Read and parse a glossary file

Files may be formatted as TeX glossary file or in yaml format suitable for reading using yaml_as_df() (see details).

read_glossary(file, format = guess_glo_fmt(file))

Arguments

file

path to the tex or yaml glossary file.

format

the glossary file format; could be either "tex" or "yaml" and will be inferred by default from the extension of file.

Value

A named list of glossary definitions with class tex_glossary and glossary. The list names are acronym entry labels (i.e., what you would pass to \gls{} when writing a tex document).

Details

For the tex format, the glossary file is expected to contain acronym entries with the form

\newacronym{label}{abbreviation}{definition}

or

\newacronym[options]{label}{abbreviation}{definition}

For the yaml format, the glossary file is expected to be able to be read with yaml_as_df(); the outer level should be the label and columns should be provided with the names def (definition) and abb (abbreviation). See Examples.

See also

as_glossary()

Examples

texfile <- system.file("glo", "glossary.tex", package = "pmtables")

x <- read_glossary(texfile)

head(x)
#> ADA   : anti-drug antibodies
#> AE    : adverse event
#> AIC   : Akaike information criterion
#> ALAG  : oral absorption lag time
#> ASCII : American Standard Code for Information I...
#> AST   : aspartate transaminase

x$WT
#> subject weight (WT)

x$SC
#> subcutaneous (SC)

yamfile <- system.file("glo", "glossary.yaml", package = "pmtables")

y <- read_glossary(yamfile)
head(y)
#> egfr : estimated glomerular filtration rate
#> bmi  : body mass index
#> wt   : weight
#> ht   : height
#> cmax : maximum concentration in the dosing inte...
#> cmin : minimum concentration in the dosing inte...

# Format of the tex glossary file
head(readLines(texfile))
#> [1] "%%%%%%%%% A"                                                                   
#> [2] "\\newacronym{ADA}{ADA}{anti-drug antibodies}"                                  
#> [3] "\\newacronym{AE}{AE}{adverse event}"                                           
#> [4] "\\newacronym{AIC}{AIC}{Akaike information criterion}"                          
#> [5] "\\newacronym{ALAG}{ALAG}{oral absorption lag time}"                            
#> [6] "\\newacronym{ASCII}{ASCII}{American Standard Code for Information Interchange}"

# Format of the yaml glossary file
head(readLines(yamfile))
#> [1] "egfr:"                                      
#> [2] "  def: estimated glomerular filtration rate"
#> [3] "  abb: eGFR"                                
#> [4] "bmi:"                                       
#> [5] "  def: body mass index"                     
#> [6] "  abb: BMI"                                 

yaml_as_df(yamfile)
#> # A tibble: 7 × 3
#>   .row  def                                          abb  
#>   <chr> <chr>                                        <chr>
#> 1 egfr  estimated glomerular filtration rate         eGFR 
#> 2 bmi   body mass index                              BMI  
#> 3 wt    weight                                       WT   
#> 4 ht    height                                       HT   
#> 5 cmax  maximum concentration in the dosing interval Cmax 
#> 6 cmin  minimum concentration in the dosing interval Cmin 
#> 7 auc   area under the concentration time curve      AUC