qicharts2

February 2020

Questions

Because I always forget this part…

Who uses Statistical Process Control charts?

(or run charts and funnel plots)
Who has used qicharts2 package in R?

Package details

install.packages("qicharts2")

library(qicharts2)

Available on CRAN
Comes with sample healthcare datasets
Created by Jacob Anhøj, a doctor in Denmark
Supercedes qichart package

Why I like this package …

Reasons to be joyful

I skim instructions
I just get healthcare data (not plants and certainly not cars)
Reproducible examples in the vignette
More than one type of SPC available

Like this

Snapshot of the vignette:

Nightingale’s Crimea…

Getting data

Copied data manually from: https://understandinguncertainty.org/node/214

library(datapasta) to copy directly to R

Saved in a script for quick retrieval later

source("Crimea.R")

Being #rstats though

install.packages("HistData")

library(HistData)

data("Nightingale")

Replot in qicharts2

Run chart code

Built on ggplot2

qic(startMonth,number,
    data     = crimeaLong,
    chart    = 'run',
    decimals = 0, 

    x.angle  = 90,
    title    = 'Run chart deaths in Crimea War',
    ylab     = 'Number of deaths',
    xlab     = 'Month'
)

Produces this

Sprinkle ggplot2 magic…

Facets

Just imagine…

Producing…

30 incident categories
10 wards
25 LSOAs

To look for signals

The magic is one line of code

qic(startMonth,number,
    data     = crimeaLong,
    chart    = 'run',
    decimals = 0, 

    x.angle  = 90,
    title    = 'Run chart deaths in Crimea War',
    ylab     = 'Number of deaths',
    xlab     = 'Month'
)

With the facet line

qic(startMonth,number,
    data     = crimeaLong,
    chart    = 'run',
    decimals = 0, 
    facets   = ~death_cause,
    x.angle  = 90,
    title    = 'Run chart deaths in Crimea War',
    ylab     = 'Number of deaths',
    xlab     = 'Month'
)

Moving Range SPC

qic(startMonth,number,
    data     = crimeaLong,
    chart    = 'mr',
    decimals = 0, 
    facet    = ~death_cause,
    x.angle  = 90,
    title    = 'SPC mr chart deaths in Crimea War',
    ylab     = 'Number of deaths',
    xlab     = 'Month'
)

mr Chart (or is that Mr Chart!)

As seen on Twitter @Letxuga007

Other SPC charts are available

Rare events - time between

The code requires a count of days difference.

Cabg = coronary artery bypass operations

# Altered slightly from the vignette

fatalities <- cabg %>% 
  filter(death) %>% 
  mutate(dt = date - lag(date))

T-chart

A point above the upper control limit is a good thing!

Breaking into the chart

Getting the data

The numbers generated to create the charts can be viewed/saved by typing:

newObject <- tchart$data

When is this useful?

In this blog: https://www.r-bloggers.com/backed-by-data/ @_johnmackintosh shows how to:

tweak the charts

And I used this code

to include only those charts with a signal

Other interesting things

Further information

Jacob has created this Flexdashboard https://hospinf.shinyapps.io/hospinf/

SPC Shiny dashboards are being discussed on the NHS-R Slack site

please join us and contribute

link: nhsrcommunity.slack.com

Twitter: @NHSrCommunity
Our Team: @DataScienceNott
Me: @Letxuga007

Follow the hashtag #rstats