tests RW ALK

spatioTemporalIndices/tests/testthat/NEAhadLengthAgeRW_betaLength/script.R → spatioTemporalIndices/tests/testthat/NEAhadLengthAgeRW/script.R

@@ -1,17 +1,17 @@
 suppressMessages(library(spatioTemporalIndices))
 
-dat_l = readRDS("NEAhadLengthAgeRW_betaLength/haddock2018-2020_length_ex_rus_reduced.rds")
-dat_alk = readRDS("NEAhadLengthAgeRW_betaLength/haddock2018-2020_age_ex_rus_reduced.rds")
+dat_l = readRDS("NEAhadLengthAgeRW/haddock2018-2020_length_ex_rus_reduced.rds")
+dat_alk = readRDS("NEAhadLengthAgeRW/haddock2018-2020_age_ex_rus_reduced.rds")
 
 conf_l = defConf(years = 2018:2020, # years to use, use all years with data by default
                  maxLength = 60, # Numeric = use directly; NULL = use input data to determine
                  minLength = 20, # Numeric = use directly; NULL = use input data to determine
                  spatioTemporal =0 ,
                  spatial =0,
-                 rwBeta0 = 1,
+                 rwBeta0 = 0,
                  dLength = 5,
                  reduceLength = 3,
-                 stratasystem = list(dsn="NEAhadLengthAgeRW_betaLength/strata", layer = "Vintertoktet_nye_strata"),
+                 stratasystem = list(dsn="NEAhadLengthAgeRW/strata", layer = "Vintertoktet_nye_strata"),
                  applyALK = 1,
                  cutoff =100)
 
@@ -21,46 +21,59 @@ conf_alk = defConf_alk(maxAge = 8,
                        minAge = 3,
                        spatioTemporal = 0,
                        spatial =0,
-                       rwBeta0 = 1,
-                       betaLength = 1)
+                       rwBeta0 = 1)
 
 confPred = defConfPred(conf=conf_l,Depth="DATA",cellsize = 200)
 
-# run model
+# run model with random walk beta0 in ALK
 run = fitModel(dat_l,conf_l, confPred,dat_alk,conf_alk,ignore.parm.uncertainty = TRUE,silent = TRUE)
 
+#RW for beta0 and beta_length in ALK
+conf_alk$rwBeta0 = 1
+conf_alk$betaLength = 1
+run2 = fitModel(dat_l,conf_l, confPred,dat_alk,conf_alk,ignore.parm.uncertainty = TRUE,silent = TRUE)
 
-#no RW for beta0 and no RW for beta_length
+#no RW for beta0 and beta_length in ALK
 conf_alk$rwBeta0 = 0
 conf_alk$betaLength = 2
-run2 = fitModel(dat_l,conf_l, confPred,dat_alk,conf_alk,ignore.parm.uncertainty = TRUE,silent = TRUE)
+run3 = fitModel(dat_l,conf_l, confPred,dat_alk,conf_alk,ignore.parm.uncertainty = TRUE,silent = TRUE)
 
 resultsOut = list(objective = run$opt$objective,
                   objective2 = run2$opt$objective,
+                  objective3 = run3$opt$objective,
                   logAgeIndex = run$rl$logAgeIndex,
-                  logAgeIndex2 = run2$rl$logAgeIndex)
-resultsOut$AIC = AIC(run,run2)
+                  logAgeIndex2 = run2$rl$logAgeIndex,
+                  logAgeIndex3 = run3$rl$logAgeIndex)
+resultsOut$AIC = AIC(run,run2,run3)
+
 
-load("NEAhadLengthAgeRW_betaLength/resultsExp.RData")
+
+load("NEAhadLengthAgeRW/resultsExp.RData")
 
 expect_equal(resultsOut$logAgeIndex, resultsExp$logAgeIndexExp,tolerance = 1e-4)
 expect_equal(resultsOut$objective, resultsExp$objectiveExp,tolerance = 1e-4)
 expect_equal(resultsOut$logAgeIndex2, resultsExp$logAgeIndex2Exp,tolerance = 1e-4)
 expect_equal(resultsOut$objective2, resultsExp$objective2Exp,tolerance = 1e-4)
+expect_equal(resultsOut$logAgeIndex3, resultsExp$logAgeIndex3Exp,tolerance = 1e-4)
+expect_equal(resultsOut$objective3, resultsExp$objective3Exp,tolerance = 1e-4)
 expect_equal(resultsOut$AIC, resultsExp$AICExp,tolerance = 1e-4)
 
 test_that("Plot runs without error", {
-  expect_silent(plotResults(run, what = "ALK", year = 2020))
+  expect_silent(plotResults(run2, what = "ALK", year = 2020))
 })
 
 
+
+
 if(FALSE){
   resultsExp = list(objectiveExp = run$opt$objective,
                     objective2Exp = run2$opt$objective,
+                    objective3Exp = run3$opt$objective,
                     logAgeIndexExp = run$rl$logAgeIndex,
                     logAgeIndex2Exp = run2$rl$logAgeIndex,
-                    AICExp = AIC(run,run2))
-  save(resultsExp,file = "NEAhadLengthAgeRW_betaLength/resultsExp.RData")
+                    logAgeIndex3Exp = run3$rl$logAgeIndex)
+  resultsExp$AICExp = AIC(run,run2,run3)
+  save(resultsExp,file = "NEAhadLengthAgeRW/resultsExp.RData")
 }
 
 

spatioTemporalIndices/tests/testthat/test-NEAhaddockRW.R

@@ -0,0 +1,2 @@
+source("NEAhadLengthAgeRW/script.R")
+