Calculate Biogas Production from Gravimetric Data
calcBgGrav calculates cumulative biogas, methane production and production rates from mass loss (gravimetric measurements) and volume measurements for any number of bottles.
calcBgGrav( # Main arguments dat, comp = NULL, temp = NULL, pres = NULL, data.struct = 'longcombo', id.name = 'id', time.name = 'time', mass.name, xCH4.name = 'xCH4', xCO2.name = NULL, xN2.name = NULL, headspace = NULL, vol.hs.name = 'vol.hs', temp.init = NULL, pres.init = NULL, pres.resid = NULL, headcomp = 'N2', cmethod = 'removed', imethod = 'linear', extrap = FALSE, addt0 = TRUE, showt0 = TRUE, std.message = !quiet, check = TRUE, temp.std = getOption('temp.std', as.numeric(NA)), pres.std = getOption('pres.std', as.numeric(NA)), unit.temp = getOption('unit.temp', 'C'), unit.pres = getOption('unit.pres', 'atm'), quiet = FALSE )
dat: a data frame with at least bottle identification code, time of measurement (as numeric, or POSIX), and bottle mass. Structure depends on data.struct argument. Additional columns can be present--these will be returned in the output data frame.
comp: (optional) a data frame with the columns bottle identification code; time of measurement, (as numeric, or POSIX); and methane concentration within dry biogas as a mole fraction, considering only methane and carbon dioxide (unless cmethod = "total") or a single numeric value. The names of these columns are specified with id.name, time.name, and xCH4.name. Default is NULL.
temp: the temperature of biogas just prior to venting. A length-one numeric vector. Degrees Celcius by default (see unit.temp argument).
pres: the absolute pressure of biogas prior to venting. A length-one numeric vector or a character vector giving the name of the column in dat with the pressure measurements. Atmospheres by default (see unit.pres argument).
data.struct: the structure of input data. The default of 'longcombo' means bottle mass and biogas composition (if available) are both in dat. The dat data frame must have bottle identification code and time columns with names specified with id.name and time.name, mass data in a single column with the name specified by mass.name, and biogas composition in a single column with the name specified by comp.name
For the data.struct = 'long' option, two separate data frames are needed, one for mass and one for composition (if available). Each data frame must have bottle identification code and time columns with names specified with id.name and time.name. The dat data frame must have mass data in a single column with the name specified by mass.name. The comp data frame must have biogas composition in a single column with the name specified by comp.name. For the data.struct = 'wide' option, two separate data frames are needed as in 'long', but there are no bottle identification code columns. Instead, in dat, mass data are in a separate column for each bottle, and column names are bottle identification codes. Here, mass.name should be the name of the first column with mass data. All following columns are assumed to also have mass data. And in comp, biogas composition data are also in a separate column for each bottle, also with bottle identification codes for column names. Here, comp.name should be the name of the first column with biogas composition data, as for dat.
id.name: name of the bottle identification code column in dat. Must be the same in all data frames used in the function. Default is "id".
time.name: name of column containing time data in dat and comp data frames. Default is "time".
mass.name: name of column containing the primary response variable (bottle mass) in dat data frame.
xCH4.name: name of column containing biogas mole fraction of methane in comp data frame. Default is "xCH4". Must be normalised so xCH4 + xCO2 = 1.0 unless cmethod = "total".
xCO2.name: name of column containing biogas mole fraction of carbon dioxide in comp data frame. Only needed if cmethod = "total".
xN2.name: name of column containing biogas mole fraction of dinitrogen in comp data frame. Only needed if cmethod = "total".
headspace: (optional) a data frame or length-one numeric vector with bottle headspace volume(s). If a data frame is used, it should at least contain a id (bottle identification code) column (see id.name) and headspace volume column (see vol.hs.name argument). Default is NULL.
vol.hs.name: name of column containing headspace volume data in optional headspace data frame. Default is "vol.hs".
temp.init: the initial headspace temperature. Optional. A length-one numeric vector. Degrees Celcius by default (see unit.temp argument). Default is NULL, which suppresses correction for initial temperature.
pres.init: the initial headspace pressure. Optional. A length-one numeric vector. Atmospheres by default (see unit.pres argument). Default is NULL, which suppresses correction for initial pressure.
pres.resid: residual headspace pressure after venting. Optional. A length-one numeric vector. Atmospheres by default (see unit.pres argument). Default is NULL.
headcomp: initial headspace composition as a chemical formula. Optional, for correcting for change in headspace density. Mixtures accepted. Default is 'N2' for pure dinitrogen.
cmethod: method for calculating cumulative methane production. Use "removed" to base production on xCH4 and gas volumes removed (default). Use "total" to base it on the sum of methane removed and methane remaining in the bottle headspace. For "removed", xCH4 should be calculated based on methane and CO2 only (xCH4 + xCO2 = 1.0).
For "total", xCH4 should be calculated including all biogas components (CH4, CO2, N2, H2S, etc.) except water.
Length one character vector.
imethod: method used for interpolation of xCH4. This is passed as the method argument to interp. Length one character vector. Default is "linear" for linear interpolation.
extrap: should comp.name be extrapolated? Length one logical vector. This is passed as the extrap argument to interp. Default is FALSE.
addt0: is the earliest time in dat data frame time zero (start time)? If not, this argument adds a row with time.name = 0 for each bottle in order to calculate production rates for the first observation. This addition is only made when time.name is numeric (or integer). Length-one logical vector. Default is TRUE. To return these additional rows in the output, see showt0.
showt0: should time zero rows be returned in the output? Can be convenient for plotting cumulative volumes. Only applies if time.name is numeric (or integer). These rows may have been present in the original data (dat) or added by the function (see addt0). Default value depends on dat time.name column content. If time.name column is numeric and contains 0 then the default value is TRUE and otherwise FALSE.
std.message: should a message with the standard conditions be displayed? Default is TRUE.
check: should input data be checked for unreasonable values (with warnings)? Default is TRUE.
temp.std: standard temperature for presentation of biogas and methane results. Length one numeric vector. Default value is 0 degrees C (set in stdVol). Argument is passed to stdVol.
pres.std: standard pressure for presentation of biogas and methane results. Length one numeric vector. Default value is 1.0 atm (101325 Pa) (set in stdVol). Argument is passed to stdVol.
unit.temp: temperature units for temp and temp.std arguments.
Default is "C". Argument is passed to stdVol.
unit.pres: pressure units for pres and pres.std arguments.
Default is "atm". Argument is passed to stdVol.
quiet: use to suppress messages. Default is FALSE.
Using mass loss data from dat and composition data from dat or comp, this function will calculate standardized biogas and methane production for each observation using a grvimetric method. See reference below for details on the method.
Standard values and units for temperature and pressure can be globally set using the function options. See stdVol.
a data frame with all the columns originally present in dat, plus others including these: - vBg: Standardized volume of biogas production for individual event.
xCH4: Calculated mole fraction of methane in biogas.
vCH4: Standardized volume of methane production for individual event.
cvBg: Standardized cumulative volume of biogas production.
cvCH4: Standardized cumulative volume of methane production.
rvBg: Production rate of biogas.
rvCH4: Production rate of methane.
Units are based on units in input data.
Hafner, S.D., Rennuit, C., Triolo, J.M., Richards, B.K. 2015. Validation of a simple gravimetric method for measuring biogas production in laboratory experiments. Biomass and Bioenergy 83 , 297-301.
Sasha D. Hafner
calcBgMan, calcBgVol, calcBgGD, summBg, interp, stdVol, options
# Combined data frame with mass and composition for \code{data.struct = 'longcombo'} (default). data('UQGravBiogas') data('UQGravSetup') cbg <- calcBgGrav(UQGravBiogas, temp = 35, pres = 1.5, id.name = 'id', time.name = 'day', mass.name = 'mass.final', xCH4.name = 'xCH4') head(cbg) # With separate mass and composition data frames data('strawMass') data('strawComp') data('strawSetup') cbg0 <- calcBgGrav(strawMass, comp = strawComp, temp = 35, pres = 1.5, data.struct = 'long', id.name = 'bottle', time.name = 'time', mass.name = 'mass', xCH4.name = 'xCH4') warnings() cbg <- calcBgGrav(strawMass, comp = strawComp, temp = 35, pres = 1.5, data.struct = 'long', id.name = 'bottle', time.name = 'time', mass.name = 'mass', xCH4.name = 'xCH4', extrap = TRUE) head(cbg)
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