High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Biogas quantity and composition can be predicted from substrate composition and additional, optional data. Lastly, inoculum and substrate mass can be determined for planning BMP experiments.
*summBg() Corrected problem with if() check with length > 1.
*summBg() Changes to error propagation so it is now based on standard error instead of standard deviation. Now results are correct even when number is replicates is unequal for inoculum bottles, substrate bottles, or VS determination.
*planBMP() New function for planning BMP experiments.
*predBg() Corrected error for value = "reactionc" where substrate (reactant) was omitted in some cases.
*predBg() New ash component for mcomp argument.
*Units (applies to multiple functions) Add mbar for pressure.
*stdVol() and functions that call it Standard conditions are automatically converted to specified units now.
*summBg() Added show.more argument to see additional ouput. Added show.rates argument to facilitate checking rates for 1% etc. criterion. Changed specification of automatic selection of BMP evaluation time based on relative rate. Now any rate and any duration can be used, e.g., when = "1p3d" for 1% per day for 3 d. Added quiet argument (default FALSE) to supress warnings.
*predBg() Slight change in protein composition for mcomp to match ADM1.
*summBg() Slight change to error propagation.
*Removed reference to two LaTeX packages that were causing problems in a vignette.
*summBg() New "0.5p" option for the when argument can be used to select those times where methane rate drops below 0.5% of cumulative production per day.
*calcCOD() Fixed an error that applied to vectorized calculations.
*cumBg() Minor fixes.
*Loading message When biogas is loaded a short message is displayed. Our hope to is to make more users aware of the mailing list and OBA, a web app interface to the biogas package.
*cumBg() New "absolute GC" method based on molar quantity of methane. Set dat.type to "gca" to use it.
Added warnings for missing observations.
*summBg() Added warnings for missing observations.
When "1p" option is used but methane production rates exceed the 1% criterion, the function throws an error. To help identify those bottles that haven't met the criterion, set when = "1p" and show.obs = TRUE to see relative rates for all bottles (rrvCH4 column).
*cumBg() Fixed bug in dat.struct = "wide" option that caused problems when the number of columns exceeded the number of rows.
*summBg() Fixed some problems with "1p" option.
Ilona Sárvári Horváth (University of Borås, Sweden) provided details on the "absolute GC" method as well as example data for testing.
Christof Holliger (École polytechnique fédérale de Lausanne, Switzerland), Konrad Koch (Technische Universität München, Germany), and Hélène Carrere (INRA Laboratoire de Biotechnologie de l'Environnement, France) provided data for testing and suggestions related to cumBg().
*cumBg() New dry argument (dry = FALSE by default) so that standardised gas volumes can be used (e.g., AMPTS II data).
If any CH4 concentration values are > 1, all are divided by 100. This allows the use of CH4 concentrations as % vol (% mol) without division first.
*sumBg() Standard deviation of BMP or similar summary is now calculated even with only one inoculum-only bottle, with a warning.
*Vignette Slight updates to "Getting started" vignette on data structures (more details in cumBg() help file).
*cumBg() When gauge = FALSE, pres.init should now be gauge pressure (pres.amb must be absolute pressure).
Fixed a bug in id column name for wide format.
*sumBg() Improved when = '1p' option (1% criterion). Criterion is now: rate <1% of cumulative CH4 per day for current observation and all following observations, and observation is >= 3 days from end of incubation.
Other problem with the when = '1p' option apparent only when rates varied significantly among replicates was fixed.
*Other minor fixes
REMOVED FUNCTIONALITY *summBg() Removed default value for inoc.m.name argument to avoid mistakes.
*cumBg() Accepts two new data structures in addition to the original "long" structure: "wide" and "longcombo". See data.struct argument. Five new example data sets have been added for use in examples to demonstrate.
Missing values (NAs) for biogas composition are now OK. They will be automatically dropped (and replaced with interpolated values if needed).
The equation for water vapor pressure calculation has been changed. Resulting changes in standardized volume will change very slightly as a result (<0.07%). (Thanks to Izabel Kronenberg.)
New pres.amb argument for use with manometric measurements and gauge pressure.
*summBg() Now possible to include effect of uncertainty in substrate mass (standard deviation) on final standard deviation in methane yield. See norm.sd.name argument.
Instead of specifying a fixed time at which to evaluate biogas production, the function can find the time when the production rate drops below 1% of cumulative production per day. This value can be different for each substrate and can be applied with or without inoculum subtraction. To use, set when = "1p".
*cumBg() Corrected calculation of initial standardized gas volume for manometric method (dat.type = "pres").
*Other minor fixes
*cumBg() New manometric method now available (use dat.type = "pres").
New option to use either cumulative or interval (default) data. See 'interval' argument.
BUG FIXES *summBg() Now returns error if 'when' argument is greater than available times for all reactors.
*cumBg() Fixed error in cmethod = "total" calculation method. Now headspace volume is correctly added to cumulative production.
*Other minor fixes
*molMass() New elements added to database. All elements with at least one stable isotope are now included. Examples: molMass('CdSiO3') molMass('FeSO4(H2O)7')
*molMass() and predBg() Additional flexibility in chemical formula specification. Both of the following are acceptable. molMass("H3C(CH2)5COOH") molMass("(C6H12O6)0.25 (H3COOH)0.75")
*summBg() New option for 'when' argument: set to "meas" to return a row for each measurement time (these may differ among reactors).
New 'sort' argument to sort results by reactor ID and time (default) or to match original order of reactor ID in setup data frame.
*predBg() New options for 'value' argument to just return chemical reactions: use "reactionn" for a numeric reaction and "reactionc" for a character version.
*vol2mol() New function for converting measured volume of CH4, CO2, and some other pure gases to moles.
*predBg() The 'mcomp' argument is more flexible now. Chemical formulas can now be mixed with macromolecule group names. See help file and predBg vignette for examples.
New option for 'value' argument: "reaction". Returns a named numeric vector with stoichiometric coefficients for the overall reaction, normalized to 1 mol of substrate.
The 'mass' argument will be set to the sum of 'mcomp' unless it is set separately. Previously the default value of 1.0 g was used even if 'mcomp' did not sum to 1.0. See help file and predBg vignette for more information.
*New vignette "Predicting methane and biogas production with the biogas package" (referred to as the "predBg vignette" above).
*predBg() 'mcomp' is now mass-based (as originally intended). Earlier versions were mole-based. See help file and predBg vignette for more information.
*Other minor bug fixes.
*The gravimetric method used in mass2vol() is described in detail in a new publication in Biomass and Bioenergy: 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. Send us an email if you would like a pdf.
There is now a biogas package mailing list. To subscribe, send a message with the subject "biogas: SUBSCRIBE" to [email protected].
*New vignette "Getting started with the biogas package"
*Standard conditions and units Standard temperature and pressure and units can now be set globally using options(). This applies to stdVol(), cumBg(), vol2mass(), and mass2vol(). This option is strongly recommended for users not using default values (1.0 atm (101325 Pa) and 0 degrees C). Also, stdVol() (and functions that use it) now displays the standard temperature and pressure.
*Checking for input errors All functions now include checks for the class and in some cases, the value, of the arguments. Functions where a column name is specified (cumBg() and summBg()) now check that the specified columns exist in the input data frames.
*cumBg() It is now possible to use a single composition value for each reactor, if it is given in a data frame with no time column (just reactor ID and xCH4). If this is the case but there is more than one composition value per reactor, an error is thrown.
For the gravimetric method, the initial headspace correction can now be applied (to the first interval only) using the headspace, vol.hs.name, headcomp, and temp.init arguments.
*summBg() Time can be totally ignored if there is a single observation for each reactor and 'when' is set to NULL.
*Measurement pressure and temperature Pressure and temperature (pres and temp arguments) both must now be specified in order to determine standardized volumes for any function with a pres or temp argument, so stdVol(), cumBg(), vol2mass(), mass2vol(). Previous versions had a default pressure of 1.0 atm. Omitting pres or temp will now throw an error or return non-standardized results (with a message).
*Column names in data frame arguments for cumBg() and summBg() Names of ID, time, volume, composition, and other columns in input data frame must now be specified using the ____.name arguments. The functions will no longer match based on position. This change is meant to avoid errors caused by incorrect positional matching when the user tried to use _____.name.
*predBg() Fixed incorrect calculation of mass when mol argument was used for input.
*molMass() The function now returns all digits--no rouding is done.
summBg *Output data frame now includes value of 'when' argument that was specified in the call.
*Will now work when only a single response ('vol.name') value is available, but only if 'when' exactly matches the time or if 'extrap' is set to TRUE.
*The 'when' argument can now be a vector, i.e., a single call can return results for different times.
*Separate contributions of substrate and inoculum are returned when 'show.obs' is set to TRUE.