check_zeroinflation: Check for zero-inflation in count models

Description Usage Arguments Details Value Examples

View source: R/check_zeroinflation.R

Description

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

Usage

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check_zeroinflation(x, tolerance = 0.05)

Arguments

x

Fitted model of class merMod, glmmTMB, glm, or glm.nb (package MASS).

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.

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.

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.

Examples

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if (require("glmmTMB")) {
  data(Salamanders)
  m <- glm(count ~ spp + mined, family = poisson, data = Salamanders)
  check_zeroinflation(m)
}

Example output

Loading required package: glmmTMB
# Check for zero-inflation

   Observed zeros: 387
  Predicted zeros: 298
            Ratio: 0.77

Model is underfitting zeros (probable zero-inflation).
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.2.15
Current Matrix version is 1.2.17
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package

performance documentation built on Oct. 1, 2021, 5:08 p.m.