LakeMetabolizer: Tools for the Analysis of Ecosystem Metabolism
Version 1.5.0

A collection of tools for the calculation of freewater metabolism.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("LakeMetabolizer")

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

Functions

GetSmithGamma Source code
KFnllDO Source code
KFnllTemp Source code
KFsmoothDO Source code
KFsmoothTemp Source code
Mode Source code
SatVaporFromTemp Source code
VaporPressure Source code
addNAs Source code
bayes.makeModel Source code
bayesFit Source code
byeShort Source code
calc.clearsky Source code
calc.freq Source code
calc.lw.net Man page Source code
calc.lw.net.base Man page Source code
calc.zeng Man page Source code
complete.inputs Source code
conquerList Source code
date2doy Source code
get.Ts Man page Source code
get.vars Man page Source code
getSchmidt Man page Source code
has.vars Man page Source code
is.day Man page Source code
is.night Man page Source code
k.cole Man page Source code
k.cole.base Man page Source code
k.crusius Man page Source code
k.crusius.base Man page Source code
k.heiskanen Man page Source code
k.heiskanen.base Man page Source code
k.macIntyre Man page Source code
k.macIntyre.base Man page Source code
k.read Man page Source code
k.read.base Man page Source code
k.read.soloviev Man page Source code
k.read.soloviev.base Man page Source code
k.vachon Man page Source code
k.vachon.base Man page Source code
k600.2.kGAS Man page Source code
k600.2.kGAS.base Man page Source code
kalmanLoopR Source code
kalmanLoopTempR Source code
load.all.data Man page Source code
load.meta Man page Source code
metab Man page Source code
metab.bayesian Man page Source code
metab.bookkeep Man page Source code
metab.kalman Man page Source code
metab.mle Man page Source code
metab.ols Man page Source code
mleLoopOE Source code
mleLoopPE Source code
mleNllOE Source code
mleNllPE Source code
o2.at.sat Man page Source code
o2.at.sat.base Man page Source code
par.to.sw Man page Source code
par.to.sw.base Man page Source code
pred.merge Source code
rmv.vars Man page Source code
round.time Source code
sun.rise.set Man page Source code
sw.to.par Man page Source code
sw.to.par.base Man page Source code
temp.kalman Man page Source code
var.indx Man page Source code
watts.in Man page Source code
wind.scale Man page Source code
wind.scale.base Man page Source code

Files

inst
inst/jags
inst/jags/bayes.mod.bothk.JAGS
inst/jags/bayes.mod.allk.JAGS
inst/jags/bayes.mod.nok.JAGS
inst/CITATION
inst/extdata
inst/extdata/sparkling.wtr
inst/extdata/troutbog.par
inst/extdata/troutbog.meta
inst/extdata/troutbog.rh
inst/extdata/mendota.rh
inst/extdata/mendota.doobs
inst/extdata/sparkling.wnd
inst/extdata/sparkling.airT
inst/extdata/mendota.meta
inst/extdata/mendota.par
inst/extdata/sparkling.rh
inst/extdata/sparkling.doobs
inst/extdata/sparkling.meta
inst/extdata/troutbog.wtr
inst/extdata/troutbog.doobs
inst/extdata/sparkling.par
inst/extdata/mendota.wnd
inst/extdata/mendota.wtr
inst/extdata/troutbog.airT
inst/extdata/troutbog.wnd
src
src/kalmanLoop.c
src/mleLoop.c
src/kalmanLoopTemp.c
NAMESPACE
demo
demo/fig_k600.R
demo/fig_timeseries.R
demo/00Index
demo/fig_metab.R
NEWS.md
R
R/helper.functions.R
R/sun.rise.set.R
R/k600.2.kGAS.R
R/k.vachon.R
R/o2.at.sat.R
R/load.all.data.R
R/getSchmidt.R
R/k.heiskanen.R
R/k.read.R
R/metab.bayesian.R
R/metab.mle.R
R/metab.ols.R
R/metab.bookkeep.R
R/k.read.soloviev.R
R/k.crusius.R
R/k.macIntyre.R
R/byeShort.R
R/addNAs.R
R/wind.scale.R
R/date2doy.R
R/temp.kalman.R
R/calc.zeng.R
R/sw.to.par.R
R/metab.R
R/k.cole.R
R/calc.lw.net.R
R/metab.kalman.R
R/load.meta.R
R/par.to.sw.R
MD5
DESCRIPTION
man
man/metab.Rd
man/getSchmidt.Rd
man/metab.bayesian.Rd
man/k600.2.kGAS.Rd
man/k.read.base.Rd
man/metab.bookkeep.Rd
man/metab.kalman.Rd
man/get.vars.Rd
man/o2.at.sat.Rd
man/metab.ols.Rd
man/par.to.sw.Rd
man/sw.to.par.Rd
man/wind.scale.Rd
man/calc.lw.net.Rd
man/calc.zeng.Rd
man/is.day.Rd
man/rmv.vars.Rd
man/k.read.Rd
man/load.meta.Rd
man/has.vars.Rd
man/get.Ts.Rd
man/var.indx.Rd
man/metab.mle.Rd
man/load.all.data.Rd
man/sun.rise.set.Rd
man/watts.in.Rd
man/is.night.Rd
man/temp.kalman.Rd
LakeMetabolizer documentation built on May 30, 2017, 12:11 a.m.