run .xml file

[rwildermuth]

Hi @gavinfay and @sgaichas,

The current atlantisom function run_truth() https://github.com/rwildermuth/atlantisom/blob/master/R/run_truth.R uses a biology .xml file "based on input from the "[...]_run.prm" file" to do some of the catch corrections (lines 216 to 262). Does the old code base use this .xml output format? I can't find it in the example output Gavin provided.

Sarah: would using just the _run.prm file work for these calculations?

Thank you, Robert

[sgaichas]

The function loading the run parameters load_runprm() is expecting xml as an input, probably because it is easier to search for the correct attributes and associated values. I think the prm file has the same information, so you can get it from there but it may be harder to code.

On the other hand, it is only pulling out a few things from that file, so you could just create it by hand. output looks like this (from NOBA model): $toutstart [1] 0

$toutinc [1] 73

$toutfinc [1] 73

$tstop [1] 52560

$nyears [1] 144

$timestep [1] 12

$timestepunit [1] "Hours"

$outputstep [1] 73

$outputstepunit [1] "days"

$hemisphere [1] "northern"

$nspp [1] 53

$nfleet [1] 27

[gavinfay]

agreed - probably easiest to create own list object. @gavinfay to do this for the fixed effort scenario.

[gavinfay]

commit d0b8785 adds function load_neus_v1_runprm() to build this object.