Package: plant 2.0.0.9001

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

5.92 score 54 stars 40 scripts 82 exports 25 dependencies

Last updated from:edbad18406. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK405
linux-devel-x86_64OK467
source / vignettesOK311
linux-release-arm64OK445
linux-release-x86_64OK448
macos-release-arm64OK293
macos-release-x86_64OK592
macos-oldrel-arm64OK362
macos-oldrel-x86_64OK739
windows-develOK632
windows-releaseFAIL34
windows-oldrelOK533
wasm-releaseOK290

Exports:%>%add_mutantadd_strategiescontrolControlcontrol_accurateDisturbance_RegimeEnvironmentenvironment_typeexpand_parametersexpand_stateexport_patch_stateFF16_EnvironmentFF16_expand_stateFF16_generate_stand_reportFF16_hyperparFF16_IndividualFF16_ParametersFF16_ParsFF16_Strategygenerate_strategygrow_individual_to_heightgrow_individual_to_sizegrow_individual_to_timehyperparIndividualintegrate_over_size_distributioninterpolate_to_heightsinterpolate_to_timesInterpolatorK93_EnvironmentK93_expand_stateK93_hyperparK93_IndividualK93_ParametersK93_ParsK93_StrategyLeafmake_FF16_hyperparmake_hyperparmake_initial_statemake_K93_hyperparmake_TF24_hyperparmake_TF24f_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_stochastic_collectscm_base_parametersseq_logseq_log_rangeseq_rangeset_initial_statestrategy_listTF24_EnvironmentTF24_expand_stateTF24_generate_stand_reportTF24_hyperparTF24_IndividualTF24_ParametersTF24_ParsTF24_plot_diagnosticsTF24_StrategyTF24f_expand_stateTF24f_generate_stand_reportTF24f_hyperparTF24f_IndividualTF24f_ParametersTF24f_Strategytidy_individualtrait_matrixutil_colour_set_opacityWeibull_Disturbance_Regime

Dependencies:BHclicpp11crayondplyrgenericsgluelifecycleloggrmagrittrodeliapillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Add strategies (or a mutant) to Parametersadd_mutant add_strategies expand_parameters mutant_parameters
Control presetscontrol control_accurate
Control parametersControl
Disturbance regimeDisturbance_Regime
Creates an environment object of specified typeEnvironment environment_type
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
Generate strategies from traitsgenerate_strategy strategy_list
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
K93 strategy parametersK93_Pars
Strategy parametersK93_Strategy
Leaf modelLeaf
Hyperparameters for FF16 physiological modelmake_FF16_hyperpar make_TF24f_hyperpar make_TF24_hyperpar
Hyperparameters for physiological modelhyperpar make_hyperpar param_hyperpar
Build an initial size distributionmake_initial_state
Hyperparameters for K93 physiological modelmake_K93_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 a stochastic patch, Collecting Outputrun_stochastic_collect
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
Create an TF24_Environment object.TF24_Environment
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
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
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