prepareTreeCompetitionTable: Prepares variables for model input
In miquelcaceres/IFNdyn: IFN forest dynamics and scenario analysis

Description Usage Arguments Value Examples

View source: R/prepareTreeCompetitionTable.R

Prepares tree and competition variables from IFN tree data for model input (used internally in model functions like IFNgrowth).

prepareTreeCompetitionTable(
  x,
  BAL = TRUE,
  BALext = FALSE,
  sortByDBH = FALSE,
  keep.vars = character(0),
  provinceFromID = FALSE,
  verbose = FALSE
)

prepareSpeciesCompetitionTable(x, provinceFromID = FALSE, verbose = FALSE)

prepareSpatialSpeciesCompetitionTable(
  x,
  nb,
  NspNmatrix,
  sigma = c(0.5, 1, 2, 4),
  provinceFromID = FALSE,
  verbose = FALSE
)

`x`	a data frame with column names.
`BAL`	A flag to indicate that basal area of larger trees (between inventories) has to be calculated.
`BALext`	A flag to indicate that basal area of larger extracted trees (between inventories) has to be calculated (requires column 'OIFFIN' in `x`).
`sortByDBH`	A flag to sort rows within each plot by increasing diameter at breast height.
`keep.vars`	A character vector with names of variables in `x` that should be copied to the output data frame.
`provinceFromID`	A flag to indicate that province should be extracted from 'ID' assuming they are IFN plot codes.
`verbose`	A flag to indicate console output during the process.
`nb`	An object of class `listw` (see functions `IFNknn` and `nb2listw`).
`NspNmatrix`	A numeric matrix with the density proportion of each species (columns) in each plot (rows).

Function prepareTreeCompetitionTable returns a data frame with as many rows as rows in the input x object and columns:

Province: Spanish province code (will be empty if provinceFromID = FALSE).
ID: Plot code.
species: Species code.
d: Tree diameter at breast height.
inv.d: Inverse of tree diameter at breast height.
ln.d: Logarithm of tree diameter at breast height.
sq.d: Square of tree diameter at breast height.
sqrt.d: Square-root of tree diameter at breast height.
h: Tree height (m).
inv.h: Inverse of tree height.
ln.h: Logarithm of tree height.
h.d: Height to diameter ratio.
N: Stand tree density.
BAL: Basal area of trees larger than the target tree.
BAL.ln.d: Basal area of larger trees divided by the logarithm of tree diameter.
BAL.ext: Basal area of trees extracted in a previous step.
G: Stand total basal area.
ln.G: Logarithm of total basal area.

Additional columns may be returned if required using keep.vars. Function prepareSpeciesCompetitionTable returns a data frame with as many rows as species in plots and columns:

Province: Spanish province code (will be empty if provinceFromID = FALSE).
ID: Plot code.
species: Species code.
G: Stand total basal area.
ln.G: Logarithm of total basal area.
ln.N: Logarithm of stand total tree density.
Nsp.N: Proportion of trees of the target species.

# Load example tree data and coordinates
data(exampleTreeData)
data(examplePlotCoords)

# Prepare input for growth/survival models
prepareTreeCompetitionTable(exampleTreeData)

# Prepare input for ingrowth models
prepareSpeciesCompetitionTable(exampleTreeData)

# Prepare input for ingrowth models including dispersal effects
nb = IFNknn(examplePlotCoords, k = 1)
Nmatrix = tapply(exampleTreeData$N, list(exampleTreeData$ID, exampleTreeData$Species),
                 sum, na.rm=T)
NspNmatrix = sweep(Nmatrix, 1, rowSums(Nmatrix, na.rm=T), "/")
NspNmatrix = rbind(NspNmatrix,c(0.5, NA, NA, NA))
rownames(NspNmatrix)[4] = "80003"
NspNmatrix = cbind(NspNmatrix, c(NA,NA,NA,0.5))
colnames(NspNmatrix)[5] = "25"
prepareSpatialSpeciesCompetitionTable(exampleTreeData, nb, NspNmatrix)