gghisse

The goal of gghisse is to provide additional ways to visualize results from hisse family models (HiSSE objects)

Installation

The development version can be installed from from GitHub with:

# install.packages("devtools")
devtools::install_github("discindo/gghisse")

A CRAN submission is forthcoming.

Web application

To see the main functionality and example code, visit the Shiny web application: https://diatom.shinyapps.io/hisse-web/

Example usage

library("gghisse")
#> Loading required package: hisse
#> Loading required package: ape
#> Loading required package: deSolve
#> Loading required package: GenSA
#> Loading required package: subplex
#> Loading required package: nloptr
#> Loading required package: dplyr
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Loading required package: ggplot2
#> Registered S3 method overwritten by 'treeio':
#>   method     from
#>   root.phylo ape
data("diatoms")
processed_hisse <- gghisse::h_process_recon(hisse_recon=diatoms$cid4_recon)
hisse_rates_plot <- gghisse::h_scatterplot(
  processed_recon=processed_hisse,
  parameter="turnover")

As gghisse is built on top of ggplot2, modifications to gghisse plots are easy with the familiar ggplot functions. For example, changing X axis tick labels:

hisse_rates_plot +
  scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos"))

Or changing the position of the legend

hisse_rates_plot +
  scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
  theme(legend.position="top")

Or using expressions (for Greek letters) in the axis labels

hisse_rates_plot +
  scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
  theme(legend.position="top") +
  labs(y=expression(paste(tau, "=", lambda, "+", mu))) +
  theme(axis.text.y=element_text(size=15))