pmx_report: Generates ggpmX report from a pre-defined template

In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

Generates ggpmX report from a pre-defined template

Description

Generates ggpmX report from a pre-defined template

Usage

pmx_report(
  contr,
  name,
  save_dir,
  plots_subdir = "ggpmx_GOF",
  output = c("all", "plots", "report"),
  template = "standing",
  footnote = output == "all",
  edit = FALSE,
  format = NULL,
  title,
  ...
)

Arguments

contr	pmxClass controller
name	character The report name
save_dir	Output directory. A directory to write the results files to
plots_subdir	Output folder name, ggpmx_GOF by default
output	character the result type, can be a standalone directory of plots or a report document as defined in the template (pdf, docx,..) ,or both
template	character ggPMX predefined template or the path to a custom rmarkdown template. Use pmx_report_template to get the list of available templates
footnote	logical TRUE to add a footnote to the generated plots. The default footnote is to add the path where the plot is saved.
edit	logical TRUE to edit the template immediately
format	character The output document format. By default, a word report is generated. User can specify one or more formats from c("word","pdf","html","all"). format "all" to generate all formats.
title	character report title (optional)
...	extra parameters depending in the template used

Details

pmx_report uses pre-defined template .Rmd to generate the report. The idea is to pass the controller as a report argument using knitr params artifact.

Examples

library(ggPMX)
# you probably want to create the report in your own directory
# But using a temp directory allows for easy cleanup

## case1: generate a single report
withr::with_tempdir({
  ctr <- theophylline()
  ctr %>% pmx_report(
    name = "my_report",
    save_dir = getwd(),
    output="report"
  )
})


## case2: generate standalone plots
withr::with_tempdir({
  ctr <- theophylline()
  ctr %>% pmx_report(
    name = "my_report",
    save_dir = getwd(),
    output="plots"
  )
})


## case3: generate both : reports + plots
## by default add footnote
## Note, you can force footnote to FALSE using footnote parameter
withr::with_tempdir({
  ctr <- theophylline()
  ctr %>% pmx_report(
    name="my_report",
    save_dir=getwd(),
    output="all"
  )
})


## case4 : generate standalone plots with footnotes
withr::with_tempdir({
  ctr <- theophylline()
  ctr %>% pmx_report(
    name="my_report",
    save_dir=getwd(),
    footnote=TRUE,
    output="plots"
  )
})


##  case6: dynamic edit
## uncomment to run
# ctr <- theophylline()
# ctr %>% pmx_report(
#   save_dir = file.path(getwd(),"case6"),
#   name="my_report",
#   output="report",
#   edit = TRUE)


## case7 : generate individual plots report
## ctr <- theophylline()
## ctr %>% pmx_report(
##   name="report2",
##   save_dir = getwd(),
##   template="individual",
##   format="all",
##   which_pages=1:2
## )

ggPMX documentation built on May 29, 2024, 1:40 a.m.