run_sims: Running a Simulation for Neutral Theory analysis
In kathalexknuts/ntsims:

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).

1 2	run_sims(k = 1, ps = 1, r = 1, n, m, Nt0, nOTU, Nlocal, Nmeta_sd, Nlocal_sd, sourc = FALSE, pool_sim = FALSE, pool_est = FALSE)

`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 May 4, 2019, 6:40 p.m.