Title:	Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results
Version:	0.2.1
Description:	This allows you to generate reporting workflows around 'nlmixr2' analyses with outputs in Word and PowerPoint. You can specify figures, tables and report structure in a user-definable 'YAML' file. Also you can use the internal functions to access the figures and tables to allow their including in other outputs (e.g. R Markdown).
URL:	https://nlmixr2.github.io/nlmixr2rpt/
BugReports:	https://github.com/nlmixr2/nlmixr2rpt/issues
License:	GPL (≥ 3)
Encoding:	UTF-8
RoxygenNote:	7.3.2
Imports:	cli, dplyr, flextable, ggforce, ggpubr, ggplot2, grDevices, stringr, nlmixr2est, nlmixr2extra (≥ 2.0.7), onbrand, rxode2, utils, xpose, xpose.nlmixr2, yaml
Suggests:	rmarkdown, ggPMX, knitr, testthat (≥ 3.0.0)
VignetteBuilder:	knitr
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2025-07-17 13:45:02 UTC; jmh
Author:	John Harrold [aut, cre]
Maintainer:	John Harrold <john.m.harrold@gmail.com>
Repository:	CRAN
Date/Publication:	2025-07-17 15:40:02 UTC

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
)

Arguments

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

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)

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

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)

Evaluate R Code in String

Description

Attempts to evaluate a string as a chunk of R code.

Usage

eval_str(estr = "", fit = NULL)

Arguments

Value

String containing the evaled as a character or the original string

Examples

res = eval_str(estr="ls()")

Gets Figure Dimensions

Description

For a given figure id and report type this will pull out the dimensions of the figure.

Usage

fetch_fdim(obnd = NULL, fid = NULL, fdim = "width", rptdetails = NULL)

Arguments

Value

ggplot object

Examples

library(onbrand)
obnd = read_template(
 template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
 mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

# This will create an example fit object to use in the examples below
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

fetch_fdim(obnd=obnd, fid="bad_figure", fdim="width", rptdetails=rptdetails)

fetch_fdim(obnd=obnd, fid="bad_figure", fdim="height", rptdetails=rptdetails)

Fetch Fit Example

Description

Creates an nlmixr2 fit example using posthoc estimation method for testing purposes. displayed on the terminal following:

Usage

fetch_fit_example(use_cache = TRUE)

Arguments

Value

Example nlmixr2 fit object

Examples

fit = fetch_fit_example()

Fetch Analysis Options

Description

Fetches analysis options from the report yaml applies it to strings.

Usage

fetch_option(rptdetails, option = NULL, fit = NULL, verbose = TRUE)

Arguments

Details

The option can be one of the following (default: NULL):

• "output_dir" - Directory to place figures that are generated (default: tempdir())

• "resolution" - Resolution of figure files (default: 300)

Value

List containing the following information about the output directory

• "isgood" - Boolean variable indicating success or failure

• "msgs" - Vector of messages

• "value" - The value of the option or the default if not specified

Examples

library(onbrand)
obnd = read_template(
 template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
 mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

# This will create an example fit object to use in the examples below
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


fetch_option(rptdetails, option="output_dir", fit=fit)

Makes nlmixr2 Parameter Estimate Table for Reporting

Description

Generates a flextable containting the parameter estimates.

Usage

gen_pest_table(obnd = NULL, fit = NULL, rptdetails = NULL, verbose = TRUE)

Arguments

Value

List with the following elements

• "isgood" - Boolean variable indicating success or failure

• "msgs" - Vector of messages

• "ft" - Parameter estimates as a flextable object

• "df" - Parameter estimates as a data.frame

Examples

library(onbrand)  
obnd = read_template(
 template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
 mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

# This will create an example fit object to use in the examples below
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

gen_pest_table(obnd = obnd, fit = fit, rptdetails = rptdetails, verbose = TRUE)

Generates ggplot Object with Error Message

Description

Takes a vector of messages and returns a ggplot object with the text in the figure. This can be used in automated figure generation to cascade an error message to the end user.

Usage

mk_error_fig(msgs)

Arguments

Value

ggplot object

Examples

mk_error_fig("This is an error")

Generates a flextable Object with Error Message

Description

Takes a vector of messages and returns a flextable object with the text in the table. This can be used in automated table generation to cascade an error message to the end user.

Usage

mk_error_tab(msgs)

Arguments

Value

list with a single flextable object

Examples

error_tab = mk_error_tab("This is an error")
error_tab$ft[[1]]

Substitutes Placehodlers in Strings

Description

Takes placeholder information from the rptyaml file and applies it to strings.

Usage

process_ph(str, rptdetails)

Arguments

Value

processed string

Examples

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

str = "This is ===CMPD==="

process_ph(str, rptdetails)

Report nlmixr2 Fit Results to PowerPoint and Word

Description

Appends nlmixr2 fit results to an onbrand report object with the content and format of the report in the supplied yaml file

Usage

report_fit(
  obnd = NULL,
  fit = NULL,
  placeholders = NULL,
  cat_covars = NULL,
  cont_covars = NULL,
  parameters = NULL,
  rptyaml = system.file(package = "nlmixr2rpt", "templates", "report_fit.yaml"),
  verbose = FALSE
)

Arguments

Value

onbrand object with the report elements added.

Examples

library(onbrand)
obnd = read_template(
 template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
 mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

# This will create an example fit object to use in the examples below
fit = fetch_fit_example()

# Appening fit results
obnd_pptx = report_fit(
 fit     = fit,
 rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml"),
 obnd    = obnd)

# Writing the report to a file
save_report(obnd, file.path(tempdir(), "report.pptx"))

Writes Figures to File

Description

Takes a figure object, optionally stamps the image, and writes to a file dimensions of the figure.

Usage

write_figure(
  p_res = NULL,
  page = NULL,
  width = 3,
  height = 3,
  resolution = NULL,
  fig_file = NULL,
  fig_stamp = NULL,
  verbose = TRUE
)

Arguments

Value

list with the following

• "isgood" - Boolean variable indicating success or failure

• "msgs" - Vector of messages

Examples

library(ggplot2)
write_figure(
 p_res = ggplot(),
 page = NULL,
 width = 3,
 height = 3,
 resolution = 200,
 fig_file = file.path(tempdir(), "write_figure_example.png"),
 fig_stamp = "stamp",
 verbose = TRUE)

Reads and Checks report_fit.yaml File

Description

Reads in the report yaml file and looks it to make sure it has all the necessary fields for the given report.

Usage

yaml_read_fit(
  obnd = NULL,
  rptyaml = NULL,
  placeholders = NULL,
  parameters = NULL,
  fit = NULL
)

Arguments

Value

List containing the following information about the report

• "isgood" - Boolean variable indicating success or failure

• "msgs" - Vector of messages

• "rpttype" - Type of onbrand report ("Word" or "PowerPoint")

• "rptfigfmt" - Default figure formatting (orientation and dimensions)

• "rpttabfmt" - Default table formatting (orientation and dimensions)

• "rptdetails" - Contents of the yaml file

• "rptcont" - Contents of the report to generate

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
yaml_read_res = yaml_read_fit(
 obnd    = obnd,
 rptyaml = system.file(package="nlmixr2rpt", "examples", "report_fit_test.yaml"),
 fit     = fit)