diff --git a/chin_tune/scripts/sim_variables.R b/chin_tune/scripts/sim_variables.R new file mode 100644 index 0000000000000000000000000000000000000000..7ecf70f0f1c533f81747f5f1c0d3057f63dea3c7 --- /dev/null +++ b/chin_tune/scripts/sim_variables.R @@ -0,0 +1,73 @@ +#### +####----1. ABOUT------------------------------------------------------------#### +#### +#### Evaluating alternative methods for modeling trap +#### efficiencies of outmigrating juvenile salmonids +#### +#### Authors: Walden et al. +#### +#### Content: R-Code for sourcing declared variables. +#### +#### This is the file for Supplement X of the manuscript. +#### + +####----2. "True" parameter values for simulated data-----------------------#### + +## Covariates +Qmin <- 500 # discharge +Qmax <- 7000 # discharge +degCmin <- 6 # temperature +degCmax <- 21 # temperature +effortmin <- 720 # effort +effortmax <- 3840 # effort +precipitation <- 0 # precipitation (yes/no) (nuisance) +nyear <- 10 # groups (random effects) + +## Set parameter values +Beta0_maxpt1 <- -3.2 # Trap efficiency max 0.10 +Beta0_maxpt25 <- -2.1 # Trap efficiency max 0.25 +Beta1 <- -0.3 # discharge +Beta2 <- 0.2 # temperature +Beta3 <- 0.2 # effort +Beta4 <- 0.0 # precipitation yes/no +Beta5 <- -0.4 # effort^2 +Beta6 <- 0.4 # discharge x temperature interaction +raneffSD <- 0.1 # year effect standard deviation +phiTrue <- 0.0002 + +####----3. Simulation variables---------------------------------------------#### + +# vector of sample sizes to test +nset <- c(50,100,150,200) +# vector of trap efficiencies to test +theseefficiencies <- c("Max efficiency 0.1","Max efficiency 0.25") +# Number of simulations to complete +nsim <- 1000 +# size of test dataset +ntest <- 100 + +####----4. Model parameters, hyperparameters, or variables------------------#### + +## For boosted regression modeling +mutuneiter <- 2000 +phituneiter <- 2000 +nu_hp=0.1 +fmu_null <- as.formula(y ~ 1) +fmu <- as.formula(y ~ 1 + + bols(discharge, intercept=FALSE) + + bols(temperature, intercept=FALSE) + + bols(effort, intercept=FALSE) + + bols(precip, intercept=FALSE) + + bbs(effort, knots=2, boundary.knots=NULL, degree=2, + df=1, center=TRUE) + + bols(temperature, intercept=FALSE, df=1) %X% + bols(discharge, intercept=FALSE, df=1) + + brandom(year) +) +fphi <- as.formula(y ~ 1) +nboot <- 100 +kfoldB <- 25 + +## For random forest modeling +seed.forest <- 234672817 +rftrees <- 2000 \ No newline at end of file