Package: plant 2.0.0.9002

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], Isaac Towers [aut], Mitchell Henry [ctb], Rafael Schouten [ctb], John Wilshire [ctb]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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

6.14 score 55 stars 42 scripts 120 exports 26 dependencies

Last updated from:bd09645dec. Checks:6 ERROR, 5 OK, 4 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR955
linux-devel-x86_64ERROR785
source / vignettesOK672
linux-release-arm64ERROR946
linux-release-x86_64OK909
macos-release-arm64NOTE825
macos-release-x86_64NOTE2960
macos-oldrel-arm64NOTE704
macos-oldrel-x86_64NOTE1132
windows-devel-arm64ERROR947
windows-devel-x86_64ERROR1435
windows-release-arm64OK934
windows-release-x86_64OK959
windows-oldrel-x86_64ERROR1024
wasm-releaseOK445

Exports:%>%add_mutantadd_strategiesbuild_scenariocheck_driver_interpolationclassify_scm_runclimate_extremecontrolControlcontrol_accurateDisturbance_RegimeEnvironmentenvironment_typeevaluate_scenarioeventsevents_defaultexpand_parametersexpand_stateexport_patch_stateFF16_EnvironmentFF16_expand_stateFF16_generate_stand_reportFF16_hyperparFF16_IndividualFF16_ParametersFF16_ParsFF16_Strategyfitness_windowfixed_point_fitnessgenerate_strategygradient_controlgrow_individual_to_heightgrow_individual_to_sizegrow_individual_to_timeharvesthyperparIndividualintegrate_over_size_distributioninterpolate_to_heightsinterpolate_to_timesK93_EnvironmentK93_expand_stateK93_hyperparK93_IndividualK93_ParametersK93_ParsK93_StrategyLeafmake_FF16_hyperparmake_hyperparmake_initial_statemake_K93_hyperparmake_TF24_hyperparmake_TF24f_hyperparmodel_idmodel_versionmutant_parametersNo_Disturbancenode_introductionsnode_schedule_times_defaultnode_schedule_times_periodicNodeScheduleoptimise_individual_rate_at_height_by_traitoptimise_individual_rate_at_size_by_traitparam_hyperparplant_log_consoleplot_size_distributionpulse_series_poissonpulse_series_recordpulse_series_regularrainfall_pulseread_scenario_mappingread_scenario_tableresource_compensation_pointresource_pulserun_plant_benchmarksrun_scenariosrun_scmrun_stochastic_collectrun_until_convergedscenario_controlscenario_generate_reportscenario_model_fingerprintscenario_run_metadatascenario_summaryscenario_to_configscm_base_parametersseq_logseq_log_rangeseq_rangeset_initial_statestand_censusstand_census_state_adjointstand_fitnessstand_gradientstand_gradient_comparestand_gradient_refusedstrategy_listTF24_EnvironmentTF24_expand_stateTF24_generate_stand_reportTF24_H_ANCHORTF24_hyperparTF24_IndividualTF24_K_s_from_whole_stemTF24_ParametersTF24_ParsTF24_plot_diagnosticsTF24_StrategyTF24f_expand_stateTF24f_generate_stand_reportTF24f_hyperparTF24f_IndividualTF24f_ParametersTF24f_Strategytidy_individualtidy_snapshotstrait_matrixutil_colour_set_opacityWeibull_Disturbance_Regime

Dependencies:BHclicpp11crayondplyrgenericsgluelifecycleloggermagrittrodeliaphylloptimpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Add strategies (or a mutant) to Parametersadd_mutant add_strategies expand_parameters mutant_parameters
Check how a driver's control points survive interpolationcheck_driver_interpolation
Control presetscontrol control_accurate
Control parametersControl
Disturbance regimeDisturbance_Regime
Creates an environment object of specified typeEnvironment environment_type
Discrete events applied during an SCM run.climate_extreme events events_default harvest node_introductions resource_pulse
Export patch state from an SCMexport_patch_state
Create an FF16_Environment object.FF16_Environment K93_Environment
Add additional state variables to the species component in output of a model.expand_state FF16_expand_state K93_expand_state TF24f_expand_state TF24_expand_state
Generates a report on stand grown with FF16 strategyFF16_generate_stand_report
Hyperparameter function for FF16 physiological modelFF16_hyperpar
Create a FF16 IndividualFF16_Individual
Setup an a model system with default or specified parametersFF16_Parameters K93_Parameters
FF16 strategy parametersFF16_Pars
Strategy parametersFF16_Strategy
Weight arrivals by a windowfitness_window
Invader fitness at a fixed pointfixed_point_fitness
Generate strategies from traitsgenerate_strategy strategy_list
The 'Control' entries a census gradient depends on.gradient_control
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
Hyperparameter function for K93 physiological modelK93_hyperpar
Create a K93 Individual or NodeK93_Individual
K93 strategy parametersK93_Pars
Strategy parametersK93_Strategy
Leaf modelLeaf
Hyperparameters for FF16 physiological modelmake_FF16_hyperpar
Hyperparameters for physiological modelhyperpar make_hyperpar param_hyperpar
Build an initial size distributionmake_initial_state
Hyperparameters for K93 physiological modelmake_K93_hyperpar
Hyperparameters for TF24 physiological modelmake_TF24f_hyperpar make_TF24_hyperpar
Scientific version of a physiological modelmodel_id model_version
No disturbance regime No_Disturbance_Regime control objectNo_Disturbance
Generate Default Node Introduction Timesnode_schedule_times_default
Periodic node introduction timesnode_schedule_times_periodic
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 loggingplant_log_console
Titleplot_size_distribution
Series of resource pulsespulse_series_poisson pulse_series_record pulse_series_regular
Gauss-Kronrod QuadratureQK
A rainfall pulse for TF24.rainfall_pulse
Whole plant light compensation pointresource_compensation_point
Check performance on current system using package benchrun_plant_benchmarks
Run SCMrun_scm
Run a stochastic patch, Collecting Outputrun_stochastic_collect
Run until the stand's block means settlerun_until_converged
Scenario evaluation framework for the TF24 / TF24f hydraulic models.build_scenario classify_scm_run evaluate_scenario read_scenario_mapping read_scenario_table run_scenarios scenario_control scenario_eval scenario_generate_report scenario_model_fingerprint scenario_run_metadata scenario_summary scenario_to_config
Basic default parameters for a given strategyscm_base_parameters
Sequence in log spaceseq_log seq_log_range seq_range
Seed Parameters with an initial patch stateset_initial_state
Metrics of a solved stand.stand_census stand_fitness
Sensitivity of the stand metrics to the ODE state at the current time.stand_census_state_adjoint
Gradient of a stand's metrics with respect to traits.stand_gradient
Compare two stand gradients.stand_gradient_compare
Which of a gradient's metrics were refused.stand_gradient_refused
Create an TF24_Environment object.TF24_Environment
Generates a report on stand grown with TF24 strategyTF24_generate_stand_report
Height at which the stem hydraulic path is anchored [m].TF24_H_ANCHOR
Hyperparameter function for TF24 physiological modelTF24_hyperpar
Create a TF24 Plant or NodeTF24_Individual
Convert a whole-stem sapwood-specific conductivity to a terminal-segment one.TF24_K_s_from_whole_stem
Setup an a TF24 system with default or specified parametersTF24_Parameters
TF24 strategy parametersTF24_Pars
Diagnostic panel plot for a TF24 standTF24_plot_diagnostics
Strategy parametersTF24_Strategy
Generates a report on stand grown with TF24f strategyTF24f_generate_stand_report
Hyperparameter function for TF24f physiological modelTF24f_hyperpar
Create a TF24f Plant or NodeTF24f_Individual
Set up a TF24f system with default or specified parametersTF24f_Parameters
Strategy parametersTF24f_Strategy
Turn `results` of plant solver, when solving individuals into a tidy data objecttidy_individual
Tidy a run's snapshotstidy_snapshots
Turn `species` component of plant solver output into a tidy data objecttidy_env tidy_patch tidy_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