Description Usage Arguments Value
This function combines the functions mom2 and sim_communities to run a full simulation (generate data and estimate).
1 2 |
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. |
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 |
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
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