R/melanoma_formatting.R

In riinuots/tidyforest: A tidyverse workflow for running and presenting a logistic regression model in R.

data_melanoma = function(){

  library(tidyverse)
  library(forcats)


  mydata = boot::melanoma

  mydata$status %>%
    factor() %>%
    fct_recode('Died'                = '1',
               'Alive'               = '2',
               'Died - other causes' = '3') %>%
    fct_relevel('Alive') -> # move Alive to front (first factor level) so the odds ratios will be relative to that
    mydata$status.factor

  mydata$sex %>%
    factor() %>%
    fct_recode('Female' = '0',
               'Male'   = '1') ->
    mydata$sex.factor

  mydata$ulcer %>%
    factor() %>%
    fct_recode('Present' = '1',
               'Absent'  = '0') ->
    mydata$ulcer.factor

  mydata$age %>%
    cut(breaks = c(4,40,60,95), include.lowest=TRUE) ->
    mydata$age.factor

  mydata$thickness %>%
    cut(breaks = c(0,0.5,1,4, max(mydata$thickness, na.rm=T)),
        include.lowest = T) ->
    mydata$stage

  mydata$stage.factor = as.factor(mydata$stage)

  mydata$stage.factor %>%
    fct_recode('Stage I'   = '[0,0.5]',
               'Stage II'  = '(0.5,1]',
               'Stage III' = '(1,4]',
               'Stage IV'  = '(4,17.4]'
    ) -> mydata$stage.factor

  mydata
}