Landscape Patterns and Species Conservation

Exercise 1+2: Code and plots

#Add your Exercise 1+2 code here. Make sure to remember to add fig.cap = 'XXX' to other chunks in this notebook that will output figures. Correctly refer to the figures in your answers

#If you decide to create separate figures per disturbance rate and/or species, insert a new code chunk (e.g. copy this one) and add a new figure caption.
ResDes<-read.csv("data/Reserves.csv",sep=',',header=T)
head(ResDes)
##   P_Dist P_Land Spec_A Spec_B Spec_C
## 1      0      0   0.00    0.0   0.00
## 2      0     10   0.00    0.0   0.00
## 3      0     20   0.00    0.0   0.00
## 4      0     30   0.00    0.3   0.58
## 5      0     40   0.28    1.0   1.00
## 6      0     50   1.00    1.0   1.00
ResDes_wide<-ResDes%>%pivot_longer(col = c(3:5), names_to = "Species")

head(ResDes_wide)
## # A tibble: 6 × 4
##   P_Dist P_Land Species value
##    <dbl>  <int> <chr>   <dbl>
## 1      0      0 Spec_A      0
## 2      0      0 Spec_B      0
## 3      0      0 Spec_C      0
## 4      0     10 Spec_A      0
## 5      0     10 Spec_B      0
## 6      0     10 Spec_C      0
#Code and figures supporting for Exercise 2 here

Disturbance_Rate <- 0 #change this for each rate (0, 0.1, 0.3, 0.5)

ResDes_wide%>%group_by(Species, P_Land)%>%filter(P_Dist == Disturbance_Rate)%>%
  ggplot() + 
  geom_line(aes(x = P_Land, y = value, color = Species),  size = 1) +
  scale_color_manual(values=c('Spec_A'='dodgerblue', 'Spec_B'='black', 'Spec_C'='firebrick'), name='Species') +
  #labs(color = 'Species')+
  xlab('Proportion of Habitat (%)') +
  ylab('Probability of Occurence') +
  theme_classic()
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

Disturbance_Rate <- 0.1 #change this for each rate (0, 0.1, 0.3, 0.5)

ResDes_wide%>%group_by(Species, P_Land)%>%filter(P_Dist == Disturbance_Rate)%>%
  ggplot() + 
  geom_line(aes(x = P_Land, y = value, color = Species),  size = 1) +
  scale_color_manual(values=c('Spec_A'='dodgerblue', 'Spec_B'='black', 'Spec_C'='firebrick'), name='Species') +
  #labs(color = 'Species')+
  xlab('Proportion of Habitat (%)') +
  ylab('Probability of Occurence') +
  theme_classic()

Disturbance_Rate <- 0.3 #change this for each rate (0, 0.1, 0.3, 0.5)

ResDes_wide%>%group_by(Species, P_Land)%>%filter(P_Dist == Disturbance_Rate)%>%
  ggplot() + 
  geom_line(aes(x = P_Land, y = value, color = Species),  size = 1) +
  scale_color_manual(values=c('Spec_A'='dodgerblue', 'Spec_B'='black', 'Spec_C'='firebrick'), name='Species') +
  #labs(color = 'Species')+
  xlab('Proportion of Habitat (%)') +
  ylab('Probability of Occurence') +
  theme_classic()

Disturbance_Rate <- 0.5 #change this for each rate (0, 0.1, 0.3, 0.5)

ResDes_wide%>%group_by(Species, P_Land)%>%filter(P_Dist == Disturbance_Rate)%>%
  ggplot() + 
  geom_line(aes(x = P_Land, y = value, color = Species),  size = 1) +
  scale_color_manual(values=c('Spec_A'='dodgerblue', 'Spec_B'='black', 'Spec_C'='firebrick'), name='Species') +
  #labs(color = 'Species')+
  xlab('Proportion of Habitat (%)') +
  ylab('Probability of Occurence') +
  theme_classic()

ResDes_wide%>%
  ggplot() + 
  geom_line(aes(x = P_Land, y = value, color = Species),  size = 1) +
  facet_grid(~P_Dist)+
  scale_color_manual(values=c('Spec_A'='dodgerblue', 'Spec_B'='black', 'Spec_C'='firebrick'),
                     name='Species') +
  xlab('Proportion of Habitat (%)') +
  ylab('Probability of Occurence') +
  theme_classic()

Exercise 1: Questions

1. Why would your answers and graphs differ from everyone else?

ANSWER HERE

2. Did the three species respond the same to the gradient in available habitat? If not how did they differ?

ANSWER HERE

3. Did you detect a threshold effect for habitat for any of the three species assessed? If so, at what amount of habitat did the threshold occur at? What species was most sensitive to changes in habitat availability?

ANSWER HERE

4. As a conservation biologist you have been tasked with advising a conservation manager the minimum amount of habitat at the landscape scale to conserve all three species, what would you recommend and why?

Exercise 2: Questions

5. Does the relationship change between the amount of habitat on the landscape and species conservation when disturbance is considered? If yes, how do the relationships change?

ANSWER HERE

6. As a conservation manager does the incorporation of disturbance change the amount of habitat at the landscape scale you would conserve? What would you recommend for each of the three levels of disturbance (0.1, 0.3, and 0.5) and why?

ANSWER HERE

Exercise 3: Figures, code and plots

#Exercise 3 - Task 2 code and figure here. Don't forget the caption!

Exercise 3: Questions

7. Comparing the initial and new reserve design, does the Number of Patches and Mean Patch Size need to increase or decrease when disturbance is considered?

ANSWER HERE

8. Based on the precautionary principle, what would you recommend to policy makers about conservation planning in your landscape?

ANSWER HERE

Overall Synthesis Question

9. Based on what you have learned in this exercise, critique the ‘Single Large or Several Small’ Reserve Design Concept. Does it seem like a robust concept for species conservation?

ANSWER HERE