LakeMetabolizer: Tools for the Analysis of Ecosystem Metabolism

A collection of tools for the calculation of freewater metabolism.

AuthorLuke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Date of publication2016-06-23 19:57:42
MaintainerLuke Winslow <lawinslow@gmail.com>
LicenseGPL (>= 2)
Version1.5.0

View on CRAN

Man pages

calc.lw.net: Estimate net long wave heat radiation

calc.zeng: Estimate sensible and latent heat fluxes

getSchmidt: Returns Schmidt number for a specific gas at a given...

get.Ts: gets surface water temperatures

get.vars: subsets data.frame according to header names

has.vars: tests data.frame for column names

is.day: determines if measurement was taken during the daytime

is.night: determines if measurement was taken during the night

k600.2.kGAS: Returns the gas exchange velocity for gas of interest w/ no...

k.read: Returns a timeseries of gas exchange velocity

k.read.base: Returns a timeseries of gas exchange velocity

load.all.data: Attemps to load and merge all timeseries data for a given...

load.meta: Loads a metadata file from the specified path

metab: Calculate metabolism

metab.bayesian: Metabolism model based on a bayesian parameter estimation...

metab.bookkeep: Metabolism model based on simple day/night summation...

metab.kalman: Metabolism calculated from parameters estimated using a...

metab.mle: Metabolism calculated from the maximum likelihood estimates...

metab.ols: Metabolism model based on a ordinary least squares parameter...

o2.at.sat: Calculates the equilibrium saturation concentration of oxygen...

par.to.sw: Convert PAR to shortwave

rmv.vars: subsets data.frame according to header names

sun.rise.set: Calculates the time of sunrise and sunset

sw.to.par: Convert shortwave radiation to PAR

temp.kalman: Smooth temperature time series using a Kalman filter/...

var.indx: finds matching column names in data.frame

watts.in: Simple estimate of energy gained by a layer of water

wind.scale: Wind Scaling U10 - exponential conversion to 10m wind speed

Files in this package

LakeMetabolizer
LakeMetabolizer/inst
LakeMetabolizer/inst/jags
LakeMetabolizer/inst/jags/bayes.mod.bothk.JAGS
LakeMetabolizer/inst/jags/bayes.mod.allk.JAGS
LakeMetabolizer/inst/jags/bayes.mod.nok.JAGS
LakeMetabolizer/inst/CITATION
LakeMetabolizer/inst/extdata
LakeMetabolizer/inst/extdata/sparkling.wtr
LakeMetabolizer/inst/extdata/troutbog.par
LakeMetabolizer/inst/extdata/troutbog.meta
LakeMetabolizer/inst/extdata/troutbog.rh
LakeMetabolizer/inst/extdata/mendota.rh
LakeMetabolizer/inst/extdata/mendota.doobs
LakeMetabolizer/inst/extdata/sparkling.wnd
LakeMetabolizer/inst/extdata/sparkling.airT
LakeMetabolizer/inst/extdata/mendota.meta
LakeMetabolizer/inst/extdata/mendota.par
LakeMetabolizer/inst/extdata/sparkling.rh
LakeMetabolizer/inst/extdata/sparkling.doobs
LakeMetabolizer/inst/extdata/sparkling.meta
LakeMetabolizer/inst/extdata/troutbog.wtr
LakeMetabolizer/inst/extdata/troutbog.doobs
LakeMetabolizer/inst/extdata/sparkling.par
LakeMetabolizer/inst/extdata/mendota.wnd
LakeMetabolizer/inst/extdata/mendota.wtr
LakeMetabolizer/inst/extdata/troutbog.airT
LakeMetabolizer/inst/extdata/troutbog.wnd
LakeMetabolizer/src
LakeMetabolizer/src/kalmanLoop.c
LakeMetabolizer/src/mleLoop.c
LakeMetabolizer/src/kalmanLoopTemp.c
LakeMetabolizer/NAMESPACE
LakeMetabolizer/demo
LakeMetabolizer/demo/fig_k600.R
LakeMetabolizer/demo/fig_timeseries.R
LakeMetabolizer/demo/00Index
LakeMetabolizer/demo/fig_metab.R
LakeMetabolizer/NEWS.md
LakeMetabolizer/R
LakeMetabolizer/R/helper.functions.R LakeMetabolizer/R/sun.rise.set.R LakeMetabolizer/R/k600.2.kGAS.R LakeMetabolizer/R/k.vachon.R LakeMetabolizer/R/o2.at.sat.R LakeMetabolizer/R/load.all.data.R LakeMetabolizer/R/getSchmidt.R LakeMetabolizer/R/k.heiskanen.R LakeMetabolizer/R/k.read.R LakeMetabolizer/R/metab.bayesian.R LakeMetabolizer/R/metab.mle.R LakeMetabolizer/R/metab.ols.R LakeMetabolizer/R/metab.bookkeep.R LakeMetabolizer/R/k.read.soloviev.R LakeMetabolizer/R/k.crusius.R LakeMetabolizer/R/k.macIntyre.R LakeMetabolizer/R/byeShort.R LakeMetabolizer/R/addNAs.R LakeMetabolizer/R/wind.scale.R LakeMetabolizer/R/date2doy.R LakeMetabolizer/R/temp.kalman.R LakeMetabolizer/R/calc.zeng.R LakeMetabolizer/R/sw.to.par.R LakeMetabolizer/R/metab.R LakeMetabolizer/R/k.cole.R LakeMetabolizer/R/calc.lw.net.R LakeMetabolizer/R/metab.kalman.R LakeMetabolizer/R/load.meta.R LakeMetabolizer/R/par.to.sw.R
LakeMetabolizer/MD5
LakeMetabolizer/DESCRIPTION
LakeMetabolizer/man
LakeMetabolizer/man/metab.Rd LakeMetabolizer/man/getSchmidt.Rd LakeMetabolizer/man/metab.bayesian.Rd LakeMetabolizer/man/k600.2.kGAS.Rd LakeMetabolizer/man/k.read.base.Rd LakeMetabolizer/man/metab.bookkeep.Rd LakeMetabolizer/man/metab.kalman.Rd LakeMetabolizer/man/get.vars.Rd LakeMetabolizer/man/o2.at.sat.Rd LakeMetabolizer/man/metab.ols.Rd LakeMetabolizer/man/par.to.sw.Rd LakeMetabolizer/man/sw.to.par.Rd LakeMetabolizer/man/wind.scale.Rd LakeMetabolizer/man/calc.lw.net.Rd LakeMetabolizer/man/calc.zeng.Rd LakeMetabolizer/man/is.day.Rd LakeMetabolizer/man/rmv.vars.Rd LakeMetabolizer/man/k.read.Rd LakeMetabolizer/man/load.meta.Rd LakeMetabolizer/man/has.vars.Rd LakeMetabolizer/man/get.Ts.Rd LakeMetabolizer/man/var.indx.Rd LakeMetabolizer/man/metab.mle.Rd LakeMetabolizer/man/load.all.data.Rd LakeMetabolizer/man/sun.rise.set.Rd LakeMetabolizer/man/watts.in.Rd LakeMetabolizer/man/is.night.Rd LakeMetabolizer/man/temp.kalman.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.