18.3: Cattle Feed

This section presents a practical application of multinomial logistic regression for a nominal dependent variable. Using a dataset on cattle, the goal is to predict which brand of feed a cow received based on its ranch, age, and weight. The section walks through the complete workflow: loading and exploring the data, fitting a multinomial model using the nnet package in R, and interpreting the results. It highlights how exploratory analysis, such as cross-tabulations, can reveal perfect predictors (like ranch) that dominate the model. The section then demonstrates how to use the fitted model to predict the feed type probabilities for a new cow (a "mysteryMoo") and, crucially, how to create informative graphics that visualize the effect of a continuous predictor (weight) on the predicted probabilities for each outcome category, making the model's implications clear and actionable.

 

Learning Objectives

By the end of this lengthy example, you will be able to:

1. Fit a multinomial logistic regression model in R using the multinom function from the nnet package for a nominal dependent variable (feed type) with multiple categorical and continuous predictors (ranch, age, weight).
2. Interpret the coefficient estimates from a multinomial model, recognizing that they are estimated relative to a baseline category (Accuration in this example) and that extremely large coefficients can indicate perfect or near-perfect predictors revealed in exploratory cross-tabulations.
3. Generate predicted probabilities for each outcome category for a new observation (a "mystery cow") using the predict function with type="prob", and identify the most likely category.
4. Create and interpret a visualization that plots the predicted probabilities for each feed type against a continuous predictor (weight), holding other predictors constant, to understand how the likelihood of each outcome changes across the range of that predictor.

 

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Example: Cattle and their Feed

Previously, we attempted to model the weight of cattle based on a few factors. Let us try something different. Let us predict the brand of food used by the cattle based on the ranch, age, and weight.

Specifically, let's first model feed type. Then, let's say that the RUR ranch sent a 21-year-old cow to slaughter at 1197 pounds. Which food brand was most likely used? What are the probabilities of each brand being used?

Solution.

Since the food brand is a nominal variable, we will use multinomial regression. The data file is cattleData. Let's load it and look at some summary statistics on it. In other words, let's know our data.

library(nnet)
cowz = read.csv("http://rur.kvasaheim.com/data/cattleData.csv")
attach(cowz)

summary(cowz)

cor.test(weight,age)
table(ranch,feedType)

Note that there is (as expected) a strong correlation between age and weight. If we are doing model selection, we will need to keep this in mind as this multicollinearity will decrease the statistical significance of those two variables. Note from the cross-tabulation that the EVA ranch only used Purina and the TCL ranch only used Rangeland (in this sample). That fact would make it really easy to predict the feed type for those ranches. The other ranches use a combination of all of the brands.

 

With this information to guide us, we fit the nominal regression model:

cowModel = multinom(feedType ~ weight + ranch + age)
summary(cowModel)

The first line fits the model. Note that the model did converge, so we can pay attention to the results. If it had not converged, we should first change the link function, then realize that the multicollinearity is a problem. Dropping one or more variables would be an appropriate action in that case.

• The results of the summary(cowModel) command gives some insight into the relationships. First, note that the coefficient estimate for ranchEVA for estimating Purina is \(20.37\). This is extremely high, meaning it is almost guaranteed that a cow from the EVA ranch will used Purina.
  But, from the cross-tabulation above, we already knew this.
• Similarly, the coefficient estimate for ranchTCL for Rangeland is a huge 22.32. This indicates a cow from the TCL ranch will most certainly use Rangeland food. Again, we knew this from our cross-tabulation.
• Note from the regression table that Accuration is missing. All feed measurements are taken with respect to that level. This is important to keep in mind if we do this by hand. It is just something to note if we are using the computer to do our calculations.

 

So, let's estimate the food used by our mystery cow. First, let's define it:

mysteryMoo = data.frame(weight=1197, age=21, ranch="RUR")

 

Now, let's predict the probabilities it used each of the feed types:

predict(cowModel, mysteryMoo, type="prob")

The results tell us that the mystery cow most likely used Steakmaker. In fact, the probability it used Steakmaker was 79%. The second most likely feed type was Accuration (13%).

  

 

Graphics

Let us talk about graphics for a bit. A two-dimensional scatter plot looks at two numeric variables. We can therefore easily plot a prediction curve when dealing with only a single dependent variable and single independent variable. If there is a second independent variable, we can plot several curves, one for each level in that second independent variable. Once we move beyond two independent variables, graphics are more difficult to do. A simple regression model like the one above may require dozens of graphics to illustrate each aspect.However, we can simplify things by focusing on only a couple independent variables at a time. The choice depends on the story you are trying to learn (or tell).

 

Graphic: Feed Type versus Weight

For this first graphic, I am consciously making the decision to plot the predicted probability on the y-axis, the cattle weight on the x-axis, and have a prediction curve for each feed type. This will allow me to see the effect of weight on the predicted food type. This means I need to select values for the other two independent variables. For the numeric age, I would typically use its mean or median, whichever was the "typical" age for these cattle.

For the selected value of the ranch, I would either select the ranch to which the mystery cow belonged (to continue that story) or the most popular ranch (to try to generalize the story). It is best to do separate graphics for all ranches so that you, the researcher, can better understand the effect of ranch on the probabilities. It is always better to do more to understand.

So, here is the code to create the predictions:

theWeights = seq(1019,1579, length=1e4)
theAge = median(age)
prRUR = predict(cowModel, newdata=data.frame(weight=theWeights, age=theAge, ranch="RUR"), type="probs")

The prRUR variable now contains 10,000 rows (one for each weight) and 5 columns (one for each feed type). The entries are the probabilities.

Now, we just plot the data and these predictions:

par(family="serif", las=1)
par(xaxs="i", yaxs="i")
par(mar=c(4,4,0,0)+0.5)
par(cex.lab=1.2, font.lab=2)

plot.new()
plot.window( xlim=c(1000,1600), ylim=c(0,1))

axis(1); axis(2)
title(xlab="Weight [lb]")
title(ylab="Probability at RUR Ranch")

lines(theWeights,prRUR[,1], col=1) # Accuration
lines(theWeights,prRUR[,2], col=2) # Purina
lines(theWeights,prRUR[,3], col=3) # Rangeland
lines(theWeights,prRUR[,4], col=4) # Steakmaker
lines(theWeights,prRUR[,5], col=5) # Wind and Rain

legend("topright", bty="n", col=1:5, lwd=2,
    legend=c("Accuration","Purina","Rangeland","Steakmaker","Wind and Rain")
    )

Note that this graphic includes a legend that lets the reader know which probability curve belongs to which feed type. Legends are rather important to include on a graphic. Remember that graphics should be stand-alone with their caption. Because a legend contains so much information, it requires a large function. To see all a legend can do, run ?"legend" in R.

Figure \(\PageIndex{1}\): Graphic of the probability for each feed type at the RUR ranch. The probabilities vary with the cow's weight. The age is held at the median, 21.

 

The figure above is the resulting graphic. Note that the predicted feed type tends to be either Steakmaker, for light cows, or Purina, for heavy cows. When the weight of the cow is middling, there is great uncertainty in which feed type it used.

It is interesting that this analysis gives us additional insight on how we can create big cows for slaughter. This suggests we should use Purina brand. This conclusion, however, is based only on the RUR ranch and a middle-aged cow. More importantly, this conclusion assumes that the data are representative of the population of interest. As this data was originally collected in conjunction with a dissertation in Animal Science, I tend to think it is representative.

From a strictly statistical standpoint, the additional insight is limited. However, if you are hired by RUR ranch to determine the best feed type, this graphic would be very persuasive for you, the decision-maker. While we could create a similar graphic for feed type against age, I am not convinced it would be helpful. Age is not something one would like to optimize like weight. In other words, I am not sure what story I would tell about it.

 

 

Important!

Don't make graphics just for fun. Make sure you create them knowing how to interpret them.