NMDS_ellipse: Generate NMDS points, group centroids and standard error...
In Jtrachsel/funfuns: Functions I Use (Title Case)

Description Usage Arguments Value Examples

Generate NMDS points, group centroids and standard error ellipses

NMDS_ellipse(
  metadata,
  OTU_table,
  grouping_set,
  distance_method = "bray",
  rand_seed = 77777,
  MDS_trymax = 1000,
  autotransform = FALSE,
  wascores = TRUE,
  expand = FALSE
)

`metadata`	A dataframe containing the metadata relating to the samples in your OTU table. Seems to break if this dataframe only has 1 column.
`OTU_table`	an OTU table with samples as rows and taxa as columns
`grouping_set`	a column name from your metadata. This column should contain information about how your samples should be grouped for centroid and ellipse calculation
`distance_method`	a single text value that describes the desired distance metric to use, must be accepted by the function vegdist()
`rand_seed`	numeric value to use as a random seed (for reproducability?)
`MDS_trymax`	number of iterations to use for the metaMDS call, default is 1000
`autotransform`	passed to vegan's metaMDS, should community data be transformed? Should be TRUE/FALSE. Default = FALSE
`wascores`	passed to vegan's metaMDS, should species scores be calculated? Should be TRUE/FALSE. Default = TRUE
`expand`	passed to vegan's metaMDS, should species scores be expanded?

Returns a list containing 3 items. [[1]] = input metadata with NMDS coordinates, group centroid coordinates for each sample. [[2]] = a dataframe containing information about the standard error confidence ellipses for each group. This datafame contains 100 points per group and is suitable for using with geom_path(). [[3]] = the ordination object created by the vegan function metaMDS().