Plant regeneration

Functions to simulate annual plant regeneration from seed recruitment or from resprouting

Usage

regeneration_seedproduction(forest, SpParams, control)

regeneration_seedrefill(seedBank, refillSpecies, refillPercent = NULL)

regeneration_seedmortality(seedBank, SpParams, minPercent = 1)

regeneration_recruitment(
  forest,
  SpParams,
  control,
  minMonthTemp,
  moistureIndex,
  verbose = FALSE
)

regeneration_resprouting(
  forest,
  internalMortality,
  SpParams,
  control,
  management_results = NULL
)

Arguments

forest

An object of class forest.

SpParams

A data frame with species parameters (see SpParamsMED and SpParamsDefinition).

control

A list with default control parameters (see defaultControl).

seedBank

A data frame with columns 'Species' and 'Percent', describing a seed bank.

refillSpecies

A string vector of species names corresponding to seed rain to refill seed bank.

refillPercent

A numeric vector of indicating the percentage of seed bank refilling (if missing then seed bank is set to 100%).

minPercent

A minimum percent of seed bank to retain entry in seedBank element of forest.

minMonthTemp

Minimum month temperature.

moistureIndex

Moisture index (annual precipitation over annual potential evapotranspiration).

verbose

Boolean flag to indicate console output during calculations.

internalMortality

A data frame with mortality occurred in the last year of simulation.

management_results

The result of calling a management function (see defaultManagementFunction).

Value

• regeneration_seedproduction returns a list of species names

• regeneration_seedrefill and regeneration_seedmortality return a copy of the input data.frame object with an update seed bank.

• regeneration_resprouting and regeneration_recruitment return a new object of class forest with the new plant cohorts.

Details

• regeneration_seedproduction evaluates if reproductive individuals (i.e. sufficiently tall individuals) are present.

• regeneration_seedrefill fills seed bank of input forest object with seed rain.

• regeneration_seedmortality updates seed bank of input forest object according to annual seed mortality.

• regeneration_recruitment evaluates recruitment from the seed bank (or local seed production if seed bank is missing). Minimum month temperature and moisture index values are used to determine if recruitment was successful. Species also require a minimum amount of light at the ground level.

• regeneration_resprouting evaluates resprouting occurs after “mortality” from die-back (including drought- or pathogen-induced dessication), cutting or burning of the aerial part in a species with resprouting ability, but not after carbon starvation or baseline mortality (unspecific mortality causes).

See also

fordyn

Author

Miquel De Cáceres Ainsa, CREAF

Examples

#Load example plot plant data
data(exampleforest)

#Default species parameterization
data(SpParamsMED)

#Initialize control parameters
control <- defaultControl("Granier")
control$recruitmentMode = "deterministic" 

#Recruitment limits
plant_parameter(exampleforest, SpParamsMED, "MinTempRecr")
#>    T1_148    T2_168    S1_165 
#>  1.083300 -3.744526  1.669536 
plant_parameter(exampleforest, SpParamsMED, "MinMoistureRecr")
#>     T1_148     T2_168     S1_165 
#> 0.10154153 0.09657161 0.22301894 

#Compare seed recruitment outcomes
regeneration_recruitment(exampleforest, SpParamsMED, control, 0, 0.25)
#> $treeData
#> [1] Species DBH     Height  N       Z50     Z95    
#> <0 rows> (or 0-length row.names)
#> 
#> $shrubData
#> [1] Species Height  Cover   Z50     Z95    
#> <0 rows> (or 0-length row.names)
#> 
#> attr(,"class")
#> [1] "forest" "list"  
regeneration_recruitment(exampleforest, SpParamsMED, control, 3, 0.25)
#> $treeData
#> [1] Species DBH     Height  N       Z50     Z95    
#> <0 rows> (or 0-length row.names)
#> 
#> $shrubData
#> [1] Species Height  Cover   Z50     Z95    
#> <0 rows> (or 0-length row.names)
#> 
#> attr(,"class")
#> [1] "forest" "list"