{ "_id": "6acecce1d9de2f3f33fc7e61", "Package": "plant", "Title": "A Package for Modelling Forest Trait Ecology and Evolution", "Version": "2.0.0.9002", "Authors@R": "c(\nperson(\"Daniel\", \"Falster\", , \"daniel.falster@unsw.edu.au\", c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9814-092X\")),\nperson(\"Richard\", \"FitzJohn\", , \"\", \"aut\"),\nperson(\"Andrew\", \"O'Reilly-Nugent\", , \"\", \"aut\"),\nperson(\"Isaac\", \"Towers\", , \"\", \"aut\"),\nperson(\"Mitchell\", \"Henry\", , \"\", \"ctb\"),\nperson(\"Rafael\", \"Schouten\", , \"\", \"ctb\"),\nperson(\"John\", \"Wilshire\", , \"\", \"ctb\")\n)", "Maintainer": "Daniel Falster ", "Description": "Solves trait, size and patch structured model from\n(Falster et al. 2016) using either method of characteristics or\nas stochastic, finite-sized population.", "Encoding": "UTF-8", "License": "AGPL (>= 3)", "Remotes": [ "richfitz/RcppR6", "traitecoevo/odelia@88cbff7", "traitecoevo/phylloptim@edaffe8" ], "URL": "https://github.com/traitecoevo/plant", "BugReports": "https://github.com/traitecoevo/plant/issues", "Config/roxygen2/version": "8.0.0", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://traitecoevo.r-universe.dev", "Date/Publication": "2026-10-13 20:01:13 UTC", "RemoteUrl": "https://github.com/traitecoevo/plant", "RemoteRef": "HEAD", "RemoteSha": "bd09645dec0f6d1850ffa96298dda1af6b295e07", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-13 23:31:34 UTC", "User": "root" }, "Author": "Daniel Falster [aut, cre] (ORCID:\n),\nRichard FitzJohn [aut],\nAndrew O'Reilly-Nugent [aut],\nIsaac Towers [aut],\nMitchell Henry [ctb],\nRafael Schouten [ctb],\nJohn Wilshire [ctb]", "_user": "traitecoevo", "_type": "src", "_file": "plant_2.0.0.9002.tar.gz", "_fileid": "https://r2.ropensci.org/730170c447c198fd32cdeb4bc22bf0cb1b90d06845a283b9a2d01e482e841df8", "_filesize": 1164238, "_sha256": "730170c447c198fd32cdeb4bc22bf0cb1b90d06845a283b9a2d01e482e841df8", "_expires": "2027-01-22T00:29:19.000Z", "_created": "2026-10-13T23:31:34.000Z", "_published": "2026-10-14T00:29:21.585Z", "_buildurl": "https://github.com/r-universe/traitecoevo/actions/runs/38484203847", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115597643280, "time": 955, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "11860410059" }, { "job": 115597643417, "time": 785, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11860017846" }, { "job": 115597643341, "time": 946, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "11859268723" }, { "job": 115597643248, "time": 909, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11859149674" }, { "job": 115597643380, "time": 704, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11860167065" }, { "job": 115597643368, "time": 1132, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11859444310" }, { "job": 115597644310, "time": 825, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11859144774" }, { "job": 115597643379, "time": 2960, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11861004597" }, { "job": 115593923045, "time": 672, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11859655773" }, { "job": 115597643227, "time": 445, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11859831975" }, { "job": 115597643272, "time": 947, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "11859174646" }, { "job": 115597643312, "time": 1435, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "11860650072" }, { "job": 115597643391, "time": 1024, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "11859423778" }, { "job": 115597643315, "time": 934, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11859109845" }, { "job": 115597643279, "time": 959, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11859318660" } ], "_upstream": "https://github.com/traitecoevo/plant", "_commit": { "id": "bd09645dec0f6d1850ffa96298dda1af6b295e07", "author": "Daniel Falster ", "committer": "GitHub ", "message": "Differentiate an FF16 species' fitness (#658)\n\nregnans's first asks of the stand gradient (#650, E1-E3) are fitness:\neach FF16 species' net reproduction ratio and offspring production as\ndifferentiable metrics, an invader's fitness with the canopy held at\nthe recorded resident, and the birth rate as a column.\n\nstand_gradient() now differentiates \".net_reproduction_ratio\" and\n\".offspring_production\" by every FF16 column, S_D and a constant\nbirth rate included; stand_fitness() reports them. An invasion replay\nkeeps its states on request, and its sweep stands in the resident's\nfield.\n\nCo-authored-by: Claude Opus 5.5 \n\n---------\n\nCo-authored-by: Claude Fable 5.1 ", "time": 1791921673 }, "_maintainer": { "name": "Daniel Falster", "email": "daniel.falster@unsw.edu.au", "login": "dfalster", "orcid": "0000-0002-9814-092X", "twitter": "@adaptive_plant", "description": "Associate Professor | @traitecoevo | @nicercode \n| orcid.org/0000-0002-9814-092X | twitter.com/adaptive_plant", "uuid": 3589590 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "odelia", "version": "== 0.7.3", "role": "LinkingTo" }, { "package": "phylloptim", "version": "== 0.10.2", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "logger", "role": "Imports" }, { 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"Control presets", "topics": [ "control", "control_accurate" ] }, { "page": "Control", "title": "Control parameters", "topics": [ "Control" ] }, { "page": "Disturbance_Regime", "title": "Disturbance regime", "topics": [ "Disturbance_Regime" ] }, { "page": "Environment", "title": "Creates an environment object of specified type", "topics": [ "Environment", "environment_type" ] }, { "page": "events", "title": "Discrete events applied during an SCM run.", "topics": [ "climate_extreme", "events", "events_default", "harvest", "node_introductions", "resource_pulse" ] }, { "page": "export_patch_state", "title": "Export patch state from an SCM", "topics": [ "export_patch_state" ] }, { "page": "FF16_Environment", "title": "Create an FF16_Environment object.", "topics": [ "FF16_Environment", "K93_Environment" ] }, { "page": "expand_state", "title": "Add additional state variables to the species component in output of a model.", "topics": [ "expand_state", "FF16_expand_state", "K93_expand_state", "TF24f_expand_state", "TF24_expand_state" ] }, { "page": "FF16_generate_stand_report", "title": "Generates a report on stand grown with FF16 strategy", "topics": [ "FF16_generate_stand_report" ] }, { "page": "FF16_hyperpar", "title": "Hyperparameter function for FF16 physiological model", "topics": [ "FF16_hyperpar" ] }, { "page": "FF16_individual", "title": "Create a FF16 Individual", "topics": [ "FF16_Individual" ] }, { "page": "FF16_Parameters", "title": "Setup an a model system with default or specified parameters", "topics": [ "FF16_Parameters", "K93_Parameters" ] }, { "page": "FF16_Pars", "title": "FF16 strategy parameters", "topics": [ "FF16_Pars" ] }, { "page": "FF16_Strategy", "title": "Strategy parameters", "topics": [ "FF16_Strategy" ] }, { "page": "fitness_window", "title": "Weight arrivals by a window", "topics": [ "fitness_window" ] }, { "page": "fixed_point_fitness", "title": "Invader fitness at a fixed point", "topics": [ "fixed_point_fitness" ] }, { "page": "generate_strategy", "title": "Generate strategies from traits", "topics": [ "generate_strategy", "strategy_list" ] }, { "page": "gradient_control", "title": "The 'Control' entries a census gradient depends on.", "topics": [ "gradient_control" ] }, { "page": "grow_individual_to_size", "title": "Grow individual to given size", "topics": [ "grow_individual_to_height", "grow_individual_to_size" ] }, { "page": "grow_individual_to_time", "title": "Grow a plant", "topics": [ "grow_individual_to_time" ] }, { "page": "Individual", "title": "Individual object", "topics": [ "Individual" ] }, { "page": "integrate_over_size_distribution", "title": "Integrate over the size distribution for each species at each time point, to give totals of each variable Integrations are performed using trapezium integration", "topics": [ "integrate_over_size_distribution" ] }, { "page": "Internals", "title": "Extract Internals from plant object", "topics": [ "Internals" ] }, { "page": "interpolate_to_heights", "title": "Interpolate data on size distributions for each species to specific heights at every time point", "topics": [ "interpolate_to_heights" ] }, { "page": "interpolate_to_times", "title": "Interpolate data on size distributions for each species to specific timer points, using specified interpolation method", "topics": [ "interpolate_to_times" ] }, { "page": "K93_hyperpar", "title": "Hyperparameter function for K93 physiological model", "topics": [ "K93_hyperpar" ] }, { "page": "K93_Individual", "title": "Create a K93 Individual or Node", "topics": [ "K93_Individual" ] }, { "page": "K93_Pars", "title": "K93 strategy parameters", "topics": [ "K93_Pars" ] }, { "page": "K93_Strategy", "title": "Strategy parameters", "topics": [ "K93_Strategy" ] }, { "page": "Leaf", "title": "Leaf model", "topics": [ "Leaf" ] }, { "page": "make_FF16_hyperpar", "title": "Hyperparameters for FF16 physiological model", "topics": [ "make_FF16_hyperpar" ] }, { "page": "Hyperparameter_functions", "title": 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"node_schedule_times_periodic" ] }, { "page": "NodeSchedule", "title": "Schedule of node introduction times", "topics": [ "NodeSchedule" ] }, { "page": "OdeControl", "title": "ODE Control parameters", "topics": [ "OdeControl" ] }, { "page": "optimise_individual_rate_at_size_by_trait", "title": "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 trait", "topics": [ "optimise_individual_rate_at_height_by_trait", "optimise_individual_rate_at_size_by_trait" ] }, { "page": "plant_log_console", "title": "Activate logging", "topics": [ "plant_log_console" ] }, { "page": "plot_size_distribution", "title": "Title", "topics": [ "plot_size_distribution" ] }, { "page": "pulse_series_poisson", "title": "Series of resource pulses", "topics": [ "pulse_series_poisson", "pulse_series_record", "pulse_series_regular" ] }, { "page": "QK", "title": "Gauss-Kronrod Quadrature", "topics": [ "QK" ] }, { "page": "rainfall_pulse", "title": "A rainfall pulse for TF24.", "topics": [ "rainfall_pulse" ] }, { "page": "resource_compensation_point", "title": "Whole plant light compensation point", "topics": [ "resource_compensation_point" ] }, { "page": "run_plant_benchmarks", "title": "Check performance on current system using package bench", "topics": [ "run_plant_benchmarks" ] }, { "page": "run_scm", "title": "Run SCM", "topics": [ "run_scm" ] }, { "page": "run_stochastic_collect", "title": "Run a stochastic patch, Collecting Output", "topics": [ "run_stochastic_collect" ] }, { "page": "run_until_converged", "title": "Run until the stand's block means settle", "topics": [ "run_until_converged" ] }, { "page": "scenario_eval", "title": "Scenario evaluation framework for the TF24 / TF24f hydraulic models.", "concept": [ "scenario_eval" ], "topics": [ "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" ] }, { "page": "scm_base_parameters", "title": "Basic default parameters for a given strategy", "topics": [ "scm_base_parameters" ] }, { "page": "seq_log", "title": "Sequence in log space", "topics": [ "seq_log", "seq_log_range", "seq_range" ] }, { "page": "set_initial_state", "title": "Seed Parameters with an initial patch state", "topics": [ "set_initial_state" ] }, { "page": "stand_census", "title": "Metrics of a solved stand.", "topics": [ "stand_census", "stand_fitness" ] }, { "page": "stand_census_state_adjoint", "title": "Sensitivity of the stand metrics to the ODE state at the current time.", "topics": [ "stand_census_state_adjoint" ] }, { "page": "stand_gradient", "title": "Gradient of a stand's metrics with respect to traits.", "topics": [ "stand_gradient" ] }, { "page": "stand_gradient_compare", "title": "Compare two stand gradients.", "topics": [ "stand_gradient_compare" ] }, { "page": "stand_gradient_refused", "title": "Which of a gradient's metrics were refused.", "topics": [ "stand_gradient_refused" ] }, { "page": "TF24_Environment", "title": "Create an TF24_Environment object.", "topics": [ "TF24_Environment" ] }, { "page": "TF24_generate_stand_report", "title": "Generates a report on stand grown with TF24 strategy", "topics": [ "TF24_generate_stand_report" ] }, { "page": "TF24_H_ANCHOR", "title": "Height at which the stem hydraulic path is anchored [m].", "topics": [ "TF24_H_ANCHOR" ] }, { "page": "TF24_hyperpar", "title": "Hyperparameter function for TF24 physiological model", "topics": [ "TF24_hyperpar" ] }, { "page": "TF24_Individual", "title": "Create a TF24 Plant or Node", "topics": [ "TF24_Individual" ] }, { "page": "TF24_K_s_from_whole_stem", "title": "Convert a whole-stem sapwood-specific conductivity to a 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