inst/doc/Reporting.R

In ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(ggplot2)
require(ubiquity)
require(officer)
require(onbrand)
require(flextable)

## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
#  fr = system_new(file_name        = "system.txt",
#                  system_file      = "mab_pk",
#                  overwrite        = TRUE,
#                  output_directory = tempdir())
#  cfg = build_system(system_file  = file.path(tempdir(), "system.txt"),
#        output_directory          = file.path(tempdir(), "output"),
#        temporary_directory       = tempdir())
#  cfg_pptx = system_rpt_read_template(cfg, "PowerPoint")
#  cfg_docx = system_rpt_read_template(cfg, "Word")
#  fr_pptx = system_rpt_template_details(cfg_pptx)
#  fr_docx = system_rpt_template_details(cfg_docx)
#  
#  tdeets = list()
#  tdeets[["pptx"]][["txt"]] = fr_pptx[["txt"]]
#  tdeets[["docx"]][["txt"]] = fr_docx[["txt"]]
#  tdeets[["pptx"]][["ft"]]  = fr_pptx[["ft"]]
#  tdeets[["docx"]][["ft"]]  = fr_docx[["ft"]]
#  
#  save(tdeets, file="Reporting.RData")

## ----echo=FALSE, eval=TRUE----------------------------------------------------
# This should create tdeets
load("Reporting.RData")

## -----------------------------------------------------------------------------
#  library(ubiquity)
#  fr = workshop_fetch(section="Reporting", overwrite=TRUE)

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = build_system("system.txt")

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  library(ggplot2)
#  p = ggplot() + annotate("text", x=0, y=0, label = "picture example")
#  imgfile = tempfile(pattern="image", fileext=".png")
#  ggsave(filename=imgfile, plot=p, height=5.15, width=9, units="in")

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  tdata =  data.frame(Parameters = c("Vp", "Cl", "Q", "Vt"),
#                      Values     = 1:4,
#                      Units      = c("L", "L/hr", "L/hr", "L") )

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  tco  = list(table     = tdata,
#              header    = TRUE,
#              first_row = FALSE)

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  tcf = list(table       = tdata,             # This element contains the table data
#             header_top  = list(              # Defining the table headers
#               Parameters = "Name",
#               Values     = "Value",
#               Units      = "Units"),
#             cwidth         = 0.8,            # Column width
#             table_autofit  = TRUE,           # Making the tables automatically fit
#             table_theme    = "theme_zebra",  # Selecting the table theme
#             first_row = FALSE)
#  

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  tfo = flextable::flextable(tdata)
#  tfo = flextable::autofit(tfo)

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  lcontent = c(1, "First major item",
#               2, "first sub bullet",
#               2, "second sub bullet",
#               3, "sub sub bullet",
#               1, "Second major item",
#               2, "first sub bullet",
#               2, "second sub bullet")

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_read_template(cfg, "PowerPoint")

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "title_slide",
#     elements = list(
#        title=list(content = "Reporting in ubiquity",
#                   type    = "text")))
#  cfg = system_rpt_add_slide(cfg,
#     template = "section_slide",
#     elements = list(
#        title=list(content = "Content Types",
#                   type    = "text")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  fr = system_rpt_template_details(cfg)

## ----message=FALSE, warning=FALSE, eval=TRUE, echo=FALSE, message=FALSE-------
trim_idx = min(c(18, length(tdeets[["pptx"]][["txt"]])))
cat(paste(tdeets[["pptx"]][["txt"]][1:trim_idx], collapse="\n"))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_list",
#     elements = list(
#        title=
#          list(content = "Lists",
#               type    = "text"),
#        sub_title=
#          list(content = "For placholders that contain lists.",
#               type    = "text"),
#        content_body=
#          list(content = lcontent,
#               type    = "list")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_text",
#     elements = list(
#        title=
#          list(content = "Figures: ggplot object",
#               type    = "text"),
#        sub_title=
#          list(content = "Using ggplot objects directly",
#               type    = "text"),
#        content_body=
#          list(content = p,
#               type    = "ggplot")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_text",
#     elements = list(
#        title=
#          list(content = "Figures: image file",
#               type    = "text"),
#        sub_title=
#          list(content = "Inserting figures from files",
#               type    = "text"),
#        content_body=
#          list(content = imgfile,
#               type    = "imagefile")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_text",
#     elements = list(
#        title=
#          list(content = "Tables: Office",
#               type    = "text"),
#        sub_title=
#          list(content = "Table in native Office format",
#               type    = "text"),
#        content_body=
#          list(content = tco,
#               type    = "table")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_text",
#     elements = list(
#        title=
#          list(content = "Tables: flextable",
#               type    = "text"),
#        sub_title=
#          list(content = "Flextables using onbrand abstraction",
#               type    = "text"),
#        content_body=
#          list(content = tcf,
#               type    = "flextable")))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg = system_rpt_add_slide(cfg,
#     template = "content_text",
#     elements = list(
#        title=
#          list(content = "Tables: flextable object",
#               type    = "text"),
#        sub_title=
#          list(content = "Flextables using a user-created flextable object",
#               type    = "text"),
#        content_body=
#          list(content = tfo,
#               type    = "flextable_object")))

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  system_rpt_save_report(cfg, output_file = "example.pptx")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  plain_text_content = paste(rep("The quick brown fox jumped over the lazy dog.", 70), collapse= " ")
#  md_text_content    = paste(rep("The *quick* <color:brown>brown</color> fox **jumped** over the ~lazy dog~.", 70), collapse=" ")
#  fpar_text_content  = officer::fpar(
#     officer::ftext("The quick ", prop=NULL),
#     officer::ftext("brown", prop=officer::fp_text(color="brown")),
#     officer::ftext(" fox jumped over the lazy dog.", prop=NULL))

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  library(ggplot2)
#  p = ggplot() + annotate("text", x=0, y=0, label = "picture example")
#  imgfile = tempfile(pattern="image", fileext=".png")
#  ggsave(filename=imgfile, plot=p, height=5.15, width=9, units="in")
#  
#  gpc = list(image   = p,
#             caption = "This is an example of an image from a ggplot object.")
#  
#  ifc  = list(image   = imgfile,
#              caption = "This is an example of an image from a file.")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  tdata =  data.frame(Parameters = c("Vp", "Cl", "Q", "Vt"),
#                      Values     = 1:4,
#                      Units      = c("L", "L/hr", "L/hr", "L") )

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  tco  = list(table     = tdata,    # This element contains the table data
#              header    = TRUE,     # These two lines control the header
#              first_row = FALSE,
#              caption   = "This creates a table using an Office theme/format.")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  tcf = list(table       = tdata,             # This element contains the table data
#             caption_format = "md",
#             caption     = "This creates a <ff:courier>flextable</ff> using the <ff:courier>onbrand</ff> abstraction",
#             header_top  = list(              # Defining the table headers
#               Parameters = "Name",
#               Values     = "Value",
#               Units      = "Units"),
#             cwidth         = 0.8,            # Column width
#             table_autofit  = TRUE,           # Making the tables automatically fit
#             table_theme    = "theme_zebra",  # Making the tables automatically fit
#             first_row = FALSE)

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  tfo = flextable::flextable(tdata)
#  tfo = flextable::autofit(tfo)
#  
#  tcfo = list(ft = tfo,
#              caption  = "This inserts a flextable object created by the user")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_read_template(cfg, "Word")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#          type="text",
#          content = list(
#            style = "Heading_1",
#            text  = "Formatting Text"))

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  fr = system_rpt_template_details(cfg)

## ----message=FALSE, warning=FALSE, eval=TRUE, echo=FALSE, message=FALSE-------
cat(paste(tdeets[["docx"]][["txt"]], collapse="\n"))

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#    type="text",
#    content = list(
#      text  = plain_text_content))

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#          type="text",
#          content = list(
#            style  = "Normal",
#            format = "md",
#            text   = md_text_content))
#  

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#          type="text",
#          content = list(
#            style  = "Normal",
#            format = "fpar",
#            text   = fpar_text_content))

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#    type     = "imagefile",
#    content  = ifc)
#  cfg = system_rpt_add_doc_content(cfg,
#    type     = "ggplot",
#    content  = gpc)

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_add_doc_content(cfg,
#    type     = "table",
#    content  = tco)
#  cfg = system_rpt_add_doc_content(cfg,
#    type     = "flextable",
#    content  = tcf)
#  cfg = system_rpt_add_doc_content(cfg,
#    type     = "flextable_object",
#    content  = tcfo)

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  system_rpt_save_report(cfg, output_file = "example.docx")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  tr = system_fetch_template(cfg, template="myOrg")

## ----message=FALSE, warning=FALSE, eval=TRUE, echo=FALSE----------------------
tdeets[["pptx"]][["ft"]]

## ----message=FALSE, warning=FALSE, eval=TRUE, echo=FALSE----------------------
tdeets[["docx"]][["ft"]]

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_read_template(cfg,
#                                 mapping  = "myOrg.yaml",
#                                 template = "myOrg.pptx")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_estimation(cfg=cfg, analysis_name="analysis_name")

## ----message=FALSE, warning=FALSE, eval=FALSE, echo=TRUE----------------------
#  cfg = system_rpt_nca(cfg=cfg, analysis_name="analysis_name")

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  rpt = system_fetch_rpt_officer_object(cfg)

## ----results="hide", message=FALSE, warning=FALSE, eval=FALSE-----------------
#  cfg  = system_set_rpt_officer_object(cfg, rpt)