biogas 1.23.0 2019 November --------------------------------------------------------------------- NEW FEATURES *calcBgMan(), calcBgVol() New simpler functions for BMP data processing. These are replacements for volumetric and manometric calculations with cumBg() *calcBgGD() Completely new function for gas density BMP (GD-BMP) calculations. biogas 1.14.1 2019 April 10 --------------------------------------------------------------------- NEW FEATURES *cumBg() Mixed cumulative/interval volumetric calculations with argument empty.name and "f1" option of imethod argument. New 'rh.resid' argument can be used for different assumptions about relative humidity in bottle headspace after venting in manometric calculations. A new 'quiet' argument suppresses messages, and is useful when processing a large number of data sets at once. *summBg() New argument 'rate.crit' allows use of gross production rates in relative duration calculations (e.g., following VDI). Relative and fixed duration criteria can be combined with arguments 'when' and 'when.min' (a new argument). For example, perhaps you want "1p3d" but at least 20 days. Now it is possible to calculate BMP (or other summaries) for multiple cumulative methane data frames simultaneously by using a list for the vol argument. Useful for evaluation of uncertainty in cumulative methane calculations. The vol.name argument can now be used for multiple response variables (e.g., both cumulative methane and biogas) in one call. BUG FIXES *cumBg() Corrected problem with error message when comp was requested for data.struct = "longcombo" even though it was not needed. Other minor bug fixes in cumBg(). biogas 1.10.3 2018 May 16 --------------------------------------------------------------------- MINOR CHANGES biogas package help file and startup message have been removed. biogas 1.10.0 2018 March 2 --------------------------------------------------------------------- BUG FIXES *summBg() Corrected another problem with if() check with length > 1. biogas 1.10.0 2018 February 5 --------------------------------------------------------------------- BUG FIXES *summBg() Corrected problem with if() check with length > 1. NEW FEATURES *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. biogas 1.9.0 2018 January 3 --------------------------------------------------------------------- BUG FIXES *predBg() Corrected error for value = "reactionc" where substrate (reactant) was omitted in some cases. NEW FEATURES *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. OTHER CHANGES *predBg() Slight change in protein composition for mcomp to match ADM1. *summBg() Slight change to error propagation. biogas 1.8.1 2017 August 11 --------------------------------------------------------------------- BUG FIXES *Removed reference to two LaTeX packages that were causing problems in a vignette. biogas 1.8.0 2017 August 9 --------------------------------------------------------------------- NEW FEATURES *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. BUG FIXES *calcCOD() Fixed an error that applied to vectorized calculations. *cumBg() Minor fixes. biogas 1.7.0 2017 February 24 --------------------------------------------------------------------- NEW FEATURES *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). BUG FIXES *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. ACKNOWLEDGEMENTS 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(). biogas 1.6.0 2016 December 16 --------------------------------------------------------------------- NEW FEATURES *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). BUG FIXES *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. biogas 1.5.0 2016 November 17 --------------------------------------------------------------------- NEW FEATURES *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". BUG FIXES *cumBg() Corrected calculation of initial standardized gas volume for manometric method (dat.type = "pres"). *Other minor fixes biogas 1.4.0 2016 May 24 --------------------------------------------------------------------- NEW FEATURES *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 biogas 1.3.0 2016 April 14 --------------------------------------------------------------------- NEW FEATURES *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. biogas 1.2.0 2015 November 13 --------------------------------------------------------------------- NEW FEATURES *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). BUG FIXES *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. NEW PUBLICATION *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. biogas 1.1.0 2015 July 29 --------------------------------------------------------------------- MAILING LIST There is now a biogas package mailing list. To subscribe, send a message with the subject "biogas: SUBSCRIBE" to saha@kbm.sdu.dk. NEW FEATURES *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. REMOVED FUNCTIONALITY *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. BUG FIXES *predBg() Fixed incorrect calculation of mass when mol argument was used for input. OTHER CHANGES *molMass() The function now returns all digits--no rouding is done. *cumBg() Calculation of methane volume in the volumetric method (default) now corrects for the (very small, < 0.4%) difference in molar volume between CH4 and biogas (this was already the case for the gravimetric method). --------------------------------------------------------------------- biogas 1.0.1 2015 May 28 --------------------------------------------------------------------- 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.