Example yaml specification file

2022-05-19

This is an example data specification document. See the [ys_help] topic for help browsing this document and for other example assets with which you can practice.

This file is located in inst/internal/analysis1.yml.

CONTENTS

SETUP__:
  description: Example PopPK analysis data set
  sponsor: example-project
  projectnumber: EXAMPK1011F
  use_internal_db: true
  glue: 
    bmiunits: "kg/m$^2$"
  flags: 
    covariate: [AGE:SCR, HT, AST:ALT]
  lookup_file: "look.yml"
  extend_file: "analysis1-ext.yml"
C:
NUM:
ID:
SUBJ: !look
TIME: !look
  label: time after first dose
  unit: hour
SEQ: 
  label: data type
  values: {observation: 0, dose: 1}
CMT:
EVID:
  make_factor: true
  lookup: true
AMT: !look
  unit: mg
DV:  !look
  unit: "micrograms/L"
  unit.tex: "$\\mu$g/L"
AGE: !look
  range: [18,50]
WT: !look
  range: [40,100]
  dots: {time_varying: true} 
CRCL:
  label: creatinine clearance
  unit: ml/min
  range: [15,150]
  dots: {time_varying: true}
ALB: !look
  range: [1.2,6]
BMI: !look
  range: [18,25]
  unit.tex: <<bmiunits>>
AAG:
  short: alpha-1-acid glycoprotein
  unit: mg/dL
  range: [50,120]
SCR: 
  about: [serum creatinine, mg/dL]
  range: [0.7,6]
AST:
  short: aspartate aminotransferase
  range: [10,36]
ALT: 
  short: alanine aminotransferase
  range: [10,35]
HT: !look
  range: [140, 222]
  unit: cm
CP: !look 
  short: Child-Pugh score
  values: {normal: 0, Pugh1: 1, Pugh2: 2, Pugh3: 3}
  dots: {updated_from_lookup: false} # these dots used in tests
TAFD:
  short: time after first dose
  unit: hours
  dots: {timecol: true}
TAD:
  about: [time after dose, hours]
  dots: {timecol: true}
LDOS:
  short: last dose amount
  unit: mg
MDV:
BLQ:
  short: below limit of quantification
  values: 
    above QL: 0
    below QL: 1
PHASE: 
  short: study phase indicator
  values: 1
  dots: {categorical: true}
STUDY: 
  short: study number
  values: {SAD: 1, MAD: 2, Renal: 3, Hepatic: 4}
RF: 
  short: renal function stage
  values: {Normal: norm, Mild: mild, Moderate: mod, Severe: sev}