Approximate Bayesian Computation with Pooled Sequencing Data
Calculate the abba portion of the D-statistic
Parameter estimation with Approximate Bayesian Computation with severa...
Calculate the baba portion of the D-statistic
Back-transform matrix of parameter values
Remove sites with incorrect depths of coverage
Check if the major allele is the same in all populations
Remove sites with missing data
Import and clean a single file containing data in popoolation2 forma...
Create SCRM command line for a model with two populations
Create SCRM command line for a parallel origin scenario
Create SCRM command line for a single origin scenario
Create a header for a _rc file of popoolation2
Draw parameters from the priors
calculate D-statistic
Perform D-statistics analysis
Compute error in model selection with Approximate Bayesian Computation
Calculate cross-validation prediction error of parameter estimation
Compute euclidean distance
Compute the fraction of exclusive sites
Compute expected heterozygosity within a population
Filter the data by the frequency of the minor allele
Compute the fraction of sites fixed between populations
Force the simulations to contain the required number of loci
Calculate FST
Calculate the mode of a distribution
Compute heterozygosity between all pairs of populations
Import multiple files containing data in PoPoolation2 format
Import a single file containing data in popoolation2 format
Parameter estimation with Approximate Bayesian Computation using rejec...
Obtain the index of SNPs inside a block with defined size
Back-transform the parameters values
Compute mean expected heterozygosity within a population
Merge posterior distributions
Compute mode of a locfit object
Perform model selection with Approximate Bayesian Computation
Parameter estimation with Approximate Bayesian Computation for multipl...
Normalize data - adjust values measured on different scales
Organize point estimates from multiple posterior distributions
Organize scrm output
Pairwise FST among populations
Randomly select blocks of a given size from several contigs
Prediction error plots for ABC
Prediction error plots for ABC using a list
Plot model misclassification
Plot the density estimation of a given parameter
Plot multiple posterior distributions
Plot the fit of a summary statistic to the target
Plot the density estimation of a given parameter
Simulation of Pooled DNA sequencing
Compute summary statistics from Pooled DNA sequencing
Pairwise FST among populations and across multiple loci
Calculate point estimates from the posterior distribution
Organize information by contig - for multiple data files
Organize information by contigs - for a single data file
Construct matrix of prior limits
Parameter estimation with Approximate Bayesian Computation using local...
Parameter estimation with Approximate Bayesian Computation using rejec...
Remove sites using quantiles of the depth of coverage
Remove sites, according to their coverage, from real data
Remove columns with zero variance
Run scrm and obtain genotypes
Compute scaled migration rates
Compute scaled migration rate limits
Compute the fraction of sites shared between populations
Leave-one-out cross validation of model selection
Perform an Approximate Bayesian Computation simulation study
Parameter estimation with Approximate Bayesian Computation for a singl...
Compute summary statistics from observed data
Posterior model probabilities
Transform matrix of parameter values
Apply a transformation to the parameters
Compute weighted point estimates
Provides functions to simulate Pool-seq data under models of demographic formation and to import Pool-seq data from real populations. Implements two ABC algorithms for performing parameter estimation and model selection using Pool-seq data. Cross-validation can also be performed to assess the accuracy of ABC estimates and model choice. Carvalho et al., (2022) <doi:10.1111/1755-0998.13834>.
Useful links