Skip to contents

Generates Tables for an nlmixr2 Report

Source: R/build_tables.R
build_tables.Rd

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
# \donttest{
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)
#> 
#> ── Building report tables 
#> → pest_table
#> → bad_table
#> 
#> ── Table generation failed 
#> → Unable to generate table
#> →  -> call:    eval, parse(text = tinfo[["cmd_proc"]])
#> →  -> message: object 'bad_table_command' not found
#> → table id: bad_table
#> → command run:
#> → bad_table_command
#> → skip_table
# }