LakeMetabolizer: Tools for the Analysis of Ecosystem Metabolism

A collection of tools for the calculation of freewater metabolism.

Author
Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Date of publication
2016-06-23 19:57:42
Maintainer
Luke Winslow <lawinslow@gmail.com>
License
GPL (>= 2)
Version
1.5.0

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