Approximate Bayesian Computation with Pooled Sequencing Data

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Documentation for package ‘poolABC’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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