R Data Analysis Examples: Tobit Models

The tobit model, also called a censored regression model, is designed to estimate linear relationships between variables when there is either left- or right-censoring in the dependent variable (also known as censoring from below and above, respectively). Censoring from above takes place when cases with a value at or above some threshold, all take on the value of that threshold, so that the true value might be equal to the threshold, but it might also be higher. In the case of censoring from below, values those that fall at or below some threshold are censored.

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 If you do not have a package installed, run: install.packages("packagename"), or if you see the version is out of date, run: update.packages().


Version info: Code for this page was tested in R Under development (unstable) (2012-11-16 r61126)
On: 2012-12-15
With: VGAM 0.9-0; GGally 0.4.2; reshape 0.8.4; plyr 1.8; ggplot2 0.9.3; knitr 0.9

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 and potential follow-up analyses.

Examples of Tobit Analysis

Example 1. In the 1980s there was a federal law restricting speedometer readings to no more than 85 mph. So if you wanted to try and predict a vehicle's top-speed from a combination of horse-power and engine size, you would get a reading no higher than 85, regardless of how fast the vehicle was really traveling. This is a classic case of right-censoring (censoring from above) of the data. The only thing we are certain of is that those vehicles were traveling at least 85 mph.

Example 2. A research project is studying the level of lead in home drinking water as a function of the age of a house and family income. The water testing kit cannot detect lead concentrations below 5 parts per billion (ppb). The EPA considers levels above 15 ppb to be dangerous. These data are an example of left-censoring (censoring from below).

Example 3. Consider the situation in which we have a measure of academic aptitude (scaled 200-800) which we want to model using reading and math test scores, as well as, the type of program the student is enrolled in (academic, general, or vocational). The problem here is that students who answer all questions on the academic aptitude test correctly receive a score of 800, even though it is likely that these students are not "truly" equal in aptitude. The same is true of students who answer all of the questions incorrectly. All such students would have a score of 200, although they may not all be of equal aptitude.

Description of the Data

For our data analysis below, we are going to expand on Example 3 from above. We have generated hypothetical data, which can be obtained from our website from within R. Note that R requires forward slashes, not back slashes when specifying a file location even if the file is on your hard drive.

dat <- read.csv("http://www.ats.ucla.edu/stat/data/tobit.csv")

The dataset contains 200 observations. The academic aptitude variable is apt, the reading and math test scores are read and math respectively. The variable prog is the type of program the student is in, it is a categorical (nominal) variable that takes on three values, academic (prog = 1), general (prog = 2), and vocational (prog = 3). The variable id is an identification variable.

Now let's look at the data descriptively. Note that in this dataset, the lowest value of apt is 352. That is, no students received a score of 200 (the lowest score possible), meaning that even though censoring from below was possible, it does not occur in the dataset.

##        id             read           math              prog    
##  Min.   :  1.0   Min.   :28.0   Min.   :33.0   academic  : 45  
##  1st Qu.: 50.8   1st Qu.:44.0   1st Qu.:45.0   general   :105  
##  Median :100.5   Median :50.0   Median :52.0   vocational: 50  
##  Mean   :100.5   Mean   :52.2   Mean   :52.6                   
##  3rd Qu.:150.2   3rd Qu.:60.0   3rd Qu.:59.0                   
##  Max.   :200.0   Max.   :76.0   Max.   :75.0                   
##       apt     
##  Min.   :352  
##  1st Qu.:576  
##  Median :633  
##  Mean   :640  
##  3rd Qu.:705  
##  Max.   :800
# function that gives the density of normal distribution
# for given mean and sd, scaled to be on a count metric
# for the histogram: count = density * sample size * bin width
f <- function(x, var, bw = 15) {
  dnorm(x, mean = mean(var), sd(var)) * length(var)  * bw

# setup base plot
p <- ggplot(dat, aes(x = apt, fill=prog))

# histogram, coloured by proportion in different programs
# with a normal distribution overlayed
p + stat_bin(binwidth=15) +
  stat_function(fun = f, size = 1,
    args = list(var = dat$apt))
plot of chunk unnamed-chunk-4

Looking at the above histogram, we can see the censoring in the values of apt, that is, there are far more cases with scores of 750 to 800 than one would expect looking at the rest of the distribution. Below is an alternative histogram that further highlights the excess of cases where apt=800. In the histogram below, the breaks option produces a histogram where each unique value of apt has its own bar (by setting breaks equal to a vector containing values from the minimum of apt to the maximum of apt). Because apt is continuous, most values of apt are unique in the dataset, although close to the center of the distribution there are a few values of apt that have two or three cases. The spike on the far right of the histogram is the bar for cases where apt=800, the height of this bar relative to all the others clearly shows the excess number of cases with this value.

p + stat_bin(binwidth = 1) + stat_function(fun = f, size = 1, args = list(var = dat$apt, 
    bw = 1))
plot of chunk unnamed-chunk-5

Next we'll explore the bivariate relationships in our dataset.

cor(dat[, c("read", "math", "apt")])
##        read   math    apt
## read 1.0000 0.6623 0.6451
## math 0.6623 1.0000 0.7333
## apt  0.6451 0.7333 1.0000
# plot matrix
ggpairs(dat[, c("read", "math", "apt")])
plot of chunk unnamed-chunk-6

In the first row of the scatterplot matrix shown above, we see the scatterplots showing the relationship between read and apt, as well as math and apt. Note the collection of cases at the top these two scatterplots, this is due to the censoring in the distribution of apt.

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.

Tobit regression

Below we run the tobit model, using the vglm function of the VGAM package.

summary(m <- vglm(apt ~ read + math + prog, tobit(Upper = 800), data = dat))
## Call:
## vglm(formula = apt ~ read + math + prog, family = tobit(Upper = 800), 
##     data = dat)
## Pearson Residuals:
##          Min    1Q Median   3Q Max
## mu      -2.6 -0.76 -0.051 0.79 4.1
## log(sd) -1.1 -0.62 -0.369 0.25 5.4
## Coefficients:
##                Estimate Std. Error z value
## (Intercept):1     209.6     32.457     6.5
## (Intercept):2       4.2      0.053    79.4
## read                2.7      0.618     4.4
## math                5.9      0.705     8.4
## proggeneral       -12.7     12.355    -1.0
## progvocational    -46.1     13.770    -3.4
## Number of linear predictors:  2 
## Names of linear predictors: mu, log(sd)
## Dispersion Parameter for tobit family:   1
## Log-likelihood: -1041 on 394 degrees of freedom
## Number of iterations: 4

Below we calculate the p-values for each of the coefficients in the model. We calculate the p-value for each coefficient using the z values and then display in a table with the coefficients. The coefficients for read, math, and prog = 3 (vocational) are statistically significant.

ctable <- coef(summary(m))
pvals <- 2 * pt(abs(ctable[, "z value"]), df.residual(m), lower.tail = FALSE)
cbind(ctable, pvals)
##                Estimate Std. Error z value      pvals
## (Intercept):1   209.555   32.45655   6.456  3.157e-10
## (Intercept):2     4.185    0.05268  79.432 1.408e-244
## read              2.698    0.61808   4.365  1.625e-05
## math              5.915    0.70480   8.392  8.673e-16
## proggeneral     -12.716   12.35467  -1.029  3.040e-01
## progvocational  -46.142   13.76971  -3.351  8.831e-04

We can test the significant of program type overall by fitting a model without program in it and using a likelihood ratio test.

m2 <- vglm(apt ~ read + math, tobit(Upper = 800), data = dat)

(p <- pchisq(2 * (logLik(m) - logLik(m2)), df = 2, lower.tail = FALSE))
## [1] 0.003155

The LRT with two degrees of freedom is associated with a p-value of 0.0032, indicating that the overall effect of prog is statistically significant.

Below we calculate the upper and lower 95% confidence intervals for the coefficients.

b <- coef(m)
se <- sqrt(diag(vcov(m)))

cbind(LL = b - qnorm(0.975) * se, UL = b + qnorm(0.975) * se)
##                     LL      UL
## (Intercept):1  145.941 273.169
## (Intercept):2    4.081   4.288
## read             1.487   3.909
## math             4.533   7.296
## proggeneral    -36.930  11.499
## progvocational -73.130 -19.154

We may also wish to examine how well our model fits the data. One way to start is with plots of the residuals to assess their absolute as well as relative (pearson) values and assumptions such as normality and homogeneity of variance.

dat$yhat <- fitted(m)[,1]
dat$rr <- resid(m, type = "response")
dat$rp <- resid(m, type = "pearson")[,1]

par(mfcol = c(2, 3))

with(dat, {
  plot(yhat, rr, main = "Fitted vs Residuals")
  plot(yhat, rp, main = "Fitted vs Pearson Residuals")
  plot(apt, rp, main = "Actual vs Pearson Residuals")
  plot(apt, yhat, main = "Actual vs Fitted")
plot of chunk unnamed-chunk-11

The graph in the bottom right was the predicted, or fitted, values plotted against the actual. This can be particularly useful when comparing competing models. We can calculate the correlation between these two as well as the squared correlation, to get a sense of how accurate our model predicts the data and how much of the variance in the outcome is accounted for by the model.

# correlation
(r <- with(dat, cor(yhat, apt)))
## [1] 0.7825
# variance accounted for
## [1] 0.6123

The correlation between the predicted and observed values of apt is 0.7825. If we square this value, we get the multiple squared correlation, this indicates predicted values share 61.23% of their variance with apt.


Long, J. S. 1997. Regression Models for Categorical and Limited Dependent Variables. Thousand Oaks, CA: Sage Publications.

McDonald, J. F. and Moffitt, R. A. 1980. The Uses of Tobit Analysis. The Review of Economics and Statistics Vol 62(2): 318-321.

Tobin, J. 1958. Estimation of relationships for limited dependent variables. Econometrica 26: 24-36.

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