Description Usage Arguments Details Value Examples
Create rarefaction curves using Jost diversities.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | getSubsamplesForDiverRare(cm, sample.size, replicates = 10,
levels = rep(c("gamma", "alpha", "beta"), 3), qs = rep(0:2, each = 3),
is.transposed = FALSE, progressBar = TRUE, verbose = TRUE)
getDiverRare(cm, sample.sizes = 10, replicates = 10,
levels = rep(c("gamma", "alpha", "beta"), 3), qs = rep(0:2, each = 3),
progressBar = TRUE, min.sample.abundance = NA,
non.rarefied.subsamples = TRUE, verbose = TRUE)
getMultiDiverRare(cm.list, min.sample.abundance.list = NA, ...)
ggDiverRare(diver.rare, multi.cm = FALSE, diversity = c(),
line.or.point = 3, point.size = 2, title = "", x.lab = "sample size",
y.lab = "diversity", ...)
|
cm |
The community matrix. |
sample.size |
An interger number representing subsample size for
rarefying community using |
replicates |
The number of replicates to repeat subsampling. |
levels |
The levels of Jost diversities in |
qs |
The order of Jost diversities in |
is.transposed |
If TRUE, then |
progressBar |
Whether to print progress bar, default to TRUE. |
sample.sizes |
The vector of subsample sizes for
rarefying community using |
min.sample.abundance |
If |
non.rarefied.subsamples |
If TRUE, as default, the subsamples will include
non rarefied ones, whose |
cm.list |
The list of community matrices. |
min.sample.abundance.list |
The list of |
diver.rare |
The rarefaction curves of one or more community matrices.
Use |
multi.cm |
If FALSE, as default, the |
diversity |
The vector of diversity included in the graph,
such as |
getSubsamplesForDiverRare
calculates subsamples for
the rarefaction using Jost diversities, given a community matrix.
getDiverRare
returns a list of subsamples calculated
from getSubsamplesForDiverRare
given a community matrix.
Note: this community matrix must not be transposed.
getMultiDiverRare
returns a list of rarefaction curves
calculated from getDiverRare
given a list of community matrices.
Note: every community matrices must not be transposed.
ggDiverRare
plots the rarefaction curves calculated
from getDiverRare
given a community matrix,
or from getMultiDiverRare
given a list of community matrices,
and returns a ggplot
object.
getSubsamplesForDiverRare
returns a list of results:
mean
is a named vector of means of each diversity measurement,
sterr
is the standard error of the mean,
subsamples
is a matrix of all subsampled points to calculate means and errors,
where the columns are diversity measurements, rows are replicates.
1 2 3 4 5 6 7 8 | diver.rare <- getSubsamplesForDiverRare(cm, 2000, 5)
diver.rare <- getDiverRare(cm, replicates=5)
multi.diver.rare <- getMultiDiverRare(cm.list, replicates=5)
gg.plot <- ggDiverRare(diver.rare)
gg.plot <- ggDiverRare(multi.diver.rare, multi.cm=T, x.trans="log", auto.scale.x=T)
|
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