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Accessing Figures and Tables

Source: vignettes/Accessing_Figures_and_Tables.Rmd
Accessing_Figures_and_Tables.Rmd

Introduction

When you create the report_fit.yaml file you have defined figures and tables for reporting. However you may want to reuse these report objects outside of Word and PowerPoint. For example you may want to use them inside of Shiny Apps or in RMarkdown document. This vignette outlines how you can build the objects outside of the nlmixr2rpt workflow.

Creating figures and tables

First we need to load the appropriate libraries. We need the onbrand library because the tables and figures are generated based on the type of report. Specifically default figure dimensions will change based on the report type. Here we initialize an empty Word report with onbrand. The report type is extracted from this object in the functions below.

library(nlmixr2rpt)
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"))

You should have an nlmixr2 fit object from your own analysis. We will load an example from this package.

Next we read in the yaml file using yaml_read_fit(). Below we are using a stripped down example for testing. The contents of the yaml file are stored in the rptdetails list element that is returned.

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

Now we can use the rptdetails object we just created to create the figures and tables using the build_figures() and build_tables() functions respectively.


bfres = build_figures(obnd       = obnd,
                      fit        = fit, 
                      rptdetails = rptdetails)

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

Using report objects in RMarkdown

You can look at the help for the two build functions above. Each of the objects they create should contain all of the information about figures and tables defined in the report_fit.yaml file. To access a figure you just need to specify the figure ID. For example the path and title of the figure containing the dv_vs_pred figure can be found here:

fig_path  = bfres$rptfigs$dv_vs_pred$figure[[1]]
fig_title = bfres$rptfigs$dv_vs_pred$title_proc

And you can include them in RMarkdown using the following:

![`r fig_title`](`r fig_path`){width=80%}
dv_vs_pred title
dv_vs_pred title

Tables are used in a similiar fashion. This code will extract the flextable object and title for the pest_table. Then it attaches the title as a caption and displays it below.

tab_ft    = btres$rpttabs$pest_table$table$ft[[1]]
tab_title = btres$rpttabs$pest_table$title_proc
tab_ft_knit = flextable::set_caption(tab_ft, caption = tab_title)

tab_ft_knit
Parameter Estimates

Parameter

Est.

SE

%RSE

Back-transformed(95%CI)

BSV(CV%)

Shrink(SD)%

Log Ka

0.476

0.203

42.7

1.61 (1.08, 2.39)

69.8

1.23%<

Log Cl

1.02

0.0754

7.42

2.76 (2.38, 3.2)

26.1

2.36%<

Log V

3.46

0.0632

1.83

31.8 (28.1, 36)

13.8

9.71%<

add.sd

0.696

0.696