netGas: Calculate the net product gas
In bgfanalyzer: Analyze Microbial Biogas Fermentation Data

netGas

R Documentation

Calculate the net product gas

Description

Two functions that allow to calculate the net amount of biogas produced by fermentations in a BGF. Both allow to subtract the amount of gas produced by blanks from fermentations, but differ in the way the netGas is calculated and also in the experimental data they need as input.

Usage

netGas(x, purity = 1, substract_blank = TRUE, pos = 7, feedback = FALSE)

netGasGC(
  x,
  purity,
  percent = TRUE,
  substract_blank = TRUE,
  pos = 7,
  na_replace = 0,
  feedback = FALSE
)

Arguments

`x`	a `BGF`
`purity`	either a `numeric` indicating the assumed purity (0 - 1) of the product gas for `netGas`, or a `character` or an `integer` referencing the column providing gas quality measurements in the `BioGasData` layer of a `BGF`.
`substract_blank`	`logic`; default is `TRUE`. Should the mean product volume produced by blanks be subtracted from fermentations? Fermentations classified as Blanks must exist in the `BGF` (`BGF$metaData$Blank==TRUE`).
`pos`	an `integer` indicating where the mass amounts of blanks in each fermentation are stored (see Note)
`feedback`	`logic`, default is `FALSE`; If `TRUE`, the function will print a feedback to the console
`percent`	`logic`; default is `TRUE`. Are the values in the column referenced by the 'purity' argument in percent or in an interval from 0 to 1?
`na_replace`	a `numeric`. The default assumed concentration of target gas at the beginning of the fermentation.

Details

The function netGas uses the 'product' column of the BioGasData layer of a BGF to calculate the 'net_product' and can be used if no gas quality measurements are available. When called, it uses the same assumed purity of the product gas for blanks and fermentations. The expected use case is the analysis of AMPTS II generated data, where a methane concentration of 100 vol.% can be assumed due to CO2 absorption units of that system.

The function netGasGC uses the 'production' column instead of the 'product' column to calculate the 'net_product' column of the BioGasData layer of a BGF. It furthermore needs a column providing gas quality measurements added to the BioGasData layer.

Value

a BGF

Note

To be able of subtracting the amount of gas produced by blank fermentations from the other fermentations, it is essential to provide the information of how much blank was used to inoculate each fermentation. If this information is not known, it can be deduced from the inoculum to substrate ratio and the working load (mass or volume) of the fermentation.

Examples

# create an example BGF
myBGF <- BGF(
        ReactorLayout = c("2*Blank","Cellulose","2*S1 ctrl","2*S1 7d","2*S1 4d",
                          "2*S2 ctrl","2*S2 4d","2*S2 6d"),
        BlankLabel = "Blank",
        name = "myBGF",
        ProcessTemp = 42,
        MeasurementType = "AMPTSV2")

# add data generated by an AMPTS II
myBGF <- add_bmp_measurement(
        x = myBGF,
        path = base::system.file("extdata","AMPTSV2.csv",package ="bgfanalyzer"))

# convert data columns
myBGF <- cols_to_numeric(myBGF)

# close gaps in data
myBGF <- close_gaps(myBGF)

# calculate netGas
myBGF <- netGas(myBGF)

# create a second example BGF
myBGF2 <- from_standard_record(
        ReactorLayout = "A",
        ProcessTemp = 80,
        InocToSubRatio = .1,
        path = base::system.file("extdata","Fermentation_A.tsv",package ="bgfanalyzer"),
        time_col = 1,
        product_col = 3)

# import gas quality data
gasq <- import_standard_record(
      ipath = base::system.file(
              "extdata",
              "gasq_A.tsv",
              package ="bgfanalyzer"),
      mkFRTime = "2025-01-15 17:00:00",
      FRTime_col = 1,
      units = "hours")

# add gas quality data to
myBGF2 <- add_BG_parameter(myBGF2,gasq,"R1",3,2,name = "H2",cut_zero = TRUE)

# ensure data integrity
myBGF2 <- update_BGF(myBGF2)

# correct NA's
myBGF2 <- na_correction(myBGF2)

# calculate production
myBGF2 <- calculate_flow_from_volume(myBGF2)

# calculate net gas based on production
myBGF2 <- netGasGC(myBGF2,substract_blank = FALSE,purity = "H2")

bgfanalyzer documentation built on Sept. 26, 2026, 5:07 p.m.