Menu Home

Modeling Trick: Impact Coding of Categorical Variables with Many Levels

One of the shortcomings of regression (both linear and logistic) is that it doesn’t handle categorical variables with a very large number of possible values (for example, postal codes). You can get around this, of course, by going to another modeling technique, such as Naive Bayes; however, you lose some of the advantages of regression — namely, the model’s explicit estimates of variables’ explanatory value, and explicit insight into and control of variable to variable dependence.

Here we discuss one modeling trick that allows us to keep categorical variables with a large number of values, and at the same time retain much of logistic regression’s power.

For this example, we will use a data set that contains all the police incidents (except homicide and manslaughter) that were reported in San Francisco for the month of June, 2012. The link to the most recent past-month’s incident data is here. The data set contains the date, time of day, and day of week that each incident was reported, along with the incident’s category, a brief description, and location (as police district, lat-long coordinates, and address to the nearest block).

Supposed we are interested in predicting the likelihood of a given incident being a violent crime, as a function of time, day, and location. We will define violent crimes ourselves, as assault, robbery, rape, kidnapping, and purse snatching. Here is the R code:

# June 2012
incidents = read.table("Sfpd_Incident_Last_Month.csv", header=T, sep=",", 

# violent - LARCENY/THEFT: 
#           -- Descript = "GRAND THEFT PURSESNATCH" 
#                         "ATTEMPTED GRAND THEFT PURSESNATCH"
#           ASSAULT
#           ROBBERY
#           KIDNAPPING

# Create violent indicator
incidents$violent = with(incidents, 
                        Category %in% c("ASSAULT", "ROBBERY", 
                                        "SEX OFFENSES, FORCIBLE", "KIDNAPPING") 
                        | Descript %in% 
                          c("GRAND THEFT PURSESNATCH", 
                            "ATTEMPTED GRAND THEFT PURSESNATCH"))

# FALSE      TRUE 
# 0.8733564 0.1266436

We see that the month’s average rate of violent incidents (excluding homicide/manslaughter) was about 13%. Is there a relationship between violence and the day of week?

modelDay = glm("violent ~ DayOfWeek", data=incidents, 

We see that the relationship is not strong at all.


Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.89213 0.07762 -24.377 <2e-16 ***
DayOfWeekMonday -0.02830 0.11874 -0.238 0.8116
DayOfWeekSaturday -0.02067 0.10941 -0.189 0.8502
DayOfWeekSunday 0.19863 0.11116 1.787 0.0739 .
DayOfWeekThursday -0.12835 0.12112 -1.060 0.2893
DayOfWeekTuesday -0.16031 0.12359 -1.297 0.1946
DayOfWeekWednesday -0.20421 0.12055 -1.694 0.0903 .

Signif. codes: 0 ‘’ 0.001 ‘’ 0.01 ‘’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

Null deviance: 6588.4 on 8669 degrees of freedom
Residual deviance: 6573.7 on 8663 degrees of freedom
AIC: 6587.7

What about time of day? The dataset records the time on the minute resolution; we will just look at the hourly resolution. We will call this model modelHr.

incidents$TimeHr = substr(incidents$Time, 1,2)
modelHr = glm("violent ~ TimeHr", data=incidents, family=binomial(link="logit"))

A little stronger, but still not very strong. The rate of violent incidents increases significantly (relative to midnight) at about 1 am; the rate is significantly lower than at midnight around late morning and noon.

              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -1.69669    0.13191 -12.862  < 2e-16 ***
  TimeHr01     0.58410    0.19004   3.074  0.00212 ** 
  TimeHr02     0.36289    0.21475   1.690  0.09106 .  
  TimeHr03     0.48928    0.24939   1.962  0.04977 *  
  TimeHr04     0.32365    0.28873   1.121  0.26232    
  TimeHr05    -0.03791    0.30957  -0.122  0.90254    
  TimeHr06    -0.55460    0.35763  -1.551  0.12096    
  TimeHr07    -0.39458    0.26627  -1.482  0.13837    
  TimeHr08    -0.31428    0.22528  -1.395  0.16299    
  TimeHr09    -0.44337    0.23940  -1.852  0.06403 .  
  TimeHr10    -0.32360    0.21912  -1.477  0.13972    
  TimeHr11    -0.61794    0.22513  -2.745  0.00605 ** 
  TimeHr12    -0.54447    0.20232  -2.691  0.00712 ** 
  TimeHr13    -0.39928    0.20580  -1.940  0.05237 .  
  TimeHr14    -0.46279    0.20539  -2.253  0.02424 *  
  TimeHr15    -0.33861    0.19483  -1.738  0.08222 .  
  TimeHr16    -0.39278    0.18848  -2.084  0.03717 *  
  TimeHr17    -0.45359    0.18741  -2.420  0.01550 *  
  TimeHr18    -0.46279    0.18971  -2.439  0.01471 *  
  TimeHr19    -0.40045    0.19352  -2.069  0.03852 *  
  TimeHr20    -0.19632    0.19043  -1.031  0.30258    
  TimeHr21     0.03771    0.19051   0.198  0.84309    
  TimeHr22     0.05408    0.17827   0.303  0.76162    
  TimeHr23    -0.37506    0.20095  -1.866  0.06197 .  
   Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 
 (Dispersion parameter for binomial family taken to be 1)
 Null deviance: 6588.4  on 8669  degrees of freedom
 Residual deviance: 6493.6  on 8646  degrees of freedom
 AIC: 6541.6

Here’s the graph. It’s interesting to see that the rate of incidents (violent or otherwise) peaks at about 5 pm.

ggplot(incidents, aes(x=TimeHr, fill=violent)) + geom_bar()


Now we add location. A visual inspection tells us that there are indeed violent incident “hot-spots”, even relative to regions where incidents in general are more frequent.

[UPDATE March 8, 2013: Thanks go to Prof. Dr. Markus Löcher, author of the RgoogleMaps package, for the improved map image. I’ve replaced the original map code and image with his.]

bb = qbbox(lat = incidents$Y, lon = incidents$X);

##download the map:
MyMap = GetMap.bbox(bb$lonR, bb$latR, destfile = "SanFrancisco.png",
tmp = PlotOnStaticMap(MyMap, lat = incidents$Y[!incidents$violent], 
                            lon = incidents$X[!incidents$violent],
                      cex=0.75,pch=20,col=rgb(0,0,1,0.5), add=FALSE);
tmp =PlotOnStaticMap(MyMap, lat = incidents$Y[incidents$violent], 
                            lon = incidents$X[incidents$violent],
                      cex=0.75,pch=20,col=rgb(1,0,0,0.5), add=TRUE);


The bad news is that location (at the block level) is a variable with a lot of possible values.

# [1] "0 Block of COLLEGE TR"     "1400 Block of KIRKWOOD CT" "900 Block of POLK ST"     
# [4] "1200 Block of LAGUNA ST"   "2400 Block of 47TH AV"     "3900 Block of ALEMANY BL" 
> length(unique(incidents$Address))
[1] 3915
# out of 8670 rows

We can try using a coarser variable, like police district, but we would see that the model is still not very predictive

modelTimeDistrict = glm("violent ~ TimeHr + PdDistrict", data=incidents, family=binomial(link="logit"))
1 - modelTimeDistrict$deviance/modelTimeDistrict$null.deviance
[1] 0.0228061

In fact, using time of day and district only reduces the deviance from the “null model” — that is, simply predicting the global rate of violent incidents — by 2%. There is always the danger, of course, that using block-level data will lead to overfit, but let’s give it a try, anyway.

To do that, we replace the categorical variable with a submodel that returns the probability of a violent incident, conditional on each category value. (in this case, the city block). In our case, it’s possible that there are city blocks that had no reported incidents — this month. That may change next month. We guard against this contingency by smoothing novel levels to the grand average. We choose to call this trick impact coding because it summarizes the impact of each category value on the outcome. (This is not standard terminology.)

# return a model of the conditional probability 
# of dependent variable (depvar) by level 
# assumes outcome is logical and not null
impactModel = function(xcol, depvar) {
  n = length(depvar)
  p = sum(depvar)/n
  # duplicate output for NA (average NA towards grand uniform average) 
  x = c(xcol,xcol)
  y = c(depvar, depvar)
  x[(1+n):(2*n)] = NA
  levelcounts = table(x, y, useNA="always")
  condprobmodel = (levelcounts[,2]+p)/(levelcounts[,1]+levelcounts[,2]+1.0) 
  # apply model example: applyImpactModel(condprobmodel,data[,varname])

# apply model to column to essentially return condprobmodel[rawx]
# both NA's and new levels are smoothed to original grand average 
applyImpactModel = function(condprobmodel, xcol) {
  naval = condprobmodel[]
  dim = length(xcol)
  condprobvec = numeric(dim) + naval
  for(nm in names(condprobmodel)) {
    if(! {
      condprobvec[xcol==nm] = condprobmodel[nm]

# convert Address variable to its impact model outcome
impact_addr_mod = impactModel(incidents$Address, incidents$violent)
incidents$impactAddr = applyImpactModel(impact_addr_mod, incidents$Address)

# check the performance of the impact model --  much more predictive than the district model
positive = incidents$violent
modelDeviance = 2*(sum(-log(incidents$impactAddr[positive]))+ 
[1] 3794.362
p = mean(positive)
nullDeviance = 2*(sum(positive)*(-log(p)) + sum(!positive)*(-log(1-p)))

1 -  modelDeviance/nullDeviance
# [1] 0.4240879

The resulting impact model alone explains 42% of the null deviance. Can we explain a little more by adding back time? We will call this model modelHrAddr.

modelHrAddr = glm("violent ~  impactAddr + TimeHr", data=incidents, family=binomial(link="logit"))

Location is the most predictive variable; but even after controlling for location, the proportion of violent incidents peaks in the early hours of the morning: from about 1 am to 4 am. The resulting model explains about 48% of the null deviance. Not great, but not bad, either.

   glm(formula = "violent ~  impactAddr + TimeHr", family = binomial(link = "logit"), 
       data = incidents)
 Deviance Residuals: 
   Min       1Q   Median       3Q      Max  
 -2.8946  -0.2529  -0.2018  -0.1629   2.9599  
             Estimate Std. Error z value   Pr(>|z|)    
 (Intercept) -4.53184    0.21611 -20.970   <2e-16 ***
 impactAddr  11.85131    0.29659  39.959    1 - modelHrAddr$deviance/modelHrAddr$null.deviance
 [1] 0.4795713

When we compare modelHr and modeHrAddr, we see that, overall, the time coefficients of modelHrAddr are less significant than those of modelHr. This indicates some correlation between time and location. This is where logistic regression’s handling of dependence is useful — a Naive Bayes model that used time and location would tend to overestimate the proportion of violent incidents at hotspots. The logistic regression model can compensate for these dependencies, and provides more accurate estimates.

And even though the impactAddr variable is less transparent than the corresponding categorical variable, the effect of time is clearer, since we have pulled out the effect of location. This is how we can make statements like “time has the following impact on the proportion of violent incidents, even after controlling for address,” even though address is a very large categorical variable, which is itself subject to possible overfitting — as well as being too large for typical logistic regression code.

Thus, while impact coding has limitations, it lets us do more than we would otherwise be able to do, especially with other categorical variables.

[EDIT: We have since automated these steps in a library called vtreat. Also, we now strongly recommend splitting your training set into two pieces, and using one piece for the vtreat::prepare() step, and only the other disjoint portion of the training data for model construction. The issue is any row of data examined during vtreat::prepare() is no longer exchangeable with even test data (let alone future data), especially for impact codes for very large categorical variables. Models trained on rows used to build the variable encodings tend to over-estimate effect sizes of the sub-models (or treated variables), under-estimate degrees of freedom, and get significances wrong. So: shared rows introduce an undesirable bias; in large data situations we can remove this bias by reserving rows for different tasks (at a cost of a small increase in variance). ]

Categories: Expository Writing Tutorials

Tagged as:

Nina Zumel

Data scientist with Win Vector LLC. I also dance, read ghost stories and folklore, and sometimes blog about it all.

4 replies

  1. Fine article :) i think you should use spatial models (eg. sar, gwr)? Using them (models) you can take into account spatial and time factor.

%d bloggers like this: