How phenological/nmr-parser works
nmr.parser is an R package for reading Bruker IVDr NMR experiment folders into analysis-ready data. The main workflow optionally discovers experiment folders with scanFolder(), then readExperiment() coordinates parameter, spectrum, title, ERETIC, QC, lipoprotein, PACS, and small-molecule readers. Individual readers are also available, and extend_lipo() derives additional lipoprotein measures; reference-table functions expose metadata independently. The README documents these capabilities and relationships; source excerpts were unavailable, so internal wiring beyond the documented orchestration is not inferred.
Main entry points: readExperiment.R Experiment reader · scanFolder.R Folder scan · readLipo.R Lipoprotein reader · readParams.R Parameter readers
Components 19
Experiment discovery
- Folder scan
R/scanFolder.R - Experiment reader
R/readExperiment.R
Experiment readers
- Parameter readers
R/readParams.R - Single parameter
R/readParam.R - Spectrum reader
R/readSpectrum.R - Title reader
R/readTitle.R - ERETIC readers
R/readEretic.R - ERETIC F80
R/readEreticF80.R
Report readers
- QC reader
R/readQc.R - Lipoprotein reader
R/readLipo.R - PACS reader
R/readPacs.R - Quant reader
R/readQuant.R
Derived data
- Lipo derivation
R/extend_lipo.R - Reference tables
R/getLipoTable.R - PACS table
R/getPacsTable.R - QC table
R/getQcTable.R - Small molecule table
R/getSmTable.R
Other components
- R user
- Bruker files
Connections 24
- R user → Folder scan: requests scan
- Folder scan → Bruker files: searches folders
- Folder scan → Experiment reader: supplies paths
- R user → Experiment reader: requests read
- Experiment reader → Parameter readers: dispatches
- Experiment reader → Spectrum reader: dispatches
- Experiment reader → Title reader: dispatches
- Experiment reader → ERETIC readers: dispatches
- Experiment reader → ERETIC F80: dispatches
- Experiment reader → QC reader: dispatches
- Experiment reader → Lipoprotein reader: dispatches
- Experiment reader → PACS reader: dispatches
- Experiment reader → Quant reader: dispatches
- Bruker files → Parameter readers: reads
- Bruker files → Single parameter: reads
- Bruker files → Spectrum reader: reads
- Bruker files → Title reader: reads
- Bruker files → ERETIC readers: reads
- Bruker files → ERETIC F80: reads
- Bruker files → QC reader: reads
- Bruker files → Lipoprotein reader: reads
- Bruker files → PACS reader: reads
- Bruker files → Quant reader: reads
- Lipoprotein reader → Lipo derivation: derives measures