installation.qmd

---
title: "Installation"
author: Luis Valente
---

## Install required software:

-   [R](https://www.r-project.org)

-   [Rstudio](https://posit.co)

-   [Figtree](https://github.com/rambaut/figtree/releases)

## Install required R packages

Open and run this script in Rstudio. This should install all required R packages (**may take a while!**).

```{r install, eval=F}
install.packages('DAISIE',dependencies = TRUE)
install.packages('DAISIEprep',dependencies = TRUE)
install.packages('ape',dependencies = TRUE)
```

**If you run into problems with 'ggtree' package.** Make sure you have the latest version of R, then use:

```{r installgg, eval=F}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ggtree")
```

Check if packages load correctly

```{r load, eval=F}
library(DAISIE)
library(ape)
library(DAISIEprep)
```