run.growthbin.manyspp: Run the model to fit growth rate in bins for many species,...
In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description Usage Arguments Examples

Run the model to fit growth rate in bins for many species, 1-4 bins. It takes a list of species, extracts growth rates for each, one at a time, from the table of growth rates, then calls run.growthfit.bin() to fit the model for the 4 bin options.

run.growthbin.manyspp(growthdata, size = "dbh", spp = spp20,
  minabund300 = 15, minTotal = 40, dbhunit = "mm",
  sdmodel = linear.model.ctr, startpar = c(0.03, 0.005),
  startsdpar = c(0.04, 0), badsdfunc = NULL, binoption = 1:4,
  noreps = 5000, noburn = 2500, noshow = 500,
  outputname = "linear.fit", path = "", ...)

`dbhunit`	'cm' or 'mm', only used for basal area
`...`	Arguments passed to `run.growthfit.bin()`.

## Not run: 
# Sample species vector from BCI: 
spp20 = c(
  'tri2tu',
  'alsebl',
  'tet2pa',
  'tachve',
  'beilpe',
  'pri2co',
  'quaras',
  'ocotwh',
  'hirttr',
  'gar2in',
  'protpa',
  'protte',
  'eugeoe',
  'virose',
  'guargu',
  'maquco',
  'jac1co',
  'cecrin',
  'cordbi',
  'micoar'
)

# Creating the complete table of biomass growth for all individuals in a 
# plot:
agb.growth = extract.growthdata(
  bciex::bci12t5mini,
  bciex::bci12t6mini,
  growthfunc = growth.biomass.indiv,
  logit = 'x',
  rounddown = FALSE,
  mindbh = 100,
  dbhunit = 'mm',
  err.limit = 4,
  maxgrow = 75
)

# Creating a vector of all species names in the agb.growth table.
allspecies = sort(unique(agb.growth$sp))

# Fitting the model for all species, 1 - 4 bins:
fit = run.growthbin.manyspp(
  growthdata = agb.growth,
  size = 'agb',
  spp = allspecies,
  minabund300 = 15,
  minTotal = 40,
  startpar = c(.03, .005),
  startsdpar = c(.04, 0)
)

## End(Not run)