Description Usage Arguments Value Note References See Also Examples
The null hypothesis for this tests is that there is no difference in gamma
diversity between the two sets of datasets sites represented in tab.a
and tab.b
, or adt.a
and adt.b
. The method for the
initial class divtable
version of this was described in
Scofield et al. (2012), while that for the allelic extension as class
link{allele_divtables}
was described in Sork et al.
(in press).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## S3 method for class 'divtable'
gammaContrastTest(tab.a, tab.b, 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:
gammaContrastTest(tab.a, tab.b, ...)
## S3 method for class 'allele_divtables'
gammaContrastTest(adt.a, adt.b,
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.a |
Site-by-source table of class |
tab.b |
Site-by-source table of class |
zero.div.adjust |
Logical, if |
n.resample |
Number of iterations for creation of the null distribution |
method |
|
adt.a |
Allelic diversity dataset of class
|
adt.b |
Allelic diversity dataset of class
|
Class diversity_test
object with the result of the test
adt.a
and adt.b
must contain the same loci
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.
gammaContrastTest3
, alphaContrastTest
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Compare gamma diversity between two diversity datasets
##
data(granaries_2002_Qlob)
data(granaries_2004_Qlob)
par(mfrow = c(1, 2))
plot(gammaAccum(granaries_2002_Qlob))
plot(gammaAccum(granaries_2004_Qlob))
gammaContrastTest(granaries_2002_Qlob, granaries_2004_Qlob)
## Compare gamma diversity between two allele datasets
##
# dat1 <- readGenalex("file-of-genotypes-sample-1.txt")
# dat2 <- readGenalex("file-of-genotypes-sample-2.txt")
# gt1 <- createAlleleTables(dat1)
# gt2 <- createAlleleTables(dat2)
# gamma.contrast <- gammaContrastTest(gt1, gt2)
|
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