effectiveness_plot: Function to plot effectiveness landscapes, with repel labels...

In pedroj/effectiveness_pckg: Effectiveness landscapes

Function to plot effectiveness landscapes, with repel labels option.

Description

Function to plot effectiveness landscapes, with repel labels option.

Usage

effectiveness_plot(q1, q2, q1.error = NULL, q2.error = NULL,
  pts.shape = NULL, pts.color = NULL, pts.size = 2, label = NA,
  label.size = 3, italic = FALSE, show.lines = TRUE, nlines = 6,
  lines.breaks = "quantile", lines.color = "grey50",
  myxlab = "QtComp", myylab = "QltComp", ...)

Arguments

q1	Numeric vector representing the "quantitative component", to plot on the X axis.
q2	Numeric vector representing the "qualitative component", to plot on the Y axis.
q1.error	Optional. Numeric vector to be used as error bars for q1.
q2.error	Optional. Numeric vector to be used as error bars for q2.
pts.shape	Optional. A grouping variable (< 7 groups) to set point shapes (e.g., family).
pts.color	Optional. A grouping variable to set point colours (e.g., family).
pts.size	Optional. Size of points.
label	Optional. A character vector of the same length as q1 and q2 providing a label for the individual points (e.g., species acronym). Note that label may be NA for some points (useful to avoid overplotting of labels).
label.size	Size of point labels.
italic	Logical. Use italic font for labels?
show.lines	Logical. Show effectiveness isolines? (default is TRUE).
nlines	Specify the number of isolines.
lines.breaks	Either a numeric vector giving break points for the contour lines, or a "style" (e.g. "quantile", "equal", or "pretty") to choose optimal breaks using classIntervals. Note that using "pretty" will override nlines, as the number of lines will be determined algorithmically. See classIntervals for more details.
lines.color	Color of the isolines.
myxlab	optional label for axis X.
myylab	optional label for axis Y.
...	Further arguments to be passed to geom_text_repel (apart from segment_size, segment_alpha, and fontface, which are already defined in this function).

Details

The script plots effectiveness landscapes as described in Schupp, E. W., Jordano, P. and Gómez, J.M. 2010. Seed dispersal effectiveness revisited: a conceptual review. New Phytologist 188: 333-353.

Value

A ggplot2 object, which can be later modified (see examples).

Examples

#------------------------------------------------------------------------
# Based on a dataset of Cecropia glaziovii frugivores.
# In this example we build the effectiveness landscape just for the 
# quantitative component, plotting its two subcomponents, visitation 
# rate and per-visit effectiveness.
#------------------------------------------------------------------------
data(cecropia)
effectiveness_plot(q1 = cecropia$totvis, q2 = cecropia$totbic, 
    myxlab= "No. visits/10h", 
    myylab="Effectiveness/vis (No. fruits handled)")
#------------------------------------------------------------------------

## Avoiding label overplotting ##
## e.g. showing only names of species with high effectiveness
labels = cecropia$code
labels[4:length(cecropia$code)] <- NA
effectiveness_plot(q1 = cecropia$totvis, q2 = cecropia$totbic, 
    label = labels, 
    myxlab= "No. visits/10h", 
    myylab="Effectiveness/vis (No. fruits handled)")
    
    
################################################

## Modify plot ##
myplot <- effectiveness_plot(q1 = cecropia$totvis, q2 = cecropia$totbic, 
    label = labels, nlines = 10, 
    myxlab= "No. visits/10h", 
    myylab="Effectiveness/vis (No. fruits handled)")
myplot + ggplot2::theme_minimal()

pedroj/effectiveness_pckg documentation built on Sept. 17, 2024, 2:15 p.m.