Calculate Cumulative Biogas Production from Pressure Data
calcBgMan (for cumulative biogas manometric) calculates cumulative biogas, methane production and production rates from individual pressure and composition measurements for any number of reactors.
calcBgMan( # Main arguments dat, comp = NULL, temp, interval = TRUE, data.struct = 'longcombo', # Column names id.name = 'id', time.name = 'time', pres.name = 'pres', comp.name = NULL, # Additional arguments pres.resid = NULL, temp.init = NULL, pres.init = NULL, rh.resid = NULL, rh.resid.init = 1, headspace = NULL, vol.hs.name = 'vol.hs', absolute = TRUE, pres.amb = NULL, # Calculation method and other settings cmethod = 'removed', imethod = 'linear', extrap = FALSE, addt0 = TRUE, showt0 = TRUE, # Warnings and messages std.message = !quiet, check = TRUE, # Units and standard conditions 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 reactor identification code; time of measurement (as numeric, or POSIX); and measured pressure in pres.unit. See Details section for details on units. Additional columns can be present--these will be returned in the output data frame. See data.struct argument for details on how data frames are structured.
comp: (optional) a data frame with the columns reactor 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. If omitted, cumulative biogas volume will still be calculated and returned (but no methane data will be returned). The names of these columns are specified with id.name, time.name, and comp.name. Default is NULL.
temp: the temperature at which headspace pressure was measured. A length-one numeric vector or length-one character vector referring to a column in dat. Degrees Celcius by default (see unit.temp argument).
interval: do biogas pressure measurements represent production only from the time interval between observations (default)? interval = FALSE means measured pressure is cumulative. For mixed manometric measurements (some observations vented, some not), use interval = TRUE, include a column for pres.resid, and, if composition was only measured for vented observations, use imethod = "f1". Default is TRUE.
data.struct: the structure of input data. The default of 'longcombo' means headspace pressure and composition in a single column. The dat data frame must have reactor identification code and time columns with names specified with id.name and time.name, volume data in a single column with the name specified by pres.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 with volume and one with composition. Each data frame must have reactor identification code and time columns with names specified with id.name and time.name. The dat data frame must have volume data in a single column with the name specified by pres.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 reactor identification code columns. Instead, in dat, volume data are in a separate column for each bottle, and column names are reactor identification codes. Here, pres.name should be the name of the first column with volume data. All following columns are assumed to also have volume data. And in comp, biogas composition data are also in a separate column for each bottle, also with reactor 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 reactor 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".
pres.name: name of column containing the primary response variable (pressure) in dat data frame. Default is dat.type value. See dat.type argument.
comp.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".
pres.resid: headspace pressure after venting. Either a single numeric value, assumed to be the same for all observations, or the name of a column in dat that contains these values for each observation. Can be absolute (default) or gauge depending on the value of absolute. Length one numeric or character vector.
temp.init: initial headspace temperature in unit.temp units. Used to determine initial gas volume.
pres.init: headspace pressure at the begining of the experiment. Can be absolute (default) or gauge depending on the value of absolute. Length one numeric vector.
rh.resid: relative humidity of the gas in the headspace after venting. If NULL (default), it is calculated for each interval as the ratio of post- to pre-venting pressure (equivalent to assuming relative water vapor concentration (mixing ratio) is the same before and after venting. If entered, typically should be 1.0. Length one numeric vector.
rh.resid.init: relative humidity of the gas in the headspace at the begining of the experiment. Typically should be 1.0 (the default). Length one numeric vector.
headspace: (optional) a data frame or length-one numeric vector with reactor headspace volume(s). If a data frame is used, it should at least contain a "id" (reactor identification code) column (see "id.name") and headspace volume column (see vol.hs.name argument). Required if cmethod = "total". Default is NULL.
vol.hs.name: name of column containing headspace volume data in optional headspace data frame. Default is "vol.hs".
absolute: is the headspace pressure measured (pres.name and pres.resid values/columns) absolute or gauge pressure? Default is TRUE.
pres.amb: absolute ambient pressure needed to calculate absolute pressure from gauge pressure measurements. In atmospheres by default (see unit.pres argument). Only a single value is accepted. If ambient pressure differed among measurements, it is necessary to convert pressures to absolute values and use absolute = TRUE instead.
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 reactor 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 reactor 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)? Currently only composition values are checked. Default is TRUE. Values are changed if outside 0, 1 (divided by 100).
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 pressure data from dat and gas composition from comp, this function will calculate standardised biogas and methane production (if comp is provided) for each observation, interpolating comp.name (from comp argument) to each time.name in dat if needed, and summing these for cumulative values. Inputs units are specified with unit.pres, and output volumes are the same as headspace volume, e.g., mL or L.
Biogas composition (comp.name column in comp) is specified as the mole fraction of methane in dry biogas, normalised so mole fractions of methane and carbon dioxide sum to unity (Richards et al. 1991). Alternatively, if cmethod is set to "total", biogas composition is the mole fraction of methane in dry biogas (include all the other gases except water).
Standard values and units for temperature and pressure can be globally set using the function options. See stdVol. To surpress volume correction to a standard temperature and pressure, leave temp as NULL (the default).
If check = TRUE, the input values of mole fraction of methane in biogas are checked, and a warning is returned if the are outside 0, 1.
See associated vignette (calcBgMan_function.Rnw) for more information.
a data frame with all the columns originally present in dat, plus these others: - vBg: Standardised volume of biogas production for individual event.
xCH4: Interpolated mole fraction of methane in biogas.
vCH4: Standardised volume of methane production for individual event. Only if comp is provided.
vhsCH4: Standardised volume of methane present in reactor headspace. Only if method = "total" is used.
cvBg: Standardised cumulative volume of biogas production.
cvCH4: Standardised cumulative volume of methane production. Only if comp is provided.
rvBg: Production rate of biogas.
rvCH4: Production rate of methane. Only if comp is provided.
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.
Hansen, T.L., Schmidt, J.E., Angelidaki, I., Marca, E., Jansen, J. la C., Mosbak, H. and Christensen, T.H. 2004. Method for determination of methane potentials of solid organic waste. Waste Management 24 , 393-400
Richards, B.K., Cummings, R.J., White, T.E., Jewell, W.J. 1991. Methods for kinetic analysis of methane fermentation in high solids biomass digesters. Biomass and Bioenergy 1: 65-73.
Sasha D. Hafner and Nanna Lojborg
cumBg, calcBgVol, calcBgGD, summBg, interp, stdVol, options
# Example with longcombo structured input data frame data("sludgeTwoBiogas") data("sludgeTwoSetup") head(sludgeTwoBiogas) head(sludgeTwoSetup) # Calculate cumulative production and rates # Pressure is gauge (not absolute) so absolute argument needed # Data structure is default of longcombo cbg <- calcBgMan(sludgeTwoBiogas, temp = 30, id.name = "id", time.name = "time.d", pres.name = "pres", comp.name = "xCH4n", temp.init = 30, pres.resid = 0, pres.init = 0, headspace = sludgeTwoSetup, vol.hs.name = "vol.hs", pres.amb = 1013, absolute = FALSE, unit.pres = "mbar") head(cbg) # Plot results ## Not run: # Not run just because it is a bit slow library(ggplot2) ggplot(cbg, aes(time.d, cvCH4, colour = factor(id))) + geom_point() + geom_line(aes(group = id)) + labs(x = "Time (d)", y = "Cumulative methane production (mL)", colour = "Bottle id") + theme_bw() ## End(Not run) # This sludgeTwoBiogas dataset has original xCH4 as well as normalized values # So "method 2" can also be used by changing comp.name and cmethod arguments cbg2 <- calcBgMan(sludgeTwoBiogas, temp = 30, id.name = "id", time.name = "time.d", pres.name = "pres", comp.name = "xCH4", temp.init = 30, pres.resid = 0, pres.init = 0, headspace = sludgeTwoSetup, vol.hs.name = "vol.hs", pres.amb = 1013, cmethod = 'total', absolute = FALSE, unit.pres = "mbar") head(cbg2) # Compare quantile(cbg2$vCH4 - cbg$vCH4) # Median difference of 0.2 mL # Example with long structured input data frame data("strawPressure") data("strawComp") data("strawSetup") # Need to specify data structure with \code{data.struct} argument # Using default values for time.name, pres.name cbg <- calcBgMan(strawPressure, comp = strawComp, temp = 31, data.struct = "long", id.name = "bottle", comp.name = "xCH4", temp.init = 21.55, pres.resid = "pres.resid", pres.init = 0, headspace = strawSetup, vol.hs.name = "headspace", pres.amb = 101.3, absolute = FALSE, unit.pres = "kPa") # Because of missing composition measurements at last time for some bottles # CH4 volume will be missing # Can estimate xCH4 here by extrapolation using argument of same name cbg2 <- calcBgMan(strawPressure, comp = strawComp, temp = 31, data.struct = "long", id.name = "bottle", comp.name = "xCH4", temp.init = 21.55, pres.resid = "pres.resid", pres.init = 0, headspace = strawSetup, vol.hs.name = "headspace", pres.amb = 101.3, absolute = FALSE, extrap = TRUE, unit.pres = "kPa") # For example with wide structured input data frame calcBgVol() help file
Useful links