Load a data specification file

ys_load(file, verbose = FALSE, ...)

ys_load_file(file, data_path = NULL, data_stem = NULL, verbose = FALSE, ...)

load_spec(...)

Arguments

file	name of yaml file containing specification
verbose	`logical`; print information to the console as the file is processed
...	other arguments to update `SETUP__`
data_path	optional path to data sets
data_stem	optional alternate stem for data files

Examples


sp <- ys_load(ys_help$file())
sp
#>  name  c d unit     short                         source           
#>  C     + + .        comment character             ysdb_internal.yml
#>  NUM   - - .        record number                 ysdb_internal.yml
#>  ID    - - .        subject identifier            ysdb_internal.yml
#>  SUBJ  + - .        subject identifier            ysdb_internal.yml
#>  TIME  - - hour     TIME                          .                
#>  SEQ   - + .        SEQ                           .                
#>  CMT   - - .        compartment number            ysdb_internal.yml
#>  EVID  - - .        event ID                      ysdb_internal.yml
#>  AMT   - - mg       dose amount                   ysdb_internal.yml
#>  DV    - - <<mugL>> dependent variable            ysdb_internal.yml
#>  AGE   - - years    age                           ysdb_internal.yml
#>  WT    - - kg       weight                        ysdb_internal.yml
#>  CRCL  - - ml/min   CRCL                          .                
#>  ALB   - - g/dL     albumin                       ysdb_internal.yml
#>  BMI   - - m2/kg    BMI                           ysdb_internal.yml
#>  AAG   - - mg/dL    alpha-1-acid glycoprotein     .                
#>  SCR   - - mg/dL    serum creatinine              .                
#>  AST   - - .        aspartate aminotransferase    .                
#>  ALT   - - .        alanine aminotransferase      .                
#>  HT    - - cm       height                        ysdb_internal.yml
#>  CP    - + .        Child-Pugh score              .                
#>  TAFD  - - hours    time after first dose         .                
#>  TAD   - - hours    time after dose               .                
#>  LDOS  - - mg       last dose amount              .                
#>  MDV   - - .        MDV                           ysdb_internal.yml
#>  BLQ   - + .        below limit of quantification .                
#>  PHASE - - .        study phase indicator         .                
#>  STUDY - + .        study number                  .                
#>  RF    + + .        renal function stage          .                

sp <- ys_load(ys_help$file(), verbose = TRUE)
#> ~ working on  ...  analysis1.yml 
#>   description ...  Example PopPK analysis data set. 
#>   sponsor     ...  example-project 
#>   lookup file ...  ysdb_internal.yml 
#> ~ working on  ...  ysdb_internal.yml 
#>   description ...  yspec internal column database 
#> ::::::::::::: ...  :::::::::::::::::::::::::::::: 
#> ~ looking up  ...  ysdb_internal.yml  --->  C 
#> ~ looking up  ...  ysdb_internal.yml  --->  NUM 
#> ~ looking up  ...  ysdb_internal.yml  --->  ID 
#> ~ looking up  ...  ysdb_internal.yml  --->  SUBJ 
#> ~ looking up  ...  ysdb_internal.yml  --->  CMT 
#> ~ looking up  ...  ysdb_internal.yml  --->  EVID 
#> ~ looking up  ...  ysdb_internal.yml  --->  AMT 
#> ~ looking up  ...  ysdb_internal.yml  --->  DV 
#> ~ looking up  ...  ysdb_internal.yml  --->  AGE 
#> ~ looking up  ...  ysdb_internal.yml  --->  WT 
#> ~ looking up  ...  ysdb_internal.yml  --->  ALB 
#> ~ looking up  ...  ysdb_internal.yml  --->  BMI 
#> ~ looking up  ...  ysdb_internal.yml  --->  HT 
#> ~ looking up  ...  ysdb_internal.yml  --->  MDV