`write.ctable` doesnt' play nicely with hooks for numbering and referencing tables

[nutterb]

write.ctable doesnt' play nicely with hooks for numbering and referencing tables

---

title: "Auto-numbering and cross-referencing of figures and tables in rmarkdown"

output: html_document

# This is a knitr hook to enable figure and table captions
# number figures
# from http://stackoverflow.com/a/18672268/1036500
library("knitr")
tn = local({
  i = 0
  function(x) {
    i <<- i + 1
    paste("<table><caption>", 'Figure ', i, ': ', x, "</caption><colgroup><col width='100'></col></colgroup><thead><tr class='header'></tr></thead><tbody></tbody></table><p>", sep = '')
  }
})
knit_hooks$set(fig.cap = function(before, options, envir) {
  if(!before)
    tn(options$fig.cap)
})
default_output_hook = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
  if (is.null(options$fig.cap) == F)  
    x
  else
    default_output_hook(x,options)
})

# number tables
# from http://stackoverflow.com/a/18672268/1036500
to = local({
  i = 0
  function(x) {
    i <<- i + 1
    paste("<table><caption>", 'Table ', i, ': ', x, "</caption><colgroup><col width='100'></col></colgroup><thead><tr class='header'></tr></thead><tbody></tbody></table><p>", sep = '')
  }
})
knit_hooks$set(tab.cap = function(before, options, envir) {
  if(!before)
    to(options$tab.cap)
})
default_output_hook = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
  if (is.null(options$tab.cap) == F)  
    x
  else
    default_output_hook(x,options)
})

library(knitr)
library(kfigr) # devtools::install_github("github mkoohafkan/kfigr")
opts_chunk$set(message=FALSE, warning=FALSE)
library(lazyWeave)
library(stringr)
options(lazyReportFormat = "markdown")

summaries

Using the knitr option "echo=F" seems to cause the problem.

data(mtcars)

mtcars$group = sample(c("Bad", "Good"), size=nrow(mtcars), replace=T)

tab1 = catconttable(data = mtcars,
                    vars = c("mpg", "cyl", "disp", "hp", "drat", "wt", "qsec", "vs", "am", "gear", "carb"),
                    normal = c("mpg", "cyl", "disp", "hp", "drat", "wt", "qsec", "vs", "am", "gear", "carb"),
                    byVar = "group")
tab = write.ctable(tab1)
tab = str_split(tab, "\n")[[1]]
tab = tab[c(6,4,5,7:length(tab))]
tab = paste(tab, collapse="\n")
cat(tab)

See r figr("ATable", T,F) for summaries of the variables in the cars dataset.

data(mtcars)

mtcars$group = sample(c("Bad", "Good"), size=nrow(mtcars), replace=T)

tab1 = catconttable(data = mtcars,
                    vars = c("mpg", "cyl", "disp", "hp", "drat", "wt", "qsec", "vs", "am", "gear", "carb"),
                    normal = c("mpg", "cyl", "disp", "hp", "drat", "wt", "qsec", "vs", "am", "gear", "carb"),
                    byVar = "group")
tab = write.ctable(tab1)
tab = str_split(tab, "\n")[[1]]
tab = tab[c(6,4,5,7:length(tab))]
tab = paste(tab, collapse="\n")
cat(tab)

See r figr("ATable2", T,F) for summaries of the variables in the cars dataset.