2024 December 4
calcBgGrav() New function for processing gravimetric BMP data.
Meant as a replacement for gravimetric processing with cumBg()fitFOM() New function for fitting first-order modelssummBg() and cumBg() warnings about missing columns fixed (thanks to Jonas Ohlsson, @jonasoh)options(scipen...) (issue #61)2020 January
if statements and logical coercion.2019 November
2019 April 10
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.
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.
Other minor bug fixes in cumBg().
2018 May 16
biogas package help file and startup message have been removed.
2018 March 2
2018 February 5
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.
2018 January 3
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.
2017 August 11
2017 August 9
calcCOD() Fixed an error that applied to vectorized calculations.
cumBg() Minor fixes.
2017 February 24
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.
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().
2016 December 16
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).
Fixed a bug in id column name for wide format.
Other problem with the when = '1p' option apparent only when rates varied significantly among replicates was fixed.
2016 November 17
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.
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
2016 May 24
New option to use either cumulative or interval (default) data. See 'interval' argument.
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
2016 April 14
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.
2015 November 13
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.
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.
2015 July 29
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.
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.
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).
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.