models.include <-

  c(

    'age', 'cox', 'cox disc', 'cox imp', 'cox imp disc', 'rfsrc', 'rfsrc imp',

    'rf-logrank', 'cox-logrank disc', 'cox-elnet disc'

  )

source('../lib/handy.R')

requirePlus('ggplot2', 'cowplot')

models.performance.all <- readTablePlus('../../output/models-performance-manual.tsv')

models.performance.all$x.labels <-

  paste0(

    models.performance.all$model,

    ifelse(models.performance.all$imputation, ' imp', ''),

    ifelse(models.performance.all$discretised, ' disc', '')

  )

# Currently different scripts quote either the area under the curve or a pre

# one-minused the area under the curve...so standardise that

big.calibration.scores <- models.performance.all$calibration.score > 0.5

models.performance.all[big.calibration.scores, c('calibration.score', 'calibration.score.lower', 'calibration.score.upper')] <-

  1 - models.performance.all[big.calibration.scores, c('calibration.score', 'calibration.score.lower', 'calibration.score.upper')]

models.performance <- data.frame()

for(model in models.include) {

  models.performance <-

    rbind(

      models.performance,

      models.performance.all[models.performance.all$x.labels == model, ]

    )

}

# Turn this into a factor with defined levels so ggplot respects the order above

models.performance$x.labels <-

  factor(models.performance$x.labels, levels = models.include)

plot.c.index <-

  ggplot(models.performance, aes(x = x.labels, y = c.index)) +

  geom_bar(stat='identity', aes(fill = model)) +

  geom_errorbar(

    aes(ymin = c.index.lower, ymax = c.index.upper), width = 0.1

  ) +

  coord_cartesian(

    ylim = c(0.75, 0.81)

  ) +

  theme(legend.position = "none")

plot.calibration <-

  ggplot(models.performance, aes(x = x.labels, y = 1 - calibration.score)) +

  geom_bar(stat='identity', aes(fill = model)) +

  geom_errorbar(

    aes(

      ymin = 1 - calibration.score.lower, ymax = 1 - calibration.score.upper

    ),

    width = 0.1

  ) +

  coord_cartesian(

    ylim = c(0.8, 1.0)

  ) +

  theme(legend.position = "none")

plot_grid(

  plot.c.index, plot.calibration,

  labels = c("A", "B"),

  align = "v", ncol = 1

)

ggsave(

  '../../output/all-models-performance.pdf',

  width = 16,

  height = 10,

  units = 'cm',

  useDingbats = FALSE

)