Overview

The biogas package is an R package for biogas research. It provides tools for processing biogas data, predicting biogas production, making conversions, and planning experiments. For example, the calcBgVol() function can be used for calculating biochemical methane potential from original measurements. The calcCOD() function can calculate the chemical oxygen demand of a compound based on a chemical formula. And the planBMP() function can suggest substrate or inoculum quantities for a biochemical methane potential (BMP) experiment based on multiple constraints.

An example

Much of the biogas package is dedicated to processing of laboratory measurements, but those functions are difficult to demonstrate in a short example. So, an alternative is the predBg() microbial stoichiometry function. With it, the theoretical maximum BMP of, say, cellulose, could be calculated with

> predBg("C6H10O5")
[1] 413.7274

and we could get a lot more information, including an estimate of biogas composition as affected by pH, for a 5:1 mixture of waste paper and waste oil with

> predBg(mcomp = c(C6H10O5 = 5/6, C54H100O7 = 1/6), mass = 1,
fd = 0.8, fs = 0.1, conc.sub = 50, pH = c(6.5, 7, 8.5),
temp = 35, value = "all")
                      form mass mol.mass      moles      COD  fs  fe  fd
1 C1.52618H2.61516O1.00000    1  36.9655 0.02705225 1.454303 0.1 0.9 0.8
2 C1.52618H2.61516O1.00000    1  36.9655 0.02705225 1.454303 0.1 0.9 0.8
3 C1.52618H2.61516O1.00000    1  36.9655 0.02705225 1.454303 0.1 0.9 0.8
  conc.sub temp  pH      hydro      fCH4      xCH4     vCH4      vCO2      vBg
1       50   35 6.5 0.09279292 0.5566161 0.5689900 365.8395 275.91411 641.7536
2       50   35 7.0 0.09279292 0.5566161 0.5864017 365.8395 256.90636 622.7459
3       50   35 8.5 0.09279292 0.5566161 0.8921576 365.8395  44.02904 409.8686
       mCH4      mCO2     mCO2Bg   mCO2.sol       cTIC      m.bio      N.req
1 0.2624617 0.5735654 0.54543300 0.02813242 0.03196140 0.08225028 0.01018521
2 0.2624617 0.5735654 0.50785807 0.06570735 0.07465048 0.08225028 0.01018521
3 0.2624617 0.5735654 0.08703757 0.48652785 0.55274693 0.08225028 0.01018521

See the vignettes and help files for more details.

Getting started

The biogas package is available from CRAN, and so can be installed directly in R with:

install.packages("biogas")

To see available vignettes, use

vignette(package = 'biogas')

and then, e.g.,

vignette('calcBgVol_function')

or

vignette('predBg_function')

Alternatively, download the vignettes from the CRAN page.

More information

• Open-access paper describing the package: https://doi.org/10.1016/j.softx.2018.06.005
• Web application interface to the package (OBA): https://biotransformers.shinyapps.io/oba1/
• YouTube playlist for OBA (shows some of what the biogas package can do): https://www.youtube.com/playlist?list=PLt5lRUaaL8JMKDyuRIrKkuloRQk6YmYhn
• Mailing list: sasha.hafner at bce.au.dk