Package index

Automatic plotting with autoplot()

Functions for producing complete plots of vegan objects using ggplot2

autoplot(<anosim>)

ggplot-based plot for objects of class "anosim"

autoplot(<cca>)

ggplot-based plot for objects of class "cca"

autoplot(<dbrda>)

ggplot-based plot for objects of class "dbrda"

autoplot(<decorana>)

ggplot-based plot for objects of class "decorana"

autoplot(<envfit>)

ggplot-based plot for envfit objects

autoplot(<fisherfit>)

Plot Fisher's log-series

autoplot(<isomap>)

ggplot-based plot for objects of class "isomap"

autoplot(<metaMDS>)

ggplot-based plot for objects of class "metaMDS"

autoplot(<permustats>)

Autoplot Graphics for vegan permustats Objects

autoplot(<poolaccum>)

ggplot-based plot for objects of class "poolaccum"

autoplot(<prc>)

ggplot-based plot for objects of class "prc"

autoplot(<prestonfit>)

Plot Preston's log-normal model of species abundance

autoplot(<rda>)

ggplot-based plot for objects of class 'rda'

autoplot(<vegan_pco>)

ggplot-based plot for objects of class "vegan_pco"

Tidy vegan objects

Functions tidying vegan objects with tidy() or fortify().

fortify(<anosim>) tidy(<anosim>)

Fortify analysis of similarities (ANOSIM) results

fortify(<cca>) tidy(<cca>)

Fortify a "cca" object.

fortify(<dbrda>) tidy(<dbrda>)

Fortify a "dbrda" object.

fortify(<decorana>) tidy(<decorana>)

Fortify a "decorana" object.

fortify(<envfit>) tidy(<envfit>)

Fortify method for envfit objects

fortify(<fisherfit>) tidy(<fisherfit>)

Tidied species rank abundance data and estimated Fisher's log-series

fortify(<isomap>) tidy(<isomap>)

Fortify isometric feature mapping results

fortify(<metaMDS>) tidy(<metaMDS>)

Fortify a "mataMDS" object.

fortify(<permustats>) tidy(<permustats>)

Fortify permutation statistics

fortify(<poolaccum>) tidy(<poolaccum>)

Fortify extrapolated species richness of a species pool

fortify(<prc>) tidy(<prc>)

Fortify a "prc" object

fortify(<prestonfit>) tidy(<prestonfit>)

Tidied species octave abundance data

fortify(<rda>) tidy(<rda>)

Fortify a "rda" object.

fortify(<renyiaccum>) tidy(<renyiaccum>)

Fortify Rényi accumulation curves

fortify(<vegan_pco>) tidy(<vegan_pco>)

Fortify a "vegan_pco" object.

Manually plotting ordination diagrams

More control over plotting of ordination diagrams can be achieved using ordiggplot() and the custom geoms provided by ggvegan

ordiggplot() ggscores()

Create a ggplot Object

Geoms

geoms for use with ordiggplot().

geom_ordi_arrow()

Add a biplot arrow layer to an ordiggplot

geom_ordi_axis()

Crosshair for axes in eigenvector methods

geom_ordi_label()

Add a label layer to an ordiggplot

geom_ordi_point()

Add a point layer to an ordiggplot

geom_ordi_text()

Add a text layer to an ordiggplot

Stats

stats for use with ordiggplot().

stat_vectorfit()

Add Fitted Vectors to Ordination plots

Utility functions

Functions that provide utilities or helpers.

add_biplot_arrows()

Adds a biplot arrow layer to an existing plot

add_biplot_centroids()

Adds a biplot arrow layer to an existing plot

add_spp_site_scores()

Adds species and site score layers to an existing plot

arrow_mul()

Scale Vectors to Data

check_user_layers()

Check user-supplied layers against list of valid layers

get_dimension_names()

Extract the names of the dimensions to plot as a character vector

label_fun()

Adds a label layer using one of a set of common geoms

layer_draw_list()

List of layers to draw for a given vegan object

scores_length()

Number of scores

valid_layers()

Valid layers for vegan objects