`check_zeroinflation()`

checks whether count models are
over- or underfitting zeros in the outcome.

## Usage

```
check_zeroinflation(x, ...)
# S3 method for default
check_zeroinflation(x, tolerance = 0.05, ...)
# S3 method for performance_simres
check_zeroinflation(
x,
tolerance = 0.1,
alternative = c("two.sided", "less", "greater"),
...
)
```

## Arguments

- x
Fitted model of class

`merMod`

,`glmmTMB`

,`glm`

, or`glm.nb`

(package**MASS**).- ...
Arguments passed down to

`simulate_residuals()`

. This only applies for models with zero-inflation component, or for models of class`glmmTMB`

from`nbinom1`

or`nbinom2`

family.- tolerance
The tolerance for the ratio of observed and predicted zeros to considered as over- or underfitting zeros. A ratio between 1 +/-

`tolerance`

is considered as OK, while a ratio beyond or below this threshold would indicate over- or underfitting.- alternative
A character string specifying the alternative hypothesis.

## Value

A list with information about the amount of predicted and observed zeros in the outcome, as well as the ratio between these two values.

## Details

If the amount of observed zeros is larger than the amount of predicted zeros, the model is underfitting zeros, which indicates a zero-inflation in the data. In such cases, it is recommended to use negative binomial or zero-inflated models.

In case of negative binomial models, models with zero-inflation component,
or hurdle models, the results from `check_zeroinflation()`

are based on
`simulate_residuals()`

, i.e. `check_zeroinflation(simulate_residuals(model))`

is internally called if necessary.

## Tests based on simulated residuals

For certain models, resp. model from certain families, tests are based on
simulated residuals (see `simulate_residuals()`

). These are usually more
accurate for testing such models than the traditionally used Pearson residuals.
However, when simulating from more complex models, such as mixed models or
models with zero-inflation, there are several important considerations.
Arguments specified in `...`

are passed to `simulate_residuals()`

, which
relies on `DHARMa::simulateResiduals()`

(and therefore, arguments in `...`

are passed further down to *DHARMa*). The defaults in DHARMa are set on the
most conservative option that works for all models. However, in many cases,
the help advises to use different settings in particular situations or for
particular models. It is recommended to read the 'Details' in
`?DHARMa::simulateResiduals`

closely to understand the implications of the
simulation process and which arguments should be modified to get the most
accurate results.

## See also

Other functions to check model assumptions and and assess model quality:
`check_autocorrelation()`

,
`check_collinearity()`

,
`check_convergence()`

,
`check_heteroscedasticity()`

,
`check_homogeneity()`

,
`check_model()`

,
`check_outliers()`

,
`check_overdispersion()`

,
`check_predictions()`

,
`check_singularity()`

## Examples

```
data(Salamanders, package = "glmmTMB")
m <- glm(count ~ spp + mined, family = poisson, data = Salamanders)
check_zeroinflation(m)
#> # Check for zero-inflation
#>
#> Observed zeros: 387
#> Predicted zeros: 298
#> Ratio: 0.77
#>
#> Model is underfitting zeros (probable zero-inflation).
# for models with zero-inflation component, it's better to carry out
# the check for zero-inflation using simulated residuals
m <- glmmTMB::glmmTMB(
count ~ spp + mined,
ziformula = ~ mined + spp,
family = poisson,
data = Salamanders
)
res <- simulate_residuals(m)
check_zeroinflation(res)
#> # Check for zero-inflation
#>
#> Observed zeros: 387
#> Predicted zeros: 387
#> Ratio: 1.00
#>
#> Model seems ok, ratio of observed and predicted zeros is within the
#> tolerance range (p > .999).
```