screeplot.cca {vegan} | R Documentation |

Screeplot methods for plotting variances of ordination axes/components
and overlaying broken stick distributions. Also, provides alternative
screeplot methods for `princomp`

and `prcomp`

.

## S3 method for class 'cca': screeplot(x, bstick = FALSE, type = c("barplot", "lines"), npcs = min(10, if (is.null(x$CCA)) x$CA$rank else x$CCA$rank), ptype = "o", bst.col = "red", bst.lty = "solid", xlab = "Component", ylab = "Inertia", main = deparse(substitute(x)), ...) ## S3 method for class 'decorana': screeplot(x, bstick = FALSE, type = c("barplot", "lines"), npcs = 4, ptype = "o", bst.col = "red", bst.lty = "solid", xlab = "Component", ylab = "Inertia", main = deparse(substitute(x)), ...) ## S3 method for class 'prcomp': screeplot(x, bstick = FALSE, type = c("barplot", "lines"), npcs = min(10, length(x$sdev)), ptype = "o", bst.col = "red", bst.lty = "solid", xlab = "Component", ylab = "Inertia", main = deparse(substitute(x)), ...) ## S3 method for class 'princomp': screeplot(x, bstick = FALSE, type = c("barplot", "lines"), npcs = min(10, length(x$sdev)), ptype = "o", bst.col = "red", bst.lty = "solid", xlab = "Component", ylab = "Inertia", main = deparse(substitute(x)), ...) bstick(n, ...) ## Default S3 method: bstick(n, tot.var = 1, ...) ## S3 method for class 'cca': bstick(n, ...) ## S3 method for class 'prcomp': bstick(n, ...) ## S3 method for class 'princomp': bstick(n, ...) ## S3 method for class 'decorana': bstick(n, ...)

`x` |
an object from which the component variances can be determined. |

`bstick` |
logical; should the broken stick distribution be drawn? |

`npcs` |
the number of components to be plotted. |

`type` |
the type of plot. |

`ptype` |
if `type == "lines"` or `bstick = TRUE` , a
character indicating the type of plotting used for the lines;
actually any of the `type` s as in `plot.default` . |

`bst.col, bst.lty` |
the colour and line type used to draw the broken stick distribution. |

`xlab, ylab, main` |
graphics parameters. |

`n` |
an object from which the variances can be extracted or the
number of variances (components) in the case of
`bstick.default` . |

`tot.var` |
the total variance to be split. |

`...` |
arguments passed to other methods. |

The functions provide screeplots for most ordination methods in
vegan and enhanced versions with broken stick for
`prcomp`

and `princomp`

.

Function `bstick`

gives the brokenstick values which are ordered
random proportions, defined as *p[i] = tot/n sum(from x=i to n) 1/x* (Legendre & Legendre 1998), where
*tot* is the total and *n* is the number of brokenstick
components (cf. `radfit`

). Broken stick has
been recommended as a stopping rule in principal component analysis
(Jackson 1993): principal components should be retained as long as
observed eigenvalues are higher than corresponding random broken stick
components.

The `bstick`

function is generic. The default needs the number of
components and the total, and specific methods extract this
information from ordination results. There also is a `bstick`

method for `cca`

. However, the broken stick model is not
strictly valid for correspondence analysis (CA), because eigenvalues
of CA are defined to be *<=1*, whereas brokenstick
components have no such restrictions. The brokenstick components are not
available for `decorana`

where the sum of eigenvalues
(total inertia) is unknown, and the eigenvalues of single axes are not
additive in detrended analysis.

Function `screeplot`

draws a plot on the currently active device,
and returns invisibly the `xy.coords`

of the points or
bars for the eigenvalues.

Function `bstick`

returns a numeric vector of broken stick
components.

Function `screeplot`

is generic from `R`

version
2.5.0. In these versions you can use plain `screeplot`

command
without suffices `cca`

, `prcomp`

etc.

Gavin L. Simpson

Jackson, D. A. (1993). Stopping rules in principal components
analysis: a comparison of heuristical and statistical
approaches. *Ecology* 74, 2204–2214.

Legendre, P. and Legendre, L. (1998) *Numerical Ecology*. 2nd English
ed. Elsevier.

`cca`

, `decorana`

, `princomp`

and
`prcomp`

for the ordination functions, and
`screeplot`

for the stock version.

data(varespec) vare.pca <- rda(varespec, scale = TRUE) bstick(vare.pca) screeplot.cca(vare.pca, bstick = TRUE, type = "lines")

[Package *vegan* version 1.16-32 Index]