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

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

library(MCE)
library(tidyverse)
library(gganimate)

Create reef zones under different conditions

KdPARs <- seq(0.05, 0.2, by = 0.01) %>%                        # Choose variable and values to compare
  map_df(function(x) {                                         # For each value
      data.frame(Light = seq(0.001, 1, length = 500)) %>%      # Make a dataframe of light levels
        mutate("Bright depths" = depth(Light, KdPAR = x),      # Add max depths given KdPAR
               "Shaded depths" = depth(Light, KdPAR = x, shade = 0.25),  # Max depths when shaded
               "Whole reef" = reef(Light),                     # Calculate default reef zonation
               "KdPAR" = x) })                                 # Include KdPAR value

Visualise

ggplot(KdPARs, 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 = KdPARs, aes(ymin = `Shaded depths`, ymax = `Bright depths`, x= `Whole reef`), colour = 
                'white', fill = 'White', alpha = 0.45) +            # Add model range
  labs(y = 'Depth (m)', x = 'Net D value') +  
  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),    
        axis.title.x = element_text(size=10),  
        axis.title.y = element_text(size=10), 
        legend.position = 'bottom') +                               # label sizes and legend position
  transition_states(KdPAR, state_length = 0, wrap = T, transition_length = 0.01) +
  labs(caption = 'parameter value: {closest_state}',
       title = expression(paste("Model sensitivity to changes in", K[dPAR]))) +
  NULL

How about the boundary depths?

KdPAR_boundaries <- seq(0.05, 0.2, by = 0.01) %>%              # Choose variable and values to compare
  map_df(function(x) {                                         # For each value
    data.frame("Upper_bound" = depth(reef_boundary(),          # Max depth for default reef boundary
                                     KdPAR = x),                     # Given a KdPAR value
               "Lower_bound" = depth(reef_boundary(), shade = 0.25,  # Shaded depth for default reef boundary
                               KdPAR = x),                    # Given a KdPAR value
                "KdPAR" = x)})                                    # Include changing variable

Plot the effect on boundary depths

ggplot() +
  geom_ribbon(data = KdPAR_boundaries, aes(x = KdPAR, ymin = Lower_bound, ymax = Upper_bound)) +  
  scale_y_reverse() +
  labs(y = 'Depth (m)', x = expression("K"["dPAR"])) +  
  theme_minimal() +                        
  theme(plot.title = element_text(size=12, hjust = 0),    
        axis.title.x = element_text(size=10),  
        axis.title.y = element_text(size=10), 
        legend.position = 'bottom')

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