### R Library: Contrast Coding Systems for categorical variables

A categorical variable of K categories is usually entered in a regression analysis as a sequence of K-1 variables, e.g. as a sequence of K-1 dummy variables. Subsequently, the regression coefficients of these K -1 variables correspond to a set of linear hypotheses on the cell means. When coding categorical variables, there are a variety of coding systems we can choose for testing different set of linear hypotheses. On this page, we will cover some of the coding schemes for categorical variables. We will show how these coding schemes are constructed and interpreted.

In R there are four built-in contrasts (dummy, deviation, helmert, orthogonal polynomial) which we will demonstrate. We will also show how to create the coding schemes using a little bit of matrix manipulation. This page is done using R 2.11 and is updated in January, 2011.

#### Coding schemes covered

 Coding Scheme Comparisons made Dummy Coding Compares each level to the reference level, intercept being the cell mean of the reference group Simple Coding Compares each level to the reference level, intercept being the grand mean Deviation Coding Compares each level to the grand mean Orthogonal Polynomial Coding Orthogonal polynomial contrasts Helmert Coding Compare levels of a variable with the mean of the subsequent levels of the variable Reverse Helmert Coding Compares levels of a variable with the mean of the previous levels of the variable Forward Difference Coding Compares adjacent levels of a variable (each level minus the next level) Backward Difference Coding Compares adjacent levels of a variable (each level minus the prior level) User-Defined Coding User-defined contrast

#### The Example Data File

The examples in this page will use data frame called hsb2 and we will focus on the categorical variable race, which has four levels (1 = Hispanic, 2 = Asian, 3 = African American and 4 = Caucasian) and we will use write as our dependent variable.  Although our example uses a variable with four levels, these coding systems work with variables that have more or fewer categories. No matter which coding system you select, you will always have a contrast matrix with one less column than levels of the original variable.  In our example, our categorical variable has four levels so we will have contrast matrices with three columns and four rows.
First, we read in the data frame over the internet and then we create a factor variable, race.f, based on race.

hsb2 = read.table('http://www.ats.ucla.edu/stat/data/hsb2.csv', header=T, sep=",")

#creating the factor variable race.f
hsb2$race.f = factor(hsb2$race, labels=c("Hispanic", "Asian", "African-Am", "Caucasian"))

Before considering any analyses, let's look at the mean of the dependent variable, write, for each level of race.  This will help in interpreting the output from later analyses.

tapply(hsb2$write, hsb2$race.f, mean)
Hispanic Asian African-Am Caucasian
46.45833    58       48.2  54.05517

#### 1. Dummy Coding

Dummy coding is probably the most commonly used coding scheme. It compares each level of the categorical variable to a fixed reference level. For example, we can choose race = 1 as the reference group and compare the mean of variable write for each level of race 2, 3 and 4 to the reference level of 1. This is the default for unordered factors in R.

Dummy Coding
 Level of race race.f1 (1 vs. 2) race.f2 (1 vs. 3) race.f3 (1 vs. 4) 1 (Hispanic) 0 0 0 2 (Asian) 1 0 0 3 (African American) 0 1 0 4 (Caucasian) 0 0 1

#the contrast matrix for categorical variable with four levels
contr.treatment(4)
2 3 4
1 0 0 0
2 1 0 0
3 0 1 0
4 0 0 1

#assigning the treatment contrasts to race.f
contrasts(hsb2$race.f) = contr.treatment(4) #the regression summary(lm(write ~ race.f, hsb2)) Residuals: Min 1Q Median 3Q Max -23.06 -5.458 0.9724 7 18.8 Coefficients: Value Std. Error t value Pr(>|t|) (Intercept) 46.4583 1.8422 25.2184 0.0000 race.f2 11.5417 3.2861 3.5122 0.0006 race.f3 1.7417 2.7325 0.6374 0.5246 race.f4 7.5968 1.9889 3.8197 0.0002 Residual standard error: 9.025 on 196 degrees of freedom Multiple R-Squared: 0.1071 F-statistic: 7.833 on 3 and 196 degrees of freedom, the p-value is 0.00005785 The parameter estimate for the first contrast compares the mean of the dependent variable, write, for levels 1 and 2 yielding 11.5417 and is statistically significant (p<.000). The t-value associated with this test is 3.5122. The results of the second contrast, comparing the mean of write for levels 1 and 3. The expected difference in variable write between group 1 and 3 is 1.7417 and is not statistically significant (t = 0.6374, p = .5246), while the third contrast is statistically significant. Notice that the intercept corresponds to the cell mean for race = Hispanic group. #### 2 Simple Coding The results of simple coding are very similar to dummy coding in that each level is compared to the reference level. The difference in the regression output between dummy coding and simple coding scheme is in the intercepts. In the dummy coding scheme, the intercept corresponds to the cell mean of the reference group, while in the simple coding scheme, the intercept corresponds to the mean of cell means. In our example below, level 1 is the reference level and race.f1 compares level 1 to level 2, race.f2 compares level 1 to level 3, and race.f3 compares level 1 to level 4. For race.f1 the coding is 3/4 for level 2, and -1/4 for all other levels. Likewise, for race.f2 the coding is 3/4 for level 3, and -1/4 for all other levels, and for race.f3 the coding is 3/4 for level 4, and -1/4 for all other levels. The general rule is that the reference group is never coded anything but -1/4 and for each contrast the level that is being contrasted is coded 3/4. Thus, for the first contrast it is level 2 which is coded 3/4 and all other level are -1/4. Since there are four groups and the values have to add to one there must be three levels coded as -1/4 and one level as 3/4. SIMPLE Coding  Level of race race.f1 (1 vs 2) race.f2 (1 vs.3) race.f3 (1 vs. 4) 1 (Hispanic) -1/4 -1/4 -1/4 2 (Asian) 3/4 -1/4 -1/4 3 (African American) -1/4 3/4 -1/4 4 (Caucasian) -1/4 -1/4 3/4 Below we show the more general rule for creating this kind of coding scheme using regression coding, where k is the number of levels of the categorical variable (in the case of the variable race.f k = 4). SIMPLE Coding  Level of race level 1 vs. 2 level 1 vs. 3 level 1 vs. 4 1 (Hispanic) -1 / k -1 / k -1 / k 2 (Asian) (k-1) / k -1 / k -1 / k 3 (African American) -1 / k (k-1) / k -1 / k 4 (Caucasian) -1 / k -1 / k (k-1) / k Let's create the contrast matrix manually using the scheme shown above. Essentially, the difference between the dummy coding scheme and the simple coding scheme is a constant matrix whose each element is 1/k if our categorical variable has k levels. #creating the contrast matrix manually by modifying the dummy coding scheme c<-contr.treatment(4) my.coding<-matrix(rep(1/4, 12), ncol=3) my.simple<-c-my.coding my.simple  2 3 4 1 -0.25 -0.25 -0.25 2 0.75 -0.25 -0.25 3 -0.25 0.75 -0.25 4 -0.25 -0.25 0.75 contrasts(hsb2$race.f)<-my.simple
summary(lm(write~race.f, hsb2))

Residuals:
Min     1Q Median 3Q  Max
-23.06 -5.458 0.9724  7 18.8

Coefficients:
Value Std. Error t value Pr(>|t|)
(Intercept) 51.6784  0.9821    52.6191  0.0000
race.f1 11.5417  3.2861     3.5122  0.0006
race.f2  1.7417  2.7325     0.6374  0.5246
race.f3  7.5968  1.9889     3.8197  0.0002

Residual standard error: 9.025 on 196 degrees of freedom
Multiple R-Squared: 0.1071
F-statistic: 7.833 on 3 and 196 degrees of freedom, the p-value is 0.00005785 

The interpretation of this output is almost the same as for the case of dummy coding. The difference lies in the intercept.
The intercept in this case is 51.6784 = (46.45833 + 58  + 48.2 + 54.05517)/4, which is the mean of cell means, sometimes referred as grand mean.

#### 3 Deviation Coding

This coding system compares the mean of the dependent variable for a given level to the overall mean of the dependent variable.  In our example below, the first comparison compares level 1 (Hispanics) to all levels of race, the second comparison compares level 2 (Asians) to all levels of race, and the third comparison compares level 3 (African Americans) to all levels of race.

As you see in the example below, the regression coding is accomplished by assigning 1 to level 1 for the first comparison (because level 1 is the level to be compared to all others), a 1 to level 2 for the second comparison (because level 2 is to be compared to all others), and 1 to level 3 for the third comparison (because level 3 is to be compared to all others).  Note that a  -1 is assigned to level 4 for all three comparisons (because it is the level that is never compared to the other levels) and all other values are assigned a 0.  This regression coding scheme yields the comparisons described above.
We will not create the contrast matrix manually because the contr.sum function creates it for us.

DEVIATION Coding
 Level of race Level 1 v. Mean Level 2 v. Mean Level 3 v. Mean 1 (Hispanic) 1 0 0 2 (Asian) 0 1 0 3 (African American) 0 0 1 4 (Caucasian) -1 -1 -1

#the contrast matrix for categorical variable with four levels
contr.sum(4)
[,1] [,2] [,3]
1    1    0    0
2    0    1    0
3    0    0    1
4   -1   -1   -1

#assigning the deviation contrasts to race.f
contrasts(hsb2$race.f) = contr.sum(4) #the regression summary(lm(write ~ race.f, hsb2)) Coefficients: Value Std. Error t value Pr(>|t|) (Intercept) 51.6784 0.9821 52.6191 0.0000 race.f1 -5.2200 1.6314 -3.1997 0.0016 race.f2 6.3216 2.1603 2.9263 0.0038 race.f3 -3.4784 1.7323 -2.0079 0.0460 The contrast estimate is the mean for level 1 minus the grand mean. However, this grand mean is not the mean of the dependent variable that is listed in the output of the means command above. Rather it is the mean of means of the dependent variable at each level of the categorical variable: (46.4583 + 58 + 48.2 + 54.0552) / 4 = 51.678375. This contrast estimate is then 46.4583 - 51.678375 = -5.220. The difference between this value and zero (the null hypothesis that the contrast coefficient is zero) is statistically significant (p = .0016), and the t-value for this test of -3.20. The results for the next two contrasts were computed in a similar manner. #### 4 Orthogonal Polynomial Coding Orthogonal polynomial coding is a form of trend analysis in that it is looking for the linear, quadratic and cubic trends in the categorical variable. This type of coding system should be used only with an ordinal variable in which the levels are equally spaced. Examples of such a variable might be income or education. The table below shows the contrast coefficients for the linear, quadratic and cubic trends for the four levels. In R it is not necessary to compute these values since this contrast can be obtained for any categorical variable by using the contr.poly function. This is also the default contrast used for ordered factor variables. For the purpose of illustration, let's create an ordered categorical variable based on the variable read. Notice that this is the only example on this page that does not use race as the categorical variable, since it is not ordered. hsb2$readcat<-cut(hsb2$read, 4, ordered = TRUE) table(readcat) readcat (28,40] (40,52] (52,64] (64,76] 22 93 55 30  tapply(hsb2$write, hsb2$readcat, mean) (28,40] (40,52] (52,64] (64,76] 42.77273 49.97849 56.56364 61.83333  POLYNOMIAL coding  Level of readcat Linear (readcat.L) Quadratic (readcat.Q) Cubic (readcat.C) 1 (28,40] -.671 .5 -.224 2 (40,52] -.224 -.5 .671 3 (52,64] .224 -.5 -.671 4 (64,76] .671 .5 .224 #the contrast matrix for categorical variable with four levels contr.poly(4) .L .Q .C 1 -0.6708204 0.5 -0.2236068 2 -0.2236068 -0.5 0.6708204 3 0.2236068 -0.5 -0.6708204 4 0.6708204 0.5 0.2236068 #assigning the orthogonal polynomial contrasts to readcat contrasts(hsb2$readcat) = contr.poly(4)

Call:
lm(formula = write ~ readcat, data = hsb2)

Residuals:
Min      1Q  Median      3Q     Max
-18.978  -5.824   1.227   5.436  17.022

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)  52.7870     0.6339  83.268   <2e-16 ***
readcat.L    14.2587     1.4841   9.607   <2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 7.726 on 196 degrees of freedom
Multiple R-squared: 0.3456,     Adjusted R-squared: 0.3356
F-statistic: 34.51 on 3 and 196 DF,  p-value: < 2.2e-16 

The regression results indicate a strong linear effect of readcat on the outcome variable write. There is not a significant quadratic effect nor a cubic effect of readcat on the outcome variable write.

#### 5 Helmert Coding

Helmert coding compares each level of a categorical variable to the mean of the subsequent levels.  Hence, the first contrast compares the mean of the dependent variable for level 1 of race with the mean of all of the subsequent levels of race (levels 2, 3, and 4), the second contrast compares the mean of the dependent variable for level 2 of race with the mean of all of the subsequent levels of race (levels 3 and 4), and the third contrast compares the mean of the dependent variable for level 3 of race with the mean of all of the subsequent levels of race (level 4).

In R there is a built-in function, contr.helmert, which, up to a scale,  corresponds to the reverse Helmert coding discussed in next section.  We will create the contrast matrix for Helmert coding manually below.

Below we see an example of Helmert regression coding.  For the first comparison (comparing level 1 with levels 2, 3 and 4) the codes are 3/4 and -1/4 -1/4 -1/4.  The second comparison compares level 2 with levels 3 and 4 and is coded 0 2/3 -1/3 -1/3.  The third comparison compares level 3 to level 4 and is coded 0 0 1/2 -1/2.

HELMERT Coding
 race.f1 race.f2 race.f3 Level of Race Level 1 v. Later Level 2 v. Later Level 3 v. Later 1 (Hispanic) 3/4 0 0 2 (Asian) -1/4 2/3 0 3 (African American) -1/4 -1/3 1/2 4 (Caucasian) -1/4 -1/3 -1/2

#helmert for factor variable with 4 levels
my.helmert = matrix(c(3/4, -1/4, -1/4, -1/4, 0, 2/3, -1/3, -1/3, 0, 0, 1/
2, -1/2), ncol = 3)
my.helmert
[,1]       [,2] [,3]
[1,]  0.75  0.0000000  0.0
[2,] -0.25  0.6666667  0.0
[3,] -0.25 -0.3333333  0.5
[4,] -0.25 -0.3333333 -0.5

#assigning the new helmert coding to race.f
contrasts(hsb2$race.f) = my.helmert #the regression summary(lm(write ~ race.f, hsb2)) Coefficients: Value Std. Error t value Pr(>|t|) (Intercept) 51.6784 0.9821 52.6191 0.0000 race.f1 -6.9601 2.1752 -3.1997 0.0016 race.f2 6.8724 2.9263 2.3485 0.0198 race.f3 -5.8552 2.1528 -2.7198 0.0071 The contrast estimate for the comparison between level 1 and the remaining levels is calculated by taking the mean of the dependent variable for level 1 and subtracting the mean of the dependent variable for levels 2, 3 and 4: 46.4583 - [(58 + 48.2 + 54.0552) / 3] = -6.960, which is statistically significant. This means that the mean of write for level 1 of race is statistically significantly different from the mean of write for levels 2 through 4. To calculate the contrast coefficient for the comparison between level 2 and the later levels, you subtract the mean of the dependent variable for levels 3 and 4 from the mean of the dependent variable for level 2: 58 - [(48.2 + 54.0552) / 2] = 6.872, which is statistically significant. The contrast estimate for the comparison between level 3 and level 4 is the difference between the mean of the dependent variable for the two levels: 48.2 - 54.0552 = -5.855, which is also statistically significant. #### 6 Reverse Helmert Coding Reverse Helmert coding (also know as difference coding) is just the opposite of Helmert coding: instead of comparing each level of categorical variable to the mean of the subsequent level(s), each is compared to the mean of the previous level(s). In our example, the first contrast codes the comparison of the mean of the dependent variable for level 2 of race to the mean of the dependent variable for level 1 of race. The second comparison compares the mean of the dependent variable level 3 of race with both levels 1 and 2 of race, and the third comparison compares the mean of the dependent variable for level 4 of race with levels 1, 2 and 3. The regression coding for reverse Helmert coding is shown below. For the first comparison, where the first and second level are compared, race.f1 is coded -1/2 and 1/2 and 0 otherwise. For the second comparison, the values of race.f2 are coded -1/3 -1/3 2/3 and 0. Finally, for the third comparison, the values of race.f3 are coded -1/4 -1/4 -/14 and 3/4. The built-in Helmert coding in R is equivalent to this coding scheme up to a constant in each column. So both give the same significance test. We will show both ways below Reverse HELMERT Coding  race.f1 race.f2 race.f3 Level of Race Level 2 v. 1 Level 3 v. 1 and 2 Level 4 v. 1, 2 and 3 1 (Hispanic) -1/2 -1/3 -1/4 2 (Asian) 1/2 -1/3 -1/4 3 (African American) 0 2/3 -1/4 4 (Caucasian) 0 0 3/4 # manually reverse helmert for factor variable with 4 leves my.rev.helmert = matrix(c(-1/2, 1/2, 0, 0, -1/3, -1/3, 2/3, 0, -1/4, -1/4, -1/4, 3/4), ncol = 3) my.rev.helmert [,1] [,2] [,3] [1,] -0.5 -0.3333333 -0.25 [2,] 0.5 -0.3333333 -0.25 [3,] 0.0 0.6666667 -0.25 [4,] 0.0 0.0000000 0.75 #assigning the reverse helmert coding to race.f contrasts(hsb2$race.f) = my.rev.helmert
#the regression
summary(lm(write ~ race.f, hsb2))

Coefficients:
Value Std. Error  t value Pr(>|t|)
(Intercept)  51.6784   0.9821    52.6191   0.0000
race.f1  11.5417   3.2861     3.5122   0.0006
race.f2  -4.0292   2.6024    -1.5483   0.1232
race.f3   3.1691   1.4880     2.1298   0.0344
# using built-in reverse Helmert coding
contrasts(hsb2$race.f) = contr.helmert(4) summary(lm(write ~ race.f, hsb2)) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 51.6784 0.9821 52.619 < 2e-16 *** race.f1 5.7708 1.6431 3.512 0.000552 *** race.f2 -1.3431 0.8675 -1.548 0.123170 race.f3 0.7923 0.3720 2.130 0.034439 *  The contrast estimate for the first comparison shown in this output was calculated by subtracting the mean of the dependent variable for level 2 of the categorical variable from the mean of the dependent variable for level 1: 58 - 46.4583 = 11.542. This result is statistically significant. The contrast estimate for the second comparison (between level 3 and the previous levels) was calculated by subtracting the mean of the dependent variable for levels 1 and 2 from that of level 3: 48.2 - [(46.4583 + 58) / 2] = -4.029. This result is not statistically significant, meaning that there is not a reliable difference between the mean of write for level 3 of race compared to the mean of write for levels 1 and 2 (Hispanics and Asians). As noted above, this type of coding system does not make much sense for a nominal variable such as race. For the comparison of level 4 and the previous levels, you take the mean of the dependent variable for the those levels and subtract it from the mean of the dependent variable for level 4: 54.0552 - [(46.4583 + 58 + 48.2) / 3] = 3.169. This result is statistically significant. #### 7 Forward Difference Coding In this coding system, the mean of the dependent variable for one level of the categorical variable is compared to the mean of the dependent variable for the next (adjacent) level. In our example below, the first comparison compares the mean of write for level 1 with the mean of write for level 2 of race (Hispanics minus Asians). The second comparison compares the mean of write for level 2 minus level 3, and the third comparison compares the mean of write for level 3 minus level 4. This type of coding may be useful with either a nominal or an ordinal variable. For the first comparison, where the first and second levels are compared, race.f1 is coded 3/4 for level 1 and the other levels are coded -1/4. For the second comparison where level 2 is compared with level 3, race.f2 is coded 1/2 1/2 -1/2 -1/2, and for the third comparison where level 3 is compared with level 4, race.f3 is coded 1/4 1/4 1/4 -3/4. FORWARD DIFFERENCE coding  race.f1 race.f2 race.f3 Level of race Level 1 v. Level 2 Level 2 v. Level 3 Level 3 v. Level 4 1 (Hispanic) 3/4 1/2 1/4 2 (Asian) -1/4 1/2 1/4 3 (African American) -1/4 -1/2 1/4 4 (Caucasian) -1/4 -1/2 -3/4 The general rule for this regression coding scheme is shown below, where k is the number of levels of the categorical variable (in this case k = 4). FORWARD DIFFERENCE regression coding  contrast 1 contrast 2 contrast 3 Level of race Level 1 v. Level 2 Level 2 v. Level 3 Level 3 v. Level 4 1 (Hispanic) (k-1)/k (k-2)/k (k-3)/k 2 (Asian) -1/k (k-2)/k (k-3)/k 3 (African American) -1/k -2/k (k-3)/k 4 (Caucasian) -1/k -2/k -3/k #forward difference for factor variable with 4 leves my.forward.diff = matrix(c(3/4, -1/4, -1/4, -1/4, 1/2, 1/2, -1/2, -1/2, 1/ 4, 1/4, 1/4, -3/4), ncol = 3) my.forward.diff [,1] [,2] [,3] [1,] 0.75 0.5 0.25 [2,] -0.25 0.5 0.25 [3,] -0.25 -0.5 0.25 [4,] -0.25 -0.5 -0.75 #assigning the forward difference coding to race.f contrasts(hsb2$race.f) = my.forward.diff
#the regression
summary(lm(write ~ race.f, hsb2))

Coefficients:
Value Std. Error  t value Pr(>|t|)
(Intercept)  51.6784   0.9821    52.6191   0.0000
race.f1 -11.5417   3.2861    -3.5122   0.0006
race.f2   9.8000   3.3878     2.8927   0.0043
race.f3  -5.8552   2.1528    -2.7198   0.0071

With this coding system, adjacent levels of the categorical variable are compared.  Hence, the mean of the dependent variable at level 1 is compared to the mean of the dependent variable at level 2:  46.4583 - 58 = -11.542, which is statistically significant.  For the comparison between levels 2 and 3, the calculation of the contrast coefficient would be 58 - 48.2 = 9.8, which is also statistically significant.  Finally, comparing levels 3 and 4, 48.2 - 54.0552 = -5.855, a statistically significant difference.  One would conclude from this that each adjacent level of race is statistically significantly different.

#### 8 Backward Difference Coding

In this coding system, the mean of the dependent variable for one level of the categorical variable is compared to the mean of the dependent variable for the prior adjacent level.  In our example below, the first comparison compares the mean of write for level 2 with the mean of write for level 1 of race (Hispanics minus Asians).  The second comparison compares the mean of write for level 3 minus level 2, and the third comparison compares the mean of write for level 4 minus level 3.  This type of coding may be useful with either a nominal or an ordinal variable.

For the first comparison, where the first and second levels are compared, race.f1 is coded -3/4 for level 1 while the other levels are coded 1/4.  For the second comparison where level 2 is compared with level 3, race.f2 is coded -1/2 -1/2 1/2 1/2, and for the third comparison where level 3 is compared with level 4, race.f3 is coded -1/4 -1/4 -1/4 3/4.

BACKWARD DIFFERENCE Coding
 race.f1 race.f2 race.f3 Level of race Level 2 v. Level 1 Level 3 v. Level 2 Level 4 v. Level 3 1 (Hispanic) - 3/4 -1/2 -1/4 2 (Asian) 1/4 -1/2 -1/4 3 (African American) 1/4 1/2 -1/4 4 (Caucasian) 1/4 1/2 3/4

The general rule for this regression coding scheme is shown below, where k is the number of levels of the categorical variable (in this case, k = 4).

BACKWARD DIFFERENCE Coding
 contrast 1 contrast 2 contrast 3 Level of race Level 1 v. Level 2 Level 2 v. Level 3 Level 3 v. Level 4 1 (Hispanic) -(k-1)/k -(k-2)/k -(k-3)/k 2 (Asian) 1/k -(k-2)/k -(k-3)/k 3 (African American) 1/k 2/k -(k-3)/k 4 (Caucasian) 1/k 2/k 3/k

#backward difference for factor variable with 4 leves
my.backward.diff = matrix(c(-3/4, 1/4, 1/4, 1/4, -1/2, -1/2, 1/2, 1/2,
-1/4, -1/4, -1/4, 3/4), ncol = 3)
my.backward.diff
[,1] [,2]  [,3]
[1,] -0.75 -0.5 -0.25
[2,]  0.25 -0.5 -0.25
[3,]  0.25  0.5 -0.25
[4,]  0.25  0.5  0.75

#assigning the backward difference coding to race.f
contrasts(hsb2$race.f) = my.backward.diff #the regression summary(lm(write ~ race.f, hsb2)) Coefficients: Value Std. Error t value Pr(>|t|) (Intercept) 51.6784 0.9821 52.6191 0.0000 race.f1 11.5417 3.2861 -3.5122 0.0006 race.f2 -9.8000 3.3878 -2.8927 0.0043 race.f3 5.8552 2.1528 2.7198 0.0071 With this coding system, adjacent levels of the categorical variable are compared, with each level compared to the prior level. Hence, the mean of the dependent variable at level 2 is compared to the mean of the dependent variable at level 1: 58 - 46.4583 = 11.542, which is statistically significant. For the comparison between levels 3 and 2, the calculation of the contrast coefficient is 48.2 - 58 = -9.8, which is also statistically significant. Finally, comparing levels 4 and 3, 54.0552 - 48.2 = 5.855, a statistically significant difference. One would conclude from this that each adjacent level of race is statistically significantly different. #### 9 User Defined Coding In R it is possible to use any general kind of coding scheme. For our example, we would like to make the following three comparisons: 1) level 1 to level 3 2) level 2 to levels 1 and 4 3) levels 1 and 2 to levels 3 and 4. In order to compare level 1 to level 3, we use the contrast coefficients 1 0 -1 0. To compare level 2 to levels 1 and 4 we use the contrast coefficients -1/2 1 0 -1/2. Finally, to compare levels 1 and 2 with levels 3 and 4 we use the coefficients 1/2 1/2 -1/2 -1/2. All these have been expressed in terms of cell means. For convenience of the calculation, we will assume that the intercept corresponds to the mean of cell means. So our initial contrast matrix looks like the following, defined as mat. The final contrast matrix (or coding scheme) turns out to be the inverse of mat transposed. #initial contrast matrix including the constant term mat = matrix(c(1/4, 1/4, 1/4, 1/4, 1, 0, -1, 0, -1/2, 1, 0, -1/2, -1/2, -1/2, 1/2, 1/2), ncol = 4) mat [,1] [,2] [,3] [,4] [1,] 0.25 1 -0.5 -0.5 [2,] 0.25 0 1.0 -0.5 [3,] 0.25 -1 0.0 0.5 [4,] 0.25 0 -0.5 0.5 mymat = solve(t(mat)) mymat [,1] [,2] [,3] [,4] [1,] 1 -0.5 -1 -1.5 [2,] 1 0.5 1 0.5 [3,] 1 -1.5 -1 -1.5 [4,] 1 1.5 1 2.5 #remove the intercept (constant) term my.contrasts<-mymat[,2:4] contrasts(hsb2$race.f) = my.contrasts
summary(lm(write ~ race.f, hsb2))

Call:
lm(formula = write ~ race.f, data = hsb2)

Residuals:
Min       1Q   Median       3Q      Max
-23.0552  -5.4583   0.9724   7.0000  18.8000

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)  51.6784     0.9821  52.619   <2e-16 ***
race.f1       1.7417     2.7325   0.637   0.5246
race.f2       6.8724     2.9263   2.348   0.0198 *
race.f3      -2.8432     1.9642  -1.448   0.1494
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 9.025 on 196 degrees of freedom
Multiple R-squared: 0.1071,     Adjusted R-squared: 0.0934
F-statistic: 7.833 on 3 and 196 DF,  p-value: 5.785e-05 

The intercept corresponds to the mean of the cell means as shown earlier. The coefficient for race.f1 corresponds to the difference in the mean of the variable write between group 3 and group 1. Similarly, the coefficient for race.f2 corresponds to the difference between group 2 and the mean of group 1 and 4, and so on.

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