Description Usage Arguments Value

View source: R/run_sims_function.R

This function combines the functions mom2 and sim_communities to run a full simulation (generate data and estimate).

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`k` |
This parameter sets the seed (also helpful for running this function in an apply loop) |

`ps` |
this parameter adjusts the amount of variation between samples, with a range between 0 and 1. This value is the probability that a given OTU's relative abundance with be permuted in a sample. Values of 0 result in homologous taxa abundance distributions across all samples. Default in 1. |

`r` |
this parameter adjusts the amount of variation between samples. Values can range from 0 to 1. r = 0 will result in a uniformly distributed relative abundance distribution within a sample. Default is 1. |

`n` |
the number of samples |

`m` |
true migration parameter |

`Nt0` |
total number of reads in each meta community samples. Note that if the argument for Nmeta_sd != 0, then this value will be the mean number of reads across meta community samples. |

`nOTU` |
number of OTUs |

`Nlocal` |
total number of reads in each local community samples. Note that if the argument for Nlocal_sd != 0, then this value will be the mean number of reads across meta community samples. |

`Nmeta_sd` |
this parameter adjusts the amount of variation in the number of reads in meta community samples. Specifically, this value is the standard deviation used in a normal distribution with mean Nmeta from which samples sizes are generated |

`Nlocal_sd` |
this parameter adjusts the amount of variation in the number of reads in local community samples. Specifically, this value is the standard deviation used in a normal distribution with mean Nlocal from which samples sizes are generated from. |

`sourc` |
to use source data in estimation of migration parameter |

`pool` |
to pool meta/source community data during data simulation and estimation |

a matrix of 4 rows: row 1 = migration parameter estimate, row 2 = mean bray curtis dissimilarity for meta community, row 3 = the estimated average shannon diversity for each sample. row 4 = average shannon diversity after the multiple samples have been generated given the inputed value for ps and OTUs with no reads across any samples are removed

kathalexknuts/ntsims documentation built on Oct. 17, 2018, 5:32 a.m.

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