load.all.data
(Package: LakeMetabolizer) :
Attemps to load and merge all timeseries data for a given site name
Loads and returns all the data available in the specified directory for a given site. All timeseries data are merged by “datetime” into a single data.frame. Data are identified by the column header information.
● Data Source:
CranContrib
● Keywords: IO, file
● Alias: load.all.data
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sun.rise.set
(Package: LakeMetabolizer) :
Calculates the time of sunrise and sunset
Calculates the time of sunrise and sunset based on latitude and date.
● Data Source:
CranContrib
● Keywords: methods
● Alias: sun.rise.set
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Estimate the amount of energy gained by a layer of water as the difference between energy entering from the top of the layer and energy leaving at the bottom. Energy gained/ lost is calculated from photosynthetically active radiation (PAR, which is then converted to watts) and an estimate of kd (light attenuation coefficient) which is derived from the depth of 1 percent surface light.
● Data Source:
CranContrib
● Keywords: math, methods
● Alias: watts.in
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is.night
(Package: LakeMetabolizer) :
determines if measurement was taken during the night
determines if measurement was taken during the nighttime
● Data Source:
CranContrib
● Keywords: methods
● Alias: is.night
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temp.kalman
(Package: LakeMetabolizer) :
Smooth temperature time series using a Kalman filter/ smoother
Smoothes a temperature time series uses a Kalman filter/ smoother.
● Data Source:
CranContrib
● Keywords:
● Alias: temp.kalman
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Returns daily time series of gross primary production (GPP), respiration (R), and net ecosystem production (NEP). Depending on the method used, other information may be returned as well. Calculations are made using one of 5 statistical methods.
● Data Source:
CranContrib
● Keywords: metabolism
● Alias: metab
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getSchmidt
(Package: LakeMetabolizer) :
Returns Schmidt number for a specific gas at a given temperature
Schmidt number is temperature dependant, and is the ratio of the kinematic viscosity of water to a diffusion coefficient. Coefficients are included for He, O2, CO2, CH4, SF6, N2O, Ar, and N2.
● Data Source:
CranContrib
● Keywords: math, methods
● Alias: getSchmidt
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metab.bayesian
(Package: LakeMetabolizer) :
Metabolism model based on a bayesian parameter estimation framework
This function runs the bayesian metabolism model on the supplied gas concentration and other supporting data. This allows for both estimates of metabolism along with uncertainty around the parameters.
● Data Source:
CranContrib
● Keywords:
● Alias: metab.bayesian
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k600.2.kGAS
(Package: LakeMetabolizer) :
Returns the gas exchange velocity for gas of interest w/ no unit conversions
Returns the gas exchange velocity for gas of interest w/ no unit conversions
● Data Source:
CranContrib
● Keywords:
● Alias: k600.2.kGAS, k600.2.kGAS.base
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k.read.base
(Package: LakeMetabolizer) :
Returns a timeseries of gas exchange velocity
Returns the gas exchange velocity based on the chosen model in units of m/day
● Data Source:
CranContrib
● Keywords: math, methods
● Alias: k.cole.base, k.crusius.base, k.heiskanen.base, k.macIntyre.base, k.read.base, k.read.soloviev.base, k.vachon.base
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providing 
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