boot.ppDeltaD |
Bootstrapping test of pairwise allelic differentiation (Delta D) between populations |
CorDdPlot |
Plot the relation between genetic differentiation (Delta D) and geographic distance |
COR_DeltaDd |
Function for calculating pairwise Delta D and correlation between genetic differentiation (Delta D) and geographic distance |
COR_Fstd |
Function for calculating pairwise Fst and correlation coefficient between Fst (Weir and Cockerham, 1984) and geographic distance |
DeltaDcorplot |
Plot correlation matrix for pairwise Delta D |
HierAr |
Calculating hierarchical allelic richness |
HierD |
Function for calculating and decomposing genetic diversity (D, q=1) and differentiation (Delta D) |
HierDjost |
Hierarchical DJost |
HierFst |
Function for calculating hierarchical genetic differentiation (Fst) (Weir B.S., 1996; Yang R.C.,1998) |
HierHe |
Function for calculating hierarchical heterozygosity |
HierJd |
Hierarchical Jaccard dissimilarity |
Hierpertest |
Test the significance among aggregates (regions, ecosystems...) |
IDIP |
Function for decomposing diversity (genetic or species diversity) and differentiation into different hierarchical levels |
Ldisper |
Test significance of dispersion among subaggregate within aggregate |
permutate.DeltaD |
Permutation test for allelic differentiation (Delta D) |
plot.aggregates |
Plot aggregates with dispersions (variances) |
plotdiff1 |
Plot genetic differentiation (Delta D) across loci |
plot_pcoa_aggregate |
Draw the aggregation plot for allelic differentiation |
print_boot_ppDeltaD |
Print the bootstrapping result for pairwise allelic differentiation (Delta D) |
pwag.permutest |
Permutation test for allelic differentiation (Delta D) among subaggregates within aggregate |
pwDeltaD |
Pairwise Shannon differentiation (Delta D) |
qD |
Function for calculating genetic diversity profile (q=0,1,2) |
qDplot |
Plot the genetic diversity profiles (q=0,1,2) |
Str |
Function for generating the structure for HierDpart format |