# input
input_filename <- "input_example.csv"

# redox options:
redox_flag  <-  0              # -3, -2, -1, 0, or 1 (see EQ3 documentation for more info)
redox_aux <- "Fe+3"            # ignored unless redox_flag is 1. Input species, e.g. "Fe+3"
default_logfO2 <- -6           # what is the default logfO2 if a redox value can't be found?

# aqueous block options
exclude <- c("Year", "Area", "Temperature")   # which columns in input file to exclude from aqueous block?
suppress <- c("N2,AQ", "CN-", "S2-2","N2H5+","N2O2-2")  # which species to suppress in aqueous block?

# charge balance options
charge_balance_on <- "none"    # "none" for no charge balance. Otherwise, "H+" or "Na+", etc.

# EQ3_Batch options
suppress_missing <- TRUE       # suppress the formation of an aqueous species if it is missing a value in the input file?
verbose <- 1                   # 2 for all messages, 1 for errors or warnings only, 0 for silent
csv_filename <- "input_processed.csv" # filename of input summary?
create_join <- TRUE            # join all forms of output together into one csv?
filename_join <- "final_report.csv" # name of final joined output

# AquaMine options
run_AquaMine <- TRUE              # Run AquaMine after EQ3 output files are generated?
AM_output_type <- "log_activity"  # Can be "molality", "log_molality", "log_gamma", or "log_activity"

# MineralMine options
run_MineralMine <- TRUE           # Run MineralMine after EQ3 output files are generated?
MM_output_type <- "affinity"      # Can be "logQoverK" or "affinity"

# RedoxMine options
run_RedoxMine <- TRUE           # Run RedoxMine after EQ3 output files are generated?
RM_output_type <- "Eh"      # Can be "Eh", "pe", "logfO2", or "Ah"

# MiscMine options
run_MiscMine <- TRUE      # Run MiscMine after EQ3 output files are generated? Mines ionic strength and charge balance results.

#db <- "tde" # which thermo database to use? Default is 'jus'.