Coral R data package

The goal of the coral package is to provide data on the species and characteristics of corals around the globe. This dataset is managed by the Coral Trait Database, and serves as a regulated repository for survey data collected on corals by many different research groups and projects.

Installation

The development version of 0.1.0 is available from GitHub with:

install.packages("devtools")
devtools::install_github("Reed-Math241/coral")

Data Format

This data is organized such that each species of coral has values for the ocean it is predominantly found in (ocean_basin), the preferred clarity of the coral’s waters (water_clarity_preference), the relative abundance of the coral (abundance_world), and the estimated geographic range of the coral (range_size) which is measured in km^2.

Example

In this example we will show you how to evaluate the global distribution of ranges of corals. These can very dramatically depending on the ecosystem and reproductive strategies of the coral.

Load Package

library(coral)
library(tidyverse)
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
#> ✓ ggplot2 3.3.3     ✓ purrr   0.3.4
#> ✓ tibble  3.0.6     ✓ dplyr   1.0.4
#> ✓ tidyr   1.1.2     ✓ stringr 1.4.0
#> ✓ readr   1.4.0     ✓ forcats 0.5.0
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag()    masks stats::lag()

Create a density plot based on the range size of corals.

pacman::p_load(ggsci)
small_coral <- coral %>% 
  filter(range_size <= 25000000)
rangesize_plot <- ggplot(data = small_coral, mapping = aes(x = range_size, color= abundance_world, fill = abundance_world)) + 
  geom_density(alpha = 0.5) + 
  labs(x = "Range of coral (km^2)", y = "Density", 
       title = "Geographic Range of All Corals", fill = "Abundance in Ocean")+
  theme_bw()+
  scale_color_tron()+
  scale_fill_tron()

Here we can see that the majority of corals have a relatively small range with a smaller number that have an exceedingly large range. These could be deep sea corals that reproduce by freely releasing offspring or they could be corals that are capable of growing in a large variety of different habitats. But we’ll leave it up to you to figure that out.