README.md

In teofiln/utilhisse: A Collection of Functions for Summarising and Visualizing 'hisse' Results

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))

teofiln/utilhisse documentation built on Sept. 3, 2020, 2:55 p.m.