I was reading this blog post:


the author describes a model to predict how many hours a day time a mammal sleeps, given its brain mass. Of course, since you cannot sleep more than 24 hrs/day, the author doesn't directly use standard linear regression, but divides the response by 24, so that it's bounded between 0 and 1 (and then he multiplies it back by 24 when making predictions, but I'm not interested in the prediction part: I'm concerned about the choice of statistical model). It also takes the log of brain mass, because the relationship between hours slept per day and brain mass seems linear on the semilog scale. Here's the relevant code, if you don't want to look at the link:

# required libraries

# filter data and transform some variables
msleep <- msleep %>% 
  filter(!is.na(brainwt)) %>% 
  mutate(log_brainwt = log10(brainwt), 
         log_bodywt = log10(bodywt), 
         log_sleep_total = log10(sleep_total),
         logit_sleep_ratio = qlogis(sleep_total/24))

# fit model
m1 <- stan_glm(
  logit_sleep_ratio ~ log_brainwt, 
  family = gaussian(), 
  data = msleep, 
  prior = normal(0, 3),
  prior_intercept = normal(0, 3))

Unless I'm mistaken, the model used here is a linear regression of the logit of the normalized hours of sleeps, on the log of brain mass, considering Gaussian errors. I don't think this is the best approach for this problem (definitely it's not the only possible one). Which approach would be appropriate? Logistic regression is not appropriate, in my opinion, because the response isn't a binary variable, but it's a true percentage. I think Beta regression would be better, but I'm open to other suggestions. I would expecially be interested in pros and cons of different suitable approaches.

Of course, statistical modeling cannot be done in a vacuum, so here is a simple plot of the data:

# simplify some names for plotting 
ex_mammals <- c("Domestic cat", "Human", "Dog", "Cow", "Rabbit",
                "Big brown bat", "House mouse", "Horse", "Golden hamster")
renaming_rules <- c(
  "Domestic cat" = "Cat", 
  "Golden hamster" = "Hamster", 
  "House mouse" = "Mouse")
ex_points <- msleep %>% 
  filter(name %in% ex_mammals) %>% 
  mutate(name = stringr::str_replace_all(name, renaming_rules))

# create labels
lab_lines <- list(
  brain_log = "Brain mass (kg., log-scaled)", 
  sleep_raw = "Sleep per day (hours)",
  sleep_log = "Sleep per day (log-hours)"

# finally, make the actual plot
ggplot(msleep) + 
  aes(x = brainwt, y = sleep_total) + 
  geom_point(color = "grey40") +
  # Circles around highlighted points + labels
  geom_point(size = 3, shape = 1, color = "grey40", data = ex_points) +
  geom_text_repel(aes(label = name), data = ex_points) + 
  # Use log scaling on x-axis
  scale_x_log10(breaks = c(.001, .01, .1, 1)) + 
    labs(x = lab_lines$brain_log, y = lab_lines$sleep_raw) 

enter image description here

  • 5
    $\begingroup$ The statistical and methodological choices analysts and authors make that get published in peer-reviewed papers are not always the best approaches or solutions. What you are pointing out is a weakness in the choice of functional form for the analysis of this data. In this instance, you clearly know more than the guys publishing this article. Rather than query this blog for support of your point of view, why not take your case directly to the guys who wrote the paper? Don't expect much in the way of a response, however, as people can become quite defensive wrt their mistakes and/or ignorance. $\endgroup$ – DJohnson Aug 29 '17 at 14:25
  • 3
    $\begingroup$ Agree with @DJohnson. I also agree with you that beta regression sounds like a more direct approach (you can use it for any bounds). Ask the authors as we would need to makes guesses about their intentions. $\endgroup$ – Tim Aug 29 '17 at 14:28
  • 2
    $\begingroup$ @DJohnson Although I agree with your comment, IMO asking for alternatives to handle these situations can be a valid question for this forum. I don't think you are denying that, but I'd want to point out providing such a 'backstory' as context might help the poster formulate his/her question. Of course, in this case Tim has also shown that the focus that this question could have ("how to handle proportions as outcomes in regression models") has already been answered elsewhere. $\endgroup$ – IWS Aug 29 '17 at 14:45
  • 5
    $\begingroup$ Oh to be a big brown bat, and breeze the blasted days away. To bat the bothers of life away, and sleep twenty hours a day. $\endgroup$ – Matthew Drury Aug 29 '17 at 15:01
  • 4
    $\begingroup$ Do you want to edit this, @DeltaV, to be about the pros & cons of different alternatives for analyzing these data, rather than why the authors chose this approach? The latter does seem to be about us making guesses about their state of mind, whereas the former would be unambiguously on topic here. As mentioned, the context can be useful & can remain, so I think a small edit / shift of emphasis is all that's necessary. $\endgroup$ – gung Aug 29 '17 at 15:42

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