In gmp26/rcljsdemo: Funnel Plot

Write me -

Cover the lung data example currently in funnel-test.R

See Vignette writing guide here

The code can be included inline bracketed with three back-ticks. See example below which imports the relevant bit of funnel-test.R

Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The html_vignette output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The html_vignette format:

• Never uses retina figures
• Has a smaller default figure size
• Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style

Vignette Info

Note the various macros within the vignette section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output:
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

Example from funnel-test.R

####################################################
# March 2016.  Test new funnel program
#
# This code may not work as I don't have access to lung.csv (Mike)
#
####################################################
# Lung data
devtools::install_github('gmp26/funnel')
library(funnel)

###
# NB from Mike. It's probably better to put the lung.csv file in the data
# directory in this package rather than use a private dropbox.
###

#
# Using CABG data since I can't access lung-data
#
load("../data/cabg.rda") # if necessary to access cabg data
x <- cabg # cabg was created by reading CABG-hospitals-03.csv into
# cabg variable and then saving it with `devtools::use_data(cabg)`

# x<-read.csv(file="~//Dropbox//DB-funnels-HSMR//funnels//lung.csv",header=T,sep=",")

N<- x$Cases
R<- N-x$deaths
xlabel<-"Number of operations per hospital"
scale<-0.8
xrange<-c(0,max(N))
xrange=c(0,600)
# ylabel<-"Mortality rate (%)"
#yrange<-c(0,max( R/N ))
ylabel<-"Survival rate (%)"
yrange<-c(0.94, 1)
#yrange=c(0,1)
names= as.character(x$X)
title<-"LCCOP data"
tails=c(0.001, 0.025)

funnel4(obs.prop=R/N,  denom=N, pred.prop=P/N, names=names,
        plot="slice", rank="precision", riskadj=F, RASRplot=F,
        plot.target=F, title=title,xrange=xrange,
        yrange=yrange, tails=tails,xlab=xlabel,ylab=ylabel,ypercent=T,
        bandcols=c("white","lightcyan","cyan")
)

# Above code fails with:
# Error in par(mar = c(3.5, trunc(max(nchar(labs[, 1]))/2) + 3, 1, 2)) :
#  invalid value specified for graphical parameter "mar"
# In addition: Warning message:
# In max(nchar(labs[, 1])) : no non-missing arguments to max; returning -Inf

# > c(3.5, trunc(max(nchar(labs[, 1]))/2) + 3, 1, 2)
# [1] 3.5 7.0 1.0 2.0
# I don't know why this value is invalid.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

knitr::kable(head(mtcars, 10))

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

gmp26/rcljsdemo documentation built on May 17, 2019, 7:28 a.m.