Marine species from sea-bed (benthic) samples

Counts of 92 benthic species at 13 sites in the North Sea following an oil exploration.

data(benthos)

Format

A matrix.

Source

Greenacre (2010).

References

Greenacre MJ (2010) Biplots in Practice. Fundacion BBVA, ISBN: 978-84-923846. https://www.fbbva.es/microsite/multivariate-statistics/biplots.html

Examples

# Confer inertia in CA between rows and columns of benthic sample data
data(benthos)
benthos %>%
  ca::ca() %>%
  as_tbl_ord() %>%
  print() -> benthos_ca
#> # A tbl_ord of class 'ca': (92 x 12) x (13 x 12)'
#> # 12 coordinates: Dim1, Dim2, ..., Dim12
#> # 
#> # Rows: [ 92 x 12 | 0 ]
#>      Dim1   Dim2   Dim3 ... | 
#>                             | 
#> 1 -1.17    0.895 -0.140     | 
#> 2 -0.552  -2.23  -0.359 ... | 
#> 3 -0.0406 -0.689  0.687     | 
#> 4  1.22    0.287 -0.700     | 
#> 5  0.312   0.142 -0.137     | 
#> 
#> # 
#> # Columns: [ 13 x 12 | 0 ]
#>     Dim1    Dim2   Dim3 ... | 
#>                             | 
#> 1 -0.173  0.262  -0.376     | 
#> 2  1.11   0.417   1.52  ... | 
#> 3 -0.226 -1.33   -0.297     | 
#> 4  1.27   0.411   1.37      | 
#> 5  0.186 -0.0884  0.568     | 
#> 
# Reproduce Exhibit 8.3
benthos_ca %>%
  confer_inertia("colprincipal") %>%
  ggbiplot(aes(label = .name)) +
  theme_bw() +
  geom_rows_point(color = "brown", size = 1) +
  geom_cols_text(color = "darkgreen")
# Reproduce Exhibit 8.4
benthos_ca %>%
  augment(.matrix = "rows") %>%
  transmute_rows(mass = .mass, sqrt_mass = sqrt(.mass)) %>%
  confer_inertia("colprincipal") %>%
  ggbiplot(aes(label = .name), scale_rows = "sqrt_mass") +
  theme_bw() +
  geom_rows_vector(color = "brown", arrow = NULL) +
  geom_rows_point(aes(size = mass), color = "brown", shape = 17) +
  scale_size_continuous(range = c(1, 4), guide = "none") +
  geom_rows_text(
    stat = "chull",
    color = "brown", hjust = "outward", vjust = "outward"
  ) +
  geom_cols_point(color = "darkgreen") +
  geom_cols_text_repel(color = "darkgreen", min.segment.length = 2)