TransectRun: Transect runs for pine, spruce, or mixed forests

In ForModLabUHel/Rprebasso: PRELES, YASSO and PREBAS models

Transect runs for pine, spruce, or mixed forests

Description

The simulations of pine or spruce or mixed forests at 7 selected points over a North-South transect. Start from seedlings!

Usage

TransectRun(
  SiteType = NA,
  initVar = NA,
  species = NA,
  nYears = 100,
  pCROBAS = pCROB,
  pPRELES = pPREL,
  AgeEffect = F,
  defaultThin = 1,
  multiThin = NA,
  multiNthin = NA,
  ClCut = 1,
  energyCut = 0,
  GVrun = 1,
  pHcMod = pHcM,
  etmodel = 0,
  pYASSO = pYAS,
  pAWEN = parsAWEN,
  multiInitClearCut = NA,
  fixBAinitClearcut = 1,
  initCLcutRatio = NA,
  multiP0 = NA,
  soilC = NA,
  weatherInput = NULL,
  weatherYasso = NA,
  litterSize = litterSizeDef,
  soilCtot = NA,
  inDclct = NA,
  inAclct = NA,
  yassoRun = 0,
  smoothP0 = 1,
  smoothETS = 1,
  smoothYear = 5,
  HcModV = HcModV_def,
  tapioPars = pTapio,
  thdPer = NA,
  limPer = NA,
  ftTapioPar = ftTapio,
  tTapioPar = tTapio,
  thinInt = -999,
  mortMod = 1,
  ECMmod = 0,
  layerPRELES = 0,
  LUEtrees = pLUEtrees,
  LUEgv = pLUEgv,
  alpharNcalc = FALSE,
  p0currClim = NA,
  TcurrClim = NA,
  PcurrClim = NA,
  ingrowth = FALSE,
  soilPar = NA,
  siteInfoDist = NA,
  modVersion = "multiSite",
  nYearsFert = 20,
  yearFert = NULL,
  deltaSiteTypeFert = 1,
  fertThin = 0,
  oldLayer = 0,
  latitude = c(60.295, 60.959, 61.377, 62.647, 64.441, 66.143, 68.203),
  TsumSBBs = matrix(-999, 7, 4),
  SMIt0 = rep(-999, 7),
  TminTmax = NA
)

Arguments

SiteType	A value between 1 to 5.
initVar	initial state of the forest. Array with nSites,VarsIn,nLayers dimentions: nSites=number of sites (7); VarsIn = initial state input variables (speciesID, age(if NA is calculated by initialAgeSeedl function),h,dbh,ba(by layer),hc,Ac(NA))
species	If the initial state of the forest is not provided (initVar) Should be 'Pine', or 'Spruce', or 'Birch' or 'Mixed'
nYears	Number of years to run the model.Default value is 100.
pCROBAS	(47 x nSpecies matrix) Matrix of parameter sets, each column corresponds to a species. Default values pCROBAS = pCROB are the parameter sets for Scots pine (Pinus sylvestris), Norway spruce (Picea abies), Silver birch (Betula pendula), European beech (Fagus sylvatica), Maritime pine (Pinus pinaster), Blue gum (Eucalyptus globulus), Black locust (Robinia pseudoacacia), Populus(in Romania), Eucalyptus grandis x Eucalyptus urophylla (in Paraguay), and Norway spruce(in Germany). Default is pCROB, print(pCROB) to see the parameter values and names.
pPRELES	A vector of PRELES parameter. Default is the boreal forest version pPREL.
AgeEffect	Carbon allocation strategy for seedlings. When True, the early growth will decrease due to age effect,by setting pCROBAS[45,]<-0.3.
defaultThin	If defaultThin = 1 (default) Finnish standard management practices are applied (ref).
multiThin	A array with thinnig inputs. Three dimensions: nSites x maxThin x 9. The first dimension is the number of sites. The second dimension, maxThin, is the number of thinnings. For the third demention, element 1 is year from the start of the simulation; element 2 is siteID; element 3 layer where thinnings are carried out; element 4 to 7 stand variables (H, D, B, Hc); element 8 parameter that indicates if the stand variables (column 4:7) are provided as fraction of the actual model outputs (value=1 means that fraction is used); element 9 is the stand density after thinning if its value is not -999.
multiNthin	A matrix with thinning inputs. Rows correspond to a thinning event. Column 1 year from the start of the simulation; column 2 is siteID; column 3 layer where thinnings are carried out; column 4 to 7 stand variables (H, D, B, Hc); column 8 parameter that indicates if the stand variables (column 4:7) are provided as fraction of the actual model outputs (value=1 means that fraction is used); column 9 is the stand density after thinning if its value is not -999; colum 10 is Sapwood area of average tree at crown base (m2) if its value is not -999 (see examples).
ClCut	Vector of Diameter (cm) threshold for clearcut. Each element correspond to a layer of the stand, if only one value is provided the same value is applied to all the layers. The different elements of the vector are for the different layers. The dominant species (highest basal area) is considered for clearcut.
energyCut	Energy cutting strategy will be applied if set to 1. Default value is 0.
GVrun
pHcMod
etmodel
pYASSO
pAWEN
multiInitClearCut	A Matrix: matrix(initClearcut,NoOfSites,5,byrow = T), where initClearcut includes those 5 variables H,dbh,BA,HC,AC, same with 'initSeedling.def'
fixBAinitClearcut
initCLcutRatio
multiP0
soilC
weatherInput	##list of weather inputs for PRELES: each variables is a matrix with nrow=nSites,columns=number of days in the simulations
weatherYasso
litterSize
soilCtot
inDclct
inAclct
yassoRun
smoothP0
smoothETS
smoothYear
HcModV	flag for the Hc model: 1 use the pipe model defined in the HcPipeMod function, different from 1 uses empirical models; default value (HcModV_def) is 1
tapioPars
thdPer
limPer
ftTapioPar
tTapioPar
thinInt
mortMod	flag for the mortality model selection (1= Reineke, 2= random (Siilipehto, 2020), 3= both models)
ECMmod	flag for the ECM modelling activation 1 -> model ECM according to Makela et al. 2022, 0 -> no ECM modelling
layerPRELES
LUEtrees	light use efficiency parameters for tree species
LUEgv	light use efficiency parameter for ground vegetation
alpharNcalc	#alphar calculations based on Nitrogen availability. deafault value is FALSE (no nitrogen impact). =1calculates N uptake
p0currClim	# vector of average annual P0 for the climIDs at current climate. if NA the first five years of the simulations will be used to calculate it.
TcurrClim	# vector of average annual temperature for the climIDs at current climate. if NA the first five years of the simulations will be used to calculate it.
PcurrClim	# vector of average annual precipitation for the climIDs current climate. if NA the first five years of the simulations will be used to calculate it.
ingrowth	# flag to simulate ingrowth
soilPar	# input a matrix (dim=nSites,3 ) with soil depth, FC, WP, for each site if NA uses the default values
modVersion	# model version to use in the simulations it can be multiSite or region
nYearsFert	number of years after thinnings for which the fertilization is effective. default values is 20 years
yearFert	simulation year when fertilization occurred
deltaSiteTypeFert	fertilization impact
fertThin	flag for implementing fertilization at thinning. the number can be used to indicate the type of thinning for now only thinning 3
oldLayer	flag for retention trees after clearcut (randomly 5-10 percent basal area is left after clearcut)
latitude	latitude of the site
TsumSBBs	initial temperature sums for bark beetle risk for the two years before the first year if not available it will be calculated using the first year
SMIt0	site vector of initial SoilMoirture index
TminTmax	array(climaIDs,ndays,2) with daily Tmin Tmax values for each climID, Tmin and Tmax will be used to calculate the Nesterov Index that will be used in the fire risk calculations

Value

The output from multiPrebas()

Examples

# Qucik examples
Pine.1 <- TransectRun(SiteType = 1, species = "Pine")
plot(Pine.1$multiOut[1, , 30, 1, 1], type = "l")

#' An example of initail sates
InitStands<-matrix(c(1,NA,1.5,0.5,0.0431969,0.,0.),nrow = 7,ncol=7,byrow = T)
Pine.i <-TransectRun(SiteType = 1, initVar = InitStands)
plot(Pine.i$multiOut[1, , 30, 1, 1], type = "l")

#An example of thinning
thinnings<-array(0,c(7,2,10))
thinnings[,,1]<- c(rep(20,7),rep(40,7)) #year from the start of the simulation
thinnings[,,2]<- 1:7 #siteID
thinnings[,,3]<- 1 #layer where thinnings are carried out
thinnings[,,4]<- 1.1 #H
thinnings[,,5]<- 1.1#D
thinnings[,,6]<- 0.5#B
thinnings[,,7]<- 1#Hc
thinnings[,,8]<- 1 #if the stand variables (column 4:7) are provided as fraction of the actual model outputs
thinnings[,,9:10] <- -999 #9 the stand density after thinning if its value is not -999.
Pine.thin <-TransectRun(SiteType = 1, initVar = InitStands,multiThin = thinnings,multiNthin = rep(2,7))
plot(Pine.thin$multiOut[1, , 30, 1, 1], type = "l")

#An example of new settings for seedlings after a clear cut
initClearcut<-c(1.5100000,0.8000000,0.0631969,0.2000000,NA) # H,dbh,BA,HC,AC
afterClearCut <- matrix(initClearcut,7,5,byrow = T)
Pine.newseed <-TransectRun(SiteType = 1, initVar = InitStands,multiThin = thinnings,multiNthin = rep(2,7),multiInitClearCut = afterClearCut)
plot(Pine.newseed$multiOut[1, , 30, 1, 1], type = "l")

ForModLabUHel/Rprebasso documentation built on April 13, 2025, 10:48 a.m.