Fortify a

Fortifies an object of class "rda" to produce a data frame of the selected axis scores in long format, suitable for plotting with ggplot2::ggplot().

Usage

# S3 method for class 'rda'
fortify(
  model,
  data = NULL,
  axes = 1:6,
  layers = c("sp", "wa", "lc", "bp", "cn"),
  const = NULL,
  ...
)

# S3 method for class 'rda'
tidy(
  x,
  data = NULL,
  axes = 1:6,
  layers = c("sp", "wa", "lc", "bp", "reg", "cn"),
  const = NULL,
  ...
)

Arguments

model, x: an object of class "rda", the result of a call to vegan::rda().
data: currently ignored.
axes: numeric; which axes to extract scores for.
layers: character; the scores to extract in the fortified object. Passed to display in the respective vegan::scores() method.
const: NULL; General scaling constant to RDA scores. See vegan::scores.rda() for the details.
...: additional arguments passed to vegan::scores.rda().

Value

A data frame (tibble) in long format containing the ordination scores. The first two components are score (the type of score in each row) and label (the text label to use on plots for this row). The remaining columns are the extracted ordination axis scores.

Details

TODO

Author

Gavin L. Simpson

Examples


library("vegan")

data(dune)
data(dune.env)

sol <- rda(dune ~ A1 + Management, data = dune.env)
head(fortify(sol))
#> # A tibble: 6 × 8
#>   score   label       rda1    rda2    rda3    rda4    pc1     pc2
#>   <fct>   <chr>      <dbl>   <dbl>   <dbl>   <dbl>  <dbl>   <dbl>
#> 1 species Achimill  0.365   0.377   0.0453 -0.147   0.362 -0.0170
#> 2 species Agrostol -0.355  -1.22    0.0240 -0.0755 -1.09   0.165 
#> 3 species Airaprae -0.215   0.169   0.0910  0.186   0.108  0.0954
#> 4 species Alopgeni  0.450  -1.17    0.173   0.0526 -0.591  0.662 
#> 5 species Anthodor  0.0626  0.493  -0.183   0.181   0.604 -0.0857
#> 6 species Bellpere  0.175   0.0832  0.196  -0.158   0.214  0.224