Description Usage Arguments Value References See Also Examples
View source: R/diversityTests-divtable.R
The null hypothesis for this tests is that there is no difference in alpha
diversity between the sites represented in tab
or adt
. The
initial (class divtable
) version of this was described in
Scofield et al. (2012), while the allelic (class
link{allele_divtables}
extension was described in Sort et al. (In
press).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## S3 method for class 'divtable'
alphaDiversityTest(tab, zero.div.adjust = TRUE,
n.resample = 10000, method = c("bootstrap", "permute"),
test.quantiles = c(0.001, 0.01, 0.05, 0.1, 0.5, 0.9, 0.95, 0.99, 0.999),
...)
## Default S3 method:
alphaDiversityTest(tab, ...)
## S3 method for class 'allele_divtables'
alphaDiversityTest(adt, zero.div.adjust = TRUE,
n.resample = 10000, method = c("bootstrap", "permute"),
test.quantiles = c(0.001, 0.01, 0.05, 0.1, 0.5, 0.9, 0.95, 0.99, 0.999),
...)
|
tab |
Site-by-source table of class |
zero.div.adjust |
Logical, if |
n.resample |
Number of iterations for creation of the null distribution |
method |
|
adt |
Allele diversity dataset of class
|
... |
Additional parameters |
An diversity_test
object with the result of the test
Scofield, D. G., Smouse, P. E., Karubian, J. and Sork, V. L. (2012) Use of alpha, beta and gamma diversity measures to characterize seed dispersal by animals. American Naturalist 180:719-732.
Sork, V. L., Smouse, P. E., Grivet, D. and Scofield, D. G. (In press) Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata N\'ee). Evolutionary Ecology.
alphaContrastTest
, alphaContrastTest3
, print.diversity_test
1 2 3 4 5 6 7 8 9 | ## Add example with class divtable
##
## Using allele diversity dataset of class allele_divtables. Compare
## allele diversity between sites in the same sample:
##
## library(readGenalex) # already loaded as a prerequisite
data(Qagr_pericarp_genotypes) # from readGenalex
gt <- createAlleleTables(Qagr_pericarp_genotypes)
alpha.test <- alphaDiversityTest(gt)
|
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