inst/scripts/table_model_success.R

In joshwlambert/relaxedDAISIE: Reproduce Relaxed-rate DAISIE Paper

# script to tally the number of models that successfully ran

model_success <- data.frame()

model <- c(
  "cr_dd", "rr_lac_dd", "rr_mu_dd", "rr_k", "rr_gam_dd", "rr_laa_dd"
)

data_name <- c("Canaries", "Comoros", "Galapagos", "Hawaii", "Marquesas",
               "New_Caledonia", "SaoTome_Principe")

for (i in seq_along(data_name)) {

  # get the files names
  files <- list.files(
    system.file(
      "extdata",
      "raw_daisie_output",
      data_name[i],
      package = "relaxedDAISIE",
      mustWork = TRUE
    )
  )

  for (j in seq_along(model)) {
    # get which files for the model
    num_files <- length(grep(
      pattern = paste(model[j], "[0-9]", sep = "_"),
      x = files
    ))

    df <- data.frame(
      Archipelago = data_name[i],
      Model = model[j],
      Success = num_files
    )
    model_success <- rbind(model_success, df)
  }
}

# format table

model_success$Archipelago <- gsub(
  pattern = "_", replacement = " ", x = model_success$Archipelago
)
model_success$Model <- toupper(model_success$Model)
model_success$Model <- gsub(
  pattern = "CR", replacement = "HR", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "_", replacement = " ", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "LAC", replacement = "$\\\\lambda^c$", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "MU", replacement = "$\\\\mu$", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "LAA", replacement = "$\\\\lambda^a$", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "RR K", replacement = "RR $K'$", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "GAM", replacement = "$\\\\gamma$", x = model_success$Model
)
model_success$Model <- gsub(
  pattern = "RR ", replacement = "RR", x = model_success$Model
)

model_success$Success <- paste0(model_success$Success, "/10")

model_success$Model <- gsub(
  pattern = " DD",
  replacement = "",
  x = model_success$Model
)


for (i in seq_len(nrow(model_success))) {
  if (i %in% seq(from = 1, to = nrow(model_success), by = 6)) {
    model_success$Archipelago[i] <- paste0(
      "\\multirow{", 6, "}{*}{", model_success$Archipelago[i], "}"
    )
  } else {
    model_success$Archipelago[i] <- ""
  }
}


print(
  xtable::xtable(
    model_success,
    display = c("s", "s", "s", "s"),
    align = "cccc",
    caption = paste0(
      "Success rate of optimisation of the models for the 10 different ",
      "starting conditions per model. Models failed most often because the ",
      "numerical integration of the likelihood became unstable and the ",
      "computer job crashed."
    ),
    label = "tab:success_rate"
  ),
  size = "small",
  math.style.exponents = TRUE,
  NA.string = "NA",
  include.rownames = FALSE,
  hline.after = sort(rep(seq(from = 0, to = nrow(model_success), by = 6), 2)),
  sanitize.colnames.function = identity,
  sanitize.text.function = force
)