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This question is partly a question from ignorance of the statistics, and part an R question. I've moved this question over from Stack Overflow since it's more about the theory.

I have growth data for multiple animals, in different habitats, across a time-span of their life. I have fitted linear regression models to each one, and as expected, there is quite a bit of variation between their growth trajectory over time. Some grow faster through time, some grow slower. What I want to calculate is the average growth trajectory among animals in each location, so that I can use that information to inform a larger model...essentially, I care about the slope of their growth/day as a predictor for a larger model. I'm not all that worried about the intercept.

My data has much more variation than the example dataset below. But, like this example, there is a mix of negative and positive slopes and variation in the length and starting points of the growth data for each individual. The data was opportunistically available in each location, so it's not like I'm working from a controlled experiment.

I'm re-writing the question with a different example dataset to better get at what I'm trying to determine, which is:

"can I just fit a regression to each animal, and average the slope coefficients within each location? Or is there a more statistically valid way to do this?"


dput(example)
structure(list(Day = c(1, 2, 3, 1, 2, 3, 3, 4, 5, 1, 2, 3, 3.5, 
4.5, 5.5, 1, 2, 3, 1, 2, 3, 1, 2, 3, 4, 5, 6), Animal = structure(c(1L, 
1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 
6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 9L), .Label = c("a", "b", 
"c", "d", "e", "f", "g", "h", "i"), class = "factor"), Growth = c(5, 
4, 3, 6, 5, 4, 7, 9, 11, 1, 2, 3, 3, 4, 5, 6, 7, 8, 3, 2, 1, 
5, 4, 3, 7, 6, 5), Location = c("X", "X", "X", "X", "X", "X", 
"X", "X", "X", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Z", 
"Z", "Z", "Z", "Z", "Z", "Z", "Z", "Z"), Var1 = c(NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, 3.5, 4.5, 5.5, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA)), row.names = c(NA, -27L), .Names = c("Day", 
"Animal", "Growth", "Location", "Var1"), class = "data.frame")

ggplot(example, aes(x=Day, y=Growth, color = Animal, group = Location)) + geom_point() + geom_smooth(method = "lm", se = FALSE) + geom_smooth(method = "lm", aes(group = Animal)) + facet_grid(.~Location)

enter image description here

Clearly, there is a problem here with fitting an overall linear regression to each location. Because of the different starting points and lengths of each regression, different animals exert undue influence over the fit of the line (namely animals "c", "e", and "I"). For example, the actual slopes in X are -1, -1, 2. If animal "c" started at point 1 the slope would be zero.

When I asked this before I got quite a few answers telling me to fit a mixed effects model with Location and Individual as random effects, then to use the coefficients for Location within that model. But this does not escape the problem of spurious slopes no matter how you set up the model:

mem = lmer(Growth ~ (Day|Animal/Location), data = example)
sjp.lmer(mem, type = "pred", vars = c("Day", "Location"))
#ignore the fact that the model doesn't converge...

enter image description here

So...is it kosher to simply take an average of the slope coefficients for the linear regression of each individual, or is there a more rigorous way to get at this?

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You can fit this in a single regression. The issue, to me, that it seems that you are dealing with is independence of observation. The example you gave is a really good example of the difference between within and between variance.

You can either do it as you see there, or you can toss everything within a regression model.

For example, each of those factors can be treated as binary variables (aka Boolean). Either the animal was in the shelter or it was not. So 1 if it was there, 0 if it was not. Doing this gives you an X by X dummy variable matrix. So for animal n, it will have a 1 in a single column and then its remaining row will be filled with zeros. This lets you put it into a regression. Then you include each of those variables (save one, which will be your baseline) within your regression model.

You regression ends up looking like this-

$growth = time + habitat_1 + habitat_2 + habitat_3 + error$.

I this case, $habitat_4$ is my baseline. The coefficients for $habitat_{1-3}$ will tell me the mean difference in growth between that habitat and $habitat_4$.

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  • $\begingroup$ I'm not sure I completely follow. I'm confused about whether overall slope within Diet (assuming the ChickWeight dataset) is a slope based on the pooled datapoints, or is based on some average of the slopes of each individual. The reason I ask is that, drawing a line through the pooled points within Diet 1, it is conceivable that the individual slopes could all be negative...but the overall slope of that cloud of points is positive. Or, is the model taking into account the slopes of each chick in which case the coefficient of the Diet 1 group would reflect a negative slope. $\endgroup$ – JHegg Oct 16 '17 at 22:15
  • $\begingroup$ My confusion still stands, but I hope my question is more clear after changing the example data. Regardless of how the regression is built, mixed-effects or simple regression, the slope within each location is not really representative of the actual slopes, due to the nature of the data. If I am trying to get at some meaningful metric of the slope of most individuals growth within location, what is the best way to do that in this case? $\endgroup$ – JHegg Oct 17 '17 at 23:56
  • $\begingroup$ ok, I will be able to clarify my advise based on the answer to the following question- Do you want the slopes respective of the location or irrespective. In other words, do you want the slope for each location, or the slope with the effect of location factored out? $\endgroup$ – JWH2006 Oct 20 '17 at 20:34
  • $\begingroup$ The slope for each location. $\endgroup$ – JHegg Oct 21 '17 at 1:25

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