run_ANOSIM | R Documentation |
The run_ANOSIM
function is used to identify the association between
the community and environmental variables by rank.
run_ANOSIM(
object,
level = c(NULL, "Kingdom", "Phylum", "Class",
"Order", "Family", "Genus",
"Species", "Strain", "unique"),
variable,
method = c("unifrac", "wunifrac", "GUniFrac", "bray", "dpcoa", "jsd"),
seedNum = 123,
alpha = 0.5)
object |
(Required). a |
level |
(Optional). character. Summarization
level (from |
variable |
(Required). character. grouping variable for test. |
method |
(Optional). character. Provide one of the currently supported
options. See
|
seedNum |
(Optional). numeric. specify seeds for reproduction (default: 123). |
alpha |
(Optional). numeric. the parameter for "GUniFrac" controlling weight on abundant lineages (default: 0.5). |
The run_ANOSIM
function is used to identify the association between
the community and environmental variables by rank, applying the distance
in profile and calculating the R statistic between community and rank variable
by permutation test to determine the significance. It can be applied to both
phyloseq::phyloseq
and SummarizedExperiment::SummarizedExperiment
object.
An ANOSIM model.
Created by Hua Zou (5/15/2022 Shenzhen China)
Clarke, K. Robert. "Nonāparametric multivariate analyses of changes in community structure." Australian journal of ecology 18.1 (1993): 117-143.
## Not run:
# phyloseq object
data("Zeybel_2022_gut")
run_ANOSIM(Zeybel_2022_gut,
level = "Phylum",
variable = "LiverFatClass",
method = "bray")
# SummarizedExperiment object
data("Zeybel_2022_protein")
run_ANOSIM(Zeybel_2022_protein,
variable = "LiverFatClass",
method = "bray")
## End(Not run)
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