# Calculate a population index via simulation from the joint precision matrix

Source:`R/get-index-sims.R`

`get_index_sims.Rd`

Calculate a population index via simulation from the joint precision matrix.
Compared to `get_index()`

, this version can be faster if bias correction was
turned on in `get_index()`

while being approximately equivalent. **This is an
experimental function.** This function usually works reasonably well, but we
make no guarantees. It is recommended to use `get_index()`

with `bias_correct = TRUE`

for final inference.

## Arguments

- obj
`predict.sdmTMB()`

output with`nsim > 0`

.- level
The confidence level.

- return_sims
Logical. Return simulation draws? The default (

`FALSE`

) is a quantile summary of those simulation draws.- area
A vector of grid cell/polyon areas for each year-grid cell (row of data) in

`obj`

. Adjust this if cells are not of unit area or not all the same area (e.g., some cells are partially over land/water). Note that the area vector is added as`log(area)`

to the raw values in`obj`

. In other words, the function assumes a log link, which typically makes sense.- est_function
Function to summarize the estimate (the expected value).

`mean()`

would be an alternative to`median()`

.- area_function
Function to apply area weighting. Assuming a log link, the

`function(x, area) x + log(area)`

default makes sense. If in natural space,`function(x, area) x * area`

makes sense.- agg_function
Function to aggregate samples within each time slice. Assuming a log link, the

`function(x) sum(exp(x))`

default makes sense. If in natural space,`function(x) sum(x)`

makes sense.

## Value

A data frame. If `return_sims = FALSE`

:

name of column (e.g.

`year`

) that was supplied to`sdmTMB()`

time argument`est`

: estimate`lwr`

: lower confidence interval value`upr`

: upper confidence interval value`log_est`

: log estimate`se`

: standard error on the log estimate

If `return_sims = TRUE`

, samples from the index values in a long-format data frame:

name of column (e.g.

`year`

) that was supplied to`sdmTMB()`

time argument`.value`

: sample value`.iteration`

: sample number

## Details

Can also be used to produce an index from a model fit with tmbstan.

This function does nothing more than summarize and reshape the matrix of simulation draws into a data frame.

## Examples

```
if (inla_installed()) {
m <- sdmTMB(density ~ 0 + as.factor(year) + depth_scaled + depth_scaled2,
data = pcod_2011, mesh = pcod_mesh_2011, family = tweedie(link = "log"),
time = "year"
)
qcs_grid_2011 <- replicate_df(qcs_grid, "year", unique(pcod_2011$year))
p <- predict(m, newdata = qcs_grid_2011, nsim = 100)
x <- get_index_sims(p)
x_sims <- get_index_sims(p, return_sims = TRUE)
if (require("ggplot2", quietly = TRUE)) {
ggplot(x, aes(year, est, ymin = lwr, ymax = upr)) +
geom_line() +
geom_ribbon(alpha = 0.4)
ggplot(x_sims, aes(as.factor(year), .value)) +
geom_violin()
}
# Demo custom functions if working in natural space:
ind <- get_index_sims(
exp(p),
agg_function = function(x) sum(x),
area_function = function(x, area) x * area
)
}
#> We generally recommend using `get_index(..., bias_correct = TRUE)`
#> rather than `get_index_sims()`.
#> We generally recommend using `get_index(..., bias_correct = TRUE)`
#> rather than `get_index_sims()`.
#> We generally recommend using `get_index(..., bias_correct = TRUE)`
#> rather than `get_index_sims()`.
```