I can’t exactly remember how I arrived to Making sense of random effects, a good post in the Distributed Ecology blog (go over there and read it). Incidentally, my working theory is that I follow Scott Chamberlain (@recology_), who follows Karthik Ram ?(@_inundata) who mentioned Edmund Hart’s (@DistribEcology) post. I liked the discussion, but I thought one could add to the explanation to make it a bit clearer.

The idea is that there are 9 individuals, assessed five times each—once under each of five different levels for a treatment—so we need to include individual as a random effect; after all, it is our experimental unit. The code to generate the data, plot it and fit the model is available in the post, but I redid data generation to make it a bit more R-ish and, dare I say, a tad more elegant:

```
library(lme4)
library(ggplot2)
# Basic dataset
idf <- data.frame(ind = factor(rep(1:9, 5)),
levs = factor(rep(c('i1', 'i2', 'i3', 'i4', 'i5'), each = 9)),
f.means = rep(c(6, 16, 2, 10, 13), each = 9),
i.eff = rep(seq(-4, 4, length = 9), 5))
# Function for individual values used in apply
ran.ind <- function(f.means, i.eff) rnorm(1, f.means + i.eff, 0.3)
# Rich showed me this version of apply that takes more than one argument
# https://smtp.biostat.wustl.edu/sympa/biostat/arc/s-news/2005-06/msg00022.html
# so we skip loops
idf$size <- apply(idf[, 3:4], 1,
function(x) do.call('ran.ind', as.list(x)))
ggplot(idf, aes(x = levs, y = size, group = ind, colour = ind)) +
geom_point() + geom_path()
# Fit linear mixed model (avoid an overall mean with -1)
m3 <- lmer(size ~ levs - 1 + (1 | ind), data = idf)
summary(m3)
# Skipping a few things
# AIC BIC logLik deviance REMLdev
# 93.84 106.5 -39.92 72.16 79.84
#Random effects:
# Groups Name Variance Std.Dev.
# ind (Intercept) 7.14676 2.67334
# Residual 0.10123 0.31816
#Number of obs: 45, groups: ind, 9
# Show fixed effects
fixef(m3)
# levsi1 levsi2 levsi3 levsi4 levsi5
# 5.824753 15.896714 2.029902 9.969462 12.870952
```

What we can do to better understand what's going on is 'adjust' the score observations by the estimated fixed effects and plot *those values* to see what we are modeling with the random effects:

```
# Substract fixed effects
idf$adjusted <- idf$size - rep(fixef(m3), each = 9)
ggplot(idf, aes(x = levs, y = adjusted, group = ind, colour = ind)) +
geom_point() + geom_path()
# Display random effects
ranef(m3)
#$ind
# (Intercept)
#1 -3.89632810
#2 -2.83054394
#3 -1.99715524
#4 -1.12733342
#5 0.06619981
#6 0.95605162
#7 2.00483963
#8 2.99947727
#9 3.82479236
```

The random effects for individual or, better, the individual-level intercepts are pretty much the lines going through the middle of the points for each individual. Furthermore, the variance for `ind`

is the variance of the random intercepts around the 'adjusted' values, which can be seen comparing the variance of random effects above (~7.15) with the result below (~7.13).

```
var(unlist(ranef(m3)))
#[1] 7.12707
```

Distributed Ecology then goes on to randomize randomize the individuals within treatment, which means that the average deviation around the adjusted means is pretty close to zero, making that variance component close to zero. I hope this explanation complements Edmund Hart's nice post.

P.S. If you happen to be in the Southern part of South America next week, I'll be here and we can have a chat (and a beer, of course).

Nice job! I’ll totally agree that’s more elegant. I knew there must have been some clever way to generate the data with apply functions that I couldn’t figure out so I just went quick and dirty with the for loops.

R is incredibly powerful, but obvious is not a word that comes to mind very often with R. Another way to do the same generation would be using plyr’s ddply.

Thank you! I was struggling with mixed models and R – and I still am. But this post + the one at Distributed Ecology brought some illuminating new insights to me. Still confused but on a higher level 🙂