Merge pull request #16 from mcolvin/referance-to-individual

Referance to individual
mcolvin · Jun 8, 2017 · 326b353 · 326b353
2 parents d545e92 + e6849d1
commit 326b353
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Showing 5 changed files with 1,417 additions and 559 deletions.
diff --git a/CPUE.Rmd b/CPUE.Rmd
@@ -17,8 +17,8 @@ rmarkdown::render("index.Rmd")
 
 ```{r,echo=FALSE,warning=FALSE, message=FALSE}
 source("R/1_global.R")
-source("R/2_functions.R")
-# source("R/3_load-and-clean.R")
+source("R/2_functions-2.R")
+source("R/3_load-and-clean.R")
 source("R/4_figures.R")
 source("R/5_tables.R")
 source("R/6-analysis-CPUE.R")
@@ -34,21 +34,63 @@ nyears<- 10
 beta0<- 2.9444
 phi<-matrix(plogis(beta0),length(segs),nyears-1)
 
-fish_density<- 10
-```
-
-#SAMPLING OUTPUT 
-segs<- c(1,2,3,4,7,8,9,11,10,13,14)
-nyears<- 10
-
-beta0<- 2.9444
-phi<-matrix(plogis(beta0),length(segs),nyears-1)
-
 sim_pop<-reference_population(segs=segs,
     bends=bends,# BENDS DATAFRAME
     fish_density=10, # FISH DENSITY PER RKM
     phi=phi) # MATRIX OF YEAR TO YEAR AND SEGEMENT SPECIFIC SURVIVALS
 
+    
+    
+    
+yyy<-catch_counts(segs=c(1,2,3,4,7,8,9,10,13,14),
+    bends=sim_pop$bendMeta,
+    abund=sim_pop$Z,
+    gears=c("GN14", "GN18", "GN41", "GN81", 
+        "MF", "OT16", "TLC1", "TLC2", "TN"),
+    catchability=c(0.00004, 0.00004, 0.00004, 
+        0.00004, 0.00004, 0.0002, 0.00004, 0.00004, 0.0002),
+    deployments=rep(8,9),
+    effort=effort,
+    occasions=3)
+   
+# returns list of values    
+    
+yyyy<- bend_samples(segs=c(1,2,3,4,7,8,9,10,13,14),
+   bends=bends,
+   abund=sim_pop$out)   
+    
+yyyyy<-samp_dat(segs=c(1,2,3,4,7,8,9,10,13,14),
+   bends=bends,
+   bend_abund=sim_pop$out,
+   ind_abund=sim_pop$Z,
+   gears=c("GN14", "GN18", "GN41", "GN81", "MF", 
+        "OT16", "TLC1", "TLC2", "TN"),
+   catchability=c(0.00004, 0.00004, 0.00004, 0.00004, 
+        0.00004, 0.0002, 0.00004, 0.00004, 0.0002),
+   deployments=rep(8,9),
+   effort=effort,
+   occasions=3)   
+names(yyyyy)  
+
+# yyyyy$cpue_long this can feed the beast below
+head(yyyyy$cpue_long)
+   
+trnd_dat<-get.trnd(segs=segs,
+    bends=bends,# BENDS DATAFRAME
+    abund=sim_pop$out,
+    abund=sim_pop$out,
+    gears=c("GN14", "GN18", "GN41", "GN81", "MF", "OT16", "TLC1", "TLC2", "TN"),
+    catchability=c(0.00004, 0.00004, 0.00004, 0.00004, 0.00004, 0.002, 0.00004, 0.00004, 0.002), #BY GEAR,
+    deployments=rep(8,9), #BY GEAR
+    effort=effort)
+
+trnd_dat<-do.call("rbind",trnd_dat)
+    
+    
+    
+    
+    
+    
 # CPUE ANALYSIS FOR TREND
 tmp<- aggregate(cpue~year+segment,sim_dat,mean)
 tmp$segment<- as.factor(tmp$segment)
@@ -86,7 +128,11 @@ sim_pop<-reference_population(segs=segs,
     bends=bends,# BENDS DATAFRAME
     fish_density=10, # FISH DENSITY PER RKM
     phi=phi) # MATRIX OF YEAR TO YEAR AND SEGEMENT SPECIFIC SURVIVALS
-
+tmp<-bend_samples(segs=c(1,2,3,4,7,8,9,10,13,14),
+                       bends=bends,
+                       abund=sim_pop$out)
+                       
+                       
   trnd_dat<-get.trnd(segs=segs,
          bends=bends,# BENDS DATAFRAME
          abund=sim_pop$out,