pedroj/effectiveness_pckg

An R package for plotting the effectiveness landscape of plant-animal mutualisms.

The effectiveness package

This is effect.lndscp, an R package for plotting the effectiveness landscape of mutualisms adding isolines of equal effectiveness values.

Effectiveness landscapes are the two-dimensional representation of the possible combinations of the quantity and the quality of mutualistic services (seed dispersal, pollination) and with elevational contours representing isoclines of effectiveness. These representations can be 2D bivariate plots of multiplicative effects of any of the seed dispersal (SDE) or pollination (PE) effectiveness components.

Installation

devtools::install_github("pedroj/effectiveness_pckg")

Usage

library(effect.lndscp)

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(cecropia$totvis, cecropia$totbic, 
    myxlab = "No. visits/10h", 
    myylab = "Effectiveness/vis (No. fruits handled)")

Based on a dataset of Prunus mahaleb frugivores.

data(prunus)
effectiveness_plot(prunus$visits, prunus$eff_per_vis, 
   pts.shape = prunus$group, label = prunus$animal,  
   myxlab = "No. visits/10h", 
   myylab = "Effectiveness/vis (No. fruits handled)")

For additional details please visit the web page here.

References

Schupp, E.W., Jordano, P. & Gómez, J.M. (2017). A general framework for effectiveness concepts in mutualisms. Ecology Letters, 20, 577–590. doi: 10.1111/ele.12764

Schupp, E.W., Jordano, P. & Gómez, J.M. (2010) Seed dispersal effectiveness revisited: A conceptual review. New Phytologist, 188, 333–353.

Schupp, E.W. (1993) Quantity, quality and the effectiveness of seed dispersal by animals. In: Frugivory and seed dispersal: ecological and evolutionary aspects (eds T.H. Fleming & A. Estrada), pp. 15–29. Springer, Dordrecht; The Netherlands.

Jordano, P. & Schupp, E.W. (2000) Seed disperser effectiveness: The quantity component and patterns of seed rain for Prunus mahaleb. Ecological Monographs, 70, 591–615.

effectiveness_pckg's Issues

Aesthetics issues

List of possible things to further implement the function:

• Error bars - when included and go out of the graph limits causes visualization problems
• Values for isolines (QC) - possibility to move further right?
• Avoid too much clustering - ggrepel options possibility to modify
• Possibility to not show grouping by shape, i.e. all points equal. Or to group by colors instead of shapes - include legend for the grouping factor

Including error bars

To implement the function I have add another function of ggplot2 to include the error bars.

But there is still a problem. When the error bars surpass the y axis they dont appear, e.g. for Brotogeris and Pyhrrura

Here an example:
Cecropia RPE.zip

Add data files for examples.

Add vignettes.