add_whatever: Add data to a 'BGF'

In bgfanalyzer: Analyze Microbial Biogas Fermentation Data

Add data to a BGF

Description

A set of functions to add data to each layer of a BGF.

Usage

add_whatever(x, layer, what, lab = "newData", feedback = FALSE)

add_ExpParam(x, what, feedback = FALSE)

add_metaData(x, what, makeCol = TRUE, lab = "newData", feedback = FALSE)

add_BG_measurement(x, reactor, time, col, measurement, feedback = FALSE)

add_BG_parameter(
  x,
  parameter,
  reactor,
  time = NULL,
  value = NULL,
  name = NULL,
  makeCol = TRUE,
  cut_zero = TRUE,
  interpolate_missing = TRUE,
  default_start = 0
)

Arguments

x	a BGF
layer	a character referring a layer of a BGF; either 'ExpParam' or 'metaData'
what	a character referring either to a list entry of the ExpParam layer, or a column of the metaData layer of a BGF
lab	a character providing the name for the new data
feedback	logic, if TRUE the function will print a feedback to the R console
makeCol	logic, default is TRUE. Should a new column be created? If FALSE the data will be added to an existing column named name
reactor	a character referring to a reactor/ fermentation of a BGF; in case of add_BG_parameter must have the same length as 'parameter'. If 'parameter' is a data.frame 'reactor' must have length 1 and specifies the reactor the measurements belong to
time	for add_BG_measurement, a numeric specifying the time that has passed since fermentation start; for add_BG_parameter either a integer indicating the position of the 'time' column in argument 'parameter' or a numeric of the same length as argument 'parameter' specifying the time that has passed since fermentation start (see Details)
col	either a character or numeric referring to an existing column of the BioGasData layer of a BGF
measurement	a numeric; measurement value to be added to the BioGasData layer of a BGF
parameter	either a data.frame with at least two columns or a numeric carrying the data to be added
value	defaults is NULL; must be an integer referring to the measurement data column in 'parameter' if 'parameter' is a data.frame
name	defaults is NULL; can be a character specifying the label of the new column being created in the BioGasData layer of a 'BGF“'
cut_zero	logic, default is TRUE. If FALSE measurements with a negative time (measurements that were acquired before the fermentation started) will NOT be removed from BioGasData
interpolate_missing	logic, default is TRUE. Indicating if missing values between to measurements should be interpolated
default_start	a numeric, a default measurement value that is assumed in the begin of the fermentation for the parameter to be added

Details

There are five functions that can be useful to add data to BGF. The first is add_whatever, which allows to add data either to the ExpParam or the metaData layer of a BGF. The functions add_ExpParam and add_metaData are wrapper functions that internally call add_whatever with the 'layer'

For add_ExpParam argument 'what' is expected to be a named vector of length 1. The name of the vector will be kept as label of a list entry in the ExpParam layer and the vectors value will be the value of that list entry.

For add_metaData argument 'what' is expected vector of the same length as number of rows in the metaData layer. It will copy that vector to the metaData layer as a new column. That column can be named using the 'lab' argument. Otherwise a standard name is created. The function checks if the chosen name already exists in metaData and will eventually generate a new name.

The function add_BG_measurement adds a single measurement value to an existing column of the BioGasData layer. To this end the user must specify to which reactor of the BGF the measurement belongs to (argument 'reactor') and at which time the measurement was taken (argument 'time'). The argument 'col' is the name or position of the column in the BioGasData layer to which the measurement should be added.

The function add_BG_parameter allows to add a new data column to the BioGasData layer of a BGF. It is very useful if not all measurements for a fermentation can be imported from the same standard record, e.g. if exhaust gas volumes are measured by one device, while the gas composition is registered by another.

Value

a BGF

Examples

# create an example BGF
myBGF <- from_AMPTSV2_report(
        ReactorLayout = c("2*Blank","Cellulose","3*neg ctrl","3*FR1","3*FR2","3*FR3"),
        BlankLabel = "Blank",
        name = "Test",
        InocToSubRatio=2,
        ProcessTemp = 52,
        path = base::system.file("extdata","AMPTSV2.csv",package = "bgfanalyzer")
        )

# add a start date to 'ExpParam'
myBGF <- add_whatever(myBGF,"ExpParam",what = c("Start date"="2026-05-04 12:00:00"))

# add organic total solutes measurements to 'metaData'
myBGF <- add_whatever(
        x = myBGF,
        layer = "metaData",
        what = c("oTS"=c(2.3,2.3,98.8,4.5,4.4,4.6,3.5,3.6,3.5,3.8,3.9,4,3.5,3.6,3.8))
        )

# add a end date to 'ExpParam'
myBGF<-add_ExpParam(x = myBGF,what =  c("End date"="2026-06-04 12:00:00"))

# add total solutes measurement to 'metaData'
myBGF<-add_metaData(
        x = myBGF,
        what =  c(3.3,3.3,99.8,6.5,6.6,6.6,6.5,6.6,6.5,6.8,6.9,6,6.5,6.6,6.8),
        lab="TS")

# add a new 'product' gas measurement for reactor 'R1' at time '49' (days) after fermentation start
myBGF<-add_BG_measurement(x = myBGF,reactor = "R1",time = 49,col = "product",measurement = 7777)

# create a second example BGF from a standard record with exhaust gas data
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 another standard record that provides additional information on the 'BioGasData' layer
Gas_comp<-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 the gas composition data to the BGF and interpolate missing values
myBGF2<-add_BG_parameter(
        x = myBGF2,
        parameter = Gas_comp,
        reactor = "R1",
        time = 3,
        value = 2,
        name = "H2",
        cut_zero = TRUE,
        interpolate_missing = TRUE)

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