reorder code

content/R/pk_prepare_dat.R

@@ -161,19 +161,19 @@ res <- rbind(res, landings, index, catchage, indexage)
 ## rm(landings, index, catchage, indexage)
 
 age_frame <- FIMS::FIMSFrame(res)
-# fishery_catch <- FIMS::m_landings(age_frame)
-# fishery_agecomp <- FIMS::m_agecomp(age_frame, "fleet1")
-# survey_index2 <- FIMS::m_index(age_frame, "survey2")
-# survey_agecomp2 <- FIMS::m_agecomp(age_frame, "survey2")
-# survey_index3 <- FIMS::m_index(age_frame, "survey3")
-# survey_agecomp3 <- FIMS::m_agecomp(age_frame, "survey3")
-# survey_index6 <- FIMS::m_index(age_frame, "survey6")
-# survey_agecomp6 <- FIMS::m_agecomp(age_frame, "survey6")
-# # need to think about how to deal with multiple fleets - only using 1 fleeet for now
-# fish_index <- methods::new(Index, nyears)
-# fish_age_comp <- methods::new(AgeComp, nyears, nages)
-# fish_index$index_data <- fishery_catch
-# fish_age_comp$age_comp_data <-
-#   fishery_agecomp * catchage$uncertainty#rep(Ncaa, each=nages)
-# 
-# FIMS::m_index(age_frame, 'survey2')
+fishery_catch <- FIMS::m_landings(age_frame)
+fishery_agecomp <- FIMS::m_agecomp(age_frame, "fleet1")
+survey_index2 <- FIMS::m_index(age_frame, "survey2")
+survey_agecomp2 <- FIMS::m_agecomp(age_frame, "survey2")
+survey_index3 <- FIMS::m_index(age_frame, "survey3")
+survey_agecomp3 <- FIMS::m_agecomp(age_frame, "survey3")
+survey_index6 <- FIMS::m_index(age_frame, "survey6")
+survey_agecomp6 <- FIMS::m_agecomp(age_frame, "survey6")
+# need to think about how to deal with multiple fleets - only using 1 fleeet for now
+fish_index <- methods::new(Index, nyears)
+fish_age_comp <- methods::new(AgeComp, nyears, nages)
+fish_index$index_data <- fishery_catch
+fish_age_comp$age_comp_data <-
+  fishery_agecomp * catchage$uncertainty#rep(Ncaa, each=nages)
+
+FIMS::m_index(age_frame, 'survey2')

content/run_pollock_tests.R

@@ -24,30 +24,28 @@ estimate_q6 <- TRUE
 estimate_F <- TRUE
 estimate_recdevs <- TRUE
 
-
-
+## Organize input lists by process
 clear()
 clear_logs()
-# source("R/pk_prepare_FIMS_inputs.R")
-source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs.R"))
+# source("R/pk_prepare_FIMS_inputs_by_process.R")
+source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs_by_process.R"))
 ## make FIMS model
 success <- CreateTMBModel()
 parameters <- list(p = get_fixed())
-obj1 <- MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
-rep1 <- obj1$report()
+obj2 <- MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
+## report values for the two models
+rep2 <- obj2$report()
 
 
-## Organize input lists by process
 clear()
 clear_logs()
-# source("R/pk_prepare_FIMS_inputs_by_process.R")
-source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs_by_process.R"))
+# source("R/pk_prepare_FIMS_inputs.R")
+source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs.R"))
 ## make FIMS model
 success <- CreateTMBModel()
 parameters <- list(p = get_fixed())
-obj2 <- MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
-## report values for the two models
-rep2 <- obj2$report()
+obj1 <- MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
+rep1 <- obj1$report()
 
 ## Test that the two models are identical
 all.equal(rep1,rep2)

content/run_pollock_tests_by_fleet.R

@@ -10,7 +10,6 @@ nages <- 10
 ages <- 1:nages
 source(file.path(getwd(), "content", "R", "pk_prepare_dat.R"))
 
-
 # test R functions: approach 1 --------------------------------------------
 clear()
 clear_logs()
@@ -224,12 +223,38 @@ obj3 <- TMB::MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
 ## report values for the two models
 rep3 <- obj3$report()
 
+
+clear()
+clear_logs()
+# source("R/pk_prepare_FIMS_inputs.R")
+estimate_fish_selex <- TRUE
+estimate_survey_selex <- TRUE
+estimate_q2 <- TRUE
+estimate_q3 <- TRUE
+estimate_q6 <- TRUE
+estimate_F <- TRUE
+estimate_recdevs <- TRUE
+source(file.path(getwd(), "content", "R", "pk_prepare_FIMS_inputs.R"))
+## make FIMS model
+success <- CreateTMBModel()
+parameters <- list(p = get_fixed())
+obj1 <- TMB::MakeADFun(data = list(), parameters, DLL = "FIMS", silent = TRUE)
+rep1 <- obj1$report()
+
 ## Parameters are in a different order but seem to match
+opt1 <- with(obj1, nlminb(par, fn, gr))
 opt3 <- with(obj3, nlminb(par, fn, gr))
 clear()
 clear_logs()
 
 
+## Test that the two models are identical
+all.equal(rep1,rep3)
+all.equal(obj1$report(opt1$par), obj3$report(opt3$par))
+sum(obj1$par)-sum(obj3$par)
+
+print(cbind(sort(opt1$par)- sort(opt3$par)))
+
 # test R functions: approach 2 --------------------------------------------
 # selectivity_double_logistic <- set_selectivity(
 #   form = "DoubleLogisticSelectivity",