nlmixr2rpt (version 0.2.2)

build_figures: Generates Figures for an nlmixr2 Report

Description

Creates figures specified in a rptyaml file

Usage

build_figures(
  obnd = NULL,
  fit = NULL,
  rptdetails = NULL,
  cat_covars = NULL,
  cont_covars = NULL,
  verbose = TRUE
)

Value

List containing the figures with the following structure:

• "rptfigs" - List of figures with names corresponding to the figure ids in the yaml file. Each figure ID contains the following elements:

  • "figure" - list of figure file names for the current fid

  • "orientation" - Figure orientation ("portrait" or "landscape")

  • "isgood" - Boolean variable indicating success or failure

  • "skip" - Boolean variable indicating whether the figure should be skipped during reporting

  • "fmsgs" - Vector of messages

  • "cmd" - Original plot generation command

  • "cmd_proc" - Plot generation command after processing for placeholders

  • "height" - Figure height

  • "width" - Figure width

  • "caption" - Caption for Word

  • "caption_proc" - Caption for Word after processing for placeholders

  • "title" - Slide title for PowerPoint

  • "title_proc" - Slide title for PowerPoint after processing for placeholders

• "isgood" - Boolean variable indicating success or failure

• "msgs" - Vector of messages

Arguments

obnd

onbrand report object to have report elements appended to

fit

nlmixr2 fit object to be reported

rptdetails

Object created when reading in rptyaml file

cat_covars

character vector of categorical covariates to overwrite defaults in yaml file

cont_covars

character vector of continuous covariates to overwrite defaults in yaml file

verbose

Boolean variable when set to TRUE (default) messages will be displayed on the terminal

Examples

# We need an onbrand object to use below
library(onbrand)
obnd = read_template(
 template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
 mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

# We also need an nlmixr fit object
fit = fetch_fit_example()

# This reads in the report details as well
rptdetails = yaml_read_fit(
 obnd    = obnd,
 rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml"),
 fit     = fit)$rptdetails

# Now we will build the figures
bfres = build_figures(obnd       = obnd,
                     fit        = fit,
                     rptdetails = rptdetails)