Permutation tests for constrained ordinations — ord

Tests the significance of a constrained ordination (ord_fit() with "rda", "cca" or "dbrda") by permutation, with vegan::anova.cca(), and returns a tidy table.

Usage

ord_test(x, by = c("model", "axis", "terms", "margin"), permutations = 999)

Arguments

x: A td_ordination from a constrained method.
by: "model" (the whole model, the default), "axis" (each constrained axis), "terms" (each term, added sequentially) or "margin" (each term given the others).
permutations: Number of permutations.

Value

A tibble with term, df, variance (or chi_square for CCA), statistic (pseudo-F) and p.value.

Examples

ord <- ord_fit(png_frogs, method = "cca", formula = ~elevation)
ord_test(ord, permutations = 199)
#> # A tibble: 2 x 5
#>   term        df chi_square statistic p.value
#>   <chr>    <dbl>      <dbl>     <dbl>   <dbl>
#> 1 Model        1      0.959      1.44   0.005
#> 2 Residual     6      4.00      NA     NA