plant

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In `expand_parameters` we repetitively specify that `mutant = FALSE`. where mutants have no effect on other plants in the community (i.e. have zero density). Changing the default setting from `TRUE...

aornugent

Initialise patch state

5

Early progress for solving patches with arbitrary initial conditions. The included test shows how this has been added to `run_scm_collect` which may or may not the desired API design, but...

aornugent

Some renaming of functions, files, classes

4

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`...

dfalster

Possible naming discrepancy introduced in #330

aornugent

Adaptive integrator should fail on NAN?

1

We ended up with an error "Maximum number of subdivisions reached". This occurs in qag.h [here](https://github.com/traitecoevo/plant/blob/f5ddd7bd7724ddbc1c77c684d292841dab168a33/inst/include/plant/qag.h#L78), when the adaptive integration of photosynthesis just keeps refining more and more. The probably...

dfalster

Add bounds (or checks) to AdaptiveInterpolator

1

Need to check that our spline doesn't go below zero, as identified in `K93` with high values of `k_I`. Reprex to follow.

aornugent

Add extra ODE(s) for water or soil resources

4

Would like to start adding competition for water and / or nitrogen. But more generally, any depleting resource. @johnWilshire and I started to map how this could work. We need...

dfalster

Variant of fixed_env functions accepting a vector of xy values

1

Suggest adding a variant of the fixed_env functions that accepts a vector of xy values and from this constructs a spline and/or a spline object itself.

dfalster

Cumulative mortality does not increase monotonically with time in some cases.

2

Mortality is non-monotonic in certain instances when looking at communities of two species. In the standard one species case, we find that all mortality~time curves are monotonic (i.e. monotonic object...

itowers1

Interpolate size distributions to specified heights and times

3

dfalster