build_tables: Generates Tables for an 'nlmixr2' Report

In nlmixr2rpt: Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results

Generates Tables for an nlmixr2 Report

Description

Creates tables specified in a rptyaml file

Usage

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

Arguments

obnd	onbrand report object to have report elements appended to
fit	nlmixr2 fit object to be reported
rptdetails	object creating 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

Value

List containing the tables with the following structure:

• "rpttabs" - List of tables with names corresponding to the table ids in the yaml file. It contains the elements from the yamle file and the following elements:

  • "table" - Result of build (t_res object)

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

  • "isgood" - Boolean variable indicating success or failure

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

  • "tmsgs" - Vector of messages

  • "cmd" - Original plot generation command

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

  • "height" - Table height

  • "width" - Table 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

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 tables 
btres = build_tables(obnd        = obnd,
                     fit        = fit, 
                     rptdetails = rptdetails)

nlmixr2rpt documentation built on June 7, 2023, 5:49 p.m.