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| Package: biogas | ||
| Type: Package | ||
| Title: Process Biogas Data and Predict Biogas Production | ||
| Version: 1.50 | ||
| Version: 1.52 | ||
| Date: 2024-12-03 | ||
| Authors@R: c(person("Sasha D.", "Hafner", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0955-0327")), | ||
| person("Charlotte", "Rennuit", role = "aut"), | ||
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| \name{calcBgGrav} | ||
| \alias{calcBgGrav} | ||
| %- Also NEED an "\alias" for EACH other topic documented here. | ||
| \title{ | ||
| Calculate Biogas Production from Gravimetric Data | ||
| } | ||
| \description{ | ||
| \code{calcBgGrav} calculates cumulative biogas, methane production and production rates from mass loss (gravimetric measurements) and volume measurements for any number of bottles. | ||
| } | ||
| \usage{ | ||
| 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 | ||
| ) | ||
| } | ||
| %- maybe also "usage" for other objects documented here. | ||
| \arguments{ | ||
| \item{dat}{ | ||
| a data frame with at least bottle identification code, time of measurement (as \code{numeric}, or \code{POSIX}), and bottle mass. | ||
| Structure depends on \code{data.struct} argument. | ||
| Additional columns can be present--these will be returned in the output data frame. | ||
| } | ||
|
|
||
| \item{comp}{ | ||
| (optional) a data frame with the columns bottle identification code; time of measurement, (as \code{numeric}, or \code{POSIX}); and methane concentration within dry biogas as a mole fraction, considering only methane and carbon dioxide (unless \code{cmethod = "total"}) or a single numeric value. | ||
| The names of these columns are specified with \code{id.name}, \code{time.name}, and \code{xCH4.name}. | ||
| Default is \code{NULL}. | ||
| } | ||
| \item{temp}{ | ||
| the temperature of biogas just prior to venting. | ||
| A length-one numeric vector. | ||
| Degrees Celcius by default (see \code{unit.temp} argument). | ||
| } | ||
| \item{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 \code{dat} with the pressure measurements. | ||
| Atmospheres by default (see \code{unit.pres} argument). | ||
| } | ||
|
|
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| \item{data.struct}{ | ||
| the structure of input data. The default of 'longcombo' means bottle mass and biogas composition (if available) are both in \code{dat}. | ||
| The \code{dat} data frame must have bottle identification code and time columns with names specified with \code{id.name} and \code{time.name}, mass data in a single column with the name specified by \code{mass.name}, and biogas composition in a single column with the name specified by \code{comp.name} | ||
| For the \code{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 \code{id.name} and \code{time.name}. | ||
| The \code{dat} data frame must have mass data in a single column with the name specified by \code{mass.name}. | ||
| The \code{comp} data frame must have biogas composition in a single column with the name specified by \code{comp.name}. | ||
| For the \code{data.struct = 'wide'} option, two separate data frames are needed as in \code{'long'}, but there are no bottle identification code columns. | ||
| Instead, in \code{dat}, mass data are in a separate column for each bottle, and column names are bottle identification codes. | ||
| Here, \code{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 \code{comp}, biogas composition data are also in a separate column for each bottle, also with bottle identification codes for column names. | ||
| Here, \code{comp.name} should be the name of the first column with biogas composition data, as for \code{dat}. | ||
| } | ||
|
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| \item{id.name}{ | ||
| name of the bottle identification code column in \code{dat}. Must be the same in all data frames used in the function. Default is \code{"id"}. | ||
| } | ||
|
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| \item{time.name}{ | ||
| name of column containing time data in \code{dat} and \code{comp} data frames. Default is \code{"time"}. | ||
| } | ||
|
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| \item{mass.name}{ | ||
| name of column containing the primary response variable (bottle mass) in \code{dat} data frame. | ||
| } | ||
|
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| \item{xCH4.name}{ | ||
| name of column containing biogas mole fraction of methane in \code{comp} data frame. Default is \code{"xCH4"}. Must be normalised so xCH4 + xCO2 = 1.0 unless \code{cmethod = "total"}. | ||
| } | ||
|
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| \item{xCO2.name}{ | ||
| name of column containing biogas mole fraction of carbon dioxide in \code{comp} data frame. | ||
| Only needed if \code{cmethod = "total"}. | ||
| } | ||
|
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| \item{xN2.name}{ | ||
| name of column containing biogas mole fraction of dinitrogen in \code{comp} data frame. | ||
| Only needed if \code{cmethod = "total"}. | ||
| } | ||
|
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| \item{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 \code{id} (bottle identification code) column (see \code{id.name}) and headspace volume column (see \code{vol.hs.name} argument). | ||
| Default is \code{NULL}. | ||
| } | ||
|
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| \item{vol.hs.name}{ | ||
| name of column containing headspace volume data in optional \code{headspace} data frame. | ||
| Default is \code{"vol.hs"}. | ||
| } | ||
|
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| \item{temp.init}{ | ||
| the initial headspace temperature. | ||
| Optional. | ||
| A length-one numeric vector. | ||
| Degrees Celcius by default (see \code{unit.temp} argument). | ||
| Default is \code{NULL}, which suppresses correction for initial temperature. | ||
| } | ||
|
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| \item{pres.init}{ | ||
| the initial headspace pressure. | ||
| Optional. | ||
| A length-one numeric vector. | ||
| Atmospheres by default (see \code{unit.pres} argument). | ||
| Default is \code{NULL}, which suppresses correction for initial pressure. | ||
| } | ||
|
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| \item{pres.resid}{ | ||
| residual headspace pressure after venting. | ||
| Optional. | ||
| A length-one numeric vector. | ||
| Atmospheres by default (see \code{unit.pres} argument). | ||
| Default is \code{NULL}. | ||
| } | ||
|
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| \item{headcomp}{ | ||
| initial headspace composition as a chemical formula. | ||
| Optional, for correcting for change in headspace density. | ||
| Mixtures accepted. | ||
| Default is \code{'N2'} for pure dinitrogen. | ||
| } | ||
|
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| \item{cmethod}{ | ||
| method for calculating cumulative methane production. | ||
| Use \code{"removed"} to base production on \code{xCH4} and gas volumes removed (default). | ||
| Use \code{"total"} to base it on the sum of methane removed and methane remaining in the bottle headspace. | ||
| For \code{"removed"}, \emph{\code{xCH4} should be calculated based on methane and CO2 only (xCH4 + xCO2 = 1.0).} | ||
| For \code{"total"}, \emph{\code{xCH4} should be calculated including all biogas components (CH4, CO2, N2, H2S, etc.) except water.} | ||
| Length one character vector. | ||
| } | ||
|
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| \item{imethod}{ | ||
| method used for interpolation of \code{xCH4}. | ||
| This is passed as the \code{method} argument to \code{\link{interp}}. | ||
| Length one character vector. | ||
| Default is \code{"linear"} for linear interpolation. | ||
| } | ||
|
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| \item{extrap}{ | ||
| should \code{comp.name} be extrapolated? | ||
| Length one logical vector. | ||
| This is passed as the \code{extrap} argument to \code{\link{interp}}. | ||
| Default is \code{FALSE}. | ||
| } | ||
|
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| item{addt0}{ | ||
| is the earliest time in \code{dat} data frame \dQuote{time zero} (start time)? | ||
| If not, this argument adds a row with \code{time.name = 0} for each bottle in order to calculate production rates for the first observation. | ||
| This addition is only made when \code{time.name} is \code{numeric} (or \code{integer}). | ||
| Length-one logical vector. | ||
| Default is \code{TRUE}. | ||
| To return these additional rows in the output, see \code{showt0}. | ||
| } | ||
|
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| \item{showt0}{ | ||
| should \dQuote{time zero} rows be returned in the output? | ||
| Can be convenient for plotting cumulative volumes. | ||
| Only applies if \code{time.name} is \code{numeric} (or \code{integer}). | ||
| These rows may have been present in the original data (\code{dat}) or added by the function (see \code{addt0}). | ||
| Default value depends on \code{dat} \code{time.name} column content. | ||
| If \code{time.name} column is numeric and contains 0 then the default value is \code{TRUE} and otherwise \code{FALSE}. | ||
| } | ||
|
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| \item{std.message}{ | ||
| should a message with the standard conditions be displayed? | ||
| Default is \code{TRUE}. | ||
| } | ||
|
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| \item{check}{ | ||
| should input data be checked for unreasonable values (with warnings)? | ||
| Default is \code{TRUE}. | ||
| } | ||
|
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| \item{temp.std}{ | ||
| standard temperature for presentation of biogas and methane results. | ||
| Length one numeric vector. | ||
| Default value is 0 degrees C (set in \code{\link{stdVol}}). | ||
| Argument is passed to \code{\link{stdVol}}. | ||
| } | ||
|
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| \item{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 \code{\link{stdVol}}). | ||
| Argument is passed to \code{\link{stdVol}}. | ||
| } | ||
|
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| \item{unit.temp}{ | ||
| temperature units for \code{temp} and \code{temp.std} arguments. | ||
| %Options are \code{"C"} (degrees Celcius), \code{"F"} (degrees Fahrenheit), and \code{"K"} (Kelvin). | ||
| Default is \code{"C"}. | ||
| Argument is passed to \code{\link{stdVol}}. | ||
| } | ||
|
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| \item{unit.pres}{ | ||
| pressure units for \code{pres} and \code{pres.std} arguments. | ||
| %Options are \code{"atm"}, \code{"Pa"}, \code{"kPa"}, \code{"hPa"}, and \code{"bar"}. | ||
| Default is \code{"atm"}. | ||
| Argument is passed to \code{\link{stdVol}}. | ||
| } | ||
|
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| \item{quiet}{ | ||
| use to suppress messages. Default is \code{FALSE}. | ||
| } | ||
|
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| } | ||
|
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| \details{ | ||
| Using mass loss data from \code{dat} and composition data from \code{dat} or \code{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. | ||
|
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| Standard values and units for temperature and pressure can be globally set using the function \code{\link{options}}. | ||
| See \code{\link{stdVol}}. | ||
|
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| } | ||
|
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| \value{ | ||
| a data frame with all the columns originally present in \code{dat}, plus others including these: | ||
| \item{vBg}{Standardized volume of biogas production for individual event.} | ||
| \item{xCH4}{Calculated mole fraction of methane in biogas.} | ||
| \item{vCH4}{Standardized volume of methane production for individual event.} | ||
| \item{cvBg}{Standardized cumulative volume of biogas production.} | ||
| \item{cvCH4}{Standardized cumulative volume of methane production.} | ||
| \item{rvBg}{Production rate of biogas.} | ||
| \item{rvCH4}{Production rate of methane.} | ||
| Units are based on units in input data. | ||
| } | ||
|
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| \references{ | ||
| 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. \emph{Biomass and Bioenergy} \bold{83}, 297-301. | ||
| } | ||
|
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| \author{ | ||
| Sasha D. Hafner | ||
| } | ||
|
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| \seealso{ | ||
| \code{\link{calcBgMan}}, | ||
| \code{\link{calcBgVol}}, | ||
| \code{\link{calcBgGD}}, | ||
| \code{\link{summBg}}, | ||
| \code{\link{interp}}, | ||
| \code{\link{stdVol}}, | ||
| \code{\link{options}} | ||
| } | ||
|
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| \examples{ | ||
|
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| data('strawMass') | ||
| data('strawComp') | ||
| data('strawSetup') | ||
|
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| 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() | ||
|
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| 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) | ||
|
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| head(cbg) | ||
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| } | ||
| %% Add one or more standard keywords, see file "KEYWORDS" in the | ||
| %% R documentation directory. | ||
| \keyword{chron} | ||
| \keyword{manip} | ||
| \concept{biogas} |
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