R/OMts_dev.R

In DLMtool/DLMtool: Data-Limited Methods Toolkit

# library(DLMtool); library(dplyr)
# OM <- testOM
# 
# DLMextra()
# library(DLMextra)
# OMs <- avail("OM")
# dflist <- list(); n <- 0
# for (om in OMs) {
#   n <- n+1
#   OM <- get(om)
#   dflist[[n]] <- data.frame(OM=om, maxage=OM@maxage)
# }
# DF <- do.call("rbind", dflist) %>% as.data.frame()
# 
# DF %>% arrange(maxage)
# 
# 
# OMts <- function(OM, ts=4, silent=FALSE) {
#   if(class(OM) != "OM") stop("Object must be class `OM`", call.=FALSE)
#   
#   OMout <- OM 
#   # Natural mortality
#   OMout@M <- OM@M/ts
#   OMout@M2 <- OM@M2/ts
#   
#   # Maximum age
#   OMout@maxage <- OM@maxage*ts
#   
#   # Growth Parameters
#   OMout@K <- OM@K/ts
#   OMout@t0 <- OM@t0 * ts
#   
#   # Effort Trends
#   OMout@EffYears <- OM@EffYears * ts
#   
#   # Interval & Years
#   OMout@interval <- OM@interval
#   OMout@nyears <- OM@nyears * ts
#   OMout@proyears <- OM@proyears * ts
#   
#   # Cpars
#   if (length(OM@cpars$M_at_Length) >0) {
#     OMout@cpars$M_at_Length <- OM@cpars$M_at_Length/ts
#   }
# 
#   if (length(OM@cpars$ageM) >0) {
#     OMout@cpars$ageM <- OM@cpars$ageM*ts
#   }
#   if (length(OM@cpars$age95) >0) {
#     OMout@cpars$age95 <- OM@cpars$age95*ts
#   }
#   
#   # At-age - can't deal with for now
#   nms <- c('M_ageArray', 'Mat_age', 'Len_age', "Wt_age", "V", "retA", "Find", 'Perr',
#            "Marray", "Karray")
#   for (nm in nms) {
#     if (!is.null(OM@cpars[[nm]]))
#       stop("Cannot convert cpars$", nm, " to different time-step. Specify externally to converted OM", call.=FALSE)
#   }
#    
#   # Message 
#   if (!silent) message("Converting from annual time-step to ", ts, ' time-steps per year')
#   OMout
# }
# 
# # Test Capelin_GSL_DFO - short-lived
# # test with curE
# 
# OM <- Lesser_Amberjack_GOM_NOAA
# OM@cpars$Len_age <- OM@cpars$Wt_age <- OM@cpars$Find <- OM@cpars$Perr <- OM@cpars$V <- 
#   OM@cpars$Marray <- NULL
# OM2 <- OMts(OM)
# 
# nsim <- 400
# OM@nsim <- nsim
# OM2@nsim <- nsim
# 
# MSE1 <- runMSE(OM, MP=c("FMSYref", "curE"), ntrials=300, parallel = TRUE, fracD=0.0001)
# MSE2 <- runMSE(OM2, MP=c("FMSYref", "curE"), ntrials=300, parallel = TRUE, fracD=0.0001)
# 
# 
# TradePlot(MSE1)
# TradePlot(MSE2)
# 
# 
# # No error test
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