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fix(hess_always): part of #394
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Kelli.Johnson committed Sep 28, 2022
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10 changes: 1 addition & 9 deletions vignettes/introduction.Rmd
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Expand Up @@ -244,8 +244,6 @@ where the output can be saved and used to build `simdf`.

```{r scenario-defaults, echo=TRUE}
simdf <- setup_scenarios_defaults()
# Get standard errors by turning on the hessian
simdf[, "hess_always"] <- TRUE
```

Column entries of `simdf` need to be quoted if they are to be evaluated later, e.g.,
Expand All @@ -259,14 +257,11 @@ you would like to help with this effort or
have ideas on how to make it work better.

Column names of `simdf` are key.
In the example above,
`hess_always` is an argument of `ss3sim_base()` and can be used directly as the column name.
In fact, you can specify any input argument to `ss3sim_base()` as a column of `simdf`.
You can specify any input argument to `ss3sim_base()` as a column of `simdf`.

{ss3sim} function Argument Description
--------------- -------------- -----------
`ss3sim_base` `bias_adjust` Perform bias adjustment
`ss3sim_base` `hess_always` Calculate hessian

For functions that are called by `ss3sim_base()` you need to use the following rules to create appropriate column names:

Expand Down Expand Up @@ -377,8 +372,6 @@ a data frame for `run_ss3sim(simdf = df)`.
df <- setup_scenarios_defaults(nscenarios = 2)
# Turn off bias adjustment and use default settings in cod EM model
df[, "bias_adjust"] <- FALSE
# Estimate the hessian
df[, "hess_always"] <- TRUE
```

### Fishing mortality
Expand Down Expand Up @@ -514,7 +507,6 @@ df[, "ce.par_int"] <- NA
df[, "ce.par_phase"] <- c(-1, 3)
df[, "scenarios"] <- c("D1-E100-F0-cod", "D1-E101-F0-M1-cod")
df[, "bias_adjust"] <- FALSE
df[, "hess_always"] <- TRUE
```

### Run self-test
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