Rename variables

[dfalster]

With building of tree2, I suggest a mass renaming of variables to improve consistency and readability across the project. @richfitz already made one round of simplifications. Here's a proposed second round of changes, any objections?

s -> mass_seed

leaf_area -> area_leaf leaf_mass -> mass_leaf bark_area -> area_bark sapwood_area -> area_sapwood heartwood_area -> area_heartwood stem_area -> area_stem stem_diameter -> diameter_stem mass_root -> root_mass total_mass -> mass_total live_mass -> mass_live above_ground_mass -> mass_above_ground

leaf_area_deployment_mass -> darea_leaf_dlive_mass

reproduction_mass_fraction -> fraction_allocation_reproduction growth_mass_fraction -> fraction_allocation_live_mass

dfecundity_dt -> reproduction_dt

net_mass_production -> net_mass_production_dt

dleaf_area_dt -> area_leaf_dt dsapwood_area_dt -> area_sapwood_dt dheartwood_area_dt -> area_heartwood_dt dbark_area_dt -> area_bark_dt dstem_area_dt -> area_stem_dt dstem_diameter_dt -> diameter_stem_dt droot_mass_dt -> mass_root_dt dlive_mass_dt -> mass_live_dt dtotal_mass_dt -> mass_total_dt dabove_ground_mass_dt -> mass_above_ground_dt dheartwood_mass_dt -> mass_heartwood_dt

These will also be modified via above changes

dheight_dleaf_area dsapwood_mass_dleaf_area dbark_mass_dleaf_area droot_mass_dleaf_area dstem_diameter_dstem_area

New variables

allocation_leaf allocation_sapwood allocation_bark allocation_root

mass_production_dt

Existing, won't be changed

assimilation_leaf respiration_leaf, respiration_bark, ,... turnover_leaf turnover_bark, ...

mortality_dt mortality_growth_dependent_dt mortality_growth_independent_dt

[richfitz]

Closed in tree2 - @dfalster to make sure this is all good.

[dfalster]

Address in 1405d9fef9999c3fed316e879e814a823f0c0534 of tree2

As far as i can tell it's done so closing.