I'm really wondering why when I keep the last line (sigma) in my function foo1 my plot call stops working BUT when I delete the last line in foo2 the plot call works fine?!
Note: My understanding is that plot should show anywhere in the function like:
foo3 <- function(x = 1:3){; plot(x); return(x); }; foo3()
I need to keep the last line but I also need to plot, is this fixable?
library(lme4)
library(emmeans)
h <- read.csv('https://raw.githubusercontent.com/hkil/m/master/h.csv')
h$year <- as.factor(h$year)
m <- lmer(scale~ year*group + (1|stid), data = h)
foo1 <- function(fit, plot = T){
vc <- VarCorr(fit)
f <- as.formula(bquote(pairwise ~ .(terms(fit)[[3]])))
ems <- emmeans(fit, f, infer = c(T, T))
if(plot) plot(ems)
## Why having this line prevents plotting?
sigma <- sqrt(sum(as.numeric(c(attr(vc[[1]], "stddev"), attr(vc, "sc")))^2))
}
###### EXAMPLE: Will NOT plot !!!
foo1(m, plot = T)
But simply delete the last line of foo1 and plot works fine!
foo2 <- function(fit, plot = T){
f <- as.formula(bquote(pairwise ~ .(terms(fit)[[3]])))
ems <- emmeans(fit, f, infer = c(T, T))
if(plot) plot(ems)
}
###### EXAMPLE: NOW plots fine !!!
foo2(m, plot = T)
The underlying cause for the unexpected behavior is that emmeans uses ggplot2 as plotting method. You may examine the code of function emmeans:::.plot.srg. This is why you can store the plot in an object (p) and print it:
foo1 <- function(fit, plot=TRUE) {
vc <- VarCorr(fit)
f <- as.formula(bquote(pairwise ~ .(terms(fit)[[3]])))
ems <- emmeans(fit, f, infer=c(TRUE, TRUE))
sigma <- sqrt(sum(as.numeric(c(attr(vc[[1]], "stddev"), attr(vc, "sc")))^2))
p <- plot(ems)
if(plot) print(p)
return(sigma)
}
foo1(m, plot=TRUE) ## plots
# [1] 126.6106
Intuitively we expect the behavior like in your foo3 <- function(x = 1:3){; plot(x); return(x); }; foo3() example:
foo2 <- function(x, plot=TRUE) {
y <- seq_len(x)^2
if(plot) plot(seq_len(x), y)
return(y)
}
foo2(20) ## plots
# [1] 1 4 9 16 25 36 49 64 81 100 121 144 169
# [14] 196 225 256 289 324 361 400
But this works differently, when one uses ggplot. When we don't store the "ggplot" object, a following line will "overwrite" the plot.
library(ggplot2)
foo3a <- function(x, plot=TRUE) {
y <- seq_len(x)^2
if(plot) ggplot(mapping=aes(seq_len(x), y)) + geom_point()
return(y) ## try to comment/un-comment this line
}
foo3a(20) ## won't plot, just output of y (depending on `return`)
Therefore we have to actually print the "ggplot" object (I show this by storing the plot in p in function foo3b), if it's not the last line of the function.
foo3b <- function(x, plot=TRUE) {
y <- seq_len(x)^2
p <- ggplot(mapping=aes(seq_len(x), y)) + geom_point()
if(plot) print(p)
return(y) ## try to comment/un-comment this line (works in both cases)
}
foo3b(20) ## plots
# [1] 1 4 9 16 25 36 49 64 81 100 121 144 169
# [14] 196 225 256 289 324 361 400
Note that the use of return also is useful.