Package index • medfate

Forest definition

Forest definition and manipulation functions

forest exampleforest exampleforest2: Description of a forest stand.

emptyforest(): Creation of an empty forest

tree2forest() shrub2forest(): Single-cohort forests

forest_mapTreeTable() forest_mapShrubTable() forest_mapWoodyTables(): Map forest plot data

forest_mergeTrees() forest_mergeShrubs() forest_reduceToDominant(): Forest complexity reduction

poblet_trees: Example forest inventory data

Species parameters

Species parameter data and utility functions.

SpParams SpParamsDefinition SpParamsMED: Data tables with species parameter definitions and values

modifySpParams() modifyCohortParams() modifyInputParams(): Modify parameters

trait_family_means: Parameter average values

Forest structure

Summarizing and displaying forest attributes

summary(<forest>) print(<summary.forest>): Summary of forest structure

plot(<forest>) shinyplot(<forest>): Plot forest attributes

Meteorology

Meteorological forcing

examplemeteo: Example daily meteorology data

Soil

Soil initialization

defaultSoilParams(): Default soil parameters

soil() summary(<soil>): Soil initialization

soil_redefineLayers(): Redefine soil layer widths

soil_retentionCurvePlot() soil_conductivityCurvePlot(): Soil water retention and conductivity plots

Simulation inputs

Simulation control and input objects

spwbInput() growthInput(): Input for simulation models

forest2aboveground() forest2belowground() forest2spwbInput() forest2growthInput(): Input for simulation models (deprecated)

defaultControl(): Control parameters for simulation models

defaultManagementFunction() defaultManagementArguments(): Default forest management actions

resetInputs(): Reset simulation inputs

Simulation functions

Simulation model functions

spwb() pwb(): Soil-plant water balance

growth_day() spwb_day(): Single-day simulation

growth(): Forest growth

fordyn(): Forest dynamics

Plots and summaries

Summaries, extraction and plots of simulation results

plot(<spwb>) plot(<aspwb>) plot(<pwb>) plot(<growth>) plot(<fordyn>): Plots simulation results

plot(<spwb_day>) plot(<growth_day>) plot(<pwb_day>): Plots simulation results for one day

summary(<spwb>) summary(<aspwb>) summary(<pwb>) summary(<growth>) summary(<fordyn>): Summarize simulation results

extract(): Extracts model outputs

shinyplot(): Shiny app with interactive plots

Post-processing

Other post-processing functions

resistances(): Soil-plant resistances

droughtStress(): Drought stress indicators

waterUseEfficiency(): Water use efficiency

fireHazard(): Fire hazard

Model analysis

Evaluation and optimization

exampleobs: Example observed data

evaluation_table() evaluation_stats() evaluation_plot() evaluation_metric(): Evaluation of simulations results

multiple_runs() optimization_function() optimization_evaluation_function() optimization_multicohort_function() optimization_evaluation_multicohort_function(): Multiple model runs and function factories for optimization routines

utils_rockOptimization(): Optimization of rock fragment content

utils_ldrExploration() utils_ldrOptimization(): Optimization of root distribution

Wildfire

Fuel characteristics and fire behaviour

fire_FCCS() fire_Rothermel(): Fire behaviour functions

fuel_stratification() fuel_FCCS(): Fuel stratification and fuel characteristics

SFM_metric: Standard fuel models (Albini 1976, Scott & Burgan 2005)