Change in bevaviour of caribouPopGrowth. Carrying capacity K is no lo…

…nger multiplied by initial population size.

Also more bug fixing.

R/caribouPopGrowth.R

@@ -27,8 +27,7 @@
 #' Given default parameters, recruitment rate is lowest \eqn{(0.5\dot{X}_t)}
 #' when \eqn{\dot{N}_t=1}, approaches a maximum of \eqn{\dot{X}_t} at
 #' intermediate population sizes, and declines to \eqn{0.6\dot{X}_t} as the
-#' population reaches carrying capacity of \eqn{k=100} times the initial
-#' population size. The post-juvenile female population in the next year
+#' population reaches carrying capacity of \eqn{K=50000}. The post-juvenile female population in the next year
 #' includes both survivors and new recruits:
 #' \eqn{\dot{N}_{t+1}=\text{min}(\dot{W}_t+\dot{J}_t,r_{max}\dot{N}_t)}.
 #'
@@ -49,7 +48,7 @@
 #' @param P_K Number. Recruitment multiplier at carrying capacity.
 #' @param a Number. Density dependence shape parameter.
 #' @param b Number. Allee effect parameter.
-#' @param K Number. Carrying capacity multiplier.
+#' @param K Number. Carrying capacity.
 #' @param r_max Number. Maximum population growth rate.
 #' @param s Number. Sex ratio.
 #' @param l_R Number. Minimum recruitment.
@@ -105,7 +104,7 @@ caribouPopGrowth <- function(N0,
                              P_K = 0.6,
                              a = 1,
                              b = 4,
-                             K = 100,
+                             K = 50000,
                              r_max = 1.3,
                              s=0.5,
                              l_R=0,
@@ -169,7 +168,7 @@ caribouPopGrowth <- function(N0,
       roundDigits=0
       doBinomial=T
     }
-    rK <- K * N0
+    rK <- K #* N0
   }
 
   if(a<0){

R/getOutputTables.R

@@ -65,14 +65,17 @@ getOutputTables <- function(caribouBayesDemogMod,
   if (!is.element("surv", names(survInput))) {
     if (sum(survInput$event, na.rm = T) > 0) {
       obsSurv <- getKMSurvivalEstimates(survInput)
-    } else {
+
+    }else{obsSurv=data.frame()} 
+
+
+    if(nrow(obsSurv)==0) {
       if(!is.element("id",names(survInput))){
         survInput$id=NA
         survInput$id[!is.na(survInput$enter)]=1
       }
       obsSurv <- unique(subset(survInput, !is.na(survInput$id),
                                select = c("Year")))
-
       obsSurv$surv <- NA
     }
   } else {

R/runScnSet.R

@@ -54,7 +54,7 @@ runScnSet <- function(scns, ePars, simNational, survAnalysisMethod = "KaplanMeie
     betaPriors <- getPriors(cs)
     minYr <- min(oo$exData$Year)
     maxYr <- max(oo$simDisturbance$Year)
-    out <- try(caribouBayesianPM(
+    out <- (caribouBayesianPM(
       survData = oo$simSurvObs, ageRatio = oo$ageRatioOut,
       disturbance = oo$simDisturbance,
       betaPriors = betaPriors, startYear = minYr, endYear = maxYr,