| .compute_Ddenom | compute_Ddenom |
| .compute_Ddenom_bjmeans | compute_Ddenom_bjmeans |
| .compute_F2_bjmeans | compute_F2_bjmeans |
| .compute_Q_bjmeans | compute_Q_bjmeans |
| .extract_allele_names | extract_allele_names |
| .extract_nonvscan_counts | extract_nonvscan_counts |
| .extract_vscan_counts | extract_vscan_counts |
| .find_indelneighbor_idx | find_indelneighbor_idx |
| .scan_allele_info | scan_allele_info |
| add.leaf | Test all possible connection of a leaf to a graph with non-admixed and or admixed edges |
| 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) |
| 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_Ddenom | compute_Ddenom |
| compute_Ddenom_bjmeans | compute_Ddenom_bjmeans |
| compute_F2_bjmeans | compute_F2_bjmeans |
| compute_Q_bjmeans | compute_Q_bjmeans |
| countdata | S4 class to represent a Count data set. |
| 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 |
| 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 | S4 class to represent a population tree or admixture graph and its underlying fitted parameter. |
| fitted.graph-class | S4 class to represent a population tree or admixture graph and its underlying fitted parameter. |
| fstats | S4 class to represent fstats results obtained with computeFstats. |
| 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 |
| 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 | S4 class to represent a population tree or admixture graph and its underlying parameter. |
| 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-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 | S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST |
| pairwisefst-class | S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST |
| plot-method | plot pairwisefst object |
| plot-method | plot fstats object |
| plot-method | plot graph in graph.params object |
| plot-method | plot pairwisefst object |
| plot_fstats | Plot F2, F3, F3star, F4, D or pairwise Fst values with their Confidence Intervals |
| pooldata | S4 class to represent a Pool-Seq data set. |
| 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 |
| pooldata2genobaypass | Convert a pooldata object into BayPass input files. |
| pooldata2genoselestim | Convert a pooldata object into SelEstim input files. |
| poolfstat | PoolFstat |
| popsync2pooldata | Convert Popoolation Sync files into a pooldata object |
| rooted.njtree.builder | Construct and root an Neighbor-Joining tree of presumably nonadmixed leaves |
| scan_allele_info | scan_allele_info |
| show-method | Show countdata object |
| show-method | Show fitted.graph object |
| show-method | Show fstats object |
| show-method | Show graph.params object |
| show-method | Show pairwisefst object |
| show-method | Show pooldata object |
| vcf2pooldata | Convert a VCF file into a pooldata object. |