build_figures {nlmixr2rpt} | R Documentation |
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
obnd |
|
fit |
|
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 |
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)