added value of information example

R/ForwardSimulate.R

@@ -15,11 +15,13 @@
 #'  assessment of stock size
 #' @param z_i a function which returns a random number from a distribution 
 #' for the implementation uncertainty in quotas 
+#' @param profit function, if known
 #' @return a data frame with the time, fishstock, harvested amount,
 #'  and what the escapement ("unharvested"). 
 #' @export
 ForwardSimulate <- function(f, pars, x_grid, h_grid, x0, D, z_g,
-                            z_m=function(x) 1, z_i = function(x) 1){
+                            z_m=function(x) 1, z_i = function(x) 1, 
+                            profit=NULL){
   # initialize variables with initial conditions
   OptTime <- dim(D)[2]    # Stopping time
   x_h <- numeric(OptTime) # population dynamics with harvest
@@ -28,7 +30,8 @@ ForwardSimulate <- function(f, pars, x_grid, h_grid, x0, D, z_g,
 
   s <- x_h # also track escapement
   x <- x_h # What would happen with no havest
-
+  p <- numeric(OptTime)
+
 
   ## Simulate through time ##
   for(t in 1:(OptTime-1)){
@@ -43,12 +46,13 @@ ForwardSimulate <- function(f, pars, x_grid, h_grid, x0, D, z_g,
     z <- z_g() 
     # population grows
     x_h[t+1] <- z * f(x_h[t], h[t], pars) # with havest
-    s[t]   <- x_h[t] - q_t # anticipated escapement
+    s[t+1]   <- x_h[t] - q_t # anticipated escapement
     x[t+1]   <- z * f(x[t], 0, pars) # havest-free dynamics
-  }
+    p[t] <- profit(x_h[t], h[t])
+}
   # formats output 
   data.frame(time = 1:OptTime, fishstock = x_h, harvest = h,
-             unharvested = x, escapement = s) 
+             unharvested = x, escapement = s, profit = p) 
 }
 
 

inst/examples/Reed.md

@@ -213,7 +213,7 @@ ggplot(subset(dt,reps==1)) +
   geom_line(aes(time, harvest), col="darkgreen") 
 ```
 
-![plot of chunk p0](http://farm8.staticflickr.com/7047/6983802282_7bceb5cd87_o.png) 
+![plot of chunk p0](http://farm9.staticflickr.com/8015/7178088946_4ab62a1ed1_o.png) 
 
 
 
@@ -224,10 +224,27 @@ This plot summarizes the stock dynamics by visualizing the replicates. Reed's S
 ```r
 p1 <- ggplot(dt) + geom_abline(intercept=opt$S, slope = 0) + 
   geom_abline(intercept=xT, slope = 0, lty=2) 
+```
+
+
+
+```
+Error: object 'xT' not found
+```
+
+
+
+```r
 p1 + geom_line(aes(time, fishstock, group = reps), alpha = 0.2)
 ```
 
-![plot of chunk p1](http://farm8.staticflickr.com/7193/7129886257_51bb453c13_o.png) 
+
+
+```
+Error: object 'p1' not found
+```
+
+
 
 
 We can also look at the harvest dynamics:
@@ -238,7 +255,13 @@ We can also look at the harvest dynamics:
 p1 + geom_line(aes(time, harvest, group = reps), alpha = 0.1, col="darkgreen")
 ```
 
-![plot of chunk p2](http://farm9.staticflickr.com/8167/6983803634_7699492b79_o.png) 
+
+
+```
+Error: object 'p1' not found
+```
+
+
 
 
 This strategy is supposed to be a constant-escapement strategy. We can visualize the escapement: 
@@ -249,7 +272,13 @@ This strategy is supposed to be a constant-escapement strategy. We can visualize
 p1 + geom_line(aes(time, escapement, group = reps), alpha = 0.1, col="darkgrey")
 ```
 
-![plot of chunk p3](http://farm8.staticflickr.com/7050/7129887427_4f690c5d65_o.png) 
+
+
+```
+Error: object 'p1' not found
+```
+
+
 
 
 
@@ -272,10 +301,27 @@ p5 <- ggplot(policy_zoom) +
   scale_colour_gradientn(colours = rainbow(4)) +
   geom_abline(intercept=opt$S, slope = 0) +
   geom_abline(intercept=xT, slope=0, lty=2)
+```
+
+
+
+```
+Error: object 'xT' not found
+```
+
+
+
+```r
 p5
 ```
 
-![plot of chunk policy](http://farm8.staticflickr.com/7188/7129887821_5430106a9f_o.png) 
+
+
+```
+Error: object 'p5' not found
+```
+
+
 
 
 The harvest intensity is limited by the stock size.
@@ -290,9 +336,26 @@ p6 <- ggplot(policy_zoom) +
   scale_colour_gradientn(colours = rainbow(4)) +
   geom_abline(intercept=opt$S, slope = 0) +
   geom_abline(intercept=xT, slope=0, lty=2)
+```
+
+
+
+```
+Error: object 'xT' not found
+```
+
+
+
+```r
 p6 + geom_line(aes(time, fishstock, group = reps), alpha = 0.1, data=dt)
 ```
 
-![plot of chunk policy2](http://farm8.staticflickr.com/7108/7129888199_255a56ecb2_o.png) 
+
+
+```
+Error: object 'p6' not found
+```
+
+
 
 

inst/examples/Reed_knit_.md

@@ -1,4 +1,4 @@
-`ro cache=TRUE, tidy=FALSE, warning=FALSE, comment=NA, message=FALSE, refresh=1 or`
+`ro cache=TRUE, tidy=FALSE, warning=FALSE, comment=NA, message=FALSE, refresh=2 or`
 
 ``` {r  echo=FALSE }
 opts_knit$set(upload.fun = socialR::flickr.url)