Search results

ROC gene-mixture: Dirichlet weight update lacks concentration pseudocounts -> emptied component is absorbing

Status: Open.

#431 In acope3/RibModelFramework;

· mikegilchrist opened on Jun 19, 2026

loadParameterObject(files) with >1 file silently drops all but the first file's traces

Status: Open.

#424 In acope3/RibModelFramework;

· mikegilchrist opened on May 28, 2026

PANSE: Trace class function getCodonSpecificParameterTraceByMixtureElementForCodon does not work for NSE rates on loading of Parameter object

bug

Status: Open.

#423 In acope3/RibModelFramework;

· acope3 opened on May 27, 2026

PANSE: getGenomeForGeneIndices returns Genome with uninitialized totalRFPCount, silently breaks CSP fits (Elongation AR = 0)

Status: Open.

#421 In acope3/RibModelFramework;

· mikegilchrist opened on May 23, 2026

FONSE: runMCMC segfaults mid-iteration on full S. cerevisiae genome (works on 8-gene test FASTA)

Status: Open.

#418 In acope3/RibModelFramework;

· mikegilchrist opened on May 22, 2026

FONSE: writeParameterObject crashes (proposedMutationParameter binding commented out for FONSEParameter)

Status: Open.

#417 In acope3/RibModelFramework;

· mikegilchrist opened on May 22, 2026

Adaptive-MCMC code paths: AA-vs-grouping audit + change list for future GeneticCode generalization

Status: Open.

#414 In acope3/RibModelFramework;

· mikegilchrist opened on May 21, 2026

Derive dM priors from non-coding genomic regions (introns / intergenic)

Status: Open.

#413 In acope3/RibModelFramework;

· mikegilchrist opened on May 21, 2026

Reform sphi prior to avoid bias toward small sphi

Status: Open.

#412 In acope3/RibModelFramework;

· mikegilchrist opened on May 21, 2026

PANSE: jointly propose Elongation and NSERate per AA (mirror ROC's joint dM/dEta)

Status: Open.

#411 In acope3/RibModelFramework;

· mikegilchrist opened on May 21, 2026

Estimate additional hyperparameters

Status: Open.

#404 In acope3/RibModelFramework;

· mikegilchrist opened on Jan 29, 2025

Allow independent fitting of mu_phi and s_phi parameters

Status: Open.

#400 In acope3/RibModelFramework;

· mikegilchrist opened on Apr 25, 2024