Forest dynamics

Function fordyn implements a forest dynamics model that simulates growth, mortality, recruitment and (optionally) management actions in a given forest stand during a period specified in the input climatic data.

Usage

fordyn(
  forest,
  soil,
  SpParams,
  meteo,
  control,
  latitude,
  elevation = NA,
  slope = NA,
  aspect = NA,
  CO2ByYear = numeric(0),
  management_function = NULL,
  management_args = NULL
)

Arguments

forest: An object of class forest. Alternatively, the output of a previous run, if continuing a previous simulation.
soil: An object of class data.frame or soil.
SpParams: A data frame with species parameters (see SpParamsMED and SpParamsDefinition).
meteo: A data frame with daily weather data series (see spwb).
control: A list with default control parameters (see defaultControl).
latitude: Latitude (in degrees).
elevation, slope, aspect: Elevation above sea level (in m), slope (in degrees) and aspect (in degrees from North).
CO2ByYear: A named numeric vector with years as names and atmospheric CO2 concentration (in ppm) as values. Used to specify annual changes in CO2 concentration along the simulation (as an alternative to specifying daily values in meteo).
management_function: A function that implements forest management actions (see details).
management_args: A list of additional arguments to be passed to the management_function.

Value

A list of class 'fordyn' with the following elements:

"StandSummary": A data frame with stand-level summaries (tree basal area, tree density, shrub cover, etc.) at the beginning of the simulation and after each simulated year.
"SpeciesSummary": A data frame with species-level summaries (tree basal area, tree density, shrub cover, etc.) at the beginning of the simulation and after each simulated year.
"CohortSummary": A data frame with cohort-level summaries (tree basal area, tree density, shrub cover, etc.) at the beginning of the simulation and after each simulated year.
"TreeTable": A data frame with tree-cohort data (species, density, diameter, height, etc.) at the beginning of the simulation (if any) and after each simulated year.
"DeadTreeTable": A data frame with dead tree-cohort data (species, density, diameter, height, etc.) at the beginning of the simulation and after each simulated year.
"CutTreeTable": A data frame with cut tree data (species, density, diameter, height, etc.) after each simulated year.
"ShrubTable": A data frame with shrub-cohort data (species, density, cover, height, etc.) at the beginning of the simulation and after each simulated year.
"DeadShrubTable": A data frame with dead shrub-cohort data (species, density, cover, height, etc.) at the beginning of the simulation (if any) and after each simulated year.
"CutShrubTable": A data frame with cut shrub data (species, density, cover, height, etc.) after each simulated year.
"ForestStructures": A list with the forest object of the stand at the beginning of the simulation and after each simulated year.
"GrowthResults": A list with the results of calling function growth for each simulated year.
"ManagementArgs": A list of management arguments to be used in another call to fordyn.
"NextInputObject": An object of class growthInput to be used in a subsequent simulation.
"NextForestObject": An object of class forest to be used in a subsequent simulation.

Details

Function fordyn simulates forest dynamics for annual time steps, building on other simulation functions. For each simulated year, the function performs the following steps:

Calls function growth to simulate daily water/carbon balance, growth and mortality processes and update the forest object.
If required, calls function management_function, using as parameters the forest object and management_args, which may result in a density reduction for existing plant cohorts and/or a set of new planted cohorts.
Simulate natural recruitment (for species present in the stand or given in a seed rain input).
Prepares the input of function growth for the next annual time step.
Store forest status, management arguments, and summaries.

To enable forest management, the user needs to provide a function that implements it, which is passed to fordyn via its argument management_function. Such function should have the following arguments:

"x": the forest object representing the stand to be managed.
"args": a list of parameters regulating the behavior of the management function.
"verbose": a logical flag to enable console output during the execution of the management function.

and return a list with the following elements:

"action": A string identifying the action performed (e.g. "thinning").
"N_tree_cut": A vector with the density of trees removed.
"Cover_shrub_cut": A vector with the cover of shrubs removed.
"planted_forest": An object of class forest with the new plant cohorts resulting from tree/shrub planting.
"management_args": A list of management arguments to be used in the next call to the management function.

An example of management function is provided in defaultManagementFunction.

References

De Cáceres M, Molowny-Horas R, Cabon A, Martínez-Vilalta J, Mencuccini M, García-Valdés R, Nadal-Sala D, Sabaté S, Martin-StPaul N, Morin X, D'Adamo F, Batllori E, Améztegui A (2023) MEDFATE 2.9.3: A trait-enabled model to simulate Mediterranean forest function and dynamics at regional scales. Geoscientific Model Development 16: 3165-3201 (https://doi.org/10.5194/gmd-16-3165-2023).

Author

Miquel De Cáceres Ainsa, CREAF

Examples

# \donttest{
#Load example daily meteorological data
data(examplemeteo)
#Prepare a two-year meteorological data with half precipitation during 
#the second year
meteo2001 <- examplemeteo
meteo2002 <- examplemeteo
meteo2002$Precipitation <- meteo2002$Precipitation/2
meteo2002$dates <- seq(as.Date("2002-01-01"), 
                           as.Date("2002-12-31"), by="day")
meteo_01_02 <- rbind(meteo2001, meteo2002)

#Load example plot plant data
data(exampleforest)

#Default species parameterization
data(SpParamsMED)

#Initialize control parameters
control <- defaultControl("Granier")

#Define soil with default soil params (4 layers)
examplesoil <- defaultSoilParams(4)

#Call simulation function
fd<-fordyn(exampleforest, examplesoil, 
           SpParamsMED, meteo_01_02, control,
           latitude = 41.82592, elevation = 100)
#> Simulating year 2001 (1/2):  (a) Growth/mortality, (b) Regeneration nT = 2 nS = 1
#> Simulating year 2002 (2/2):  (a) Growth/mortality, (b) Regeneration nT = 2 nS = 1

#Stand-level summaries
fd$StandSummary
#>   Step NumTreeSpecies NumTreeCohorts NumShrubSpecies NumShrubCohorts
#> 1    0              2              2               1               1
#> 2    1              2              2               1               1
#> 3    2              2              2               1               1
#>   TreeDensityLive TreeBasalAreaLive DominantTreeHeight DominantTreeDiameter
#> 1        552.0000          25.03330           800.0000             37.55000
#> 2        551.3663          25.20814           806.2122             37.66571
#> 3        550.7272          25.36317           811.8206             37.77070
#>   QuadraticMeanTreeDiameter HartBeckingIndex ShrubCoverLive BasalAreaDead
#> 1                  24.02949         53.20353       3.750000    0.00000000
#> 2                  24.12711         52.82391       3.092051    0.03917375
#> 3                  24.21523         52.48941       3.133367    0.03979292
#>   ShrubCoverDead BasalAreaCut ShrubCoverCut
#> 1    0.000000000            0             0
#> 2    0.005308898            0             0
#> 3    0.004781110            0             0

#Tree table by annual steps
fd$TreeTable
#>   Step Year Cohort          Species      DBH   Height        N Z50  Z95 ObsID
#> 1    0   NA T1_148 Pinus halepensis 37.55000 800.0000 168.0000 100  600  <NA>
#> 2    0   NA T2_168     Quercus ilex 14.60000 660.0000 384.0000 300 1000  <NA>
#> 3    1 2001 T1_148 Pinus halepensis 37.66571 806.2122 167.6992 100  600  <NA>
#> 4    1 2001 T2_168     Quercus ilex 14.71218 663.4915 383.6671 300 1000  <NA>
#> 5    2 2002 T1_148 Pinus halepensis 37.77070 811.8206 167.3957 100  600  <NA>
#> 6    2 2002 T2_168     Quercus ilex 14.81392 666.6497 383.3315 300 1000  <NA>

#Dead tree table by annual steps
fd$DeadTreeTable
#>   Step Year Cohort          Species      DBH   Height         N N_starvation
#> 1    1 2001 T1_148 Pinus halepensis 37.66571 806.2122 0.3007828            0
#> 2    1 2001 T2_168     Quercus ilex 14.71218 663.4915 0.3328893            0
#> 3    2 2002 T1_148 Pinus halepensis 37.77070 811.8206 0.3035177            0
#> 4    2 2002 T2_168     Quercus ilex 14.81392 666.6497 0.3356219            0
#>   N_dessication N_burnt Z50  Z95 ObsID
#> 1             0       0 100  600  <NA>
#> 2             0       0 300 1000  <NA>
#> 3             0       0 100  600  <NA>
#> 4             0       0 300 1000  <NA>
# }