An object of class divtable
, a diversity table, holds site (rows) by
membership (columns) count data expressed using numeric
values. Such
data could represent (for example) numbers of individuals observed of
specific species, numbers of seeds observed originating from different
parental trees, or, as a component of class allele_divtables
,
counts of alleles observed for a specific genetic locus. This is the basic
data object of the dispersalDiversity
package, and is
accepted by the function diversity
, which generates
descriptive statistics, and the functions alphaDiversityTest
,
gammaContrastTest
and many others that test for differences
in the structure of diversity.
A divtable
can be assembled by hand, but more typically
data will be read into a matrix
or data.frame
or assembled
into a table
or xtabs
and then converted to a
divtable
using as.divtable
. All functions in the
dispersalDiversity
package that accept divtable
also
have a default method that will convert matrix
, data.frame
,
table
and xtabs
to divtable
using
as.divtable
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Generate divtables, starting with random site-species pairs with a
## log-normal distribution of abundances
set.seed(42)
t <- data.frame(site = sample(n.sites, n.samples, replace = TRUE),
source = round(rlnorm(n.samples, .1, 1) + 0.5))
head(t)
## Using table
as.divtable(table(t))
## Using xtabs
as.divtable(xtabs(~ site + species, data = t))
## More complicated, create 'matrix' intermediary
as.divtable(do.call(rbind, lapply(split(t, t$site),
function(x) table(x$source))))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.