POISSON REGRESSION | STATA DATA

ANALYSIS EXAMPLES
Version info: Code for this page was tested in Stata 12.

Poisson regression is used to model count variables.

Please note: The purpose of this page is to show how to use various data
analysis commands. It does not cover all aspects of the research process
which researchers are expected to do. In particular, it does not cover data
cleaning and checking, verification of assumptions, model diagnostics or
potential follow-up analyses.

Examples of Poisson regression

Example 1. The number of persons killed by mule or horse kicks in the
Prussian army per year. Ladislaus Bortkiewicz collected data from 20
volumes of Preussischen Statistik. These data were collected on 10 corps
of the Prussian army in the late 1800s over the course of 20 years.

Example 2. The number of people in line in front of you at the grocery

store. Predictors may include the number of items currently offered at a
special discounted price and whether a special event (e.g., a holiday, a big
sporting event) is three or fewer days away.

Example 3. The number of awards earned by students at one high

school. Predictors of the number of awards earned include the type of
program in which the student was enrolled (e.g., vocational, general or
academic) and the score on their final exam in math.

Description of the data

For the purpose of illustration, we have simulated a data set for Example 3
above. In this example, num_awards is the outcome variable and
indicates the number of awards earned by students at a high school in a
year, math is a continuous predictor variable and represents students
scores on their math final exam, and prog is a categorical predictor
variable with three levels indicating the type of program in which the
students were enrolled.

Lets start with loading the data and looking at some descriptive statistics.
use
https://stats.idre.ucla.edu/stat/stata/dae/poisson_sim,
clear

sum num_awards math

Variable | Obs Mean Std. Dev.

Min Max
-------------+-----------------------------------------
---------------
num_awards | 200 .63 1.052921
0 6
math | 200 52.645 9.368448
33 75
Each variable has 200 valid observations and their distributions seem quite
reasonable. In this particular the unconditional mean and variance of our
outcome variable are not extremely different.

Lets continue with our description of the variables in this dataset. The table
below shows the average numbers of awards by program type and seems
to suggest that program type is a good candidate for predicting the number
of awards, our outcome variable, because the mean value of the outcome
appears to vary by prog.

tabstat num_awards, by(prog) stats(mean sd n)

Summary for variables: num_awards

by categories of: prog (type of program)

prog | mean sd N
---------+------------------------------
general | .2 .4045199 45
academic | 1 1.278521 105
vocation | .24 .5174506 50
---------+------------------------------
Total | .63 1.052921 200
----------------------------------------
histogram num_awards, discrete freq scheme(s1mono)
(start=0, width=1)
Analysis methods you might consider
Below is a list of some analysis methods you may have
encountered. Some of the methods listed are quite reasonable, while
others have either fallen out of favor or have limitations.

Poisson regression Poisson regression is often used for modeling

count data. Poisson regression has a number of extensions useful for
count models.
Negative binomial regression Negative binomial regression can be
used for over-dispersed count data, that is when the conditional
variance exceeds the conditional mean. It can be considered as a
generalization of Poisson regression since it has the same mean
structure as Poisson regression and it has an extra parameter to
model the over-dispersion. If the conditional distribution of the
outcome variable is over-dispersed, the confidence intervals for
Negative binomial regression are likely to be narrower as compared to
those from a Poisson regression.
Zero-inflated regression model Zero-inflated models attempt to
account for excess zeros. In other words, two kinds of zeros are
thought to exist in the data, "true zeros" and "excess zeros". Zero-
inflated models estimate two equations simultaneously, one for the
count model and one for the excess zeros.
OLS regression Count outcome variables are sometimes log-
transformed and analyzed using OLS regression. Many issues arise
with this approach, including loss of data due to undefined values
 generated by taking the log of zero (which is undefined) and biased
estimates.

Poisson regression
Below we use the poisson command to estimate a Poisson regression
model. The i. before prog indicates that it is a factor variable (i.e.,
categorical variable), and that it should be included in the model as a series
of indicator variables.

We use the vce(robust) option to obtain robust standard errors for the
parameter estimates as recommended by Cameron and Trivedi (2009) to
control for mild violation of underlying assumptions.

poisson num_awards i.prog math, vce(robust)

Iteration 0: log pseudolikelihood = -182.75759

Iteration 1: log pseudolikelihood = -182.75225
Iteration 2: log pseudolikelihood = -182.75225

Poisson regression
Number of obs = 200

Wald chi2(3) = 80.15

Prob > chi2 = 0.0000

Log pseudolikelihood = -182.75225
Pseudo R2 = 0.2118

----------------------------------------------------
--------------------------
| Robust
num_awards | Coef. Std. Err. z
P>|z| [95% Conf. Interval]
-------------+--------------------------------------
--------------------------
prog |
2 | 1.083859 .3218538 3.37
0.001 .4530373 1.714681
3 | .3698092 .4014221 0.92
0.357 -.4169637 1.156582
|
math | .0701524 .0104614 6.71
0.000 .0496485 .0906563
 _cons | -5.247124 .6476195 -8.10
0.000 -6.516435 -3.977814
----------------------------------------------------
--------------------------

The output begins with the iteration log, which gives the values of the
log of pseudolikelihoods starting with the null model. The last value in
the iteration log is the final value of the log of pseudolikelihood for the
full model and is displayed again. Because we asked for robust
standard errors, the maximized likelihood is actually a
pseudolikelihood. The estimates of the parameters are maximum
likelihood estimates and the estimation of the variance-covariance
matrix of the parameter estimates leads to the pseudolikelihood. Log
pseudolikelihood values can be used to compare models.
The header information is presented next. On the right-hand side, the
number of observations used in the analysis (200) is given, along with
the Wald chi-square statistic with three degrees of freedom for the full
model, followed by the p-value for the chi-square. This is a test
that all of the estimated coefficients are equal to zeroa test of the
model as a whole. From the p-value, we can see that the model is
statistically significant. The header also includes a pseudo-R2, which
is 0.21 in this example.
Below the header you will find the Poisson regression coefficients for
each of the variables along with robust standard errors, z-scores, p-
values and 95% confidence intervals for the coefficients. The
coefficient for math is .07. This means that the expected increase in
log count for a one-unit increase in math is .07. The indicator
variable 2.prog is the expected difference in log count between group
2 (prog=2) and the reference group (prog=1). Compared to level 1
of prog, the expected log count for level 2 of prog increases by about
1.1. The indicator variable 3.prog is the expected difference in log
count between group 3 (prog=3) and the reference group
(prog=1). Compared to level 1 of prog, the expected log count for
level 3 of prog increases by about .37. To determine if prog itself,
overall, is statistically significant, we can use the test command to
obtain the two degrees-of-freedom test of this variable.

The two degree-of-freedom chi-square test indicates that prog, taken

together, is a statistically significant predictor of num_awards.

test 2.prog 3.prog

( 1) [num_awards]2.prog = 0
( 2) [num_awards]3.prog = 0
 chi2( 2) = 14.76
Prob > chi2 = 0.0006
To help assess the fit of the model, the estat gof command can be used to
obtain the goodness-of-fit chi-squared test. This is not a test of the model
coefficients (which we saw in the header information), but a test of the
model form: Does the poisson model form fit our data?

estat gof

Goodness-of-fit chi2 = 189.4496

Prob > chi2(196) = 0.6182

Pearson goodness-of-fit = 212.1437

Prob > chi2(196) = 0.2040
We conclude that the model fits reasonably well because the goodness-of-
fit chi-squared test is not statistically significant. If the test had been
statistically significant, it would indicate that the data do not fit the model
well. In that situation, we may try to determine if there are omitted predictor
variables, if our linearity assumption holds and/or if there is an issue of
over-dispersion.

Sometimes, we might want to present the regression results as incident

rate ratios, we can use the irroption. These IRR values are equal to our
coefficients from the output above exponentiated.

poisson, irr

Poisson regression
Number of obs = 200
Wald
chi2(3) = 80.15
Prob
> chi2 = 0.0000
Log pseudolikelihood = -182.75225
Pseudo R2 = 0.2118

-------------------------------------------------------
-----------------------
| Robust
num_awards | IRR Std. Err. z P>|z|
[95% Conf. Interval]
-------------+-----------------------------------------
-----------------------
prog |
 | 2 2.956065 .9514208 3.37 0.001
1.573083 5.554903
3 | 1.447458 .5810418 0.92 0.357
.6590449 3.179049
|
math | 1.072672 .0112216 6.71 0.000
1.050902 1.094893
-------------------------------------------------------
-----------------------
The output above indicates that the incident rate for 2.prog is 2.96 times
the incident rate for the reference group (1.prog). Likewise, the incident
rate for 3.prog is 1.45 times the incident rate for the reference group
holding the other variables constant. The percent change in the incident
rate of num_awards is an increase of 7% for every unit increase in math.

Recall the form of our model equation:

log(num_awards) = Intercept + b1(prog=2) + b2(prog=3) + b3math.

This implies:

num_awards = exp(Intercept + b1(prog=2) + b2(prog=3)+ b3math) =

exp(Intercept) * exp(b1(prog=2)) * exp(b2(prog=3)) * exp(b3math)
The coefficients have an additive effect in the log(y) scale and the IRR
have a multiplicative effect in the y scale.

For additional information on the various metrics in which the results can be
presented, and the interpretation of such, please see Regression Models
for Categorical Dependent Variables Using Stata, Second Edition by J.
Scott Long and Jeremy Freese (2006).

To understand the model better, we can use the margins command. Below
we use the margins command to calculate the predicted counts at each
level of prog, holding all other variables (in this example, math) in the
model at their mean values.

margins prog, atmeans

Adjusted predictions
Number of obs = 200
Model VCE : Robust

Expression : Predicted number of events, predict()

at : 1.prog = .225 (mean)
 2.prog = .525 (mean)
3.prog = .25 (mean)
math = 52.645 (mean)

----------------------------------------------------
--------------------------
| Delta-method
| Margin Std. Err. z
P>|z| [95% Conf. Interval]
-------------+--------------------------------------
--------------------------
prog |
1 | .211411 .0627844 3.37
0.001 .0883558 .3344661
2 | .6249446 .0887008 7.05
0.000 .4510943 .7987949
3 | .3060086 .0828648 3.69
0.000 .1435966 .4684205
----------------------------------------------------
--------------------------
In the output above, we see that the predicted number of events for level 1
of prog is about .21, holding math at its mean. The predicted number of
events for level 2 of prog is higher at .62, and the predicted number of
events for level 3 of prog is about .31. Note that the predicted count of
level 2 of prog is (.6249446/.211411) = 2.96 times higher than the
predicted count for level 1 of prog. This matches what we saw in the IRR
output table.

Below we will obtain the predicted counts for values of math that range
from 35 to 75 in increments of 10.

margins, at(math=(35(10)75)) vsquish

Predictive margins
Number of obs = 200
Model VCE : Robust

Expression : Predicted number of events, predict()

1._at : math = 35
2._at : math = 45
3._at : math = 55
4._at : math = 65
5._at : math = 75
 ----------------------------------------------------
--------------------------
| Delta-method
| Margin Std. Err. z
P>|z| [95% Conf. Interval]
-------------+--------------------------------------
--------------------------
_at |
1 | .1311326 .0358696 3.66
0.000 .0608295 .2014358
2 | .2644714 .047518 5.57
0.000 .1713379 .3576049
3 | .5333923 .0575203 9.27
0.000 .4206546 .64613
4 | 1.075758 .1220143 8.82
0.000 .8366147 1.314902
5 | 2.169615 .4115856 5.27
0.000 1.362922 2.976308
----------------------------------------------------
--------------------------
The table above shows that with prog at its observed values
and math held at 35 for all observations, the average predicted count (or
average number of awards) is about .13; when math = 75, the average
predicted count is about 2.17. If we compare the predicted counts at math
= 35 and math = 45, we can see that the ratio is (.2644714/.1311326) =
2.017. This matches the IRR of 1.0727 for a 10 unit change: 1.0727^10 =
2.017.

The user-written fitstat command (as well as Statas estat commands) can
be used to obtain additional information that may be helpful if you want to
compare models. You can type search fitstat to download this program
(see How can I used the search command to search for programs and get
additional help? for more information about using search).

fitstat

Measures of Fit for poisson of num_awards

Log-Lik Intercept Only: -231.864 Log-Lik

Full Model: -182.752
D(195): 365.505 LR(3):
98.223
Prob > LR:
0.000
 McFadden's R2: 0.212 McFadden's
Adj R2: 0.190
ML (Cox-Snell) R2: 0.388 Cragg-
Uhler(Nagelkerke) R2: 0.430
AIC: 1.878 AIC*n:
375.505
BIC: -667.667 BIC':
-82.328
BIC used by Stata: 386.698 AIC used by
Stata: 373.505
You can graph the predicted number of events with the commands
below. The graph indicates that the most awards are predicted for those in
the academic program (prog = 2), especially if the student has a high math
score. The lowest number of predicted awards is for those students in the
general program (prog = 1).

predict c
separate c, by(prog)
twoway scatter c1 c2 c3 math, connect(l l l) sort ///
ytitle("Predicted Count") ylabel( ,nogrid)
legend(rows(3)) ///
legend(ring(0) position(10)) scheme(s1mono)

Things to consider
If overdispersion seems to be an issue, we should first check if our
model is appropriately specified, such as omitted variables and
functional forms. For example, if we omitted the predictor
 variable prog in the example above, our model would seem to have a
problem with over-dispersion. In other words, a mis-specified model
could present a symptom like an over-dispersion problem.
Assuming that the model is correctly specified, you may want to check
for overdispersion. There are several ways to do this including the
likelihood ratio test of over-dispersion parameter alpha by running the
same regression model using negative binomial distribution (nbreg).
One common cause of over-dispersion is excess zeros, which in turn
are generated by an additional data generating process. In this
situation, zero-inflated model should be considered.
If the data generating process does not allow for any 0s (such as the
number of days spent in the hospital), then a zero-truncated model
may be more appropriate.
Count data often have an exposure variable, which indicates the
number of times the event could have happened. This variable should
be incorporated into a Poisson model with the use of the exp() option.
The outcome variable in a Poisson regression cannot have negative
numbers, and the exposure cannot have 0s.
In Stata, a Poisson model can be estimated via glm command with
the log link and the Poisson family.
You will need to use the glm command to obtain the residuals to
check other assumptions of the Poisson model (see Cameron and
Trivedi (1998) and Dupont (2002) for more information).
Many different measures of pseudo-R-squared exist. They all attempt
to provide information similar to that provided by R-squared in OLS
regression, even though none of them can be interpreted exactly as
R-squared in OLS regression is interpreted. For a discussion of
various pseudo-R-squares, see Long and Freese (2006) or our FAQ
page What are pseudo R-squareds?.
Poisson regression is estimated via maximum likelihood estimation. It
usually requires a large sample size.

See also
Annotated output for the poisson command
Stata FAQ: How can I use countfit in choosing a count model?
Stata online manual
poisson
Stata FAQs
How are the standard errors and confidence intervals computed
for incidence-rate ratios (IRRs) by poisson and nbreg?

References
 Cameron, A. C. and Trivedi, P. K. (2009). Microeconometrics Using
Stata. College Station, TX: Stata Press.
Cameron, A. C. and Trivedi, P. K. (1998). Regression Analysis of
Count Data. New York: Cambridge Press.
Cameron, A. C. Advances in Count Data Regression Talk for the
Applied Statistics Workshop, March 28,
2009. http://cameron.econ.ucdavis.edu/racd/count.html .
Dupont, W. D. (2002). Statistical Modeling for Biomedical
Researchers: A Simple Introduction to the Analysis of Complex
Data. New York: Cambridge Press.
Long, J. S. (1997). Regression Models for Categorical and Limited
Dependent Variables. Thousand Oaks, CA: Sage Publications.
Long, J. S. and Freese, J. (2006). Regression Models for Categorical
Dependent Variables Using Stata, Second Edition. College Station,
TX: Stata Press.