dfalster
commented
5 years ago Updated list, from develop branch, commit ee692a705e3c444207c361ee1d6424ee5aca8e98:
➜ plant git:(develop) grep -r TODO .
./man/Internals.Rd:\title{Internals TODO}
./man/Internals.Rd:Internals TODO
./vignettes/physiology.Rmd:# TODO: can we get groups as headers spanning multiple columns?
./tests/testthat/test-stochastic-patch-runner.R: ## TODO: more tests on collect output
./tests/testthat/test-species.R:## TODO: The tests here really warrant splitting into different chunks
./tests/testthat/test-strategy-ff16-reference-comparison.R: ## TODO: Check with Daniel here -- might need updating.
./tests/testthat/test-strategy-ff16-reference-comparison.R: ## TODO: This is due to issues with how we think about size; see notes
./tests/testthat/test-strategy-ff16-reference-comparison.R: ## TODO: Check what growth variables look like before running
./tests/testthat/test-strategy-ff16-reference-comparison.R: ## TODO: add lcp_whole_plant test to refference comparison
./tests/testthat/test-build-schedule.R:## TODO: Not yet done.
./tests/testthat/test-cohort.R:## TODO: This is all just ported over from tree1 and needs splitting
./tests/testthat/test-cohort.R: ## TODO: Not done yet:
./tests/testthat/test-plant-runner.R:## TODO: another useful function could be to construct splines for
./tests/testthat/test-scm.R: ## TODO: The unlist here is annoying...
./tests/testthat/test-scm.R: ## ## TODO: This is a fairly inadequate set of tests; none of the failure
./tests/testthat/test-scm.R: ## # TODO: This needs implementing; requires get/set of the ODE solver
./tests/testthat/test-patch.R:## TODO: Test add_seeds(vector<double>)
./tests/testthat/test-patch.R: ## TODO: This is something that needs validating: the seed_rain and
./tests/testthat/test-patch.R: ## TODO: This is not really a test, but we need to look at this and
./r/plant.R: ## TODO: This could also be done by better configuring the
./r/plant.R: # TODO: size index uses index from 0
./r/plant.R: ## TODO: Consider making this an error, or making the test a bit better.
./r/plant.R: # TODO: size index uses index from 0
./r/scm_support.R: ## TODO: This needs to be made to work with the output of
./r/equilibrium.R: min_seed_rain <- 1e-10 # TODO: should also be in the controls?
./r/equilibrium.R: ## TODO: This is annoying, but turns out to be a problem for getting
./r/equilibrium.R: ## TODO: most of the plant_log_eq things here should be DEBUG not INFO?
./r/equilibrium.R: ## TODO: don't do anything if we don't have at least 2 species?
./r/equilibrium.R: ## TODO: This was p$control$equilibrium_inviable_test, but I think
./r/fitness_trait_space.R: ## TODO: It seems a crying shame to throws all this information
./r/ff16.R: ## TODO: k_I should actually be in default parameter set, so perhaps don't pass into function?
./r/ff16.R: ## TODO: Remove the 0.5 hardcoded default for k_I here, and deal
./r/util.R: ## TODO: This uses an implementation detail of RcppR6 that is not
./TODO.md:# TODO
Binary file ./.git/index matches
./.git/COMMIT_EDITMSG:# modified: TODO.md
./inst/RcppR6_classes.yml: # TODO: This is broken:
./inst/RcppR6_classes.yml: # TODO: Not 100% sure this is needed from R:
./inst/RcppR6_classes.yml: # TODO: Not 100% sure this is needed from R:
./inst/include/plant/plant.h: // TODO: maybe reuse intervals? default false
./inst/include/plant/control.h:// TODO: Eventually I need to make sure that the numbers here are
./inst/include/plant/stochastic_patch.h: // TODO: No support here for setting *vectors* of species. Might
./inst/include/plant/stochastic_patch_runner.h: // TODO: consider renaming CohortSchedule -> Schedule
./inst/include/plant/get_state.h:// TODO: Might be worth moving this into the main interface? Not sure
./inst/include/plant/get_state.h: // TODO: this should work (also up in get_state(Cohort<T>, ...)).
./inst/include/plant/internals.h:// TODO: extra_state bounds, upper and lower limits
./inst/include/plant/parameters.h:// TODO: I will possibly move out the "Patch" parameters out into
./inst/include/plant/parameters.h:// TODO: Will require some free functions on the R side:
./inst/include/plant/parameters.h:// TODO: Consider adding this to scm_utils.h perhaps?
./inst/include/plant/stochastic_species.h: // TODO: Here, and elsewhere, consider using a
./inst/include/plant/stochastic_species.h:// TODO: This is going to change...
./inst/include/plant/stochastic_species.h: // TODO: also simplify r_heights for Species?
./inst/include/plant/RcppR6_support.hpp: // TODO: need to deal with failure here (i.e. R_NilValue), or we
./inst/include/plant/ff16_strategy.h: // TODO : expose this so can access state_names directly
./inst/include/plant/cohort.h:// TODO: Eventually change to growth rate given size
./inst/include/plant/species.h: // TODO: Should the seed be recomputed here?
./inst/include/plant/util.h:// TODO: Probably move these out to their own file?
./inst/include/plant/patch.h:// TODO: We should only be recomputing the light environment for the
./inst/include/plant/scm.h: // TODO: These are liable to change to return all species at once by
./inst/include/plant/scm.h: // TODO: This causes this to happen too often, given we usually get
./inst/include/plant/scm.h: // all the errors I think? (see TODO in class definition)
./inst/include/plant/scm.h: // TODO: I think we need to scale this by total area; that should be
./inst/include/plant/ode_solver.h:// TODO: Need to go through and sort out the logic here; it might be
./inst/include/plant/ode_solver.h: // TODO: Not clear that this is the right thing here; should just
./inst/docs/vignettes/physiology.Rmd:# TODO: can we get groups as headers spanning multiple columns?
./inst/docs/R/utils.R:#TODO - everything from here down can be deleted I think
./inst/docs/patch.Rmd:<!-- TODO: should really start here using a patch with fixed seed rain -->
./inst/docs/Individuals.Rmd:<!-- TODO: next bit is a bit vague -->
./inst/docs/Individuals.Rmd:<!-- TODO: PlantPlus
./inst/docs/Individuals.Rmd:TODO: Revise with new Plant Plus
./inst/docs/Individuals.Rmd:TODO: Revise with new Plant Plus
./inst/docs/Individuals.Rmd:<!-- # TODO: PlantPlus revise once LCP available
./inst/docs/Individuals.Rmd:<!-- TODO: Remove below once lap works -->
./inst/docs/Individuals.Rmd:<!-- # TODO: PlantPlus revise once LCP available
./inst/docs/physiology.Rmd:# TODO: can we get groups as headers spanning multiple columns?
./inst/reference_plant_ff16/extra.R: ## TODO: These are hard-coded for now, but the upper limit could be
./src/ff16_strategy.cpp:// TODO: Document consistent argument order: l, b, s, h, r
./src/ff16_strategy.cpp:// TODO: Document ordering of different types of variables (size
./src/ff16_strategy.cpp:// TODO: Consider moving to activating as an initialisation list?
./src/ff16_strategy.cpp:// TODO: Ordering below here needs working on, probably as @dfalster
./src/ff16_strategy.cpp:// TODO: Change top two to use mass_live_dt
./src/ff16_strategy.cpp:// TODO: Do we not track root mass change?
./src/ff16_strategy.cpp: // TODO: MODIFY THIS SO WE PASS THE AREA_LEAF WE RECOMPUTER
./src/tk_spline.cpp: // TODO sort x and y, rather than returning an error
Scattered through the code