Description Usage Arguments Details Value References See Also Examples

View source: R/score.sim.control.q

In the call to haplo.score, the sim.control parameter is a list of parameters that control the simulations. This list is created by this function, score.sim.control, making it easy to change the default values.

1 | ```
score.sim.control(p.threshold=0.25, min.sim=1000, max.sim=20000.,verbose=FALSE)
``` |

`p.threshold ` |
A paremeter used to determine p-value precision from Besag and Clifford (1991). For a p-value calculated after min.sim simulations, continue doing simulations until the p-value's sample standard error is less than p.threshold * p-value. The dafault value for p.threshold = 1/4 corresponds approximately to having a two-sided 95% confidence interval for the p-value with a width as wide as the p-value itself. Therefore, simulations are more precise for smaller p-values. Additionally, since simulations are stopped as soon as this criteria is met, p-values may be biased high. |

`min.sim ` |
The minimum number of simulations to run. To run exactly min.sim simulations, set max.sim = min.sim. Also, if run-time is an issue, a lower minimum (e.g. 500) may be useful, especially when doing simulations in haplo.score.slide. |

`max.sim ` |
The upper limit of simulations allowed. When the number of simulations reaches max.sim, p-values are approximated based on simulation results at that time. |

`verbose` |
Logical, if (T)rue, print updates from every simulation to the screen. If (F)alse, do not print these details. |

In simulations for haplo.score, employ the simulation p-value precision criteria of Besag and Clifford (1991). The criteria ensures both the global and the maximum score statistic simulated p-values be precise for small p-values. First, perform min.sim simulations to guarantee sufficient precision for the score statistics on individual haplotypes. Then continue simulations as needed until simulated p-values for both the global and max score statistics meet precision requirements set by p.threshold.

A list of the control parameters:

`p.threshold` |
As described above |

`min.sim` |
As described above. |

`max.sim` |
As described above |

`verbose` |
As described above |

Besag, J and Clifford, P. "Sequential Monte Carlo p-values." Biometrika. 78, no. 2 (1991): 301-304.

1 2 3 4 | ```
# it would be used in haplo.score as appears below
#
# score.sim.500 <- haplo.score(y, geno, trait.type="gaussian", simulate=T,
# sim.control=score.sim.control(min.sim=500, max.sim=2000)
``` |

haplo.stats documentation built on April 11, 2018, 5:03 p.m.

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