---
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 = 40,
nyears_experiment = 60,
ramp_years = 60, # ramp years should almost always be set to the same as nyears_experiment
mindate = as.Date("2001-05-01"),
# ── Temperature — warm patch ───────────────────────────
base_temp_warm = 11,
amplitude_warm = 14,
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 = 200, K_cold = 200, # reduced from 500; needed for density signal in critical-period function
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 = 2, A_cold_target = 0,
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_current",
# ── Population ─────────────────────────────────────────
n_fish_per_strat = 50,
start_wt = 0.5,
wt_sd = 0.05,
# ── Movement cost ──────────────────────────────────────
movecost_c = 0.1,
movecost_b = 0.3,
sigma_bold = 0.002,
tau = 0.001,
# ── Survival ──────────────────────────────────────────
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 = 0.1, # reduced from 0.1; prevents overcompensatory recruitment cycles (see diagnostic session)
# ── 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))
)
```
### Plot scenario habitat specs.
#### Null: cold habitat only
* Cold habitat only; warm habitat total unavailable. This is effectively equivalent to running a simulation with only resident fish.
*Note that we specify warm habitat conditions (temp, food availability, survival, etc.), these have no bearing on the results because area is always 0; fish can never occupy the warm habitat*
```{r}
plot_habitat(build_habitat(scenarios[["null_cold"]]), exp_start_date = scenarios[["null_cold"]]$mindate + years(scenarios[["null_cold"]]$nyears_burnin))
```
#### Multiplicative temperature
* Thermal regimes are ~multiplicative of each other: maximum thermal heterogeneity during summer, but heterogeneity collapses to ~0 during winter (everything is cold).
* Habitat area is equal during burn-in; cold habitat is entirely replaced by warm habitat over experiment
```{r}
plot_habitat(build_habitat(scenarios[["temp_mult"]]), exp_start_date = scenarios[["temp_mult"]]$mindate + years(scenarios[["temp_mult"]]$nyears_burnin))
```
#### Offset temperature
* Thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Everything else the same as is base parameter set
```{r}
plot_habitat(build_habitat(scenarios[["temp_offset"]]), exp_start_date = scenarios[["temp_offset"]]$mindate + years(scenarios[["temp_offset"]]$nyears_burnin))
```
#### Pcmax: warm-high, cold-low
* As above, thermal regimes are offset of each other: warm habitat is 5-10 degrees warmer than the cold habitat. Warm habitat persists overwinter
* Threshold Pcmax is high in the warm habitat and low in the cold habitat (gradients/controls on food availability and foraging opportunity)
```{r}
plot_habitat(build_habitat(scenarios[["temp_offset_diffP"]]), exp_start_date = scenarios[["temp_offset_diffP"]]$mindate + years(scenarios[["temp_offset_diffP"]]$nyears_burnin))
```
## Write R file
```{r}
#| eval: false
#| purl: false
file.remove("ScenarioDefs.R")
quarto::qmd_to_r_script("ScenarioDefs.qmd")
```
