| sonicLength-package | Calibration of Number of Length Variants |
| A1 | HTLV-1 Fragment Length Data |
| dfrag | Simple Fragment Length Distribution |
| estAbund | estimate Abundances from sonicated samples |
| Ey.given.x | E-Step for Abundance Estimation |
| maxEM | maximum likelihood estimates relative abundances |
| maxEM.iter.control | iteration controls |
| mstep | M-step to maximize theta |
| pfrag | Simple Fragment Length Distribution |
| phi.update.lframe | estimate phi |
| pr.y.given.x | E-Step for Abundance Estimation |
| qfrag | Simple Fragment Length Distribution |
| rfrag | Simple Fragment Length Distribution |
| simSonic | Simulate Sonicated Data |
| sonicLength | Calibration of Number of Length Variants |