iNEXT_pq {MiscMetabar} | R Documentation |
iNterpolation and EXTrapolation of Hill numbers (with iNEXT)
Description
Usage
iNEXT_pq(physeq, merge_sample_by = NULL, ...)
Arguments
physeq |
(required): a |
merge_sample_by |
(default: NULL) if not |
... |
Other arguments for the |
Value
see iNEXT::iNEXT()
documentation
Author(s)
Adrien Taudière
This function is mainly a wrapper of the work of others.
Please make a reference to iNEXT::iNEXT()
if you
use this function.
Examples
if (requireNamespace("iNEXT")) {
data("GlobalPatterns", package = "phyloseq")
GPsubset <- subset_taxa(
GlobalPatterns,
GlobalPatterns@tax_table[, 1] == "Bacteria"
)
GPsubset <- subset_taxa(
GPsubset,
rowSums(GPsubset@otu_table) > 20000
)
GPsubset <- subset_taxa(
GPsubset,
rowSums(is.na(GPsubset@tax_table)) == 0
)
GPsubset@sam_data$human <- GPsubset@sam_data$SampleType %in%
c("Skin", "Feces", "Tong")
res_iNEXT <- iNEXT_pq(
GPsubset,
merge_sample_by = "human",
q = 1,
datatype = "abundance",
nboot = 2
)
iNEXT::ggiNEXT(res_iNEXT)
iNEXT::ggiNEXT(res_iNEXT, type = 2)
iNEXT::ggiNEXT(res_iNEXT, type = 3)
}
[Package MiscMetabar version 0.9.1 Index]