LakeMetabolizer: Tools for the Analysis of Ecosystem Metabolism

A collection of tools for the calculation of freewater metabolism.

Install the latest version of this package by entering the following in R:
install.packages("LakeMetabolizer")
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

Functions

calc.lw.net Man page
calc.lw.net.base Man page
calc.zeng Man page
getSchmidt Man page
get.Ts Man page
get.vars Man page
has.vars Man page
is.day Man page
is.night Man page
k600.2.kGAS Man page
k600.2.kGAS.base Man page
k.cole Man page
k.cole.base Man page
k.crusius Man page
k.crusius.base Man page
k.heiskanen Man page
k.heiskanen.base Man page
k.macIntyre Man page
k.macIntyre.base Man page
k.read Man page
k.read.base Man page
k.read.soloviev Man page
k.read.soloviev.base Man page
k.vachon Man page
k.vachon.base Man page
load.all.data Man page
load.meta Man page
metab Man page
metab.bayesian Man page
metab.bookkeep Man page
metab.kalman Man page
metab.mle Man page
metab.ols Man page
o2.at.sat Man page
o2.at.sat.base Man page
par.to.sw Man page
par.to.sw.base Man page
rmv.vars Man page
sun.rise.set Man page
sw.to.par Man page
sw.to.par.base Man page
temp.kalman Man page
var.indx Man page
watts.in Man page
wind.scale Man page
wind.scale.base Man page

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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