library(devtools)
library(challengeR)

data_matrix <- read.csv("C:/Users/a446r/Desktop/csv_files/data_matrix_NaN.csv") # type ?read.csv for help
bootstrapSamples <- 10

naTreat = 'na.rm'
# naTreat = 0

challenge <- as.challenge(data_matrix,
                          by = "task",
                          algorithm = "alg_name",
                          case = "case",
                          value = "value",
                          na.treat = naTreat,
                          smallBetter = TRUE)


ranking1 <- challenge %>% aggregateThenRank(FUN = mean, na.treat = naTreat, ties.method = "min")
ranking2 <- challenge %>% rankThenAggregate(FUN = mean, ties.method = "min")
ranking3 <- challenge %>% testThenRank(alpha = 0.05,
                                    p.adjust.method = "none", 
                                    na.treat = naTreat,
                                    ties.method = "min" )



# Get Consensus Ranking ---------------------------------------------------


meanRanks1 <- ranking1 %>% consensus(method = "euclidean")
meanRanks2 <- ranking2 %>% consensus(method = "euclidean")
meanRanks3 <- ranking3 %>% consensus(method = "euclidean")


# Prepare Bootsrapped Versions --------------------------------------------

if (bootstrapSamples > 0) {
  set.seed(1)
  rankingBootstrapped1 <- ranking1 %>% bootstrap(nboot = bootstrapSamples)
  rankingBootstrapped2 <- ranking2 %>% bootstrap(nboot = bootstrapSamples)
  rankingBootstrapped3 <- ranking3 %>% bootstrap(nboot = bootstrapSamples)
  ranking1_bootstrap <- rankingBootstrapped1
  ranking2_bootstrap <- rankingBootstrapped2
  ranking3_bootstrap <- rankingBootstrapped3
}


## Generate the reports 


# AggregateThenRank -------------------------------------------------------


ranking1 %>%
  report(consensus = meanRanks1,
         title = "AggregateThenRank with Na threat",
         file = "AggregateThenRank",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)


# AggregateThenRank with Bootstrap -----------------------------------------


ranking1_bootstrap %>%
  report(consensus = meanRanks1,
         title = "AggregateThenRank with Na threat and Bootstrap",
         file = "AggregateThenRank_bootstrap",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)



# RankThenAggregate -------------------------------------------------------


ranking2 %>%
  report(consensus = meanRanks2,
         title = "RankThenAggregate with Na threat",
         file = "RankThenAggregate",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)


# RankThenAggregate with Bootstrap -----------------------------------------


ranking2_bootstrap %>%
  report(consensus = meanRanks2,
         title = "RankThenAggregate with Na threat and Bootstrap",
         file = "RankThenAggregate_bootstrap",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)


# TestThenRank ------------------------------------------------------------


ranking3 %>%
  report(consensus = meanRanks3,
         title = "TestThenRank with Na threat",
         file = "TestThenRank",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)

# TestThenRank with Bootstrap ---------------------------------------------


ranking3_bootstrap %>%
  report(consensus = meanRanks3,
         title = "TestThenRank with Na threat and Bootstrap",
         file = "TestThenRank_bootstrap",
         format = "PDF",
         clean = TRUE,
         open = FALSE,)