more experiments - beta distributed interannual variation in recruitm…

…ent.
LandSciTech · Aug 29, 2024 · d2c1ac9 · d2c1ac9
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Showing 4 changed files with 25 additions and 9 deletions.
diff --git a/R/getPriors.R b/R/getPriors.R
@@ -85,7 +85,7 @@ getPriors <- function(modList = NULL,
                       sSigmaMax = 0.18,
                       rIntSE = 0.25,
                       rSigmaMin =0.00001,
-                      rSigmaMax = 0.79,
+                      rSigmaMax =0.7,
                       qMin=0, qMax =0.6, 
                       uMin = 0, uMax = 0.2, 
                       zMin = 0, zMax = 0.2, 

diff --git a/inst/templates/JAGS_template.txt b/inst/templates/JAGS_template.txt
@@ -10,6 +10,15 @@ for(k in 1:nCounts){
 
 #Survival
 for(k in 1:nYears){
+	#Note adjustment as in Johnson et al 2020.
+  #mu.S[k] <- min(1,exp(l.Saf + anthro[k]*beta.Saf))
+  #sig.S[k] <- cv.S*mu.S[k]
+  #Get beta distribution parameters from mean and sd
+  #alpha.S[k] <- max(0.01,((1-mu.S[k])/sig.S[k]^2 - 1/mu.S[k]) * mu.S[k]^2)
+  #beta.S[k] <- max(0.01,alpha.S[k] * (1/mu.S[k] - 1))
+  #Saf2[k]~dbeta(alpha.S[k],beta.S[k])
+  #S.annual.KM[k] <- min((Saf2[k]*46-0.5)/45,1)
+
 	#Adult female survival - process variance
 	epsilon.Saf[k]~dnorm(0,tau.Saf)
 	log(Saf2[k]) <- l.Saf + anthro[k]*beta.Saf + epsilon.Saf[k]
@@ -20,11 +29,17 @@ for(k in 1:nYears){
 
 #Recruitment
 for(k in 1:nYears){
-    fixedEffect[k] <- l.R + anthro[k]*beta.Rec.anthro + fire[k]*beta.Rec.fire
-	  sig.R[k]<-cv.R*fixedEffect[k]^2
-	  tau.R[k]<-pow(sig.R[k], -2)
-		epsilon.R[k]~dnorm(0,tau.R[k])
-		log(R[k]) <-  fixedEffect[k]+ epsilon.R[k]
+    mu.R[k] <- min(1,exp(l.R + anthro[k]*beta.Rec.anthro + fire[k]*beta.Rec.fire))
+    sig.R[k] <- cv.R*mu.R[k]
+    #Get beta distribution parameters from mean and sd
+    alpha.R[k] <- max(0.01,((1-mu.R[k])/sig.R[k]^2 - 1/mu.R[k]) * mu.R[k]^2)
+    beta.R[k] <- max(0.01,alpha.R[k] * (1/mu.R[k] - 1))
+    R[k]~dbeta(alpha.R[k],beta.R[k])
+
+	  #sig.R[k]<-cv.R*exp(fixedEffect[k])
+	  #tau.R[k]<-pow(sig.R[k], -2)
+		#epsilon.R[k]~dnorm(0,tau.R[k])
+		#log(R[k]) <-  fixedEffect[k]+ epsilon.R[k]
 }
 
 #Growth
@@ -55,6 +70,7 @@ for(k in 2:nYears){
 
 	#NOTE truncate distribution to ensure intercept between 0 and (45+0.5)/46.
 	l.Saf ~ dnorm(l.Saf.Prior1,pow(l.Saf.Prior2,-2)) T(-10,-0.01092911)
+	#cv.S~dunif(sig.Saf.Prior1,sig.Saf.Prior2)
 	sig.Saf~dunif(sig.Saf.Prior1,sig.Saf.Prior2)
 	tau.Saf<-pow(sig.Saf, -2)
 

diff --git a/man/getPriors.Rd b/man/getPriors.Rd
diff --git a/tests/testthat/test-caribouBayesianPM.R b/tests/testthat/test-caribouBayesianPM.R
@@ -246,8 +246,8 @@ test_that("results match expected", {
   manyObs <- doScn(nCollar = 2000, rQuantile = 0.9, sQuantile = 0.9)
   doPlot(manyObs, title = "2000 collars")
 
-  fewCollarObs <- doScn(nCollar = 0, rQuantile = 0.9, sQuantile = 0.9)
-  doPlot(fewCollarObs, title = "5 collars")
+  fewCollarObs <- doScn(nCollar = 5, rQuantile = 0.9, sQuantile = 0.9)
+  doPlot(fewCollarObs, title = "5 collars")#,var="Adult female survival")
 
   difMany <- calcDif(manyObs$obs.all)
   difFew <- calcDif(fewCollarObs$obs.all)