Cleaned "trend" option

Set Env. Variance at 8% ==> SD ~28%

inst/ShinyApp/server.R

@@ -1134,24 +1134,24 @@ server <- function(input, output, session){
 
         if(input$pop_trend == "growth") {
           if(input$pop_trend_strength == "weak") {
-            param$pop_growth_mean <- 1.01
+            param$pop_growth_mean <- growth_weak
           } else if(input$pop_trend_strength == "average"){
-            param$pop_growth_mean <- 1.03
+            param$pop_growth_mean <- growth_average
           } else {
-            param$pop_growth_mean <- 1.06
+            param$pop_growth_mean <- growth_strong
           }
         } else if(input$pop_trend == "decline"){
           if(input$pop_trend_strength == "weak") {
-            param$pop_growth_mean <- 0.99
+            param$pop_growth_mean <- decline_weak
           } else if(input$pop_trend_strength == "average"){
-            param$pop_growth_mean <- 0.97
+            param$pop_growth_mean <- decline_average
           } else {
-            param$pop_growth_mean <- 0.94
+            param$pop_growth_mean <- decline_strong
           }
         } else {
-          param$pop_growth_mean <- 1
+          param$pop_growth_mean <- pop_stable
         }
-        param$pop_growth_se <- 0
+        param$pop_growth_se <- trend_se
 
 
         # Case 3 : Values directly provided (i.e., not from expert elicitation)
@@ -1237,9 +1237,8 @@ server <- function(input, output, session){
     rMAX_species <- rMAX_spp(surv = tail(param$survivals,1), afr = min(which(param$fecundities != 0)))
     param$rMAX_species <- rMAX_species
 
-    ## We define theta = 1 for simplicity - given large uncertainty of real shape of density-dependence in nature
-    #param$theta <- theta_spp(rMAX_species)
     param$theta <- fixed_theta
+    #param$theta <- theta_spp(rMAX_species)
 
     param$vr_calibrated <- calibrate_params(
       inits = init_calib(s = param$survivals, f = param$fecundities, lam0 = param$pop_growth_mean),

inst/ShinyApp/ui.R

@@ -21,17 +21,29 @@ rm(list = ls(all.names = TRUE))
 
 
   ##### Fixed parameters #####
-
-  # We define theta = 1 for simplicity - given large uncertainty of real shape of density-dependence in nature
+  # We define theta = 1 (same as in PBR) - for simplicity, given large uncertainty of real shape of density-dependence in nature
   fixed_theta = 1
 
-  # Coefficient of environmental variation -- set at 8%, based on values found for birds in the literature
-    ## (Saeher & Engen 2002) between 7% et 14%, so about 10%
-    ## (Sther et al. 2005) : mostly between 2.5% et 10%, so about 6%
-  coeff_var_environ = 0.08
+  # Coefficient of environmental variation (SD)
+    ## Environnmental variance set at 8%, based on values found for birds in the literature:
+    ## (Saeher & Engen 2002) : between 7% et 14 ==> average : 10%
+    ## (Sther et al. 2005) : between 2.5% et 10% ==> average : 6%
+  coeff_var_environ = sqrt(0.08) # SD ~28%
 
   # Coverage probability used for lower/upper interval input values
   CP = 0.99
+
+  # Values of pop_growth (assumed), when the "trend" option is chosen
+  growth_weak <- 1.05
+  growth_average <- 1.10
+  growth_strong <- 1.15
+
+  decline_weak <- 0.97
+  decline_average <- 0.94
+  decline_strong <- 0.91
+
+  pop_stable <- 1
+  trend_se <- 0.03 # SE to use for pop_growth, when the "trend" option is chosen
 }
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