update main

[andybeet]

Bug fixes

• Correct accounting of interdetrital flows.
  • This added a second stage to the EE calculation, first calculating flows between living (+ gears) and detritus, then calculating initial EE of detritus, and based on initial EE, adding interdetrital flows equal to (1-initial EE) * flow rate. PR fixed interdetrital flows (EEs and ecosim equilibrium), removed a det… #161
• Ability to run models without any stanzas. PR Pb fixes #162
• Fix missing/infinte X (CAN WE EXPLAIN WHY THIS HAPPENED?) Yes (KA note). This is warned about in check.rpath.params() and happens when certain parameters are missing certain required inputs. It isn't "fixed" in that models with these problems are underspecified and won't work. The "fix" is to trap the error with a slightly more intelligent error message directing the user towards which parameters may be missing. Also, there are many fewer of these errors now that the "estimate unknown PB" feature was added (previously the most common missing parameter error trigger in our test set).
• Fix of ordering assumption in create.rpath.params. Previous code assumed that all stanzas of a particular species were grouped together in the main model, not interspersed in the main table with other stanza species. PR Stanza order fix #164
• Better warning messages

Minor Changes

• New vignette to describe xml -> rpath PR xml parsing functions + #166
  • Included sample eiixml file for use in vignette
• Documentation fixes

New Features

• Can now estimate unknown PB from B and EE (like EwE) PR Pb fixes #162
• Create rpath objects from EwE exported models (from XLM format) PR xml parsing functions + #166