In Jack-H-Laverick/MCE: Modelling Community Transitions Across Coral Reef Depth Gradients

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(MCE)
library(dplyr)

data.frame(Light = seq(0.0065, 1, length = 500)) %>%         # Choose light levels
  mutate("Bright depths" = depth(Light),                # Calculate depths
         "Shaded depths" = depth(Light, shade = 0.25),  # Calculate depths
         "Shallow community" = shallow(Light),
         "Mesophotic community" = mesophotic(Light),
         "Whole reef" = reef(Light)) -> depth.distribution   # Calculate community values

knitr::kable(depth.distribution[1:5,], format="html") %>% 
  kableExtra::kable_styling(bootstrap_options = "striped", full_width = T)

boundaries <- data.frame(Boundary = c("lower", "upper"),
                         Depth = c(depth(reef_boundary()), depth(reef_boundary(), shade = 0.25)))

knitr::kable(boundaries, format="html") %>% 
  kableExtra::kable_styling(bootstrap_options = "striped", full_width = T)

library(ggplot2)

ggplot(depth.distribution, aes(y= `Bright depths`, x= `Whole reef`)) + 
  annotate("rect", xmin=-1,xmax=0, ymin=-Inf,
           ymax=Inf, fill="steelblue2", alpha=0.75)+                # Box from -1 to 0
  annotate("rect", xmin=0, xmax=1, ymin=-Inf,
           ymax=Inf, fill="tan2", alpha=0.75)+                      # Box from 0 to 1
  geom_ribbon(data = depth.distribution, aes(ymin = `Shaded depths`, ymax = `Bright depths`, x= `Whole reef`), colour = 
                'white', fill = 'White', alpha = 0.45) +            # Add model range
  geom_point(data = boundaries, aes(x = 0, y = Depth)) +
  scale_y_reverse() +
  coord_cartesian(ylim = c(100, 0), xlim = c(-0.65,0.65)) +
  annotate("text", label="Shallow", y=93, x=-0.35, col="Black")+
  annotate("text", label="observations", y=100, x=-0.35, col="Black")+
  annotate("text", label="Mesophotic", y=93, x=0.35, col="Black")+
  annotate("text", label="observations", y=100, x=0.35, col="Black")+
  theme_minimal() +                        
  theme(plot.title = element_text(size=12, hjust = 0.5),    
        axis.title.x = element_text(size=10),  
        axis.title.y = element_text(size=10), 
        legend.position = 'bottom') +                              # label sizes and legend position
  NULL

Jack-H-Laverick/MCE documentation built on May 9, 2020, 3:58 p.m.