Analyze Microbial Biogas Fermentation Data

Provides a new S3 class object and relevant methods to analyze biogas fermentation data. It includes three workflows. One is specialized to a commercially available lab-scale fermentation system (see e.g. Nwaigwe (2018) ). The second provides more flexibility and allows to import data from plain text files. The last workflow offers the most flexibility as it doesn't expect external input files but relays on interactive user input. Although the focus is set on biogas fermentations, concepts and workflows may be also applicable to other fermentations even if not a gaseous product is measured. Furthermore, it provides functions that bridge to established plot engines (e.g. 'ggplot2' or 'plotly') for data visualisation. 'bgfanalyzer' catches up an idea of Hafner et al. (2018) of using R to standardize research within the biogas field. For more details on standardization efforts within the biogas research field see Hollinger et al. (2016) and Hollinger et al. (2021) .

bgfanalyzer

The goal of bgfanalyzer is to help standardizing the analysis of biogas fermentation data, through a novel S3 object class, the BGF. Th package ships with methods allowing object creation based on external files, object manipulation, as well as visualizing and exporting BGF’s .

Installation

You can install the development version of bgfanalyzer from GitHub with:

# install.packages("pak")
pak::pak("BlackiXP/bgfanalyzer")

Example

The package comes with an example data set ‘LabScaleBiogas’

library(bgfanalyzer)
myBGF <- LabscaleBiogas
myBGF
#> 'LabscaleBiogas' - a BGF with 15 fermentation(s)
#> 
#> 
#> $ExpParam: 11 experimental paramerters
#> $metaData: 16 meta variables
#> $BioGasData: 735 observations of 7 fermentation variables
#> 
#> 
#>                   yield    sd_yield production sd_production time_production
#> Blank     -2.997602e-14  2.88499567     75.325    5.26794552             1.0
#> Cellulose  2.899017e+01          NA    182.260            NA             3.0
#> S1 ctrl    6.188975e+02  9.87799079    700.350    0.77781746             3.0
#> S1 7d      2.618791e+02  9.49000623    359.790    6.49124025             3.0
#> S1 4d      1.087374e+03 11.21296479    644.655   20.73944189             3.0
#> S2 ctrl    7.781660e+01  0.02079726    119.845    0.04949747             1.0
#> S2 4d      4.011575e+02  2.21973211    110.935    0.21920310             2.0
#> S2 6d      1.335888e+02 42.32196395    128.480   25.54069694             4.5
#>           sd_time_production
#> Blank               0.000000
#> Cellulose                 NA
#> S1 ctrl             0.000000
#> S1 7d               0.000000
#> S1 4d               0.000000
#> S2 ctrl             0.000000
#> S2 4d               0.000000
#> S2 6d               3.535534

The data of a BGF can be plotted with simplest methods:

plot(myBGF)

This plot is produced by the minimum data needed to set up a BGF, the accumulated exhaust gas volumes of each fermentation part of the BGF. Upon further processing, other parameters can be visualized using advanced plotting methods, such as plot_curve() or bgf_plot():

# plot the production
plot_curve(myBGF,production,reactor)

# plot the yield
bgf_plot(myBGF,type="yield_box")