neutral.rand | R Documentation |
Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664) several times on ramdomly picked samples and with 16S rRNA gene copy number corrected rarefaction.
neutral.rand( data, n = NULL, s = NULL, rRNA = NULL, rn = NULL, cores = 1, naming = NULL )
data |
A phyloseq object |
n |
Integer. Number of times to repeat analysis |
s |
Integer. Number of random samples to for each repetition. |
rRNA |
What Greengenes database version was used to find OTUs. Atm only "v13.5" is available. Alternatively, A dataframe with two variables: "ID" is the OTU id matched by names in x and "Copy" is the copy number. |
rn |
Integer. Number of reads to sample for rarefaction |
cores |
Integer. Number of cores to use for parallel computing. |
naming |
Optional. A list for naming the output e.g. list(Time="1 Week",Type="Gut") |
A list of length two; first element contains fit statistics, the second element contains predictions.
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