Package: plant 2.0.0.9000

Daniel Falster

plant: A Package for Modelling Forest Trait Ecology and Evolution

Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.

Authors:Daniel Falster [aut, cre], Richard FitzJohn [aut], Andrew O'Reilly-Nugent [aut], Mitchell Henry [ctb], Rafael Schouten [ctb], Isaac Towers [ctb], John Wilshire [ctb]

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plant.pdf |plant.html✨
plant/json (API)

# Install 'plant' in R:
install.packages('plant', repos = c('https://traitecoevo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/traitecoevo/plant/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp

5.87 score 53 stars 86 exports 25 dependencies

Last updated 4 days agofrom:6dd5cae58f. Checks:1 OK, 8 NOTE, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 13 2025
R-4.5-win-x86_64NOTEMar 13 2025
R-4.5-mac-x86_64ERRORMar 13 2025
R-4.5-mac-aarch64NOTEMar 13 2025
R-4.5-linux-x86_64NOTEMar 13 2025
R-4.4-win-x86_64NOTEMar 13 2025
R-4.4-mac-x86_64ERRORMar 13 2025
R-4.4-mac-aarch64NOTEMar 13 2025
R-4.4-linux-x86_64NOTEMar 13 2025
R-4.3-win-x86_64NOTEMar 13 2025
R-4.3-mac-x86_64ERRORMar 13 2025
R-4.3-mac-aarch64NOTEMar 13 2025

Exports:%>%build_scheduleControlDisturbance_Regimeenvironment_typeexpand_parametersfast_controlFF16_EnvironmentFF16_expand_stateFF16_fixed_environmentFF16_generate_stand_reportFF16_hyperparFF16_IndividualFF16_make_environmentFF16_ParametersFF16_StrategyFF16r_hyperparFF16r_IndividualFF16r_make_environmentFF16r_ParametersFF16r_StrategyFF16w_fixed_environmentFF16w_hyperparFF16w_IndividualFF16w_make_environmentFF16w_Strategygrow_individual_to_heightgrow_individual_to_sizegrow_individual_to_timehyperparIndividualintegrate_over_size_distributioninterpolate_to_heightsinterpolate_to_timesInterpolatorK93_EnvironmentK93_fixed_environmentK93_hyperparK93_IndividualK93_make_environmentK93_ParametersK93_Strategymake_environmentmake_FF16_hyperparmake_FF16r_hyperparmake_FF16w_hyperparmake_hyperparmake_K93_hyperparmake_patchmake_scm_integratemake_TF24_hyperparmutant_parametersNo_Disturbancenode_schedule_times_defaultNodeScheduleoptimise_individual_rate_at_height_by_traitoptimise_individual_rate_at_size_by_traitparam_hyperparplant_log_consoleplot_size_distributionresource_compensation_pointrun_plant_benchmarksrun_scmrun_scm_collectrun_stochastic_collectscm_base_controlscm_base_parametersscm_patchscm_stateseq_logseq_log_rangeseq_rangestrategy_listTF24_EnvironmentTF24_fixed_environmentTF24_generate_stand_reportTF24_hyperparTF24_IndividualTF24_make_environmentTF24_ParametersTF24_Strategytidy_individualtidy_patchtrait_matrixutil_colour_set_opacityWeibull_Disturbance_Regime

Dependencies:BHclicpp11crayondplyrfansigenericsgluelifecycleloggrmagrittrpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Getting started with the plant model

Rendered fromplant.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2024-05-22
Started: 2015-05-29

Readme and manuals

Help Manual

Help pageTopics
Build Node Schedulebuild_schedule
Control parametersControl
Disturbance regimeDisturbance_Regime
Make environment objects for a strategyenvironment_type make_environment
Setup parameters to run resindets or mutantsexpand_parameters mutant_parameters
Fast Control Defaultsfast_control
Create an FF16_Environment object.FF16_Environment K93_Environment TF24_Environment
Add additional state variables to the species component in output of FF16 model.FF16_expand_state
Construct a fixed environment for a modelFF16w_fixed_environment FF16_fixed_environment K93_fixed_environment TF24_fixed_environment
Generates a report on stand grown with FF16 strategyFF16_generate_stand_report
Hyperparameter function for FF16 physiological modelFF16_hyperpar
Create a FF16 IndividualFF16_Individual
create a model Environment objectFF16r_make_environment FF16w_make_environment FF16_make_environment K93_make_environment TF24_make_environment
Setup an a model system with default or specified parametersFF16r_Parameters FF16_Parameters K93_Parameters TF24_Parameters
Strategy parametersFF16_Strategy
Create a test environment for FF16 startegyFF16r_test_environment FF16w_test_environment FF16_test_environment K93_test_environment TF24_test_environment
Hyperparameter function for FF16r physiological modelFF16r_hyperpar
Create a FF16r Plant or NodeFF16r_Individual
Strategy parametersFF16r_Strategy
Create a FF16w Plant or NodeFF16w_Individual FF16w_Parameters
Strategy parametersFF16w_Strategy
Grow individual to given sizegrow_individual_to_height grow_individual_to_size
Grow a plantgrow_individual_to_time
Individual objectIndividual
Integrate over the size distribution for each species at each time point, to give totals of each variable Integrations are performed using trapezium integrationintegrate_over_size_distribution
Extract Internals from plant objectInternals
Interpolate data on size distributions for each species to specific heights at every time pointinterpolate_to_heights
Interpolate data on size distributions for each species to specific timer points, using specified interpolation methodinterpolate_to_times
Spline interpolationInterpolator
Hyperparameter function for K93 physiological modelK93_hyperpar
Create a K93 Individual or NodeK93_Individual
Strategy parametersK93_Strategy
Hyperparameters for FF16 physiological modelmake_FF16_hyperpar
Hyperparameters for FF16r physiological modelmake_FF16r_hyperpar
Hyperparameters for FF16w physiological modelFF16w_hyperpar make_FF16w_hyperpar
Hyperparameters for FF16 physiological modelhyperpar make_hyperpar param_hyperpar
Hyperparameters for K93 physiological modelmake_K93_hyperpar
Reconstruct a patchmake_patch scm_patch scm_state
Integrate SCM variablesmake_scm_integrate
Hyperparameters for TF24 physiological modelmake_TF24_hyperpar
No disturbance regime No_Disturbance_Regime control objectNo_Disturbance
Generate Default Node Introduction Timesnode_schedule_times_default
Schedule of node introduction timesNodeSchedule
ODE Control parametersOdeControl
The function `optimise_individual_rate_at_height_by_trait` and `optimise_individual_rate_at_size_by_trait` solve for the maximum of some rate (e.g. growth rate) at a specified height within the interval of the bounds of a given traitoptimise_individual_rate_at_height_by_trait optimise_individual_rate_at_size_by_trait
Activate logging with loggrplant_log_console
Titleplot_size_distribution
Gauss-Kronrod QuadratureQK
Whole plant light compensation pointresource_compensation_point
Check performance on current system using package benchrun_plant_benchmarks
Run SCMrun_scm
Run the SCM, Collecting Outputrun_scm_collect
Run a stochastic patch, Collecting Outputrun_stochastic_collect
Sensible, fast (ish) SCM control settingsscm_base_control
Basic default parameters for a given strategyscm_base_parameters
Sequence in log spaceseq_log seq_log_range seq_range
Create a list of Strategiesstrategy_list
Generates a report on stand grown with TF24 strategyTF24_generate_stand_report
Hyperparameter function for TF24 physiological modelTF24_hyperpar
Create a TF24 Plant or NodeTF24_Individual
Strategy parametersTF24_Strategy
Turn `env` component of solver output into a tidy data objecttidy_env
Turn `results` of plant solver, when solving individuals into a tidy data objecttidy_individual
Turns output of plant solver into a tidy data objecttidy_patch
Turn `species` component of plant solver output into a tidy data objecttidy_species
Create trait matrixtrait_matrix
Make colours transparentutil_colour_set_opacity
Weibull disturbance regime The frequency of disturbance in a meta-population of patches follows a Weibull distributionWeibull_Disturbance_Regime