Type:	Package
Title:	'ggplot2' Plots for the 'vegan' Package
Version:	0.2.1
Depends:	R (≥ 4.1.0)
Imports:	vegan (≥ 2.3-0), dplyr, tibble, vctrs, ggplot2, grid, tidyr, ggrepel, generics
Suggests:	testthat (≥ 3.0.0), vdiffr (≥ 1.0.0), permute, withr
Description:	Functions to produce 'ggplot2'-based plots of objects produced by functions in the 'vegan' package. Provides 'fortify()', 'autoplot()', and 'tidy()' methods for many of 'vegan”s functions. The aim of 'ggvegan' is to make it easier to work within the 'tidyverse' with 'vegan'.
License:	GPL-2
ByteCompile:	true
RoxygenNote:	7.3.3
Encoding:	UTF-8
Config/testthat/edition:	3
Language:	en-GB
NeedsCompilation:	no
Packaged:	2026-02-23 11:44:48 UTC; gavin
Author:	Gavin L. Simpson [aut, cre], Jari Oksanen [aut], Didzis Elferts [ctb]
Maintainer:	Gavin L. Simpson <ucfagls@gmail.com>
Repository:	CRAN
Date/Publication:	2026-02-27 20:30:02 UTC

Add Fitted Vectors to Ordination plots

Description

Fits arrows to show the direction of fastest increase in continuous environmental variables in ordination space.The arrows are scaled relative to their correlation coefficient, and they can be added to an ordination plot with geom_ordi_arrow().

Usage

stat_vectorfit(
  mapping = NULL,
  data = NULL,
  geom = "text",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  edata = NULL,
  formula = NULL,
  arrow.mul = NULL,
  ...
)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

Examples

library("vegan")
library("ggplot2")

data(mite, mite.env)
m <- metaMDS(mite, trace = FALSE, trymax = 100)

## add fitted vectors for continuous variables
ordiggplot(m) +
  geom_ordi_point("sites") +
  geom_ordi_arrow("sites", stat = "vectorfit", edata = mite.env)

## can be faceted
ordiggplot(m) + geom_ordi_point("sites") +
  geom_ordi_arrow("sites", stat = "vectorfit", edata = mite.env) +
  facet_wrap(mite.env$Topo)

Adds a biplot arrow layer to an existing plot

Description

Adds a biplot arrow layer to an existing plot

Usage

add_biplot_arrows(object, plt, vars, arrow.col = "navy")

Arguments

Adds a biplot arrow layer to an existing plot

Description

Adds a biplot arrow layer to an existing plot

Usage

add_biplot_centroids(object, plt, vars, arrow.col = "navy")

Arguments

Adds species and site score layers to an existing plot

Description

Adds species and site score layers to an existing plot

Usage

add_spp_site_scores(object, plt, vars, geom, draw_list, arrows)

Arguments

Scale Vectors to Data

Description

Scale vector arrows to fill proportion of the data.

Usage

arrow_mul(arrows, data, at = c(0, 0), fill = 0.75)

Arguments

Value

a numeric multiplier that will scale the arrows

Author(s)

Gavin L. Simpson

ggplot-based plot for objects of class "anosim"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::anosim().

Usage

## S3 method for class 'anosim'
autoplot(
  object,
  notch = TRUE,
  varwidth = TRUE,
  xlab = NULL,
  ylab = NULL,
  title = "Analysis of similarities",
  subtitle = NULL,
  caption = bquote(R == .(r) * "," ~ P == .(p)),
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Didzis Elferts. Modifications by Gavin L. Simpson.

Examples

library("vegan")

data(dune)
data(dune.env)
dune.dist <- vegdist(dune)
dune.ano <- with(dune.env, anosim(dune.dist, Management))

autoplot(dune.ano, notch = FALSE)

ggplot-based plot for objects of class "cca"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::cca() or vegan::capscale().

Usage

## S3 method for class 'cca'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("species", "sites", "biplot", "centroids"),
  legend.position = "right",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab = NULL,
  xlab = NULL,
  arrow.col = "navy",
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")
data(dune)
data(dune.env)

sol <- cca(dune ~ A1 + Management, data = dune.env)
autoplot(sol)

ggplot-based plot for objects of class "dbrda"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::dbrda().

Usage

## S3 method for class 'dbrda'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("sites", "biplot", "centroids"),
  legend.position = "none",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab = NULL,
  xlab = NULL,
  const = NULL,
  arrow.col = "navy",
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune, dune.env)

dune_dbrda <- dbrda(
  dune ~ A1 + Moisture + Use + Management,
  data = dune.env
)
autoplot(dune_dbrda)

ggplot-based plot for objects of class "decorana"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::decorana().

Usage

## S3 method for class 'decorana'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("sites", "species"),
  legend.position = "right",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab,
  xlab,
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")
data(dune)

sol <- decorana(dune)
autoplot(sol)
autoplot(sol, layers = "species", geom = "text")

ggplot-based plot for envfit objects

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::envfit().

Usage

## S3 method for class 'envfit'
autoplot(
  object,
  geom = c("label", "text", "label_repel", "text_repel"),
  line.col = "black",
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")
data(varespec, varechem)
ord1 <- metaMDS(varespec)
fit1 <- envfit(ord1, varechem, perm = 199)

autoplot(fit1, geom = 'label_repel')

data(dune, dune.env)
ord2 <- cca(dune)
fit2 <- envfit(ord2 ~ Moisture + A1, dune.env, perm = 199)

autoplot(fit2)

Plot Fisher's log-series

Description

Draws a bar plot of species rank abundance with Fisher's log-series superimposed.

Usage

## S3 method for class 'fisherfit'
autoplot(
  object,
  show.fitted = TRUE,
  xlab = "Abundance",
  ylab = "Number of Species",
  title = "Fisher's log-series distribution",
  bar.col = NA,
  bar.fill = "grey35",
  line.col = "red",
  linewidth = 0.7,
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(BCI)
mod <- fisherfit(BCI[5,])
autoplot(mod)

ggplot-based plot for objects of class "isomap"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::isomap().

Usage

## S3 method for class 'isomap'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  network = TRUE,
  line.col = "grey85",
  linewidth = 0.7,
  xlab = NULL,
  ylab = NULL,
  title = "Isometric feature mapping",
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(BCI)
dis <- vegdist(BCI)
ord <- isomap(dis, k = 3)

autoplot(ord)

autoplot(ord, geom = "text")

ggplot-based plot for objects of class "metaMDS"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::metaMDS().

Usage

## S3 method for class 'metaMDS'
autoplot(
  object,
  geom = c("point", "text"),
  layers = c("species", "sites"),
  legend.position = "right",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab,
  xlab,
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

sol <- metaMDS(dune)
autoplot(sol)

Autoplot Graphics for vegan permustats Objects

Description

Alternatives for lattice graphics functions vegan::densityplot.permustats(), vegan::densityplot.permustats() and vegan::boxplot.permustats().

Usage

## S3 method for class 'permustats'
autoplot(
  object,
  plot = c("box", "violin", "density", "qqnorm"),
  scale = FALSE,
  facet = FALSE,
  gg.params = list(),
  ...
)

Arguments

Details

Function fortify() returns a data frame with variables permutations (numeric) and term (factor labelling the permutation). The result of fortify() can be used to custom build diagnostic plots. autoplot() provides basic plots of vegan::permustats() objects with limited flexibility.

Value

Returns a ggplot object.

Examples

library("vegan")

data(dune, dune.env)
mod <- cca(dune ~ A1 + Management + Moisture, dune.env)
(ano <- anova(mod, by = "onedf"))
pstat <- permustats(ano)
head(fortify(pstat))
autoplot(pstat, "box")


if (requireNamespace("ggplot2")) {
  library("ggplot2")

  # avoid overplotting x-axis text
  autoplot(pstat, "violin") +
    scale_x_discrete(guide = guide_axis(n.dodge = 2))

  autoplot(pstat, "qqnorm", facet = TRUE) +
    geom_qq_line()
}

autoplot(pstat, "density", facet = TRUE)

ggplot-based plot for objects of class "poolaccum"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::poolaccum().

Usage

## S3 method for class 'poolaccum'
autoplot(
  object,
  facet = TRUE,
  ribbon = facet,
  ncol = NULL,
  ribbon.alpha = 0.3,
  xlab = "Size",
  ylab = "Richness",
  title = "Accumulated species richness",
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Didzis Elferts & Gavin L. Simpson

Examples

library("vegan")

data(BCI)
pool <- poolaccum(BCI)

autoplot(pool)

## Turn off facetting; turns off ribbon too
autoplot(pool, facet = FALSE)

ggplot-based plot for objects of class "prc"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::prc().

Usage

## S3 method for class 'prc'
autoplot(
  object,
  select,
  xlab,
  ylab,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  legend.position = "top",
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(pyrifos)
week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))

## Fit PRC model
mod <- prc(pyrifos, dose, week)

## plot
want <- colSums(pyrifos) >= 300
autoplot(mod, select = want)

Plot Preston's log-normal model of species abundance

Description

Draws a bar plot of species rank abundance with Preston's log-normal model superimposed.

Usage

## S3 method for class 'prestonfit'
autoplot(
  object,
  show.fitted = TRUE,
  xlab = "Abundance",
  ylab = "Number of Species",
  title = "Preston's lognormal distribution",
  subtitle = NULL,
  caption = NULL,
  bar.col = NA,
  bar.fill = "grey35",
  line.col = "red",
  linewidth = 0.7,
  ...
)

Arguments

Value

A ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(BCI)
pfit <- prestonfit(colSums(BCI))
autoplot(pfit)

ggplot-based plot for objects of class 'rda'

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::rda().

Usage

## S3 method for class 'rda'
autoplot(
  object,
  axes = c(1, 2),
  geom = c("point", "text"),
  layers = c("species", "sites", "biplot", "centroids"),
  arrows = TRUE,
  legend.position = "none",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab = NULL,
  xlab = NULL,
  const = NULL,
  arrow.col = "navy",
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

pca <- rda(dune)
autoplot(pca)

## Just the species scores
autoplot(pca, layers = "species")

ggplot-based plot for objects of class "vegan_pco"

Description

Produces a multi-layer ggplot object representing the output of objects produced by vegan::pco().

Usage

## S3 method for class 'vegan_pco'
autoplot(
  object,
  geom = "point",
  legend.position = "right",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ylab = NULL,
  xlab = NULL,
  ...
)

Arguments

Details

TODO

Value

Returns a ggplot object.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

sol <- pco(dune)
autoplot(sol)

Check user-supplied layers against list of valid layers

Description

Check user-supplied layers against list of valid layers

Usage

check_user_layers(user, valid, message = FALSE)

Arguments

Fortify analysis of similarities (ANOSIM) results

Description

Prepares a fortified version of results from vegan::anosim() objects.

Usage

## S3 method for class 'anosim'
fortify(model, data, ...)

## S3 method for class 'anosim'
tidy(x, data, ...)

Arguments

Value

A data frame with columns Rank and Class with ranks of dissimilarity.

Author(s)

Original implementation by Didzis Elferts. Modification to tibbles by Gavin L. Simpson.

Examples

library("vegan")

library("ggplot2")
data(dune, dune.env)
dune.dist <- vegdist(dune)
dune.ano <- with(dune.env, anosim(dune.dist, Management))

df <- fortify(dune.ano)

ggplot(df, aes(x = class, y = rank)) +
    geom_boxplot(notch = FALSE, varwidth = TRUE)

Fortify a "cca" object.

Description

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

Usage

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

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

Arguments

Details

TODO

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.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)
data(dune.env)

sol <- cca(dune ~ A1 + Management, data = dune.env)
head(fortify(sol))

Fortify a "dbrda" object.

Description

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

Usage

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

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

Arguments

Details

TODO

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.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)
data(dune.env)

sol <- dbrda(dune ~ A1 + Management, data = dune.env)
head(fortify(sol))

Fortify a "decorana" object.

Description

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

Usage

## S3 method for class 'decorana'
fortify(model, data, axes = 1:4, layers = c("sites", "species"), ...)

## S3 method for class 'decorana'
tidy(x, data, axes = 1:4, layers = c("sites", "species"), ...)

Arguments

Details

TODO

Value

A data frame in long format containing the ordination scores. The first two components are the axis scores.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

sol <- decorana(dune)
head(fortify(sol))
head(fortify(sol, layers = "species"))

Fortify method for envfit objects

Description

Produces a tidy data frame from the results of an vegan::envfit() object.

Usage

## S3 method for class 'envfit'
fortify(model, data, ...)

## S3 method for class 'envfit'
tidy(x, data, ...)

Arguments

Value

A data frame with columns label, type, containing the label for, and whether each row refers to, the fitted vector or factor. Remaining variables are coordinates on the respective ordination axes returned by vegan::scores.envfit().

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(varespec, varechem)
ord <- metaMDS(varespec)
fit <- envfit(ord, varechem, perm = 199)

fortify(fit)

data(dune, dune.env)
ord <- ca(dune)
fit <- envfit(ord ~ Moisture + A1, dune.env, perm = 199)

fortify(fit)

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

Description

Prepares a data frame of results from a vegan::fisherfit()) object suitable for plotting with ggplot2::ggplot()).

Usage

## S3 method for class 'fisherfit'
fortify(model, data, ...)

## S3 method for class 'fisherfit'
tidy(x, data, ...)

Arguments

Value

A data frame with columns 'Rank' and 'Abundance'. Additionally, Fisher's \alpha and the nuisance parameter are returned as attributes 'alpha' and 'k' respectively.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(BCI)
mod <- fisherfit(BCI[5,])
head(fortify(mod))

Fortify isometric feature mapping results

Description

Prepares fortified versions of results from vegan::isomap() objects.

Usage

## S3 method for class 'isomap'
fortify(model, data = NULL, axes = NULL, what = c("sites", "network"), ...)

## S3 method for class 'isomap'
tidy(x, data = NULL, axes = NULL, what = c("sites", "network"), ...)

Arguments

Details

Two different objects can be created from the results of an vegan::isomap() object. The first is the standard scores representation of fortified ordinations in vegan, which results in a wide data frame where rows contain observations and column the coordinates of observations on the MDS axes. Because ISOMAP also produces a network or sorts, the coordinates of the edges of the network can also be returned in a tidy format using what = "network".

Value

A data frame. For what = "sites", the data frame contains one variable per dimension of the multidimensional scaling embedding of the dissimilarities. Variables are named "DimX" with "X" being an integer. An additional variable is label, containing a label for each observation. For what = "network", the data frame contains four variables containing the coordinates in the chosen MDS axes for the start and end points of the network edges.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

library("ggplot2")
data(BCI)
dis <- vegdist(BCI)
ord <- isomap(dis, k = 3)

df <- fortify(ord, data = data.frame(Richness = specnumber(BCI)))
net <- fortify(ord, what = "network", axes = 1:2)

ggplot(df, aes(x = dim1, y = dim2)) +
    geom_segment(data = net,
                 aes(x = xfrom, y = yfrom,
                     xend = xto, yend = yto),
                 colour = "grey85", size = 0.8) +
    geom_point(aes(size = Richness)) +
    coord_fixed()

Fortify a "mataMDS" object.

Description

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

Usage

## S3 method for class 'metaMDS'
fortify(model, data, axes = 1:2, layers = c("sites", "species"), ...)

## S3 method for class 'metaMDS'
tidy(x, data, layers = c("sites", "species"), ...)

Arguments

Details

TODO

Value

A data frame in long format containing the ordination scores. The first two components are the axis scores.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

ord <- metaMDS(dune)
head(fortify(ord))

Fortify permutation statistics

Description

Fortify permutation statistics

Usage

## S3 method for class 'permustats'
fortify(model, data, scale = FALSE, ...)

## S3 method for class 'permustats'
tidy(x, data, scale = FALSE, ...)

Arguments

Value

A tibble with columns permutations, and terms containing the values of tests statistics under the null hypothesis, and a factor labelling the permutation, respectively.

Examples

library("vegan")
data(dune, dune.env, package = "vegan")
mod <- adonis2(dune ~ Management + A1, data = dune.env)
## use permustats
perm <- permustats(mod)

Fortify extrapolated species richness of a species pool

Description

Prepares a fortified version of results from vegan::poolaccum() objects.

Usage

## S3 method for class 'poolaccum'
fortify(model, data, alpha = 0.05, ...)

## S3 method for class 'poolaccum'
tidy(x, data, alpha = 0.05, ...)

Arguments

Value

A data frame with columns index, size, richness, lower, upper, and std_dev, containing the richness index, permutation richness estimator, sample size, upper and lower 1 - \alpha quantile interval, and standard deviation of permutation estimates, respectively.

Author(s)

Gavin L. Simpson & Didzis Elferts

Examples

library("vegan")
library("ggplot2")
data(BCI)
pool <- poolaccum(BCI)
df <- fortify(pool)
df

ggplot(df, aes(x = size, y = richness, colour = index)) +
    geom_ribbon(aes(ymin = lower, ymax = upper, x = size, fill = index),
                alpha = 0.3, inherit.aes = FALSE) +
    geom_line() +
    facet_wrap(~ index)

Fortify a "prc" object

Description

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

Usage

## S3 method for class 'prc'
fortify(model, data, scaling = "symmetric", axis = 1, ...)

## S3 method for class 'prc'
tidy(x, data, scaling = "symmetric", axis = 1, ...)

Arguments

Details

TODO

Value

A data frame in long format containing the ordination scores. The first three components are the Time, Treatment, and associated Response. The last two components, score and label are an indicator factor and a label for the rows for use in plotting.

Author(s)

Gavin L. Simpson

Examples

library("vegan")
data(pyrifos)
week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
ditch <- gl(12, 1, length=132)

pyrifos_prc <- prc(pyrifos, dose, week)
fortify(pyrifos_prc)

Tidied species octave abundance data

Description

Prepares a data frame of results from a vegan::prestonfit() object suitable for plotting with ggplot2::ggplot().

Usage

## S3 method for class 'prestonfit'
fortify(model, data, ...)

## S3 method for class 'prestonfit'
tidy(x, data, ...)

Arguments

Value

A data frame with columns ⁠'Octave'`` and ⁠'Abundance'“.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(BCI)
pfit <- prestonfit(colSums(BCI))
fortify(pfit)

Fortify a "rda" object.

Description

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

Details

TODO

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.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)
data(dune.env)

sol <- rda(dune ~ A1 + Management, data = dune.env)
head(fortify(sol))

Fortify Rényi accumulation curves

Description

Prepares a fortified version of results from vegan::renyiaccum() objects.

Usage

## S3 method for class 'renyiaccum'
fortify(model, data, ...)

## S3 method for class 'renyiaccum'
tidy(x, data, ...)

Arguments

Value

A data frame (tibble) is returned. What is returned depends on how vegan::renyiaccum() was called. If raw = FALSE, then a data frame with columns site, scale, mean, std_dev, min, max, q2.5, and q97.5, containing the accumulated sites, the Rényi scale, and summary statistics of the Rényi accumulation curves. An additional column collector will be present if collector = TRUE was used in the vegan::renyiaccum() call. If raw = TRUE, then a data frame with columns site, permutation, scale, and diversity, containing the site and permutation identifiers, Rényi scale, and the Rényi diversity, respectively.

Author(s)

Gavin L. Simpson much rewritten from an original by Didzis Elferts.

Examples

library("vegan")
library("ggplot2")
data(BCI)
pool <- renyiaccum(BCI)
df <- fortify(pool)
df

ggplot(df, aes(x = site, y = mean)) +
    geom_ribbon(aes(ymin = q2.5, ymax = q97.5, x = site),
                alpha = 0.2, inherit.aes = FALSE) +
    geom_line() +
    facet_wrap(~ scale)

Fortify a "vegan_pco" object.

Description

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

Usage

## S3 method for class 'vegan_pco'
fortify(model, data = NULL, axes = 1:6, ...)

## S3 method for class 'vegan_pco'
tidy(x, data = NULL, axes = 1:6, const = NULL, ...)

Arguments

Details

TODO

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.

Author(s)

Gavin L. Simpson

Examples

library("vegan")

data(dune)

sol <- pco(dune)
head(fortify(sol))

Add a biplot arrow layer to an ordiggplot

Description

Add a biplot arrow layer to an ordiggplot

Usage

geom_ordi_arrow(
  score,
  data,
  text = TRUE,
  box = FALSE,
  arrow.params = list(),
  text.params = list(),
  ...
)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

Crosshair for axes in eigenvector methods

Description

Crosshair for axes in eigenvector methods

Usage

geom_ordi_axis(lty = 3, ...)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

Add a label layer to an ordiggplot

Description

Add a label layer to an ordiggplot

Usage

geom_ordi_label(score, data, ...)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

Add a point layer to an ordiggplot

Description

Add a point layer to an ordiggplot

Usage

geom_ordi_point(score, data, ...)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

Add a text layer to an ordiggplot

Description

Add a text layer to an ordiggplot

Usage

geom_ordi_text(score, data, ...)

Arguments

Value

Returns a ggplot2 layer or a list of such layers: a "LayerInstance" object that inherits from classes "Layer", "ggproto", and "gg".

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

Description

Find the character vector of names for the two dimensions of data to be plotted.

Usage

get_dimension_names(object)

Arguments

Value

A length 2 character vector of dimension names.

Author(s)

Gavin L. Simpson

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

Description

Adds labels to a plot using one of ggplot2::geom_label(), ggplot2::geom_text(), ggrepel::geom_label_repel() or ggrepel::geom_text_repel().

Usage

label_fun(data, geom = c("label", "text", "label_repel", "text_repel"), vars)

Arguments

Author(s)

Gavin L. Simpson

List of layers to draw for a given vegan object

Description

List of layers to draw for a given vegan object

Usage

layer_draw_list(valid, layers = NULL, available = NULL)

Arguments

Create a ggplot Object

Description

Function ordiggplot sets up an ordination graph but draws no result. You can add new graphical elements to this plot with ⁠geom_ordi_*⁠ function of this package, or you can use standard ggplot2 ⁠geom_*⁠ functions and use ggscores as their data argument.

Usage

ordiggplot(model, axes = c(1, 2), arrow.mul, ...)

ggscores(score)

Arguments

Details

The ggvegan package has two contrasting approaches to draw ordination plots. The autoplot functions (e.g. autoplot.rda(), autoplot.cca(), and autoplot.metaMDS) draw a complete plot with one command, but the design is hard-coded in the function. However, you can add new elements to the graph.

In contrast, function ordiggplot() only sets up an ordination plot, and does not draw anything. It allows you to add layers to the plot one by one with full flexibility of the ggplot2 functions. There are some specific functions ⁠geom_ordi_*⁠ functions that are similar as similarly named ⁠geom_*⁠ functions. For these you need to give the type of ordination scores to be added, and in addition, you can give any ⁠geom_*⁠ function arguments to modify the plot. Alternatively, you can use any ggplot2 function and in its data argument use ggscores() function to select the data elements for the function.

The ordiggplot() function extracts results using fortify() functions of this package, and it accepts the arguments of those functions. This allows setting, e.g., the scaling of ordination axes.

Value

Returns a ggplot object.

Examples

library("vegan")
library("ggplot2")
data(dune, dune.env, varespec, varechem)
m <- cca(dune ~ Management + A1, dune.env)

## use geom_ordi_* functions
ordiggplot(m) + geom_ordi_axis() +
  geom_ordi_point("sites") +
  geom_ordi_text("species", col = "darkblue",
                 mapping = aes(fontface = "italic")) +
  geom_ordi_label("centroids") +
  geom_ordi_arrow("biplot")

## use ggscores + standard geom_* functions
ordiggplot(m, scaling = "sites") +
  geom_point(data = ggscores("sites")) +
  geom_text(data = ggscores("species"),
            mapping = aes(fontface = "italic")) +
  geom_label(data = ggscores("centroids"), fill = "yellow") +
  geom_ordi_arrow("biplot")

## Messy arrow biplot for PCA
m <- rda(dune)
ordiggplot(m) +
  geom_ordi_axis() +
  geom_ordi_point("sites") +
  geom_ordi_arrow("species")

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

generics

tidy

ggplot2

autoplot, fortify

Number of scores

Description

Returns the number of scores returns in object 'x“.

Usage

scores_length(x)

Arguments

Value

a numeric vector of length 1 with the number of scores.

Author(s)

Gavin L. Simpson

Valid layers for vegan objects

Description

Valid layers for vegan objects

Usage

valid_layers(object, ...)

## S3 method for class 'rda'
valid_layers(object, ...)

## S3 method for class 'cca'
valid_layers(object, ...)

## S3 method for class 'dbrda'
valid_layers(object, ...)

Arguments

Value

A character vector of valid ordination layers for the provided object.