add.leaf                Test all possible connection of a leaf to a
                        graph with non-admixed and or admixed edges
bjack_cov               bjack_cov
block_sum               block_sum
block_sum2              block_sum2
compare.fitted.fstats   Compare fitted f2, f3 and f4 f-statistics of an
                        admixture graph with estimated ones
compute.f4ratio         Compute F4ratio (estimation of admixture rate)
                        from an fstats object
compute.fstats          Estimate the F-statistics (F2, F3, F3star, F4,
                        Dstat) and within and across population
                        diversity
compute.pairwiseFST     Compute pairwise population population FST
                        matrix (and possibly all pairwise SNP-specific
                        FST)
computeFST              Compute Fst from Pool-Seq data or Count data
compute_F3fromF2        compute_F3fromF2
compute_F3fromF2samples
                        compute_F3fromF2samples
compute_F4DfromF2samples
                        compute_F4DfromF2samples
compute_F4fromF2        compute_F4fromF2
compute_F4fromF2samples
                        compute_F4fromF2samples
compute_H1              compute_H1
compute_Q2              compute_Q2
compute_QmatfromF2samples
                        compute_QmatfromF2samples
compute_blockDdenom     compute_blockDdenom
compute_snpFstAov       compute_snpFstAov
compute_snpHierFstAov   compute_snpHierFstAov
compute_snpQ1           compute_snpQ1
compute_snpQ1onepop     compute_snpQ1onepop
compute_snpQ1rw         compute_snpQ1rw
compute_snpQ2           compute_snpQ2
compute_snpQ2onepair    compute_snpQ2onepair
compute_snpQ2rw         compute_snpQ2rw
countdata-class         S4 class to represent a Count data set.
countdata.subset        Create a subset of a countdata object that
                        contains count data as a function of pop or SNP
                        indexes
countdata2genobaypass   Convert a countdata object into BayPass input
                        files.
data.merge              Merge two pooldata or countdata objects
extract_allele_names    extract_allele_names
extract_nonvscan_counts
                        extract_nonvscan_counts
extract_vscan_counts    extract_vscan_counts
find.tree.popset        Find sets of populations that may used as
                        scaffold tree
find_indelneighbor_idx
                        find_indelneighbor_idx
fit.graph               Estimate parameters of an admixture graph
fitted.graph-class      S4 class to represent a population tree or
                        admixture graph and its underlying fitted
                        parameter.
fstats-class            S4 class to represent fstats results obtained
                        with computeFstats.
generate.graph.params   Generate a graph parameter object to fit
                        admixture graph to observed fstats
generate.jackknife.blocks
                        Generate block coordinates for block-jackknife
generateF3names         generateF3names
generateF4names         generateF4names
genobaypass2countdata   Convert BayPass allele count input files into a
                        coundata object
genobaypass2pooldata    Convert BayPass read count and haploid pool
                        size input files into a pooldata object
genoselestim2pooldata   Convert SelEstim read count input files into a
                        pooldata object
genotreemix2countdata   Convert allele count input files from the
                        Treemix program into a coundata object
graph.builder           Implement a graph builder heuristic by
                        successively adding leaves to an initial graph
graph.params-class      S4 class to represent a population tree or
                        admixture graph and its underlying parameter.
graph.params2qpGraphFiles
                        Generate files for the qpGraph software from a
                        graph.params object
graph.params2symbolic.fstats
                        Provide a symbolic representation of all the
                        F-statistics and the model system of equations
heatmap,pairwisefst-method
                        Show pairwisefst object
is.countdata            Check countdata objects
is.fitted.graph         Check fitted.graph objects
is.fstats               Check fstats objects
is.graph.params         Check graph.params objects
is.pairwisefst          Check pairwisefst objects
is.pooldata             Check pooldata objects
make.example.files      Create example files
pairwisefst-class       S4 class to represent a pairwise Fst results
                        obtained with the compute.pairwiseFST
plot,fitted.graph-method
                        plot pairwisefst object
plot,fstats-method      plot fstats object
plot,graph.params-method
                        plot graph in graph.params object
plot,pairwisefst-method
                        plot pairwisefst object
plot_fstats             Plot F2, F3, F3star, F4, D or pairwise Fst
                        values with their Confidence Intervals
pooldata-class          S4 class to represent a Pool-Seq data set.
pooldata.subset         Create a subset of the pooldata object that
                        contains Pool-Seq data as a function of pool
                        and/or SNP indexes
pooldata2diyabc         Convert a pooldata object into DIYABC input
                        files.
pooldata2genobaypass    Convert a pooldata object into BayPass input
                        files.
pooldata2genoselestim   Convert a pooldata object into SelEstim input
                        files.
poolify                 Create a (pseudo-)pooled sample from a set of
                        samples (using random-allele sampling)
poppair_idx             poppair_idx
popsync2pooldata        Convert Popoolation Sync files into a pooldata
                        object
randomallele.pca        PCA of a pooldata or countdata object using a
                        random allele approach
rooted.njtree.builder   Construct and root an Neighbor-Joining tree of
                        presumably nonadmixed leaves
scan_allele_info        scan_allele_info
show,countdata-method   Show countdata object
show,fitted.graph-method
                        Show fitted.graph object
show,fstats-method      Show fstats object
show,graph.params-method
                        Show graph.params object
show,pairwisefst-method
                        Show pairwisefst object
show,pooldata-method    Show pooldata object
sim.readcounts          Simulate read counts from count data and return
                        a pooldata object
simureads_mono          simureads_mono
simureads_poly          simureads_poly
sliding.windows.fstat   Compute sliding window estimates of
                        F-statistics or ratio of F-statistics over the
                        genome
vcf2pooldata            Convert a VCF file into a pooldata object.
