inst/doc/write2.R

In arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries

## ----include = FALSE------------------------------------------------------------------------------
knitr::opts_chunk$set(eval = FALSE, message = FALSE)

## -------------------------------------------------------------------------------------------------
#  library(arsenal)
#  library(magrittr)
#  data(mockstudy)
#  tmpdir <- tempdir()

## -------------------------------------------------------------------------------------------------
#  mylabels <- list(sex = "SEX", age ="Age, yrs")
#  tab1 <- tableby(arm ~ sex + age, data=mockstudy)
#  
#  write2html(
#    tab1, paste0(tmpdir, "/test.tableby.html"), quiet = TRUE,
#    title = "My test table",      # passed to summary.tableby
#    labelTranslations = mylabels, # passed to summary.tableby
#    total = FALSE                 # passed to summary.tableby
#  )

## -------------------------------------------------------------------------------------------------
#  tab2 <- modelsum(alk.phos ~ arm + ps + hgb, adjust= ~ age + sex, family = "gaussian", data = mockstudy)
#  
#  write2pdf(
#    tab2, paste0(tmpdir, "/test.modelsum.pdf"), quiet = TRUE,
#    title = "My test table", # passed to summary.modelsum
#    show.intercept = FALSE,  # passed to summary.modelsum
#    digits = 5               # passed to summary.modelsum
#  )

## -------------------------------------------------------------------------------------------------
#  mockstudy[, c("arm", "sex", "mdquality.s")] %>%
#    table(useNA = "ifany") %>%
#    freqlist(groupBy = c("arm", "sex")) %>%
#    write2word(
#      paste0(tmpdir, "/test.freqlist.doc"), quiet = TRUE,
#      single = FALSE,         # passed to summary.freqlist
#      title = "My cool title" # passed to summary.freqlist
#    )

## -------------------------------------------------------------------------------------------------
#  mockstudy %>%
#    head() %>%
#    knitr::kable() %>%
#    write2html(paste0(tmpdir, "/test.kable.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  mockstudy %>%
#    head() %>%
#    xtable::xtable(caption = "My xtable") %>%
#    write2pdf(
#      paste0(tmpdir, "/test.xtable.pdf"), quiet = TRUE,
#      comment = FALSE, # passed to print.xtable to turn off the default message about xtable version
#      include.rownames = FALSE, # passed to print.xtable
#      caption.placement = "top" # passed to print.xtable
#    )

## -------------------------------------------------------------------------------------------------
#  mockstudy %>%
#    head() %>%
#    xtable::xtable(caption = "My xtable") %>%
#    write2html(
#      paste0(tmpdir, "/test.xtable.html"), quiet = TRUE,
#      type = "html",            # passed to print.xtable
#      comment = FALSE, # passed to print.xtable to turn off the default message about xtable version
#      include.rownames = FALSE, # passed to print.xtable
#      caption.placement = "top" # passed to print.xtable
#    )

## -------------------------------------------------------------------------------------------------
#  write2word(pander::pander_return(head(mockstudy)), file = paste0(tmpdir, "/test.pander.doc"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  mylist <- list(
#    tableby(sex ~ age, data = mockstudy),
#    freqlist(table(mockstudy[, c("sex", "arm")])),
#    knitr::kable(head(mockstudy))
#  )
#  
#  write2pdf(mylist, paste0(tmpdir, "/test.mylist.pdf"), quiet = TRUE)
#  

## -------------------------------------------------------------------------------------------------
#  mylist2 <- list(
#    "# Header 1",
#    "This is a small paragraph introducing tableby.",
#    tableby(sex ~ age, data = mockstudy),
#    "<hr>",
#    "# Header 2",
#    "<font color='red'>I can change color of my text!</font>"
#  )
#  write2html(mylist2, paste0(tmpdir, "/test.mylist2.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  write2pdf(list(mylist2, mylist), paste0(tmpdir, "/test.mylists.pdf"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  lm(age ~ sex, data = mockstudy) %>%
#    summary() %>%
#    write2pdf(paste0(tmpdir, "/test.lm.pdf"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  tab4 <- tableby(arm ~ sex + age, data=mockstudy)
#  write2html(verbatim(tab4), paste0(tmpdir, "/test.print.tableby.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  chr <- paste0("MyVector", 1:10)
#  write2pdf(verbatim(chr), paste0(tmpdir, "/test.character.pdf"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  write2pdf(verbatim(tab4, chr), paste0(tmpdir, "/test.verbatim.pdf"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  mylist3 <- list(
#    yaml(title = "Test YAML Title", author = "My cool author name"),
#    "# Header 1",
#    "This is a small paragraph introducing tableby.",
#    tableby(sex ~ age, data = mockstudy)
#  )
#  write2html(mylist3, paste0(tmpdir, "/test.yaml.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  mylist4 <- list(
#    "# Header 1",
#    "This is a small paragraph introducing tableby.",
#    yaml(title = "Test YAML Title"),
#    tableby(sex ~ age, data = mockstudy),
#    yaml(author = "My cool author name")
#  )
#  write2html(mylist4, paste0(tmpdir, "/test.yaml2.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  mylist5 <- list(
#    "# What is 1 + 2?",
#    code.chunk(a <- 1, b <- 2),
#    code.chunk(a + b, chunk.opts = "r echo=FALSE, eval=TRUE")
#  )
#  write2html(mylist5, paste0(tmpdir, "/test.code.chunk.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  write2html(
#    knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.quiet.html"),
#    quiet = TRUE # passed to rmarkdown::render
#  )

## -------------------------------------------------------------------------------------------------
#  write2html(
#    knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.keep.rmd.html"),
#    quiet = TRUE, # passed to rmarkdown::render
#    keep.rmd = TRUE
#  )

## -------------------------------------------------------------------------------------------------
#  write2html(
#    knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.dont.render.html"),
#    render. = FALSE
#  )

## -------------------------------------------------------------------------------------------------
#  mylist2 <- list(
#    "# Header 1",
#    "This is a small paragraph introducing tableby.",
#    tableby(sex ~ age, data = mockstudy),
#    "<hr>",
#    "# Header 2",
#    "<font color='red'>I can change color of my text!</font>"
#  )
#  write2html(mylist2, paste0(tmpdir, "/test.mylist2.html"), quiet = TRUE)

## -------------------------------------------------------------------------------------------------
#  write2html(
#    knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.theme.html"),
#    quiet = TRUE,  # passed to rmarkdown::render
#    theme = "yeti" # passed to rmarkdown::html_document
#  )

## -------------------------------------------------------------------------------------------------
#  write2(
#    knitr::kable(head(mockstudy[, 1:4])), paste0(tmpdir, "/test.kable.rtf"),
#    quiet = TRUE,  # passed to rmarkdown::render
#    output_format = rmarkdown::rtf_document
#  )

## -------------------------------------------------------------------------------------------------
#  mylist5 <- list(
#    yaml("header-includes" = list("\\usepackage[labelformat=empty]{caption}")),
#    "# Header 1",
#    "This is a small paragraph introducing tableby.",
#    tableby(sex ~ age, data = mockstudy)
#  )
#  write2pdf(mylist5, paste0(tmpdir, "/test.noprefixes.pdf"), title = "My tableby")

## -------------------------------------------------------------------------------------------------
#  mylist6 <- list(
#    summary(tableby(sex ~ age, data = mockstudy), title = "A Title for tableby"),
#    summary(modelsum(age ~ sex, data = mockstudy), title = "A Title for modelsum"),
#    summary(freqlist(~ sex, data = mockstudy), title = "A Title for freqlist")
#  )
#  write2pdf(mylist6, paste0(tmpdir, "/test.multiple.titles.pdf"))