README.Rmd

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# gghisse

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The goal of `gghisse` is to provide additional ways to visualize results from `hisse` family models ([HiSSE](https://cran.r-project.org/web/packages/hisse/index.html) objects)

## Installation

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The development version can be installed from from [GitHub](https://github.com/) with:

``` r
# 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

```{r}
library("gghisse")
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:

```{r}
hisse_rates_plot +
  scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos"))
```

Or changing the  position of the legend

```{r}
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

```{r}
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))
```