---
title: "Define Scenarios & Experiments"
---
```{r, include = FALSE}
library(tidyverse)
library(lubridate)
library(ggpubr)
library(egg)
```
***if any changes are made, need to re-run `qmd_to_r_script()` at end, in console***
**Purpose:** This script defines parameter sets for each scenario/experiment.
```{r include=FALSE}
#| cache: false
source("Habitat.R")
```
## Default parameters
Set the default/base parameter values that each experiment will adjust. Note that both the habitat and simulation parameters are rolled into a single list here.
```{r}
base_params <- list(
# ── Timeline ──────────────────────────────────────────
nyears_burnin = 50,
nyears_experiment = 50,
ramp_years = 0,
mindate = as.Date("2001-05-01"),
# ── Temperature — warm patch ───────────────────────────
base_temp_warm = 15,
amplitude_warm = 9.5,
peak_doy_warm = 196,
temp_min_warm = 0.5,
temp_noise_warm = 0,
# ── Temperature — cold patch ───────────────────────────
base_temp_cold = 6.6,
amplitude_cold = 8.4,
peak_doy_cold = 196,
temp_min_cold = 0.3,
temp_noise_cold = 0,
# ── Patch burn-in values ───────────────────────────────
pcmax_warm = 0.5, pcmax_cold = 0.5,
A_warm = 1.0, A_cold = 1.0,
K_warm = 400, K_cold = 400,
S_max_warm = 0.9994, S_max_cold = 0.9994,
# ── Experiment targets (NA = no change) ───────────────
pcmax_warm_target = NA, pcmax_cold_target = NA,
A_warm_target = NA, A_cold_target = NA,
K_warm_target = NA, K_cold_target = NA,
S_max_warm_target = NA, S_max_cold_target = NA,
# ── Behavioural / movement ─────────────────────────────
move_stochastic = "prob",
food_densdepen = "hyperbolic",
sense_environment = "density_all",
# ── Population ─────────────────────────────────────────
n_fish_per_strat = 50,
start_wt = 0.5,
wt_sd = 0.05,
# ── Movement cost ──────────────────────────────────────
movecost_c = 0.0, # previously 0.1. 0.0 is effective no cost
movecost_b = 0.3,
sigma_bold = 0.002,
tau = 0.001,
# ── Survival ──────────────────────────────────────────
s_min = 0.96,
s_w0 = 5,
s_k = 0.8,
T1_mort = 30,
T9_mort = 25.8,
K9_starv = 0.55,
K1_starv = 0.45,
MaxDensity4Growth = 50,
# Critical-period consumption-based survival (Elliott 1989)
# Applies fncSurviveConsumption() to age-0 fry for their first crit_period_days.
# Parameterised so that sustained pcmax_dd ≤ crit_pcmax_lo ≈ 1% 60-day survival;
# sustained pcmax_dd ≥ crit_pcmax_hi ≈ 99% 60-day survival (negligible cost).
crit_pcmax_lo = 0.30,
crit_pcmax_hi = 0.40,
crit_period_days = 60L,
# ── Competition ───────────────────────────────────────
dominance_beta = 1,
age_structured_competition = TRUE,
# ── Reproduction ──────────────────────────────────────
egg_wt = 0.07,
repro_cost = 0.2,
sigma_fecund = 0.085,
egg_surv = 0.15,
# ── Seeds ─────────────────────────────────────────────
hab_seed = 123,
sim_seed = 7843
)
```
## Define scenarios
Define scenarios as variants on the default parameters
```{r}
scenarios <- list(
# null_cold = modifyList(base_params, list(A_warm = 0,
# A_warm_target = NA)),
# temp_mult = base_params,
# temp_offset = modifyList(base_params, list(base_temp_warm = 15,
# amplitude_warm = 9.5,
# temp_min_warm = 0.5,
# base_temp_cold = 6.6,
# amplitude_cold = 8.4,
# temp_min_cold = 0)),
# temp_offset_diffP = modifyList(base_params, list(base_temp_warm = 15,
# amplitude_warm = 9.5,
# temp_min_warm = 0.5,
# base_temp_cold = 6.6,
# amplitude_cold = 8.4,
# temp_min_cold = 0,
# pcmax_warm = 0.6,
# pcmax_cold = 0.4)),
# Fixed habitat scenarios: changing habitat availability is tested by comparing among scenarios
### Null (cold only)
TempOffset_ColdOnly_95percold = modifyList(base_params, list(A_cold = 1.9,
A_warm = 0)),
TempOffset_ColdOnly_75percold = modifyList(base_params, list(A_cold = 1.5,
A_warm = 0)),
TempOffset_ColdOnly_50percold = modifyList(base_params, list(A_cold = 1.0,
A_warm = 0)),
TempOffset_ColdOnly_25percold = modifyList(base_params, list(A_cold = 0.5,
A_warm = 0)),
TempOffset_ColdOnly_05percold = modifyList(base_params, list(A_cold = 0.1,
A_warm = 0)),
### Cold + Warm, same Pcmax
TempOffset_ColdWarm_95percold = modifyList(base_params, list(A_cold = 1.9,
A_warm = 0.1)),
TempOffset_ColdWarm_75percold = modifyList(base_params, list(A_cold = 1.5,
A_warm = 0.5)),
TempOffset_ColdWarm_50percold = modifyList(base_params, list(A_cold = 1.0,
A_warm = 1.0)),
TempOffset_ColdWarm_25percold = modifyList(base_params, list(A_cold = 0.5,
A_warm = 1.5)),
TempOffset_ColdWarm_05percold = modifyList(base_params, list(A_cold = 0.1,
A_warm = 1.9)),
### Cold + Warm, high Pcmax in warm
TempOffset_ColdWarm_95percold_highPwarm = modifyList(base_params, list(A_cold = 1.9,
A_warm = 0.1,
pcmax_warm = 0.6)),
TempOffset_ColdWarm_75percold_highPwarm = modifyList(base_params, list(A_cold = 1.5,
A_warm = 0.5,
pcmax_warm = 0.6)),
TempOffset_ColdWarm_50percold_highPwarm = modifyList(base_params, list(A_cold = 1.0,
A_warm = 1.0,
pcmax_warm = 0.6)),
TempOffset_ColdWarm_25percold_highPwarm = modifyList(base_params, list(A_cold = 0.5,
A_warm = 1.5,
pcmax_warm = 0.6)),
TempOffset_ColdWarm_05percold_highPwarm = modifyList(base_params, list(A_cold = 0.1,
A_warm = 1.9,
pcmax_warm = 0.6))
)
```
## Plot scenario habitat specs.
### Fixed habitat: cold only (null)
#### 95% cold / 5% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 95% cold, 5% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdOnly_95percold"]]), exp_start_date = scenarios[["TempOffset_ColdOnly_95percold"]]$mindate + years(scenarios[["TempOffset_ColdOnly_95percold"]]$nyears_burnin))
```
#### 75% cold / 25% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 75% cold, 25% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdOnly_75percold"]]), exp_start_date = scenarios[["TempOffset_ColdOnly_75percold"]]$mindate + years(scenarios[["TempOffset_ColdOnly_75percold"]]$nyears_burnin))
```
#### 50% cold / 50% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 50% cold, 50% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdOnly_50percold"]]), exp_start_date = scenarios[["TempOffset_ColdOnly_50percold"]]$mindate + years(scenarios[["TempOffset_ColdOnly_50percold"]]$nyears_burnin))
```
#### 25% cold / 75% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 25% cold, 75% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdOnly_25percold"]]), exp_start_date = scenarios[["TempOffset_ColdOnly_25percold"]]$mindate + years(scenarios[["TempOffset_ColdOnly_25percold"]]$nyears_burnin))
```
#### 5% cold / 95% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 5% cold, 95% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdOnly_05percold"]]), exp_start_date = scenarios[["TempOffset_ColdOnly_05percold"]]$mindate + years(scenarios[["TempOffset_ColdOnly_05percold"]]$nyears_burnin))
```
### Fixed habitat: cold + warm (same pcmax)
#### 95% cold / 5% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 95% cold, 5% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_95percold"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_95percold"]]$mindate + years(scenarios[["TempOffset_ColdWarm_95percold"]]$nyears_burnin))
```
#### 75% cold / 25% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 75% cold, 25% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_75percold"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_75percold"]]$mindate + years(scenarios[["TempOffset_ColdWarm_75percold"]]$nyears_burnin))
```
#### 50% cold / 50% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 50% cold, 50% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_50percold"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_50percold"]]$mindate + years(scenarios[["TempOffset_ColdWarm_50percold"]]$nyears_burnin))
```
#### 25% cold / 75% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 25% cold, 75% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_25percold"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_25percold"]]$mindate + years(scenarios[["TempOffset_ColdWarm_25percold"]]$nyears_burnin))
```
#### 5% cold / 95% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 5% cold, 95% warm
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_05percold"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_05percold"]]$mindate + years(scenarios[["TempOffset_ColdWarm_05percold"]]$nyears_burnin))
```
### Fixed habitat: cold + warm, high P
#### 95% cold / 5% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 95% cold, 5% warm
* Maximum P_cmax is 10% greater in warm (0.6) relative to cold (0.5)
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_95percold_highPwarm"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_95percold_highPwarm"]]$mindate + years(scenarios[["TempOffset_ColdWarm_95percold_highPwarm"]]$nyears_burnin))
```
#### 75% cold / 25% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 75% cold, 25% warm
* Maximum P_cmax is 10% greater in warm (0.6) relative to cold (0.5)
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_75percold_highPwarm"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_75percold_highPwarm"]]$mindate + years(scenarios[["TempOffset_ColdWarm_75percold_highPwarm"]]$nyears_burnin))
```
#### 50% cold / 50% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 50% cold, 50% warm
* Maximum P_cmax is 10% greater in warm (0.6) relative to cold (0.5)
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_50percold_highPwarm"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_50percold_highPwarm"]]$mindate + years(scenarios[["TempOffset_ColdWarm_50percold_highPwarm"]]$nyears_burnin))
```
#### 25% cold / 75% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 25% cold, 75% warm
* Maximum P_cmax is 10% greater in warm (0.6) relative to cold (0.5)
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_25percold_highPwarm"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_25percold_highPwarm"]]$mindate + years(scenarios[["TempOffset_ColdWarm_25percold_highPwarm"]]$nyears_burnin))
```
#### 5% cold / 95% warm
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Habitat availability is fixed throughout the simulation: 5% cold, 95% warm
* Maximum P_cmax is 10% greater in warm (0.6) relative to cold (0.5)
```{r}
plot_habitat(build_habitat(scenarios[["TempOffset_ColdWarm_05percold_highPwarm"]]), exp_start_date = scenarios[["TempOffset_ColdWarm_05percold_highPwarm"]]$mindate + years(scenarios[["TempOffset_ColdWarm_05percold_highPwarm"]]$nyears_burnin))
```
## Write R file
```{r}
#| eval: false
#| purl: false
file.remove("ScenarioDefs.R")
quarto::qmd_to_r_script("ScenarioDefs.qmd")
```
