Analysis of Similarity (ANOSIM)

Source: R/gv_ANOSIM.R

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)

Arguments

object

(Required). a phyloseq::phyloseq or SummarizedExperiment::SummarizedExperiment object.

level

(Optional). character. Summarization level (from rank_names(pseq), default: NULL).

variable

(Required). character. grouping variable for test.

method

(Optional). character. Provide one of the currently supported options. See distanceMethodList for a detailed list of the supported options and links to accompanying documentation. Options include:

  • "bray": bray crutis distance.

  • "unifrac" : unweighted UniFrac distance.

  • "wunifrac": weighted-UniFrac distance.

  • "GUniFrac": The variance-adjusted weighted UniFrac distances (default: alpha=0.5).

  • "dpcoa": sample-wise distance used in Double Principle Coordinate Analysis.

  • "jsd": Jensen-Shannon Divergence. Alternatively, you can provide a character string that defines a custom distance method, if it has the form described in designdist (default: "bray").

seedNum

(Optional). numeric. specify seeds for reproduction (default: 123).

alpha

(Optional). numeric. the parameter for "GUniFrac" controlling weight on abundant lineages (default: 0.5).

Value

An ANOSIM model.

Details

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.

References

Clarke, K. Robert. "Non‐parametric multivariate analyses of changes in community structure." Australian journal of ecology 18.1 (1993): 117-143.

Author

Created by Hua Zou (5/15/2022 Shenzhen China)

Examples


if (FALSE) {

# 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")
}