MULTINOMIAL LOGISTIC REGRESSION | R DATA ANALYSIS

EXAMPLES

Multinomial logistic regression is used to model nominal outcome variables, in which

the log odds of the outcomes are modeled as a linear combination of the predictor
variables.
This page uses the following packages. Make sure that you can load them before
trying to run the examples on this page. If you do not have a package installed, run:
install.packages("packagename"), or if you see the version is out of date, run:
update.packages().
require(foreign)
require(nnet)
require(ggplot2)
require(reshape2)

Version info: Code for this page was tested in R version 3.1.0
(2014-04-10)
On: 2014-06-13
With: reshape2 1.2.2; ggplot2 0.9.3.1; nnet 7.3-8; foreign 0.8-61;
knitr 1.5
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 multinomial logistic regression
Example 1. People’s occupational choices might be influenced by their parents’
occupations and their own education level. We can study the relationship of one’s
occupation choice with education level and father’s occupation. The occupational
choices will be the outcome variable which consists of categories of occupations.
Example 2. A biologist may be interested in food choices that alligators make. Adult
alligators might have different preferences from young ones. The outcome variable
here will be the types of food, and the predictor variables might be size of the
alligators and other environmental variables.
Example 3. Entering high school students make program choices among general
program, vocational program and academic program. Their choice might be modeled
using their writing score and their social economic status.
Description of the data
For our data analysis example, we will expand the third example using the hsbdemo
data set. Let’s first read in the data.
ml <- read.dta("https://stats.idre.ucla.edu/stat/data/hsbdemo.dta")

The data set contains variables on 200 students. The outcome variable is prog,
program type. The predictor variables are social economic status, ses, a three-level
categorical variable and writing score, write, a continuous variable. Let’s start with
getting some descriptive statistics of the variables of interest.
with(ml, table(ses, prog))

## prog
## ses general academic vocation
## low 16 19 12
## middle 20 44 31
## high 9 42 7

with(ml, do.call(rbind, tapply(write, prog, function(x) c(M = mean(x), SD = sd(x)))))

## M SD
## general 51.33 9.398
## academic 56.26 7.943
## vocation 46.76 9.319

Analysis methods you might consider

Multinomial logistic regression, the focus of this page.

Multinomial probit regression, similar to multinomial logistic regression with
independent normal error terms.
Multiple-group discriminant function analysis. A multivariate method for
multinomial outcome variables
Multiple logistic regression analyses, one for each pair of outcomes: One
problem with this approach is that each analysis is potentially run on a different
sample. The other problem is that without constraining the logistic models, we
can end up with the probability of choosing all possible outcome categories
greater than 1.
 Collapsing number of categories to two and then doing a logistic regression:
This approach suffers from loss of information and changes the original
research questions to very different ones.
Ordinal logistic regression: If the outcome variable is truly ordered and if it also
satisfies the assumption of proportional odds, then switching to ordinal logistic
regression will make the model more parsimonious.
Alternative-specific multinomial probit regression, which allows different error
structures therefore allows to relax the IIA assumption. This requires that the
data structure be choice-specific.
Nested logit model, another way to relax the IIA assumption, also requires the
data structure be choice-specific.

Multinomial logistic regression

Below we use the multinom function from the nnet package to estimate a
multinomial logistic regression model. There are other functions in other R packages
capable of multinomial regression. We chose the multinom function because it does
not require the data to be reshaped (as the mlogit package does) and to mirror the
example code found in Hilbe’s Logistic Regression Models.
Before running our model. We then choose the level of our outcome that we wish to
use as our baseline and specify this in the relevel function. Then, we run our model
using multinom. The multinom package does not include p-value calculation for the
regression coefficients, so we calculate p-values using Wald tests (here z-tests).
ml$prog2 <- relevel(ml$prog, ref = "academic")
test <- multinom(prog2 ~ ses + write, data = ml)

## # weights: 15 (8 variable)
## initial value 219.722458
## iter 10 value 179.982880
## final value 179.981726
## converged

summary(test)

## Call:
## multinom(formula = prog2 ~ ses + write, data = ml)
##
## Coefficients:
## (Intercept) sesmiddle seshigh write
## general 2.852 -0.5333 -1.1628 -0.05793
## vocation 5.218 0.2914 -0.9827 -0.11360
##
## Std. Errors:
## (Intercept) sesmiddle seshigh write
## general 1.166 0.4437 0.5142 0.02141
## vocation 1.164 0.4764 0.5956 0.02222
##
## Residual Deviance: 360
## AIC: 376
z <- summary(test)$coefficients/summary(test)$standard.errors
z

## (Intercept) sesmiddle seshigh write

## general 2.445 -1.2018 -2.261 -2.706
## vocation 4.485 0.6117 -1.650 -5.113

# 2-tailed z test
p <- (1 - pnorm(abs(z), 0, 1)) * 2
p

## (Intercept) sesmiddle seshigh write

## general 1.448e-02 0.2294 0.02374 6.819e-03
## vocation 7.299e-06 0.5408 0.09895 3.176e-07

We first see that some output is generated by running the model, even though
we are assigning the model to a new R object. This model-running output
includes some iteration history and includes the final negative log-likelihood
179.981726. This value multiplied by two is then seen in the model summary as
the Residual Deviance and it can be used in comparisons of nested models,
but we won’t show an example of comparing models on this page.
The model summary output has a block of coefficients and a block of standard
errors. Each of these blocks has one row of values corresponding to a model
equation. Focusing on the block of coefficients, we can look at the first row
comparing prog = "general" to our baseline prog = "academic" and the
second row comparing prog = "vocation" to our baseline prog =
"academic". If we consider our coefficients from the first row to be \(b_1\) and
our coefficients from the second row to be \(b_2\), we can write our model
equations:
$$ln\left(\frac{P(prog=general)}{P(prog=academic)}\right) = b_{10} + b_{11}
(ses=2) + b_{12}(ses=3) + b_{13}write$$ $$ln\left(\frac{P(prog=vocation)}
{P(prog=academic)}\right) = b_{20} + b_{21}(ses=2) + b_{22}(ses=3) +
b_{23}write$$

A one-unit increase in the variable write is associated with the

decrease in the log odds of being in general program vs. academic
program in the amount of .058 \(b_{13}\).
A one-unit increase in the variable write is associated with the
decrease in the log odds of being in vocation program vs. academic
program. in the amount of .1136 \(b_{23}\).
The log odds of being in general program vs. in academic program will
decrease by 1.163 if moving from ses="low" to ses="high"\(b_{12}\).
The log odds of being in general program vs. in academic program will
decrease by 0.533 if moving from ses="low"to ses="middle"\(b_{11}\),
 although this coefficient is not significant.
The log odds of being in vocation program vs. in academic program will
decrease by 0.983 if moving from ses="low" to ses="high"\(b_{22}\).
The log odds of being in vocation program vs. in academic program will
increase by 0.291 if moving from ses="low" to ses="middle"\(b_{21}\),
although this coefficient is not signficant.

The ratio of the probability of choosing one outcome category over the probability of
choosing the baseline category is often referred as relative risk (and it is also
sometimes referred as odds as we have just used to described the regression
parameters above). The relative risk is the right-hand side linear equation
exponentiated, leading to the fact that the exponentiated regression coefficients are
relative risk ratios for a unit change in the predictor variable. We can exponentiate
the coefficients from our model to see these risk ratios.
## extract the coefficients from the model and exponentiate
exp(coef(test))

## (Intercept) sesmiddle seshigh write

## general 17.33 0.5867 0.3126 0.9437
## vocation 184.61 1.3383 0.3743 0.8926

The relative risk ratio for a one-unit increase in the variable write is .9437 for
being in general program vs. academic program.
The relative risk ratio switching from ses = 1 to 3 is .3126 for being in general
program vs. academic program.

You can also use predicted probabilities to help you understand the model. You can
calculate predicted probabilities for each of our outcome levels using the fitted
function. We can start by generating the predicted probabilities for the observations
in our dataset and viewing the first few rows
head(pp <- fitted(test))

## academic general vocation

## 1 0.1483 0.3382 0.5135
## 2 0.1202 0.1806 0.6992
## 3 0.4187 0.2368 0.3445
## 4 0.1727 0.3508 0.4765
## 5 0.1001 0.1689 0.7309
## 6 0.3534 0.2378 0.4088

Next, if we want to examine the changes in predicted probability associated with one
of our two variables, we can create small datasets varying one variable while holding
the other constant. We will first do this holding write at its mean and examining the
predicted probabilities for each level of ses.
dses <- data.frame(ses = c("low", "middle", "high"), write = mean(ml$write))
predict(test, newdata = dses, "probs")

## academic general vocation

## 1 0.4397 0.3582 0.2021
## 2 0.4777 0.2283 0.2939
## 3 0.7009 0.1785 0.1206

Another way to understand the model using the predicted probabilities is to look at
the averaged predicted probabilities for different values of the continuous predictor
variable write within each level of ses.
dwrite <- data.frame(ses = rep(c("low", "middle", "high"), each = 41), write = rep(c(30:70),
3))

## store the predicted probabilities for each value of ses and write
pp.write <- cbind(dwrite, predict(test, newdata = dwrite, type = "probs", se = TRUE))

## calculate the mean probabilities within each level of ses

by(pp.write[, 3:5], pp.write$ses, colMeans)

## pp.write$ses: high
## academic general vocation
## 0.6164 0.1808 0.2028
## --------------------------------------------------------
## pp.write$ses: low
## academic general vocation
## 0.3973 0.3278 0.2749
## --------------------------------------------------------
## pp.write$ses: middle
## academic general vocation
## 0.4256 0.2011 0.3733

Sometimes, a couple of plots can convey a good deal amount of information. Using
the predictions we generated for the pp.write object above, we can plot the
predicted probabilities against the writing score by the level of ses for different
levels of the outcome variable.
## melt data set to long for ggplot2
lpp <- melt(pp.write, id.vars = c("ses", "write"), value.name = "probability")
head(lpp) # view first few rows

## ses write variable probability

## 1 low 30 academic 0.09844
## 2 low 31 academic 0.10717
## 3 low 32 academic 0.11650
## 4 low 33 academic 0.12646
## 5 low 34 academic 0.13705
## 6 low 35 academic 0.14828

## plot predicted probabilities across write values for each level of ses
## facetted by program type
ggplot(lpp, aes(x = write, y = probability, colour = ses)) + geom_line() + facet_grid(variable ~
., scales = "free")
Things to consider

The Independence of Irrelevant Alternatives (IIA) assumption: Roughly, the IIA

assumption means that adding or deleting alternative outcome categories
does not affect the odds among the remaining outcomes. There are alternative
modeling methods, such as alternative-specific multinomial probit model, or
nested logit model to relax the IIA assumption.
Diagnostics and model fit: Unlike logistic regression where there are many
statistics for performing model diagnostics, it is not as straightforward to do
diagnostics with multinomial logistic regression models. For the purpose of
detecting outliers or influential data points, one can run separate logit models
and use the diagnostics tools on each model.
Sample size: Multinomial regression uses a maximum likelihood estimation
method, it requires a large sample size. It also uses multiple equations. This
implies that it requires an even larger sample size than ordinal or binary logistic
regression.
Complete or quasi-complete separation: Complete separation means that the
outcome variable separate a predictor variable completely, leading perfect
prediction by the predictor variable.
Perfect prediction means that only one value of a predictor variable is
associated with only one value of the response variable. But you can tell from
the output of the regression coefficients that something is wrong. You can then
do a two-way tabulation of the outcome variable with the problematic variable
to confirm this and then rerun the model without the problematic variable.
Empty cells or small cells: You should check for empty or small cells by doing a
cross-tabulation between categorical predictors and the outcome variable. If a
cell has very few cases (a small cell), the model may become unstable or it
 might not even run at all.

See also

Applied Logistic Regression (Second Edition) (/examples/alr2/) by David

Hosmer and Stanley Lemeshow
An Introduction to Categorical Data Analysis (/examples/icda/) by Alan Agresti
Logistic Regression Models by Joseph M. Hilbe

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