# Read .isox test data
df <- 
  system.file("extdata", "testfile_dual_inlet_new.isox", package = "isoorbi") |>
  orbi_read_isox() |> # reads .isox test data
  orbi_simplify_isox() |> # optionally: keeps only most important columns; equivalent to simplify check box in IsoX
  # check for issues
  orbi_flag_satellite_peaks() |> # removes minor signals that were reported by IsoX in the same tolerance window where the peak of interest is
  orbi_flag_weak_isotopocules(min_percent = 10) |> # removes signals of isotopocules that were not detected at least in min_percent scans
  orbi_flag_outliers(agc_fold_cutoff = 2) |> # removes outlying scans that have more than 2 times or less than 1/2 times the average number of ions in the Orbitrap analyzer; another method: agc_window (see function documentation for more details)
  orbi_define_basepeak(basepeak_def = "M0") # sets one isotopocule in the dataset as the base peak (denominator) for ratio calculation

df |> orbi_plot_raw_data(isotopocule = "15N", y = tic * it.ms, y_scale = "log")

# define blocks
df_w_blocks <-
  df |>
  # general definition
  orbi_define_blocks_for_dual_inlet(
    ref_block_time.min = 10, # the reference block is 10 min long
    sample_block_time.min = 10, # the sample block is 10 min long
    startup_time.min = 5, # there is 5 min of data before the reference block starts, to stabilize spray conditions
    change_over_time.min = 2, # it takes 2 min to make sure the right solution is measured after switching the valve
    sample_block_name = "sample",
    ref_block_name = "reference"
  ) |> 
  # fine adjustments
  orbi_adjust_block(block = 1, shift_start_time.min = 2) |> # the 1st reference block is shorter by 2 min, cut from the start
  orbi_adjust_block(block = 4, set_start_time.min = 38, set_end_time.min = 44) # the start and end of the 2nd reference block are manually set

# get blocks info
blocks_info <- df_w_blocks |> orbi_get_blocks_info()
blocks_info |> knitr::kable()

# calculate summary
df_summary <- 
  df_w_blocks |>
  # segment (optional)
  orbi_segment_blocks(into_segments = 3) |>
  # calculate results, including for the unused parts of the data blocks
  orbi_summarize_results(
    ratio_method = "sum",
    include_unused_data = TRUE
  )