poilogMLE: maximum likelihood estimation for the Poisson lognormal
In texmexseq: Treatment Effect eXplorer for Microbial Ecology eXperiments (using Sequence Counts)

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/texmexseq.R

Fit a set of OTU counts to the Poisson lognormal distribution.

1 2	poilogMLE(n, start.mu, start.sig, trunc=TRUE, method='L-BFGS-B', control=list(fnscale=length(n)), ...)

`n`	vector of observed counts
`start.mu`	initial estimate for the lognormal mean
`start.sig`	initial estimate for the lognormal standard deviation
`trunc`	remove weight from zero counts?
`method`	optimization method for `optim`
`control`	list of parameters for `optim`
`...`	further parameters to go to `optim`

The function estimates parameters mean mu and standard deviation sig.

The parameters must be given starting values for the optimization procedure. The default values here worked well when fitting OTUs in the referenced paper.

The function uses the optimization procedures in optim to make the maximum likelihood estimate. The method and control arguments are passed to optim.

A zero-truncated distribution (see dpoilog) is assumed by default. Truncation should only be turned off if all the known OTUs of the sequenced community are known. In most cases, this is not applicable, since it is usually not possible to know if an OTU had zero counts because it is not present in the environment or if it is present but in low abundance.

`par`	Maximum likelihood estimates of the parameters
`p`	Approximate fraction of OTUs revealed by the sample
`logLval`	Log likelihood of the data given the estimated parameters

Scott Olesen swo@mit.edu

dpoilog optim

# create some random data
x <- rpoilog(S=1000, mu=-2.0, sig=2.0, keep0=FALSE)

# fit that data
res <- poilogMLE(x, 2.0, -2.0)

# the results should be fairly robust to the starting parameters
res2 <- poilogMLE(x, 1.0, 0.5)

Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggplot2