.kalmanmetab.mlemetab.olso2.at.sato2.at.sat.basepar.to.swpar.to.sw.basermv.varssun.rise.setsw.to.parsw.to.par.basetemp.kalmanvar.indxwatts.inwind.scalewind.scale.base

Dependencies:plyrRcpprLakeAnalyzer

Readme and manuals

Help Manual

Help pageTopics
Estimate net long wave heat radiationcalc.lw.net calc.lw.net.base
Estimate sensible and latent heat fluxescalc.zeng
gets surface water temperaturesget.Ts
subsets data.frame according to header namesget.vars
Returns Schmidt number for a specific gas at a given temperaturegetSchmidt
tests data.frame for column nameshas.vars
determines if measurement was taken during the daytimeis.day
determines if measurement was taken during the nightis.night
Returns a timeseries of gas exchange velocityk.cole k.crusius k.heiskanen k.macIntyre k.read k.read.soloviev k.vachon
Returns a timeseries of gas exchange velocityk.cole.base k.crusius.base k.heiskanen.base k.macIntyre.base k.read.base k.read.soloviev.base k.vachon.base
Returns the gas exchange velocity for gas of interest w/ no unit conversionsk600.2.kGAS k600.2.kGAS.base
Attemps to load and merge all timeseries data for a given site nameload.all.data
Loads a metadata file from the specified pathload.meta
Calculate metabolismmetab
Metabolism model based on a bayesian parameter estimation frameworkmetab.bayesian
Metabolism model based on simple day/night summation NEP-interpreted changes in DO.metab.bookkeep
Metabolism calculated from parameters estimated using a Kalman filtermetab.kalman
Metabolism calculated from the maximum likelihood estimates of the parameters in a standard linear regression modelmetab.mle
Metabolism model based on a ordinary least squares parameter estimation framework.metab.ols
Calculates the equilibrium saturation concentration of oxygen in water at the supplied conditionso2.at.sat o2.at.sat.base
Convert PAR to shortwavepar.to.sw par.to.sw.base
subsets data.frame according to header namesrmv.vars
Calculates the time of sunrise and sunsetsun.rise.set
Convert shortwave radiation to PARsw.to.par sw.to.par.base
Smooth temperature time series using a Kalman filter/ smoothertemp.kalman
finds matching column names in data.framevar.indx
Simple estimate of energy gained by a layer of waterwatts.in
Wind Scaling U10 - exponential conversion to 10m wind speedwind.scale wind.scale.base