doc/nddspiro_format.md

In jipp3r/nddspiro.R: Extracts Spirometry Data From ndd XML Files

nddspiro output format

Details of the format of extracted data

General principles

Generally, data are extracted at 'Test' level from the ndd database. 'Trials' (the component parts of 'Tests') are returned as sets of columns in descending order of their 'Rank' (1 being the best). The 'Rank' is given to them either automatically, or as a result of user review in the ndd software. Each row therefore represents the results of a single test. The exception is that for tests which incorporate a 'Pre' and 'Post' stage (before and after reversibility testing, for example), each stage appears as a separate row.

Format

Columns within the dataframe describe the following details: nddTestID Character vector. ndd database internal (unique) identifier for the test. patientID Character vector. Entered by the user at the point of testing. nddPatientID Character vector. ndd database internal (unique) identifier for the patient. lastName Character vector. Entered by the user at the point of testing. firstName Character vector. Entered by the user at the point of testing. height Double. Height in meters, entered by the user at the point of testing. weight Double. Weight in kilograms, entered by the user at the point of testing. ethnicity Character vector with levels. Entered by the user at the point of testing. gender Character vector with 2 levels. Entered by the user at the point of testing. dob Date. Date of birth. Entered by the user at the point of testing. calcdob Logical. ndd parameter which is TRUE if date of birth has been calculated from age. testDate Date. Date of the test. testType Character vector with levels. ndd database identifier for type of test performed e.g. "MVV", "SVC", "DLCO", "FRC", "FVC" testStage Character vector with levels. ndd database identifier for stage of test e.g. "Pre", "Post", "Base", "Level" nddTrialID Character vector. ndd database internal (unique) identifier for the trial (which represents a single manoeuvre within a test). deviceID Character vector. ndd equipment (unique) identifier. age Double. Calculated age at the time of the test (years). PredictedSet Character vector. Identifies the reference range used by ndd software to generate lower limit of normal (lln) and predicted (pred) values for each measurement.

For each requested measure, 4 columns. Column titles are appended by "_1", "_2", "_3"... to indicate 1st, 2nd and 3rd... ranked trial. The number of trials given can be altered using the nddspiro.read(... traces=n) parameter.

[repeating block begins] measure_value Double. Values for given measure. measure_unit Character vector. Unit for given measure. measure_pred Double. Predicted value for given measure, based on the PredictedSet measure_lln Double. Lower limit of normal for given measure, based on the PredictedSet

[repeating block ends]

Optional- z scores based on GLI-2012 (Quanjer) references are given if requested using nddspiro-read(... add_gli=TRUE) parameter. Z scors represent the number of standard deviations from the predicted (population mean) value. Typically z=-1.64 (10th centile) is considered abnormal for spirometry. The given values are calculated from Rank=1 trial. gli_z_fev1 FEV1 z score gli_z_fvc FVC z score gli_z_fev1fvc FEV1/FVC z score gli_z_fef2575 FEF25-75 z score

ndd measurement identifiers

These can be passed to nddspiro.read() as a list, and may be one or more of: FEV1 FEV6 FVC FEV1_FVC PEFR FEF2575 FET BEV EOTV VCmax ...other measures according to ndd equipment*

jipp3r/nddspiro.R documentation built on May 27, 2019, 2 a.m.