spparea.sq: Number of species in replicated, randomly-placed quadrats of...
In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description Usage Arguments Details Value Note Arguments details Examples

Function for calculating the number of species in replicated, randomly-placed quadrats of various areas.

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spparea.sq(censdata, spcolumn = "sp", size, rectdim = 1,
  mindbh = NULL, plotdim = c(1000, 500), replicates = 10,
  unidennames = c("**", "UNID", "uniden", "UNIDEN"))

`censdata`	A table of plot census data.
`spcolumn`	name of the column in the table having the species; defaults to 'sp', but can be set to 'genus'for 'family'if desired
`size`	A vector of quadrat sizes, referring to the x-dimension of a rectangular quadrat.
`rectdim`	the ratio of y to x dimensions of the rectangles; rectdim=1 (the default) for squares
`mindbh`	The minimum diameter above which the counts are done. Trees smaller than `mindbh` are excluded. If `NULL`, all living trees are included.
`plotdim`	The x and y dimensions of the plot.
`replicates`	the number of random quadrats to create, of each size
`unidennames`	a vector of species names that should not be included in species counts (see the function unidentified.species()

Species are counted as the number of unique values of sp in the R Analytical Table; unidentified species are not counted, based on a default unidennames; see the function unidentified.species in utilitiesCTFS.r.

A list of two components. The first is a table giving the mean number (and SD) of individuals and species in all quadrat sizes submitted. The second is a table giving the number of individuals and species in every random quadrat created.

In addition, a graph of species vs. individuals in every quadrat is created as the program runs. This can also be used to calculate genus- or family-area curves with use of the spcolumn argument. The censdata table must have a new column added, for example the genus for every record, then spcolumn can be set to 'genus'.

Randomly-placed quadrats produce statistically preferable species-area curves than checkerboards of non-overlapping quadrats. If required, though, the function abundanceperquad() offers a fast way to count the number of species in checkerboard-type quadrats of different sizes.

censdata can be either full or stem
censdata
sizeRefers to the dimension (side) of the square, and can be a vector; replicates is the number of random draws per dimension.

## Not run: 
speciesPerArea = spparea.sq(
  bciex::bci12t6mini,
  size = c(10, 20, 50),
  mindbh = 10,
  plotdim = c(1000, 500),
  replicates = 5,
  unidennames = c('unid')
)
rowmatch = match(bciex::bci12t6mini$sp, bciex::bci_species$sp)
bciex::bci12t6mini$Genus = bciex::bci_species$Genus[rowmatch]
genusPerArea = spparea.sq(
  bciex::bci12t6mini,
  spcolumn = 'Genus',
  size = c(10, 20, 50),
  mindbh = 10,
  plotdim = c(1000, 500),
  replicates = 5,
  unidennames = c('unid')
)

## End(Not run)