## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.height = 5, 
  fig.width = 7
)

## ----setup--------------------------------------------------------------------
library(FunnelPlotR)

## ----dtsetup------------------------------------------------------------------
library(COUNT)
data(medpar)
medpar$provnum<-factor(medpar$provnum)
medpar$los<-as.numeric(medpar$los)

# Logistic model to predict LOS, LOS is quite overdispersed
mod<- glm(los ~ hmo + died + age80 + factor(type), family="poisson", data=medpar)

#Get predicted value for ratio
medpar$prds<- predict(mod, newdata = medpar, type="response")

# Draw plot, returning just the plot object
funnel_plot(medpar, denominator=prds, numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE)


## ----highlight----------------------------------------------------------------
# Draw plot, returning just the plot object
funnel_plot(medpar, denominator=prds, numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, highlight="030002")




## ----plottheme1---------------------------------------------------------------

funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, theme = funnel_grey() )


## ----plottheme2---------------------------------------------------------------
library(ggplot2)

new_funnel_theme <-
  funnel_grey()+
    theme(plot.title = element_text(face="bold", colour="red", size=6), # Change plot title
          legend.background = element_rect(fill="brown"), # Alter legend background colour
          axis.title.y = element_text(angle=0)  #Rotate y axis label
    )


funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, theme = new_funnel_theme)


## ----colours------------------------------------------------------------------
funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, theme = funnel_grey(),
            plot_cols = c("#FF7F0EFF", "#000000", "#1F77B4FF","#1F77B4FF", "#9467BDFF", "#9467BDFF", "#2CA02CFF", "#2CA02CFF"))

## ----funnelscales-------------------------------------------------------------
## Changing labels
funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, x_range=c(0, 400), y_range=c(0,2))


## ----funnellabels1------------------------------------------------------------
funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99 ,label = "outlier"
            , draw_unadjusted = TRUE, title = "Vignette funnel plot"
            , x_label = "x-axis", y_label = "y-axis")

## ----funnellabels2------------------------------------------------------------
funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99
            , draw_unadjusted = TRUE, title = "Vignette funnel plot"
            , x_label = "x-axis", y_label = "y-axis"
            , highlight= "030002", label = "highlight")

## ----cutoutplot---------------------------------------------------------------
# Original funnel plot object
fp <-
funnel_plot(medpar, denominator=prds,numerator=los
            , group = provnum, limit=99, label = "outlier"
            , draw_unadjusted = TRUE)

# Extract just the plot
my_plot <- plot(fp)

# Add an additional geom to plot
my_plot +
  geom_vline(aes(xintercept=400), linetype = "dashed", colour="red", linewidth=2)