How to plot predicted margins when they are specified with 'at'? - r

Question

We can get marginal effects of a linear model with margins::margins() and can select variables of interest with option variables.
fit <- lm(mpg ~ factor(vs) + gear:factor(vs) + qsec, mtcars)
library(margins)
marg1 <- margins(fit, variables="vs")
> summary(marg1)
factor AME SE z p lower upper
vs1 4.8023 2.6769 1.7940 0.0728 -0.4443 10.0490
The package has a implemented method plot.margins, so we can plot the marginal effects
plot(marg1)
at allows us to specify the values at which to calculate the marginal effects:
marg2 <- margins(fit, variables="vs", at=list(gear=c(3, 4, 5)))
> summary(marg2)
factor gear AME SE z p lower upper
vs1 3.0000 2.8606 3.3642 0.8503 0.3952 -3.7332 9.4544
vs1 4.0000 5.6849 2.6713 2.1282 0.0333 0.4493 10.9206
vs1 5.0000 8.5093 3.8523 2.2089 0.0272 0.9588 16.0597
However, attempting to plot these specified margins will yield an error:
plot(marg2)
Error in `[.data.frame`(summ, , names(attributes(x)[["at"]]), drop = FALSE) :
undefined columns selected
Since the margins package claims to be "an R-port of Stata's 'margins' command ", I'd expect a plot similar to the one Stata gives:
So, how can we plot the predicted margins when they are specified with at?
edit:
Note that this is not really an ordinary interaction plot, since
with(mtcars[mtcars$gear %in% c(3, 4, 5), ],
interaction.plot(gear, vs, mpg, pch=rep(1, 2), type="b"))
gives a different output:

Answer 1

The error comes from what seems to be a bug in the plot method for objects of class "margins", plot.margins.
This is an attempt to correct it. The changes are in the function body, just execute this or save it in a file "plotmargins.R" and then source("plotmargins.R").
plot.margins <-
function (x, pos = seq_along(marginal_effects(x, with_at = FALSE)),
which = colnames(marginal_effects(x, with_at = FALSE)), labels = gsub("^dydx_",
"", which), horizontal = FALSE, xlab = "", ylab = "Average Marginal Effect",
level = 0.95, pch = 21, points.col = "black", points.bg = "black",
las = 1, cex = 1, lwd = 2, zeroline = TRUE, zero.col = "gray",
...)
{
pars <- list(...)
summ <- summary(x, level = level, by_factor = TRUE)
MEs <- summ[, "AME", drop = TRUE]
lower <- summ[, ncol(summ) - 1L]
upper <- summ[, ncol(summ)]
r <- max(upper) - min(lower)
#--- changes start here
nms <- intersect(names(summ), names(attributes(x)[["at"]]))
at_levels <- unique(summ[, nms, drop = FALSE])
#--- changes end here
n_at_levels <- nrow(at_levels)
if (n_at_levels > 1) {
pos2 <- rep(pos, each = n_at_levels)
pos2 <- pos2 + seq(from = -0.2, to = 0.2, length.out = n_at_levels)
}
else {
pos2 <- pos
}
if (isTRUE(horizontal)) {
xlim <- if ("xlim" %in% names(pars))
xlim
else c(min(lower) - 0.04 * r, max(upper) + 0.04 * r)
ylim <- if ("ylim" %in% names(pars))
xlim
else c(min(pos2) - (0.04 * min(pos2)), max(pos2) + (0.04 *
max(pos2)))
}
else {
xlim <- if ("xlim" %in% names(pars))
xlim
else c(min(pos2) - (0.04 * min(pos2)), max(pos2) + (0.04 *
max(pos2)))
ylim <- if ("ylim" %in% names(pars))
xlim
else c(min(lower) - 0.04 * r, max(upper) + 0.04 * r)
}
if (isTRUE(horizontal)) {
plot(NA, xlim = xlim, ylim = ylim, yaxt = "n", xlab = ylab,
ylab = xlab, las = las, ...)
if (isTRUE(zeroline)) {
abline(v = 0, col = zero.col)
}
points(MEs, pos2, col = points.col, bg = points.bg, pch = pch)
axis(2, at = pos, labels = as.character(labels), las = las)
mapply(function(pos, upper, lower, lwd) {
segments(upper, pos, lower, pos, col = points.col,
lwd = lwd)
}, pos2, upper, lower, seq(max(lwd), 0.25, length.out = length(MEs)))
}
else {
plot(NA, xlim = xlim, ylim = ylim, xaxt = "n", xlab = xlab,
ylab = ylab, las = las, ...)
if (isTRUE(zeroline)) {
abline(h = 0, col = zero.col)
}
points(pos2, MEs, col = points.col, bg = points.bg, pch = pch)
axis(1, at = pos, labels = as.character(labels), las = las)
mapply(function(pos, upper, lower, lwd) {
segments(pos, upper, pos, lower, col = points.col,
lwd = lwd)
}, pos2, upper, lower, seq(max(lwd), 0.25, length.out = length(MEs)))
}
invisible(x)
}
Now your code and the graph.
source("plotmargins.R")
marg2 <- margins(fit, variables = "vs",
at = list(gear = c(3, 4, 5)))
plot(marg2)