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Backfill utility for descriptions

Source: R/utils.R
desc_from_comments.Rd

A slightly more generic approach to getting model descriptions.

Usage

desc_from_comments(
  xpdb,
  start_check = ".*description",
  maxlines = 5,
  remove = paste0(start_check, ":\\s*"),
  extra_proc = c,
  collapse = " "
)

Arguments

xpdb

<xpose_data> or <xp_xtras> object

start_check

Regular expression used to mark start of description. This is tested case-insensitively.

maxlines

If the number of lines after description to the first code block is more than 1, this allows a limit.

remove

By default, the start check and a colon, with optional whitespace. A regex.

extra_proc

Any extra processing that might be desired prior to collapsing the description lines. This should be a vectorized function.

collapse

Character to use when collapsing multiple lines.

Value

The description-updated <xpose_data) object

See also

set_prop()

Examples


# This has a description, but it's not visible by default
pheno_base
#> 
#> ── ~ xp_xtras object 
#> Model description: na
#> run6.lst overview: 
#>  - Software: nonmem 7.5.0 
#>  - Attached files (memory usage 495.2 Kb): 
#>    + obs tabs: $prob no.1: run6tab 
#>    + sim tabs: <none> 
#>    + output files: run6.cor, run6.cov, run6.ext, run6.grd, run6.phi, run6.shk 
#>    + special: <none> 
#>  - gg_theme: theme_readable 
#>  - xp_theme: xp_xtra_theme new_x$xp_theme 
#>  - Options: dir = ~/Step 3/Step 5/Step 6, quiet = FALSE, manual_import = NULL, cvtype = exact

# It can be added with the following
pheno_base %>%
  desc_from_comments()
#> 
#> ── ~ xp_xtras object 
#> Model description: Final structural version of the model: 1 CMT Block IIV on
#> CL+V Add Error
#> run6.lst overview: 
#>  - Software: nonmem 7.5.0 
#>  - Attached files (memory usage 495.4 Kb): 
#>    + obs tabs: $prob no.1: run6tab 
#>    + sim tabs: <none> 
#>    + output files: run6.cor, run6.cov, run6.ext, run6.grd, run6.phi, run6.shk 
#>    + special: <none> 
#>  - gg_theme: theme_readable 
#>  - xp_theme: xp_xtra_theme new_x$xp_theme 
#>  - Options: dir = ~/Step 3/Step 5/Step 6, quiet = FALSE, manual_import = NULL, cvtype = exact

# Extra processing for preference can also implemented
pheno_base %>%
  desc_from_comments(extra_proc = tolower)
#> 
#> ── ~ xp_xtras object 
#> Model description: final structural version of the model: 1 cmt block iiv on
#> cl+v add error
#> run6.lst overview: 
#>  - Software: nonmem 7.5.0 
#>  - Attached files (memory usage 495.4 Kb): 
#>    + obs tabs: $prob no.1: run6tab 
#>    + sim tabs: <none> 
#>    + output files: run6.cor, run6.cov, run6.ext, run6.grd, run6.phi, run6.shk 
#>    + special: <none> 
#>  - gg_theme: theme_readable 
#>  - xp_theme: xp_xtra_theme new_x$xp_theme 
#>  - Options: dir = ~/Step 3/Step 5/Step 6, quiet = FALSE, manual_import = NULL, cvtype = exact

# If a run label ($PROB) would make a good description, use the
# following instead:
pkpd_m3 %>%
  set_prop(descr=get_prop(pkpd_m3,"label"))
#> 
#> ── ~ xp_xtras object 
#> Model description: Simulated PKPD
#> run.lst overview: 
#>  - Software: nonmem 7.5.0 
#>  - Attached files (memory usage 1.6 Mb): 
#>    + obs tabs: $prob no.1: output.fit, pars.fit 
#>    + sim tabs: <none> 
#>    + output files: run.cor, run.cov, run.ext, run.grd, run.phi, run.shk 
#>    + special: <none> 
#>  - gg_theme: theme_readable 
#>  - xp_theme: xp_xtra_theme new_x$xp_theme 
#>  - Options: dir = ~/pkpdm3, quiet = FALSE, manual_import = NULL, cvtype = exact