Question

I’m trying to use R to do some modelling, I’ve started to use BodyWeight library, since I’ve seen some examples online. Just to understand and get used to the commands.

I’ve come to my final model, with estimates and I was wondering how to plot these estimates, but I haven’t seen anything online..

Is there a way to plot the values of the estimates with a line, and dots for the values of each observation?

Where can I find information about how to do this, do I have to extract the values myself or it is possible to say plot the estimates of these model?

I’m only starting with R. Any help is welcome.

Thank you

Answer 1

There is no function that just plots the output of a model, since there are usually many different possible ways of plotting the output.

Take a look at the predict function for whatever model type you are using (for example, linear regressions using lm have a predict.lm function).

Then choose a plotting system (you will likely want different panels for different levels of diet, so use either ggplot2 or lattice). Then see if you can describe more clearly in words how you want the plot to look. Then update your question if you get stuck.

---

Now we’ve identified which dataset you are using, here’s a possible plot:

#Run your model
model <- lme(weight ~ Time + Diet, BodyWeight, ~ 1 | Rat)
summary(model)

#Predict the values
#predict.lme is a pain because you have to specify which rat
#you are interested in, but we don't want that
#manually predicting things instead
times <- seq.int(0, 65, 0.1)
mcf <- model$coefficients$fixed
predicted <- 
  mcf["(Intercept)"] + 
  rep.int(mcf["Time"] * times, nlevels(BodyWeight$Diet)) + 
  rep(c(0, mcf["Diet2"], mcf["Diet3"]), each = length(times))
prediction_data <- data.frame(
  weight = predicted,
  Time   = rep.int(times, nlevels(BodyWeight$Diet)),
  Diet   = rep(levels(BodyWeight$Diet), each = length(times))
)  

#Draw the plot (using ggplot2)
(p <- ggplot(BodyWeight, aes(Time, weight, colour = Diet)) + 
  geom_point() +
  geom_line(data = prediction_data)
)