| abba | Calculate the abba portion of the D-statistic |
| ABC | Parameter estimation with Approximate Bayesian Computation... |
| baba | Calculate the baba portion of the D-statistic |
| BTmatrix | Back-transform matrix of parameter values |
| checkCoverage | Remove sites with incorrect depths of coverage |
| checkMajor | Check if the major allele is the same in all populations |
| checkMissing | Remove sites with missing data |
| cleanData | Import and clean a single file containing data in... |
| cmd2pops | Create SCRM command line for a model with two populations |
| cmdParallel | Create SCRM command line for a parallel origin scenario |
| cmdSingle | Create SCRM command line for a single origin scenario |
| createHeader | Create a header for a _rc file of popoolation2 |
| createParams | Draw parameters from the priors |
| D.stat | calculate D-statistic |
| D.statPool | Perform D-statistics analysis |
| errorABC | Calculate cross-validation prediction error of parameter... |
| error_modelSel | Compute error in model selection with Approximate Bayesian... |
| euclidean | Compute euclidean distance |
| exclusive | Compute the fraction of exclusive sites |
| Expected_Het | Compute expected heterozygosity within a population |
| filterData | Filter the data by the frequency of the minor allele |
| fixed | Compute the fraction of sites fixed between populations |
| forceLocus | Force the simulations to contain the required number of loci |
| getFst | Calculate FST |
| getmode | Calculate the mode of a distribution |
| Het_Between | Compute heterozygosity between all pairs of populations |
| importContigs | Import multiple files containing data in PoPoolation2 format |
| importData | Import a single file containing data in 'popoolation2' format |
| index.rejABC | Parameter estimation with Approximate Bayesian Computation... |
| indexSNPs | Obtain the index of SNPs inside a block with defined size |
| inverse_trans | Back-transform the parameters values |
| limits | Matrix of prior limits |
| meanExpected_Het | Compute mean expected heterozygosity within a population |
| mergepost | Merge posterior distributions |
| mode_locfit | Compute mode of a locfit object |
| modelSelect | Perform model selection with Approximate Bayesian Computation |
| multipleABC | Parameter estimation with Approximate Bayesian Computation... |
| myparams | Matrix of simulated parameter values |
| normalise | Normalize data - adjust values measured on different scales |
| organize.poststat | Organize point estimates from multiple posterior... |
| organizeSCRM | Organize scrm output |
| pairFST | Pairwise FST among populations |
| params | Matrix of simulated parameter values |
| pickWindows | Randomly select blocks of a given size from several contigs |
| plot_error | Prediction error plots for ABC |
| plot_errorABC | Prediction error plots for ABC using a list |
| plot_msel | Plot model misclassification |
| plot_param | Plot the density estimation of a given parameter |
| plot_Posteriors | Plot multiple posterior distributions |
| plot_stats | Plot the fit of a summary statistic to the target |
| plot_weighted | Plot the density estimation of a given parameter |
| poolSim | Simulation of Pooled DNA sequencing |
| poolStats | Compute summary statistics from Pooled DNA sequencing |
| popsFST | Pairwise FST among populations and across multiple loci |
| poststat | Calculate point estimates from the posterior distribution |
| prepareData | Organize information by contig - for multiple data files |
| prepareFile | Organize information by contigs - for a single data file |
| priorsMatrix | Construct matrix of prior limits |
| rc1 | Data frame with an example of observed data |
| rc2 | Data frame with an example of observed data |
| regABC | Parameter estimation with Approximate Bayesian Computation... |
| rejABC | Parameter estimation with Approximate Bayesian Computation... |
| remove_quantileReads | Remove sites using quantiles of the depth of coverage |
| remove_realReads | Remove sites, according to their coverage, from real data |
| removeVar | Remove columns with zero variance |
| runSCRM | Run scrm and obtain genotypes |
| scaled.migration | Compute scaled migration rates |
| scaledPrior | Compute scaled migration rate limits |
| shared | Compute the fraction of sites shared between populations |
| sim_modelSel | Leave-one-out cross validation of model selection |
| simulationABC | Perform an Approximate Bayesian Computation simulation study |
| singleABC | Parameter estimation with Approximate Bayesian Computation... |
| statsContig | Compute summary statistics from observed data |
| summary_modelSelect | Posterior model probabilities |
| sumstats | Matrix of summary statistics computed from simulated data |
| Tmatrix | Transform matrix of parameter values |
| tranf | Apply a transformation to the parameters |
| weighted_stats | Compute weighted point estimates |
