add_bmp_measurement: Supportive data import functions

In bgfanalyzer: Analyze Microbial Biogas Fermentation Data

Supportive data import functions

Description

A set of internal functions that bridge the data import and object creation when using from_AMPTSV2_report or from_standard_record to create an BGF. These functions are not meant for direct user interaction.

Usage

add_bmp_measurement(x, path, mode = "auto", feedback = FALSE)

add_standard_record(
  x,
  path,
  header = TRUE,
  dec = ".",
  sep = "\t",
  units = "hours",
  time_col = "time",
  RName = "R1",
  product_col = "GCounter..ml.",
  feedback = TRUE
)

add_ExpPara(x, rawReport, feedback = FALSE)

add_ExpSetup(x, rawReport, feedback = FALSE)

sort_AMPTSV2_reactors(x, rawReport, feedback = FALSE)

sort_standardReport(x, rawReport, RName, product_col)

Arguments

x	a BGF
path	a path pointing to an external data file. Either a .csv-file generated by the AMPTS II (BioProcess Control; Lund; Sweden), or a text-file with at least biogas production (cumulative volume) and time data.
mode	the mode add_bmp_measurement treats the imported data at path. Currently only 'auto' and 'AMPTSV2' are the only implemented options.
feedback	logic; if TRUE the function will print a textual feedback to the console
header	logic; does the matrix like structure at path has a header
dec	a single character specifying the decimal separator
sep	a single character specifying the column separator
units	the desired unit of the time difference calculated by calc_FR_time
time_col	a character specifying the name of the column with time information in the external data file
RName	a character specifying the reactor name of the biogas fermentation to be added. Defaults to 'R1'
product_col	a character specifying the name of the column with the cumulative biogas volume data in the external data file
rawReport	either a list or a data.frame created by read_raw_AMPTSV2_report or import_standard_record, respectively.

Details

The function add_bmp_mesurement is called by from_AMPTSV2_report. It imports a .csv-file created by the AMPTS II (BioProcess Control; Lund; Sweden) from a location on the system specified in path and adds it to a BGF specified in x.

Internally, add_bmp_mesurement calls read_raw_AMPTSV2_report to import the external file to a list and then it calls add_ExpPara, add_ExpSetup and sort_AMPTSV2_reactors to transfer the data to the BGF.

The function add_standard_record is similar to add_bmp_measurement, put in this case path must point to an external text file with a matrix like data structure. This matrix must have at least two columns, one with information on when the measurement was recorded (time_col), the other with a cumulative biogas volume measurement (product_col). Additional columns can be present and will be imported as well.

Internally, add_standard_record calls import_standard_record to import the data and next it calls calc_FR_time to calculate a standardized fermentation time for the imported data set. Finally, it calls sort_standardReport to transfer the imported data to the BGF The function will not remove empty rows resulting from object creation within the BGF. Thus, it is advised to use update_BGF to ensure the integrity of the BGF.

The function add_ExpPara is called by add_bmp_measurement and acts as a wrapper for add_ExpParam to transfer experimental meta data to a BGF object. It expects a list created by read_raw_AMPTSV2_report as a second argument.

Similarly,the function add_ExpSetup is also called by add_bmp_measurement, but acts as a wrapper for add_metaData to transfer fermentation meta data to a BGF object. Consequently it also expects a list created by read_raw_AMPTSV2_report as a second argument.

In addition, sort_AMPTSV2_reactors is also called by add_bmp_measurement and acts as a wrapper for add_BG_measurement and alter_BG_measurement to transfer cumulative biogas volume and biogas flow data to a BGF. Like the former two functions, it expects a list generated via read_raw_AMPTSV2_report as second argument

Additional details...

Value

a BGF

Examples

# create an example BGF
myBGF <- BGF(ReactorLayout = c("2*Blank","Cellulose","3*neg ctrl","3*FR1","3*FR2","3*FR3"),
              name = "myBGF",
              ProcessTemp = 52,
              MeasurementType = "AMPTSV2")

myBGF # print the BGF

# add data from external files
myBGF <- add_bmp_measurement(
        x = myBGF,
        path = base::system.file("extdata","AMPTSV2.csv",package = "bgfanalyzer"))

myBGF # print the BGF

# create another example BGF
myBGF2 <- BGF("A")

myBGF2 # print the BGF

# add data from an external file (standard record)
myBGF2 <- add_standard_record(
        x = myBGF2,
        path = base::system.file("extdata","Fermentation_B.tsv",package = "bgfanalyzer"),
        RName = "R1",
        time_col = "UTC",
        product_col = "GCounter..ml.")

myBGF2 # print the BGF

# create an additional example BGF
myBGF3 <- BGF(c("2*Blank","Cellulose","3*neg ctrl","3*FR1","3*FR2","3*FR3"))

myBGF3 # print the BGF

# import standard record
rawReport <- read_raw_AMPTSV2_report(
        path = base::system.file("extdata","AMPTSV2.csv",package = "bgfanalyzer"))

# add experimental meta data to BGF
myBGF3 <- add_ExpPara(myBGF3,rawReport,TRUE)

myBGF3 # print the BGF

# add fermentation meta data to BGF
myBGF3 <- add_ExpSetup(myBGF3,rawReport,TRUE)

myBGF3 # print the BGF

# add biogas volume and flow data
myBGF3 <- sort_AMPTSV2_reactors(myBGF3,rawReport)

myBGF3 # print the BGF

# create an empty example BGF
myBGF4 <- BGF("myBGF4")

myBGF4 # print the BGF

# import a standard record
rawReport2 <- import_standard_record(
        ipath = base::system.file("extdata","Fermentation_B.tsv",package = "bgfanalyzer"))

# calculate a fermentaion/ observation time
rawReport2<-calc_FR_time(rawReport2,1,units="hours")

# add imported data to BGF
myBGF4 <- sort_standardReport(myBGF4,rawReport2,"R1",3)

myBGF4 # print BGF

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