put in some mods to vignette

vignettes/00-spm-example.Rmd

@@ -94,9 +94,7 @@ inp <- spmR::dat2list(here::here("examples","BSAI NRS","spm.dat"))
 fc <- data.frame(Year=inp$fixed_catch[,1], mean=inp$fixed_catch[,2], type='C')# |> 
 names(fc) <- c("Year", "mean", "type")
 fc <- fc |>  expand_grid(Alt=c(1,3,5,7)) |> mutate(Alt=as.factor(Alt), ub=mean,lb=mean)
-fc
-p1$data
-p1 + geom_point(data=fc,aes(x=Year,y=mean))
+plotSPM(df) + geom_point(data=fc,aes(x=Year,y=mean))
 #p1$data
 ```
 
@@ -131,11 +129,10 @@ plotSPM(df)
 
 First we'll run this model with only 3-years fixed catch assumed
 
-```{r goa_fhs,eval=TRUE,echo=FALSE}
-# df <- runSPM(here::here("examples","goa_flathead/maia"),run=TRUE)
+```{r goa_fhs,eval=TRUE,echo=TRUE}
 inp <- spmR::dat2list(here::here("examples","goa_flathead","spmorig.dat"))
 spmR::list2dat(inp,here::here("examples","goa_flathead","spm.dat"))
-bdf <- runSPM(here::here("examples","goa_flathead"),run=TRUE)
+bdf <- runSPM(here::here("examples","goa_flathead"),run=FALSE)
 df <- readr::read_csv(here::here("examples","goa_flathead","spm_summary.csv"))
 plotSPM(df)
 # p1<- plotSPM(df)
@@ -151,7 +148,7 @@ inp$nyrs_fixed_catch <- 5
 inp$fixed_catch <- rbind(inp$fixed_catch, c(2025, 1100), c(2026, 1100))
 inp$fixed_catch
 spmR::list2dat(inp,here::here("examples","goa_flathead","spm.dat"))
-bdf <- runSPM(here::here("examples","goa_flathead"),run=TRUE)
+bdf <- runSPM(here::here("examples","goa_flathead"),run=FALSE)
 
 df <- readr::read_csv(here::here("examples","goa_flathead","spm_summary.csv"))
 plotSPM(df)