| ABC | Parameter estimation with Approximate Bayesian Computation with several targets |
| cleanData | Import and clean a single file containing data in 'popoolation2' format |
| 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 |
| error_modelSel | Compute error in model selection with Approximate Bayesian Computation |
| forceLocus | Force the simulations to contain the required number of loci |
| getmode | Calculate the mode of a distribution |
| importContigs | Import multiple files containing data in PoPoolation2 format |
| index.rejABC | Parameter estimation with Approximate Bayesian Computation using rejection sampling and recording just the index of accepted simulations |
| limits | Matrix of prior limits |
| mergepost | Merge posterior distributions |
| modelSelect | Perform model selection with Approximate Bayesian Computation |
| mode_locfit | Compute mode of a locfit object |
| multipleABC | Parameter estimation with Approximate Bayesian Computation for multiple targets |
| myparams | Matrix of simulated parameter values |
| params | Matrix of simulated parameter values |
| 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 |
| 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 using local linear regression |
| rejABC | Parameter estimation with Approximate Bayesian Computation using rejection sampling |
| remove_quantileReads | Remove sites using quantiles of the depth of coverage |
| remove_realReads | Remove sites, according to their coverage, from real data |
| runSCRM | Run scrm and obtain genotypes |
| scaled.migration | Compute scaled migration rates |
| scaledPrior | Compute scaled migration rate limits |
| simulationABC | Perform an Approximate Bayesian Computation simulation study |
| sim_modelSel | Leave-one-out cross validation of model selection |
| singleABC | Parameter estimation with Approximate Bayesian Computation for a single target |
| summary_modelSelect | Posterior model probabilities |
| sumstats | Matrix of summary statistics computed from simulated data |