| Title: | Compares the Distribution of Sister Clades Through a Phylogeny |
|---|---|
| Description: | An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped. |
| Authors: | Michael Krabbe Borregaard |
| Maintainer: | Michael Krabbe Borregaard <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.4.1 |
| Built: | 2025-01-19 04:00:22 UTC |
| Source: | https://github.com/mkborregaard/nodiv |
The package implements Borregaard et al. (2014) method for identifying nodes in a phylogeny associated with divergent distributions. The main algorithm goes through each node in the phylogeny and relates node overlap to a null model. The package also provides functions for preparing the data sets, for exploratory plots and further analysis.
| Package: | nodiv |
| Type: | Package |
| Version: | 1.4.0 |
| Date: | 2020-05-26 |
| License: | MIT |
The workflow starts by creating a nodiv_data data object, which makes sure that the phylogeny, the species distributions and the spatial coordinates of sites are matched correctly. The function takes a number of data types. There are several functions for exploratory data analysis, including plot, summary, richness, Node_occupancy, Node_size etc. The core of the package are the functions Nodesig, which compares the distributions of the two clades descending from a node, and Node_analysis, which applies this function to all nodes in the phylogeny and summarizes the results as a nodiv_result object. There is a set of functions for interpretation of the results, including plot, plotSOS, and summary. The package also provides basic functions for plotting and manipulating data sets that combine spatial distributions with phylogenies, e.g. subsample, plot_grid and plot_points.
Note that the package may still be unstable - if you experience problems, try cloning the github repository instead: library(devtools); install_github("mkborregaard/nodiv"), or feel free to contact the maintainer.
Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <[email protected]>
Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>
data(coquettes) res <- Node_analysis(coquettes, 50, "rdtable") opar <- par(mfrow = c(1,2)) plot(res) plotSOS(res, 28, shapefill = terrain.colors(64)) summary(res) par(opar)data(coquettes) res <- Node_analysis(coquettes, 50, "rdtable") opar <- par(mfrow = c(1,2)) plot(res) plotSOS(res, 28, shapefill = terrain.colors(64)) summary(res) par(opar)
nodiv data object
Takes a shapefile, e.g. as points or polygons, and adds it to the data object
add_shape(distrib_data, shape)add_shape(distrib_data, shape)
distrib_data |
An object of type |
shape |
A GIS shapefile, from e.g. packages |
Returns the object with the new shapefile
Michael Krabbe Borregaard
# remove the shapefile from coquettes data(coquettes) sh <- coquettes$shape coquettes$shape <- NULL # and add it back in coquettes <- add_shape(coquettes, sh)# remove the shapefile from coquettes data(coquettes) sh <- coquettes$shape coquettes$shape <- NULL # and add it back in coquettes <- add_shape(coquettes, sh)
Returns the internal (ape) node numbers corresponding to certain nodes in the phylogeny
basal_node(tree) nodenumbers(tree) nodes(tree, all = FALSE) Descendants(node, tree) Parent(node, tree) Sister(node, tree) MostRecentAncestor(tips, tree)basal_node(tree) nodenumbers(tree) nodes(tree, all = FALSE) Descendants(node, tree) Parent(node, tree) Sister(node, tree) MostRecentAncestor(tips, tree)
tree |
An object of type |
node |
The internal node number of a focal node in the phylogeny |
all |
Give all node labels in order of occurrence. If FALSE, only non-empty node labels will be shown in alphabetical order |
tips |
The species to find the most recent common ancestor for |
Parent gives the code immediately basal to the focal node, Descendants gives the nodes descending from the focal node, and Sister gives the sister node(s). MostRecentAncestor gives the most recent common node for the given tips.
The internal (ape) node number of the node
Michael Krabbe Borregaard
Phylogeny and distributions for the coquette clade of hummingbirds in Ecuador, Peru and Colombia
data(coquettes)data(coquettes)
a nodiv_data object with the phylogeny and distributions of all species
Graham, C.H., Parra, J.L., Tinoco, B.A., Stiles, F.G. & McGuire, J.A. (2012). Untangling the influence of ecological and evolutionary factors on trait variation across hummingbird assemblages. Ecology, 93, S99-S111.
data(coquettes) plot(coquettes, shapefill = terrain.colors(64), pch = 21)data(coquettes) plot(coquettes, shapefill = terrain.colors(64), pch = 21)
Functions to collect and display data with matching species distributions and phylogenies
distrib_data(commatrix, coords = NULL, proj4string_in = CRS(as.character(NA)), type = c("auto", "grid", "points"), shape = NULL) nodiv_data(phylo, commatrix, coords, proj4string_in = CRS(as.character(NA)), type = c("auto", "grid", "points"), shape = NULL) ## S3 method for class 'distrib_data' summary(object, ...) ## S3 method for class 'nodiv_data' summary(object, ...) ## S3 method for class 'distrib_data' plot(x, ...) ## S3 method for class 'nodiv_data' plot(x, ...) ## S3 method for class 'distrib_data' identify(x, ...)distrib_data(commatrix, coords = NULL, proj4string_in = CRS(as.character(NA)), type = c("auto", "grid", "points"), shape = NULL) nodiv_data(phylo, commatrix, coords, proj4string_in = CRS(as.character(NA)), type = c("auto", "grid", "points"), shape = NULL) ## S3 method for class 'distrib_data' summary(object, ...) ## S3 method for class 'nodiv_data' summary(object, ...) ## S3 method for class 'distrib_data' plot(x, ...) ## S3 method for class 'nodiv_data' plot(x, ...) ## S3 method for class 'distrib_data' identify(x, ...)
phylo |
A phylogeny in ape's phylo format, with tip.labels that correspond to the species names in commatrix |
commatrix |
A community matrix or data.frame of species distributions, with species as columns, sites as rows, and 0/1 denoting the absence or presence of a species in a given site. Alternatively, the functions accept a |
coords |
The coordinates of all sites in the data. The input can be of a variety of different formats. Can be a |
proj4string_in |
Projection string as defined in package |
type |
A descriptor of whether the sites are point (community) sites, or the centres of regular grid cells. If omitted or set to |
shape |
An optional shapefile to overlay plots upon. |
object |
An object of type distrib_data or nodiv_data |
x |
An object of type distrib_data or nodiv_data |
... |
Further arguments to be passed to the plotting function |
When making an object of type 'grid', the coordinates will be stored as SpatialPixels from package sp. This may result in a warning if there are rows or columns in the grid without data. The function removes these. This may affect plotting, but can otherwise be ignored.
The distrib_data function produces an object of type distrib_data, which has the following components:
coords |
A |
comm |
The community matrix |
type |
A character vector describing the type of data |
species |
A list of species names |
shape |
An optional slot detailing a shapefile object for plotting the data |
The nodiv_data function produces an object of type nodiv_data, which contains the additional component:
phylo |
A phylogeny of type |
Michael Krabbe Borregaard
Takes an object of type distrib_data or nodiv_data, and puts the point distributions on a grid. Can also be used for resampling grid data at a coarser scale. If the comm matrix has abundances (any one value larger than 1), they are summed across points in the grid cell.
gridData(dist_data, cellsize_x = 1, cellsize_y = cellsize_x, xll_corner, yll_corner)gridData(dist_data, cellsize_x = 1, cellsize_y = cellsize_x, xll_corner, yll_corner)
dist_data |
An object of type |
cellsize_x |
The size of the bins along the X (longitudinal) axis, in units of the spatial coordinates of the original points |
cellsize_y |
The size of the bins along the Y (latitudinal) axis, in units of the spatial coordinates of the original points |
xll_corner |
The x coordinate of the lower left corner of the lower left grid cell of the intended grid. The corner must be left of all points in the data set |
yll_corner |
The y coordinate of the lower left corner of the lower left grid cell of the intended grid. The corner must be below all points in the data set |
The return value is the original dist_data object with gridded distribution data
Michael Krabbe Borregaard
distrib_data, ~~~
data(coquettes) new <- gridData(coquettes, 2) plot_richness(new)data(coquettes) new <- gridData(coquettes, 2) plot_richness(new)
Goes through each node in the phylogeny, and compares the distribution overlap of sister clades to that expected from a null mode that considers node size, species richness and range size.
Node_analysis(nodiv_data, repeats = 100, method = c("rdtable", "quasiswap"), cores = 1, log_parallel_progress = FALSE) ## S3 method for class 'nodiv_result' summary(object, ...) ## S3 method for class 'nodiv_result' print(x, printlen = 4, ...) ## S3 method for class 'nodiv_result' plot(x, label = nodenumbers(x), zlim = 0:1, ...)Node_analysis(nodiv_data, repeats = 100, method = c("rdtable", "quasiswap"), cores = 1, log_parallel_progress = FALSE) ## S3 method for class 'nodiv_result' summary(object, ...) ## S3 method for class 'nodiv_result' print(x, printlen = 4, ...) ## S3 method for class 'nodiv_result' plot(x, label = nodenumbers(x), zlim = 0:1, ...)
nodiv_data |
An object created by the |
repeats |
Number of null communities to create at each node |
method |
The null model algorithm used to simulate random communities |
cores |
The number of cores to use in the computation. Note that multi-core processing is yet unimplemented. |
log_parallel_progress |
If this is TRUE, the results from each node will be saved as an '.rda' file in the working directory. Useful for large parallel computations. |
object |
The |
x |
The |
printlen |
The number of species to print to screen |
label |
The text to use for labelling nodes in the plot |
zlim |
The values of GND to use for the extremes of the color scale on the plot |
... |
Further arguments to be passed to the function |
The "rdtable" algorithm is efficient, but may underestimate the deviation between nodes. It should primarily be used for exploratory data analysis. Note that the more robust "quasiswap" algorithm may take days to run on larger data sets.
The plot function for nodiv_result plots the phylogenetic tree with colored symbols at the nodes. The color and size the nodes are proportional with the GND value of the node.
The result is an object of type nodiv_result, which has the following components:
GND |
A numeric vector between 0 and 1 describing the distributional divergence associated with a node |
SOS |
A numeric matrix given the SOS of values, which expresses the difference between empirical and expected species richness of each clade at each site |
It also includes all the elements of the nodiv_data object:
coords |
A |
comm |
The community matrix |
type |
A character vector describing the type of data |
species |
A list of species names |
shape |
An optional slot detailing a shapefile object for plotting the data |
phylo |
A phylogeny of type |
Michael Krabbe Borregaard
Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283
data(coquettes) res <- Node_analysis(coquettes, 50, "rdtable") opar <- par(mfrow = c(1,2)) plot(res) plotSOS(res, 28, shapefill = terrain.colors(64)) summary(res) par(opar)data(coquettes) res <- Node_analysis(coquettes, 50, "rdtable") opar <- par(mfrow = c(1,2)) plot(res) plotSOS(res, 28, shapefill = terrain.colors(64)) summary(res) par(opar)
Functions that summarize the species that descend from a node, and their distribution.
Node_size(nodiv_data, node = NULL) Node_sites(nodiv_data, node, names = TRUE) Node_species(nodiv_data, node, names = TRUE) Node_occupancy(nodiv_data, node = NULL)Node_size(nodiv_data, node = NULL) Node_sites(nodiv_data, node, names = TRUE) Node_species(nodiv_data, node, names = TRUE) Node_occupancy(nodiv_data, node = NULL)
node |
A character or numeric variable specifying one or more nodes in the phylogeny |
nodiv_data |
An object of type |
names |
If |
If no node is specified in Node_size or Node_occupancy, the function will calculate the value for all nodes in the phylogeny
For Node_size and Node_occupancy the number of species or number of occupied sites of the nodes; or a vector giving this value for all nodes. For Node_species or Node_sites a character vector of names of species descending from a node, or the sites where they occur.
Michael Krabbe Borregaard
Compares the overlap of species richness of a pair of sister clades to the expectation from a null model. By default, the function compares the two descendants from the basal node of the phylogeny
Nodesig(nodiv_data, Node_sp = NULL, repeats = 100, method = c("rdtable", "quasiswap"), show = T)Nodesig(nodiv_data, Node_sp = NULL, repeats = 100, method = c("rdtable", "quasiswap"), show = T)
nodiv_data |
An object of type |
Node_sp |
A character or numeric vector indicating which species that belong to one of the clades. If NULL, the species of a descendant from the basal node of nodiv_data is chosen randomly |
repeats |
The number of repeats to use for the null model |
method |
The null model algorithm used in the calculations |
show |
Should a progress bar be printed during calculations? |
The \"rdtable\" algorithm is efficient, but may underestimate the deviation between nodes. It should primarily be used for exploratory data analysis. Note that the more robust \"quasiswap\" algorithm may take hours to run on data sets with a few hundred species.
The return value is a list with 5 elements:
SR |
A numeric vector of the standardized difference between the empirical and simulated species richness for one node in each site |
rval |
The rank of the empirical species richness of one node in the distribution of simulated values |
nodeemp |
The numerical species richness in each site |
nodemeans |
The mean simulated species richness of one node in each site |
nodesds |
The standard deviation of the simulated species richness of one node in each site |
Michael Krabbe Borregaard
Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283
data(coquettes) res <- Nodesig(coquettes, repeats = 50) hist(res$rval, xlim = 0:1)data(coquettes) res <- Nodesig(coquettes, repeats = 50) hist(res$rval, xlim = 0:1)
distrib_data objects
Calculates the species richness and site occupancy of a distrib_data object
Nspecies(distrib_data) Nsites(distrib_data) richness(distrib_data, sites = NULL) occupancy(distrib_data, species = NULL) sites(distrib_data) species(distrib_data) coords(distrib_data)Nspecies(distrib_data) Nsites(distrib_data) richness(distrib_data, sites = NULL) occupancy(distrib_data, species = NULL) sites(distrib_data) species(distrib_data) coords(distrib_data)
distrib_data |
An object of type |
sites |
The site for which to return the richness |
species |
The species for which to return the occupancy |
Nspecies gives the number of species in the dataset, and Nsites the number of sites.
richness gives a numeric vector with the species richness of all sites.
occupancy gives the number of sites occupied by all species.
sites gives a list of site names in the object.
species gives a list of species names in the object.
nodes gives a node labels or node numbers
coords returns the spatial coordinates of points or grid cell centers
Michael Krabbe Borregaard
distrib_data objects
Gives the species in a site, or the sites occupied by a species, in a distrib_data object
occurrences(distrib_data, species, value = c("index", "names", "logical", "raw")) assemblage(distrib_data, site, value = c("index", "names", "logical", "raw"))occurrences(distrib_data, species, value = c("index", "names", "logical", "raw")) assemblage(distrib_data, site, value = c("index", "names", "logical", "raw"))
distrib_data |
An object of type |
species |
The number or name of a species in the data set |
site |
The number or name of a site in the data set |
value |
The type of data to return, see below. |
type = "01" gives a vector of 0s and 1s from the community matrix
type = "logical" gives a logical vector identifying species or sites
type = "index" gives the index number of species or sites in the community matrix
Michael Krabbe Borregaard
This is just the ape::plot.phylo method, which is imported and exported directly by the nodiv package. These functions plot phylogenetic trees on the current graphical device.
phyplot(x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE, edge.color = "black", edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", lab4ut = NULL, tip.color = "black", plot = TRUE, rotate.tree = 0, open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)phyplot(x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE, edge.color = "black", edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", lab4ut = NULL, tip.color = "black", plot = TRUE, rotate.tree = 0, open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)
x |
an object of class |
type |
a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial" or any unambiguous abbreviation of these. |
use.edge.length |
a logical indicating whether to use the edge
lengths of the phylogeny to draw the branches (the default) or not
(if |
node.pos |
a numeric taking the value 1 or 2 which specifies the
vertical position of the nodes with respect to their descendants. If
|
show.tip.label |
a logical indicating whether to show the tip
labels on the phylogeny (defaults to |
show.node.label |
a logical indicating whether to show the node
labels on the phylogeny (defaults to |
edge.color |
a vector of mode character giving the colours used
to draw the branches of the plotted phylogeny. These are taken to be
in the same order than the component |
edge.width |
a numeric vector giving the width of the branches of
the plotted phylogeny. These are taken to be in the same order than
the component |
edge.lty |
same than the previous argument but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash. |
font |
an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic). |
cex |
a numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters. |
adj |
a numeric specifying the justification of the text strings
of the labels: 0 (left-justification), 0.5 (centering), or 1
(right-justification). This option has no effect if |
srt |
a numeric giving how much the labels are rotated in degrees
(negative values are allowed resulting in clock-like rotation); the
value has an effect respectively to the value of
|
no.margin |
a logical. If |
root.edge |
a logical indicating whether to draw the root edge (defaults to FALSE); this has no effect if ‘use.edge.length = FALSE’ or if ‘type = "unrooted"’. |
label.offset |
a numeric giving the space between the nodes and
the tips of the phylogeny and their corresponding labels. This
option has no effect if |
underscore |
a logical specifying whether the underscores in tip
labels should be written as spaces (the default) or left as are (if
|
x.lim |
a numeric vector of length one or two giving the limit(s)
of the x-axis. If |
y.lim |
same than above for the y-axis. |
direction |
a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards". |
lab4ut |
(= labels for unrooted trees) a character string
specifying the display of tip labels for unrooted trees (can be
abbreviated): either |
tip.color |
the colours used for the tip labels, eventually recycled (see examples). |
plot |
a logical controlling whether to draw the tree. If
|
rotate.tree |
for "fan", "unrooted", or "radial" trees: the rotation of the whole tree in degrees (negative values are accepted). |
open.angle |
if |
node.depth |
an integer value (1 or 2) used if branch lengths are not used to plot the tree; 1: the node depths are proportional to the number of tips descending from each node (the default and was the only possibility previously), 2: they are evenly spaced. |
align.tip.label |
a logical value or an integer. If TRUE, the tips are aligned and dotted lines are drawn between the tips of the tree and the labels. If an integer, the tips are aligned and this gives the type of the lines (lty). |
... |
further arguments to be passed to |
The font format of the labels of the nodes and the tips is the same.
If no.margin = TRUE, the margins are set to zero and are not
restored after plotting the tree, so that the user can access the
coordinates system of the plot.
The option ‘node.pos’ allows the user to alter the vertical position
(i.e., ordinates) of the nodes. If node.pos = 1, then the
ordinate of a node is the mean of the ordinates of its direct
descendants (nodes and/or tips). If node.pos = 2, then the
ordinate of a node is the mean of the ordinates of all the tips of
which it is the ancestor. If node.pos = NULL (the default),
then its value is determined with respect to other options: if
type = "phylogram" then ‘node.pos = 1’; if type =
"cladogram" and use.edge.length = FALSE then ‘node.pos = 2’;
if type = "cladogram" and use.edge.length = TRUE then
‘node.pos = 1’. Remember that in this last situation, the branch
lengths make sense when projected on the x-axis.
If adj is not specified, then the value is determined with
respect to direction: if direction = "leftwards" then
adj = 1 (0 otherwise).
If the arguments x.lim and y.lim are not specified by the
user, they are determined roughly by the function. This may not always
give a nice result: the user may check these values with the
(invisibly) returned list (see “Value:”).
If you resize manually the graphical device (windows or X11) you may need to replot the tree.
plot.phylo returns invisibly a list with the following
components which values are those used for the current plot:
type |
|
use.edge.length |
|
node.pos |
|
node.depth |
|
show.tip.label |
|
show.node.label |
|
font |
|
cex |
|
adj |
|
srt |
|
no.margin |
|
label.offset |
|
x.lim |
|
y.lim |
|
direction |
|
tip.color |
|
Ntip |
|
Nnode |
|
root.time |
The argument asp cannot be passed with ....
Emmanuel Paradis
A wrapper for the plot.phylo function defined in package ape, which is useful for plotting the values at each node
plot_nodes_phylo(variable, tree, label = variable, main = deparse(substitute(variable)), zlim = NULL, col, show.legend = TRUE, sig.cutoff, nodes, roundoff = TRUE, show.tip.label = NULL, cex = NULL, ...)plot_nodes_phylo(variable, tree, label = variable, main = deparse(substitute(variable)), zlim = NULL, col, show.legend = TRUE, sig.cutoff, nodes, roundoff = TRUE, show.tip.label = NULL, cex = NULL, ...)
variable |
The variable to be plotted |
label |
The text to write in each node label |
tree |
The phylogeny to plot, in the |
main |
The title text |
zlim |
The values to use for the most extreme colors of the color scale |
col |
The color palette used to create the color scale |
show.legend |
Should a legend for the color scale be plotted? |
sig.cutoff |
The minimum value for nodes to be plotted on the tree, useful for trees with many nodes |
nodes |
The nodes to be plotted on the tree |
roundoff |
Whether to round values when writing them as nodelabel text |
show.tip.label |
Show tip labels on the tree |
cex |
Controls the size of the node symbols |
... |
Further arguments to pass to plot.phylo |
Michael Krabbe Borregaard
data(coquettes) Clade_occupancy <- Node_occupancy(coquettes) plot_nodes_phylo(Clade_occupancy, coquettes$phylo, cex = 0.7)data(coquettes) Clade_occupancy <- Node_occupancy(coquettes) plot_nodes_phylo(Clade_occupancy, coquettes$phylo, cex = 0.7)
Plots a variable either as colored points or as a colored raster. plot_sitestat is a wrapper function that dispatches the other functions according to the type of distrib_data.
plot_points(x, coords, col, shape = NULL, shapefill = "grey", zlim= NULL, zoom_to_points = FALSE, pch = 16, bg = par("bg"), legend = TRUE, ...) plot_grid(x, coords, col, shape = NULL, shapefill = "grey", shapeborder = NA, zlim = NULL, zoom_to_points = FALSE, legend = TRUE, gridcol, gridlwd, gridsites, overlay_shape = FALSE, colscale = c("equal_interval","quantiles"), legendlabels = NULL, ...) plot_species(distrib_data, species, col = c("darkgreen", "red"), ...)plot_points(x, coords, col, shape = NULL, shapefill = "grey", zlim= NULL, zoom_to_points = FALSE, pch = 16, bg = par("bg"), legend = TRUE, ...) plot_grid(x, coords, col, shape = NULL, shapefill = "grey", shapeborder = NA, zlim = NULL, zoom_to_points = FALSE, legend = TRUE, gridcol, gridlwd, gridsites, overlay_shape = FALSE, colscale = c("equal_interval","quantiles"), legendlabels = NULL, ...) plot_species(distrib_data, species, col = c("darkgreen", "red"), ...)
x |
A numerical variable to be plotted using a color scale |
coords |
A matrix or |
col |
The color palette to use for the color scale. Can be given as color names, a vector of hex colors from a call to a color palette (e.g., |
shape |
A shape file giving a map to use as a background for the plot |
shapefill |
If shape is a polygon, the color to use to fill the polygons. If shape is a line shapefile, the color to use for plotting lines |
shapeborder |
If shape is a polygon, the color to use for plotting the line border |
zlim |
The values to use for the extremes of the color scale |
zoom_to_points |
Given a shapefile, the function will set the outer limits of the plot to the bounding box of the shapefile. If |
pch |
The point character to use for plotting points |
bg |
The central color of points when using a pch value between 21 and 25 |
distrib_data |
An object of type |
legend |
Whether to plot a color legend |
species |
The number or name of the species to be plotted |
gridcol |
If specified, plots the sampling grid cell borders in this color |
gridlwd |
If specified, set the line width of overlaid grid cell borders |
gridsites |
If specified, which grid cells to draw cell borders around |
overlay_shape |
Whether to overlay the shape file border on top of the points - only works if shape is a vector shapefile |
colscale |
Specifies whether to define the colors on an equal interval or a quantile-based color scale |
legendlabels |
Specifies custom labels for the colorbar legend |
... |
Additional arguments to pass to plot |
Note that if shape is a raster object, the points may shift relative to the background when resizing the image. This seems to be due to a bug in the raster package.
Michael Krabbe Borregaard
Create a raster or point plot showing the species richness of an object. Useful for comparing the species richness of sister clades
plot_richness(distrib_data, ...) plot_node(nodiv_data, node = basal_node(nodiv_data), sites = NULL, ...)plot_richness(distrib_data, ...) plot_node(nodiv_data, node = basal_node(nodiv_data), sites = NULL, ...)
distrib_data |
An object of types |
nodiv_data |
An object of types |
node |
The name or internal number of the node to be plotted |
sites |
If |
... |
Further arguments to pass to the plotting function |
The plot will be done as a spatial grid or as colored points, depending on the type of the nodiv_result object. plot_richness plots the richness of the entire dataset, whereas plot_node plots the species richness of a given node.
If distrib_data has type = raster, a raster object of the SOS values is returned.
Michael Krabbe Borregaard
nodiv data objects
Adds, plots or reads site statistics from objects in the nodiv package
add_sitestat(distrib_data, site_stat, site = NULL) plot_sitestat(distrib_data, x, shape = NULL, type = c("auto", "points", "grid"), ...) sitestat(distrib_data, statname = NULL, site = NULL)add_sitestat(distrib_data, site_stat, site = NULL) plot_sitestat(distrib_data, x, shape = NULL, type = c("auto", "points", "grid"), ...) sitestat(distrib_data, statname = NULL, site = NULL)
distrib_data |
An object of type |
site_stat |
A site statistic, such as species richness or mean temperature. This can be a vector or a data.frame. If
|
site |
A character or numeric variable specifying the sites in which to enter or read sitestat |
statname |
The name of a sitestatistic in the |
x |
A variable to plot on sites, can either be a numeric variable, or the name of a
sitestatistic in the |
shape |
A shape file giving a map to use as a background for the plot |
type |
A character vector describing the type of data |
... |
Further arguments to the plotting function |
add_sitestat returns the object with the new sitestat inside.
sitestat returns the named sitestatistic.
Michael Krabbe Borregaard
SOS gives the SOS value for the node, used in the interpretation of node-based analysis of species distributions after running Node_analysis. plotSOS plots the values on a map. GND gives the GND values.
SOS(nodiv_result, node) plotSOS(nodiv_result, node, zlim, ...) GND(nodiv_result, node = NULL)SOS(nodiv_result, node) plotSOS(nodiv_result, node, zlim, ...) GND(nodiv_result, node = NULL)
nodiv_result |
The result of running |
node |
The node label or node number specifying the node to plot. Optional for |
zlim |
The values to use for the extremes of the color palette |
... |
Further arguments to pass to the plotting function |
The first descendant clade (i.e. the first returned by a call to Descendants) is associated with positive SOS values, the second descendant clade is associated with negative values. The plot will be done as a spatial grid or as colored points, depending on the type of the nodiv_result object. If the nodiv_result object has a shape object of type raster, this will be plotted normally in the background - but resizing the window will cause the plots/pixels and the underlying raster object to lose alignment, due to a bug in the raster package.
SOS returns a numerical vector with the SOS values. If nodiv_result has type raster, a raster object of the SOS values is returned by plotSOS.
Michael Krabbe Borregaard
Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283
nodiv data objects
Adds, or reads species statistics from objects in the nodiv package
add_species_stat(distrib_data, species_stat, specs = NULL) species_stat(distrib_data, statname = NULL, specs = NULL)add_species_stat(distrib_data, species_stat, specs = NULL) species_stat(distrib_data, statname = NULL, specs = NULL)
distrib_data |
An object of type |
species_stat |
A species statistic, such as body size or cold tolerance. This can be a vector or a data.frame. If
|
specs |
A character or numeric variable specifying the species of interest, or for which species_stat is specified |
statname |
The name of a species statistic in the |
add_species_stat returns the object with the new species_stat inside.
species_stat returns the named sitestatistic.
Michael Krabbe Borregaard
Takes an object of type distrib_data or nodiv_data, and subsamples it to contain certain species or sites, while keeping the integrity of the data.
subsample(x, ...) ## S3 method for class 'distrib_data' subsample(x, sites = NULL, species = NULL, ...) ## S3 method for class 'nodiv_data' subsample(x, sites = NULL, species = NULL, node = NULL, ...) ## S3 method for class 'nodiv_result' subsample(x, node = NULL, ...)subsample(x, ...) ## S3 method for class 'distrib_data' subsample(x, sites = NULL, species = NULL, ...) ## S3 method for class 'nodiv_data' subsample(x, sites = NULL, species = NULL, node = NULL, ...) ## S3 method for class 'nodiv_result' subsample(x, node = NULL, ...)
x |
An object of type |
sites |
A numeric or character vector identifying the sites to keep in the new object. If specified, the function will subsample the data object to only include the defined sites, and the species that exist there. If sites == \"all\", all sites will be kept when subsampling for species, even if no species now exist in the sites. |
species |
A numeric or character vector identifying the species to keep in the new object. If specified, the function will subsample the data object to only include the defined species, and the sites where they exist. |
node |
A numeric or character vector identifying a node in the phylogeny. Only species descending from this node will be kept in the new object, and the sites where they exist. |
... |
Further arguments to the subsample function |
The return value is a new object of the same type as x
Michael Krabbe Borregaard
distrib_data, ~~~
data(coquettes) new <- subsample(coquettes, sites = which(richness(coquettes) > 3)) plot(new, show.tip = FALSE)data(coquettes) new <- subsample(coquettes, sites = which(richness(coquettes) > 3)) plot(new, show.tip = FALSE)
Plots site statistics from objects in the nodiv package
two_color_map(distrib_data, vec1, vec2, res = 10, showlegend = T, legend_coords = c(0.2, 0.26, 0.36, 0.44), type = c("auto", "grid", "points"), colour = c("green_purple", "green_red_purple_cyan"), ...)two_color_map(distrib_data, vec1, vec2, res = 10, showlegend = T, legend_coords = c(0.2, 0.26, 0.36, 0.44), type = c("auto", "grid", "points"), colour = c("green_purple", "green_red_purple_cyan"), ...)
distrib_data |
An object of type |
vec1 |
A site statistic to be plotted, such as species richness or mean temperature. This can be a vector of values or the name of a site statistic in distrib_data. |
vec2 |
The oter site statistic to be plotted. |
res |
The resolution of colors on the color legend |
showlegend |
A boolean specifying whether to show the legend |
legend_coords |
A vector x1, x2, y1, y2 specifying the location and extent of the color legend |
type |
To specify whether to plot as spatial points or a grid |
colour |
What colour scheme to use for plotting |
... |
Further arguements to the plotting function |
A data.frame giving codes and indices of the colors shown in the plot
Michael Krabbe Borregaard
distrib_data objects to the nodiv version >= 1.1 format
Creates the species_stats element
update_object(distrib_data)update_object(distrib_data)
distrib_data |
An object of type |
An updated version of the object
Michael Krabbe Borregaard