## ----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)