In gevamaimon/CLSAR: Helper Functions for CLSA Data

knitr::opts_chunk$set(echo = FALSE)

library(CLSAR)
library(pander)
library(ggplot2)
library(knitr)

# keep tables from splitting accross multiple lines, format numbers
panderOptions("table.split.table", Inf)
panderOptions("digits", 2)
panderOptions("round", 2)
panderOptions("keep.trailing.zeros", TRUE)
options(digits = 4)

# A Prefix nulling hook.

# Make sure to keep the default for normal processing.
default_output_hook <- knitr::knit_hooks$get("output")

# Output hooks handle normal R console output.
knitr::knit_hooks$set( output = function(x, options) {

  comment <- knitr::opts_current$get("comment")
  if( is.na(comment) ) comment <- ""
  can_null <- grepl( paste0( comment, "\\s*\\[\\d?\\]" ),
                     x, perl = TRUE)
  do_null <- isTRUE( knitr::opts_current$get("null_prefix") )
  if( can_null && do_null ) {
    # By default R print output aligns at the right brace.
    align_index <- regexpr( "\\]", x )[1] - 1
    # Two cases: start or newline
    re <- paste0( "^.{", align_index, "}\\]")
    rep <- comment
    x <- gsub( re, rep,  x )
    re <- paste0( "\\\n.{", align_index, "}\\]")
    rep <- paste0( "\n", comment )
    x <- gsub( re, rep,  x )
  }

  default_output_hook( x, options )

})

knitr::opts_template$set("kill_prefix"=list(comment=NA, null_prefix=TRUE))

# load the tracking, comprehensive and mcq data
data.list <- loadCLSAData("path")

# split the data list into tracking, comprehensice and mcq data
tra <- data.list[[1]]
cop <- data.list[[2]]
tra.mcq <- data.list[[3]]
cop.mcq <- data.list[[4]]
rm(data.list)

# create the age sex categories for tra and cop dataframes
tra$sexAgeCat <- createSexAgeCateg(ageVec = tra$AGE_NMBR_TRM,
                                   sexVec = tra$SEX_ASK_TRM,
                                   categoryNum = 8)
cop$sexAgeCat <- createSexAgeCateg(ageVec = cop$AGE_NMBR_COM,
                                   sexVec = cop$SEX_ASK_COM,
                                   categoryNum = 8)