[simplify interface] Some renaming of functions, files, classes

[dfalster]

Gradually thinking some renaming of functions, files, classes will help make the material more accessible. For example:

Variables and functions:

• [ ] height -> individual_size (#223)
• [x] plant -> individual
• [x] cohort -> node
• [x] compute_vars_phys --> compute_vital_rates
• [x] area_leaf_above -> competition (or other)
• [x] germination_probability -> establishment_probability
• [x] seed_rain -> offspring_arrival_rate
• custom environments and strategies go in a models folder

files:

• [x] plant.h -> individuals.h
• [ ] ff16strategy -> strategy_ff16
• [ ] Move supporting tools (like qag, qk, ode) into subfolders?

[aornugent]

It strikes me that there is significant duplication for simple environments. K93Environment and FF16Environment are effectively the same.

Brainstorming, with no consideration for how this will affect compilation, there might be room for components that are not specific to one strategy but part of a larger class of models.

For example:

inst
├──include
|   ├── evolutionary
|   |   ├── StochasticPatch.h
|   |   └── StochasticSpecies.h
|   ├── fish
|   |   └── 3DEnvironment.h
|   ├── generic
|   |   ├── Cohort.h
|   |   ├── Environment.h
|   |   ├── Individual.h
|   |   ├── Patch.h
|   |   ├── Species
|   |   └── Strategy.h
|   ├── models
|   |   ├── FF16.h
|   |   ├── FF16evo.h
|   |   ├── FF16r.h
|   |   └── K93.h
|   ├── numeric
|   |   ├── QAG.h
|   |   ├── Lorenz.h
|   |   ├── QK.h
|   |   |    .....
|   ├── plant
|   |   ├── LightEnvironment.h
|   |   └── WaterEnvironment.h
|   └── SCM.h
└── RcppR6_classes.yml

would permit FF16 and K93 to use the same plant\LightEnvironment, while still providing room to specialise.

[aornugent]

• [x] Update names of utility functions, e.g. grow_plant_to_size -> grow_individual_to_size
• [ ] Change name of result in utility functions e.g. res$plant -> res$individual

[aornugent]

• [ ] change lai_error in run_scm_error to e.g. competition_error

[dfalster]

Note @devmitch - I added something to the list, rename cohort to node

[dfalster]

• [ ]scm_base_parameters -> FF16_system or parameters?
• [ ] scm_base_control -> system_control or delete. We already have Control()
• [ ] fast_control() -> system_control_fast()
• [ ] expand_parameters -> add_strategies (see #410 )
• [ ] run_scm -> solve_system