feat: numerous improvements to wild model

Report.qmd

@@ -1,6 +1,6 @@
 # Condor Populations Project 3
 
-Emily Fowler, Menna Ellaqanny, Michael Thomas
+Emily Fowler, Menna Ellaqany, Michael Thomas
 
 ```{r}
 source("project.R")
@@ -30,6 +30,11 @@ simulate_condor_population(0.659, 0.086, 0.086)
 simulate_condor_population(0.659, 0.138, 0.069)
 ```
 
+### Double Clutching
+```{r}
+simulate_condor_population(0.659, 0.138, 0.069, dc = TRUE)
+```
+
 ## Part E.  Consider year 1, immature, and adult mortalities of 0.659, 0.099, and 0.099,  respectively. 
 
 ```{r}

project.R

@@ -42,6 +42,7 @@ simulate_condor_population_inner <- function(rd1, rdI, rdA,
                                              c_Y0, c_Y1, c_I, c_A,
                                              w_Y0, w_Y1, w_I, w_A,
                                              nyears, captive_dc) {
+  captive_prod <- if (captive_dc) captive_productivity_rate_dc else captive_productivity_rate
   for (t in (length(c_Y0) + 1):nyears) {
     # model captive population changes (year 1, immature, and adult)
     c_Y1[t] <- c_Y0[t - 1] - # last year's population
@@ -57,7 +58,7 @@ simulate_condor_population_inner <- function(rd1, rdI, rdA,
       captive_immature_to_adult_rate * c_I[t - 1] # inflow from immature
 
     # model new births in captive population
-    c_Y0[t] <- captive_productivity_rate * (c_A[t] / 2)
+    c_Y0[t] <- captive_prod * (c_A[t] / 2)
 
     # sum of all population groups
     last_captive_population <- c_Y0[t - 1] + c_Y1[t - 1] + c_I[t - 1] + c_A[t - 1]
@@ -70,25 +71,21 @@ simulate_condor_population_inner <- function(rd1, rdI, rdA,
     c_Y1[t] <- c_Y1[t] - released_to_wild
 
     # carrying capacity death rate
-    last_wild_population <- w_Y0[t - 1] + w_Y1[t - 1] + c_I[t - 1] + c_A[t - 1]
+    last_wild_population <- w_Y0[t - 1] + w_Y1[t - 1] + w_I[t - 1] + w_A[t - 1]
-    approx_wild_growth_rate <- (wild_productivity_rate * (w_A[t - 1] / 2) + released_to_wild) / last_wild_population
+    rd_carrying <- (last_wild_population / wild_carrying_capacity) # P / M
-    rd_carrying <- approx_wild_growth_rate * (last_wild_population / wild_carrying_capacity) # r * P / M
 
-    w_Y1[t] <- (w_Y0[t - 1] + # inflow from year zero
+    w_Y1[t] <- w_Y0[t - 1] - # inflow from year zero
-      released_to_wild) * # inflow from captive
+      rd1 * w_Y1[t - 1] # outflow to deaths (death rate)
-      (1 - rd1) * # outflow to deaths (death rate)
-      (1 - rd_carrying) # outflow to deaths (carrying capacity)
 
     w_I[t] <- w_I[t - 1] + # last year's population
-      w_Y1[t - 1] - # inflow from year one
+      w_Y1[t - 1] + # inflow from year one
+      released_to_wild * (1 - rd_carrying) - # inflow from captive
       w_I[t - 1] * wild_immature_to_adult_rate - # outflow to adult
-      w_I[t - 1] * rdI - # outflow to deaths (death rate)
+      w_I[t - 1] * rdI # outflow to deaths (death rate)
-      w_I[t - 1] * rd_carrying # outflow to deaths (carrying capacity)
 
     w_A[t] <- w_A[t - 1] + # last year's population
       w_I[t - 1] * wild_immature_to_adult_rate - # inflow from immature
-      w_A[t - 1] * rdA - # outflow to deaths (death rate)
+      w_A[t - 1] * rdA # outflow to deaths (death rate)
-      w_A[t - 1] * rd_carrying # outflow to deaths (carrying capacity)
 
     w_Y0[t] <- wild_productivity_rate * (w_A[t] / 2) *
       (1 - rd_carrying) # deaths due to carrying capacity
@@ -123,7 +120,7 @@ plot_populations <- function(c_Y0, c_Y1, c_I, c_A,
   plot(
     years,
     w_Y0,
-    ylim = c(0, wild_carrying_capacity + 100),
+    ylim = c(0, wild_carrying_capacity),
     col = "red",
     main = "Condor Population in the Wild",
     xlab = "Time (years)",
@@ -133,13 +130,15 @@ plot_populations <- function(c_Y0, c_Y1, c_I, c_A,
   points(years, w_I, col = "darkgreen")
   points(years, w_A, col = "blue")
   points(years, wild_population)
+
+  print(wild_population)
 }
 
 # Simulates the Condor population over time using the given parameters.
 # * `rd1` - death rate of year one birds
 # * `rdI` - death rate of immature birds
 # * `rdA` - death rate of adult birds
-simulate_condor_population <- function(rd1, rdI, rdA) {
+simulate_condor_population <- function(rd1, rdI, rdA, dc = FALSE) {
   # captive population groups
   c_Y0 <- c(30)
   c_Y1 <- c(30)
@@ -147,16 +146,16 @@ simulate_condor_population <- function(rd1, rdI, rdA) {
   c_A <- c(30)
 
   # wild population groups
-  w_Y0 <- c(100)
+  w_Y0 <- c(30)
-  w_Y1 <- c(100)
+  w_Y1 <- c(30)
-  w_I <- c(100)
+  w_I <- c(30)
-  w_A <- c(100)
+  w_A <- c(30)
 
   list2env(simulate_condor_population_inner(
     rd1, rdI, rdA,
     c_Y0, c_Y1, c_I, c_A,
     w_Y0, w_Y1, w_I, w_A,
-    simulation_years, FALSE
+    simulation_years, dc
   ), envir = environment())
 
   plot_populations(
@@ -173,29 +172,31 @@ simulate_part_f <- function(rd1, rdI, rdA) {
   c_A <- c(30)
 
   # wild population groups
-  w_Y0 <- c(100)
+  w_Y0 <- c(30)
-  w_Y1 <- c(100)
+  w_Y1 <- c(30)
-  w_I <- c(100)
+  w_I <- c(30)
-  w_A <- c(100)
+  w_A <- c(30)
+
+  sdc <- 5
 
   # simulate first 5 years
   list2env(simulate_condor_population_inner(
     rd1, rdI, rdA,
     c_Y0, c_Y1, c_I, c_A,
     w_Y0, w_Y1, w_I, w_A,
-    5, TRUE
+    sdc, TRUE
   ), envir = environment())
 
   # release all in captivity
-  w_Y0[5] <- w_Y0[5] + c_Y0[5]
+  w_Y0[sdc] <- w_Y0[sdc] + c_Y0[sdc]
-  w_Y1[5] <- w_Y1[5] + c_Y1[5]
+  w_Y1[sdc] <- w_Y1[sdc] + c_Y1[sdc]
-  w_I[5] <- w_I[5] + c_I[5]
+  w_I[sdc] <- w_I[sdc] + c_I[sdc]
-  w_A[5] <- w_A[5] + c_A[5]
+  w_A[sdc] <- w_A[sdc] + c_A[sdc]
 
-  c_Y0[5] <- 0
+  c_Y0[sdc] <- 0
-  c_Y1[5] <- 0
+  c_Y1[sdc] <- 0
-  c_I[5] <- 0
+  c_I[sdc] <- 0
-  c_A[5] <- 0
+  c_A[sdc] <- 0
 
   # continue simulation
   list2env(simulate_condor_population_inner(