Accessors: Grab important output from a list of fits
In hillarykoch/powerTCR: Model-Based Comparative Analysis of the TCR Repertoire

Description Usage Arguments Value Author(s) See Also Examples

These are convenient accessors that will grab important output from a list of fits from fdiscgammagpd. They will grab the maximum likelihood estimates and/or the negative log likelihood for the maximum likelihood estimates.

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get_mle(fits)
get_nllh(fits)
get_diversity(fits)

fits

A list of fits output from fdiscgammagpd.

A list of out either maximum likelihood estimates (get_mle) or negative log likelihoods (get nllh) corresponding to the list of fits. For get_diversity, a data frame of diversity estimates (species richness, Shannon entropy, clonality, and proportion of highly stimulated clones) for the samples.

hbk5086@psu.edu

fdiscgammagpd

# Here is a good workflow using fdiscgammagpd:
# Choose quantiles for every sample repertoire in the same manner.
# Then fit the model in the same manner as well.

data("repertoires")

thresholds <- list()
fits <- list()
for(i in 1:2){
    thresholds[[i]] <- unique(round(quantile(repertoires[[i]], c(.8,.85,.9,.95))))
    fits[[i]] <- fdiscgammagpd(repertoires[[i]], useq = thresholds[[i]],
                                shift = min(repertoires[[i]]))
}
names(fits) <- c("fit1", "fit2")

mles <- get_mle(fits)
nllhs <- get_nllh(fits)
diversity_ests <- get_diversity(fits)

mles
nllhs
diversity_ests