Package: bgfanalyzer 1.1.0

Maximilian Strick

bgfanalyzer: 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) <doi:10.1115/ES2018-7553>). 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) <doi:10.1016/j.softx.2018.06.005> 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) <doi:10.2166/wst.2016.336> and Hollinger et al. (2021) <doi:10.2166/wst.2020.569>.

Authors:Maximilian Strick [aut, cre, cph]

bgfanalyzer_1.1.0.tar.gz
bgfanalyzer_1.1.0.zip(r-4.7-any)bgfanalyzer_1.1.0.zip(r-4.6-any)
bgfanalyzer_1.1.0.tar.gz(r-4.7-any)bgfanalyzer_1.1.0.tar.gz(r-4.6-any)
bgfanalyzer_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bgfanalyzer/json (API)

# Install 'bgfanalyzer' in R:
install.packages('bgfanalyzer', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.30 score 58 exports 66 dependencies

Last updated from:c1ebb89295. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK159
source / vignettesOK214
linux-releaseOK152
windows-develOK95
windows-releaseOK107
wasm-releaseOK131

Exports:add_BG_measurementadd_BG_parameteradd_bmp_measurementadd_ExpParaadd_ExpParamadd_ExpSetupadd_metaDataadd_standard_recordadd_whateveralter_BG_measurementalter_whateverBGFbgf_interpolationbgf_plotboxplot_yieldcalc_FR_timecalc_inoc_matrix_from_metaDatacalc_yieldcalculate_flow_from_volumeclose_gapscolplot_yieldcols_to_numericcorrect_RLayoutfrom_AMPTSV2_reportfrom_standard_recordget_BlankLabelget_blanksget_Excludedget_layerget_MeasurementTypeget_ReactorLayoutget_whateverget_yield_summaryimport_BGF_objectimport_standard_recordmerge_BGFna_correctionnetGasnetGasGCnew_BGFplot_curveplot_netProduct_by_Layoutplot_product_curveplot_production_curveplot_rel_production_curveread_raw_AMPTSV2_reportrelative_productionsave_BGFsave_BioGasDatasave_ExpParamsave_metaDatasort_AMPTSV2_reactorssort_standardReportsubset_BGFsummarize_yieldtrim_FR_timeupdate_BGFvalidate_BGF

Dependencies:askpassbase64encbslibcachemclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyamlzoo

Creating a BGF from a Commercial Fermentation System
Whats this vignette is about | The 'AMPTSV2'-type BGF | Background | The commercial fermentation system | The CFS Workflow | BGF subsetting | Behind the scenes | Step 1: Object creation | Step 2: Adding data | Step 3: Data correction | Step 4: net gas calculation | Step 5: calculate relative production | Step 6: yield calculation and summary

Last update: 2026-09-26
Started: 2026-09-26

Creating a BGF from a Custom Fermentation System
Whats this vignette is about | Background | Object creation | Adding additional data to BioGasData-layer | NA removal through data inter- and extrapolation | Further data processing | Adding further fermentations | Same reactor layout | Different reactor layout

Last update: 2026-09-26
Started: 2026-09-26

Creating a BGF without Input Files
What this vignette is about | Setting up a manual BGF | Modify ExpParam | Modify metaData | Modify BioGasData | manual BGF's allow max flexibility

Last update: 2026-09-26
Started: 2026-09-26

Introducing the bgfanalyzer Package
Introduction | Background - A Microbial Biogas Fermentation | The BGF Concept | BGF structure | Building a BGF | Visualizing fermentation data | The product curve | The net product per layout curve | The production curve | The relative production curve | yield plots | Further information

Last update: 2026-09-26
Started: 2026-09-26

Readme and manuals

Help Manual

Help pageTopics
Supportive data import functionsadd_bmp_measurement add_ExpPara add_ExpSetup add_standard_record sort_AMPTSV2_reactors sort_standardReport
Add data to a 'BGF'add_BG_measurement add_BG_parameter add_ExpParam add_metaData add_whatever
Alter data within a 'BGF'alter_BG_measurement alter_whatever
Helper to set up a 'BGF' objectBGF from_AMPTSV2_report from_standard_record
The default color set to be used by 'bgf_plot'BGF_defaultcolors
Data interpolation algorithmbgf_interpolation
Advanced 'BGF' visualizationbgf_plot boxplot_yield colplot_yield plot_curve plot_netProduct_by_Layout plot_production_curve plot_product_curve plot_rel_production_curve
Calculate Fermentation Timecalc_FR_time
Calculate an inoculation matrixcalc_inoc_matrix_from_metaData
Data transformation functionscalculate_flow_from_volume calc_yield relative_production summarize_yield
Close gaps in dataclose_gaps na_correction
Data correction functionscols_to_numeric correct_RLayout
Extract information from a BGFget_BlankLabel get_blanks get_Excluded get_layer get_MeasurementType get_ReactorLayout get_whatever get_yield_summary
Data import functionsimport_BGF_object import_standard_record read_raw_AMPTSV2_report
A data set resulting from a lab scale biogas fermentationLabscaleBiogas
The reactor layout of the lab scale biogas exampleLabscaleBiogasLayout
Calculate the net product gasnetGas netGasGC
Constructor to set up a Bio Gas Fermentation objectnew_BGF
Plot a Biogas Fermentationplot.BGF
Print a Biogas Fermentationprint.BGF
Save a 'BGF' to an external filesave_BGF save_BioGasData save_ExpParam save_metaData
Split or merge 'BGF''smerge_BGF subset_BGF
Re-orientate fermentations of a 'BGF' by timetrim_FR_time
Validation of data integrityupdate_BGF validate_BGF