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Example on how to change and run a model
Change_Model_Specs.Rmd
Example use of ebswp
library for setting up a new
model
Read in an existing model
Now use process error tuned file to fix the vales in the “ssb” files
d3 <- d2
d3$n_avo <- d1$n_avo
d3$ob_avo <- d1$ob_avo
d3$ob_avo_std <- d1$ob_avo_std
d3$wt_avo <- d1$wt_avo
d3$yrs_avo <- d1$yrs_avo
write_dat(output_file="runs/dat/pm_ssb0new.dat", indata=d3)
# Create directory and copy key files
dir.create("runs/ssb0")
file.copy("runs/ssb0_origProcTune/control.dat","runs/ssb0/",overwrite = TRUE)
file.copy("runs/avon2/compweights.ctl","runs/ssb0/",overwrite = TRUE)
file.remove("runs/ssb0/pm")
file.symlink("../../src/pm","runs/ssb0/pm")
# Read pm.dat, then write (e.g.,)
pm.dat<-read_table("runs/ProcTune/pm.dat",col_names=FALSE)
# Add some description of the rows...
row.names(pm.dat) <- c("Desc","main","sel","ctl","altFmsy","cov","wtage","cpue","temp","q")
pm.dat
pm.dat[1,] <- "Updated_SSB0_to_proctune1"
pm.dat[2,] <- "../dat/pm_ssb0new.dat"
writeLines(as.character(pm.dat$X1),"runs/ssb0/pm.dat")
For SSB1
#d1 <- read_dat("runs/dat/pm_avon2.dat")
d2 <- read_dat("runs/dat/pm_ssb1.dat")
d3 <- d2
d3$n_avo <- d1$n_avo
d3$ob_avo <- d1$ob_avo
d3$ob_avo_std <- d1$ob_avo_std
d3$wt_avo <- d1$wt_avo
d3$yrs_avo <- d1$yrs_avo
write_dat(output_file="runs/dat/pm_ssb1new.dat", indata=d3)
# Create directory and copy key files
dir.create("runs/ssb1")
file.copy("runs/ProcTune/control.dat","runs/ssb1/",overwrite = TRUE)
file.copy("runs/avon2/compweights.ctl","runs/ssb1/",overwrite = TRUE)
file.remove("runs/ssb1/pm")
file.symlink("../../src/pm","runs/ssb1/pm")
# Read pm.dat, then write (e.g.,)
pm.dat<-read_table("runs/ProcTune/pm.dat",col_names=FALSE)
# Add some description of the rows...
pm.dat[1,] <- "Updated_SSB1_to_proctune"
pm.dat[2,] <- "../dat/pm_ssb1new.dat"
writeLines(as.character(pm.dat$X1),"runs/ssb1/pm.dat")
And SSB2
#d1 <- read_dat("runs/dat/pm_proctune1.dat")
d2 <- read_dat("runs/dat/pm_ssb2.dat")
d3 <- d2
d3$n_avo <- d1$n_avo
d3$ob_avo <- d1$ob_avo
d3$ob_avo_std <- d1$ob_avo_std
d3$wt_avo <- d1$wt_avo
d3$yrs_avo <- d1$yrs_avo
write_dat(output_file="runs/dat/pm_ssb2new.dat", indata=d3)
# Create directory and copy key files
dir.create("runs/ssb2")
file.copy("runs/ProcTune/control.dat","runs/ssb2/",overwrite = TRUE)
file.copy("runs/avon2/compweights.ctl","runs/ssb2/",overwrite = TRUE)
file.remove("runs/ssb2/pm")
file.symlink("../../src/pm","runs/ssb2/pm")
# Read pm.dat, then write (e.g.,)
pm.dat<-read_table("runs/ProcTune/pm.dat",col_names=FALSE)
# Add some description of the rows...
pm.dat[1,] <- "Updated_SSB2_to_proctune"
pm.dat[2,] <- "../dat/pm_ssb2new.dat"
writeLines(as.character(pm.dat$X1),"runs/ssb2/pm.dat")
And obs-error run
d1 <- read_dat("runs/dat/pm_avon2.dat")
d2 <- read_dat("runs/dat/std_tune.dat")
d3 <- d2
d3$n_avo <- d1$n_avo
d3$ob_avo <- d1$ob_avo
d3$ob_avo_std <- d1$ob_avo_std
d3$wt_avo <- d1$wt_avo
d3$yrs_avo <- d1$yrs_avo
write_dat(output_file="runs/dat/obs_err_tune.dat", indata=d3)
# Files already in "tune" dir
file.remove("runs/tune/pm")
file.symlink("../../src/pm","runs/tune/pm")
# Read pm.dat, then write (e.g.,)
pm.dat<-read_table("runs/tune/pm.dat",col_names=FALSE)
# Add some description of the rows...
pm.dat[1,] <- "Obs_error_tuning"
pm.dat[2,] <- "../dat/obs_err_tune.dat"
writeLines(as.character(pm.dat$X1),"runs/tune/pm.dat")
Now run them all in parallel
mod_dir <- c("ProcTune","ssb0","ssb1","ssb2")
mod_names <- c("Proc_error_Tune","ssb0","ssb1","ssb2")
# output=TRUE default, also check on spm
res <- run_model()
#res <- get_results()
tab_fit(res, mod_scen = c(1:2)) |> gt::gt()
tab_fit(res, mod_scen = c(1:4)) |> gt::gt()
tab_ref(res, mod_scen = c(1:4)) |> gt::gt() |> gt::fmt_markdown()
# See if different from base
tail(sc2)
ctl <-read_dat("runs/ProcTune/control.dat")
ctlb <-read_dat("runs/base22/control.dat")
diff <- purrr::map_lgl(names(ctl), ~ !identical(ctl[[.]], ctlb[[.]]))
sum(diff)
names(ctl[diff])
cbind(ctl[diff][2],ctlb[diff][2])
names(ctl)
ctl[56]
write_dat("runs/base22/control.dat",ctl)
# Set an initial working directory
mod_names <- c("AVON Full","Proc_tune")
mod_dir <- c("avon2", "ProcTune")
# Note, 0.2 CV for selectivity variability nails it (from base22)
# Read, adjust, write...
sc <-read_table("runs/dat/scmed22P.dat",col_names = FALSE); names(sc) <- c("Year","fsh","bts","ats")
tail(sc )
# Iterated on selectivity
sc2 <- sc |> mutate(ats = ifelse(ats>0,.138,0))
write.table(sc2,file="runs/dat/scmed22P.dat",col.names = FALSE,row.names = FALSE)
#modtune <- run_model(Output=TRUE)
modtune<-get_results()
tab_fit(modtune, mod_scen = c(1,2)) |> gt::gt()
tab_ref(modtune, mod_scen = c(1,2)) |> gt::gt()
tab_ref(modlst, mod_scen = c(4,5)) |> gt::gt()
(modlst[[4]]$nextyrssbs)
(modlst[[4]]$nextyrssb.sd)
(modtune[[1]]$nextyrssbs)
names(modtune)