Atlnts 289 mortality

[andybeet]

Mortality

• Updated the three core processing R scripts to accommodate mortality output and plotting
  • get_atl_paramfiles (added paths to mort.txt, and specificMort.txt)
  • process_atl_output (read in and save as RDS files)
  • make_atlantis_diagnostic_figures (plot variety of figures)

Atlantis tools

For these new plots to function correctly atlantistools was forked and modified. You will now need to install atlantistools from https://github.com/andybeet/atlantistools to take advantage of new functions

• added load_mort
• created load_spec_mort
• changed previous load_spec_mort to load_spec_pred_mort
• added get_cohorts
• modified plot_line to take ylim argument
• modified processed_txt to take removeZeros argument

These changes will be documented in the package update

[jcaracappa1]

looks good