countreg logo

Count Data Regression

Overview

The core of the R package countreg consists of functions for a variety of count data regression models:

  • nbreg(): Negative binomial regression (type 1 and 2), including both constant and varying dispersion parameters which can depend on regressors.
  • zeroinfl() and hurdle(): Zero-inflated and hurdle models for count data based on Poisson, geometric, negative binomial, and binomial distributions. These allow for excess zeros compared to the unadjusted underlying distributions (or also a deficit of zeros in case of the hurdle model).
  • zerotrunc(): Zero-truncated count regression based on Poisson, geometric, and negative binomial distributions. These models can be employed for the zero-truncated count part of hurdle models.
  • FLXMRnegbin(): Finite mixtures of negative binomial regressions via driver for the flexmix package.
  • MBnegbin(): Model-based boosting of negative binomial regressions via driver for the mboost package.

Previously available functions for graphical goodness-of-fit assessment (rootograms, PIT histograms, Q-Q plots based on randomized quantile residulas, etc.) are now provided in the topmodels package.

Distribution functions (d/p/q/r) for the different zero-truncated, zero-inflated, and hurdle count distributions are availabe in the distributions3 package along with corresponding distribution objects.

Installation

The latest development version can be installed from R-universe:

install.packages("countreg", repos = "https://zeileis.R-universe.dev")

License

The package is available under the General Public License version 3 or version 2

Illustration

For demonstrating some of the available count regression models we analyze the number of male satellites around nesting female horseshoe crabs during mating. Because larger females that are in better condition tend to attract more satellites we consider their carapace width and color as (numeric) regressor variables. Package and data can be loaded and tranformed via:

library("countreg")
## Loading required package: MASS
data("CrabSatellites", package = "countreg")
cs <- CrabSatellites |>
  transform(color = as.numeric(color)) |>
  subset(select = c("satellites", "width", "color"))

The following four count models are compared: a Poisson generalized linear model via glm(), a negative binomial regression with nbreg(), a negative binomial hurdle model with hurdle(), and a zero-inflated negative binomial model with zeroinfl().

cs_p    <-      glm(satellites ~ ., data = cs, family = poisson)
cs_nb   <-    nbreg(satellites ~ ., data = cs)
cs_hnb  <-   hurdle(satellites ~ ., data = cs, dist = "negbin")
cs_zinb <- zeroinfl(satellites ~ ., data = cs, dist = "negbin")

The glm() function is from base R, all other models are from countreg. All negative binomial models employ the type 2 parameterization. The hurdle and zero-inflated models employ binary models for the zero hurdle and zero-inflated part, respectively.

For a quick overview we compare the estimated coefficients from all parts of the models and compute their BIC.

cbind(
  poisson = coef(cs_p),
  nb = coef(cs_nb, model = "mu"),
  hnb_count = coef(cs_hnb, model = "count"),
  hnb_zero = coef(cs_hnb, model = "zero"),
  zinb_count = coef(cs_zinb, model = "count"),
  zinb_zero = coef(cs_zinb, model = "zero")
)
##                poisson         nb   hnb_count    hnb_zero zinb_count  zinb_zero
## (Intercept) -2.5199832 -3.2409843 0.428566899 -10.0708390 0.29870287 10.4341839
## width        0.1495725  0.1776543 0.037845165   0.4583097 0.04171687 -0.4890186
## color       -0.1694036 -0.1815656 0.006928678  -0.5090467 0.01866320  0.6068262
BIC(cs_p, cs_nb, cs_hnb, cs_zinb)
##         df      BIC
## cs_p     3 930.9589
## cs_nb    4 769.5455
## cs_hnb   7 736.7985
## cs_zinb  7 736.8958

This shows that

  • The number of male satellites increase with width and decrease with color of the female carapace.
  • The effect of the regressors mostly distinguishes between having any satellites or not while the expectation in the count part has almost no dependency on the regressors.
  • There is overdispersion in the number of satellites because the negative binomial models fit much better than the simple Poisson model.
  • There is only litte difference between the hurdle and zero-inflated model (except that the sign in the zero part is flipped because one models the probability to exceed zero while the other models the probability of an excess zero).

The summary of the hurdle negative binomial model provides further details such as the non-significance of the regressors in the count part and the estimate of the overdispersion parameter theta.

summary(cs_hnb)
## 
## Call:
## hurdle(formula = satellites ~ ., data = cs, dist = "negbin")
## 
## Pearson residuals:
##     Min      1Q  Median      3Q     Max 
## -1.3835 -0.7244 -0.2636  0.5557  3.6080 
## 
## Count model coefficients (truncated negbin with log link):
##             Estimate Std. Error z value Pr(>|z|)    
## (Intercept) 0.428567   0.941077   0.455    0.649    
## width       0.037845   0.032749   1.156    0.248    
## color       0.006929   0.091078   0.076    0.939    
## Log(theta)  1.527382   0.352950   4.327 1.51e-05 ***
## Zero hurdle model coefficients (binomial with logit link):
##             Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -10.0708     2.8065  -3.588 0.000333 ***
## width         0.4583     0.1040   4.407 1.05e-05 ***
## color        -0.5090     0.2237  -2.276 0.022862 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
## 
## Theta: count = 4.6061
## Number of iterations in BFGS optimization: 17 
## Log-likelihood: -350.4 on 7 Df