plotAcceptanceRatios

<p>An Rcpp trace object initialized with <code>initializeTraceObject</code>.</p>

trace

main

<p>Plots acceptance ratios for codon-specific parameters. Will be by amino acid for ROC and FONSE models, but will be by codon for PA and PANSE models. Note assumes estimating parameters for all codons.</p>

Is a collection of models to analyze genome scale codon
data using a Bayesian framework. Provides visualization
routines and checkpointing for model fittings. Currently
published models to analyze gene data for selection on codon
usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist
et al. (2015) <doi:10.1093/gbe/evv087>), and ROC with phi
(Wallace & Drummond (2013) <doi:10.1093/molbev/mst051>). In
addition 'AnaCoDa' contains three currently unpublished models.
The FONSE (First order approximation On NonSense Error) model
analyzes gene data for selection on codon usage against of
nonsense error rates. The PA (PAusing time) and PANSE (PAusing
time + NonSense Error) models use ribosome footprinting data to
analyze estimate ribosome pausing times with and without
nonsense error rate from ribosome footprinting data.

plotAcceptanceRatios: Plot Acceptance ratios

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