I have been trying to produce a conditional plot using coplot function
(http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/coplot.html) for a
binary response ("Presence" in my case) variable and one continuous variable
("Overstory") given a specific levels of the other continuous variable ("Ivy").
But, my codes produces an overlapping graph. Also, I want to use three equal
intervals for "Ivy" (i.e.,33.3 each), but I could not figure out how. Here is
my data and codes I used:
dat <- structure(list(Presence = c(0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,
0L, 1L, 1L, 1L, 0L, 0L), Cover.size = c(7400, 2730, 2782, 1408,
5400, 4170, 630, 1120, 720, 1080, 1197, 2160, 1638, 2850, 2420,
90, 1017, 1260, 700, 1540, 100, 2720, 792, 360, 3048, 2620, 6253,
6253, 740, 2520, 3520), Ivy = c(10L, 90L, 0L, 40L, 100L, 100L,
100L, 90L, 50L, 95L, 95L, 95L, 0L, 85L, 10L, 5L, 5L, 80L, 70L,
70L, 0L, 0L, 0L, 0L, 0L, 90L, 0L, 0L, 6L, 50L, 15L), Overstory = c(6L,
4L, 4L, 4L, 3L, 6L, 5L, 4L, 5L, 8L, 8L, 8L, 8L, 8L, 6L, 6L, 9L,
12L, 12L, 7L, 12L, 16L, 16L, 16L, 16L, 13L, 14L, 14L, 14L, 12L,
12L), Moist = c(13.65, 15.3, 15.95, 17.2, 22.95, 18.25, 19.3,
18.75, 17, 21.3, 17.7, 28, 20.85, 19.85, 24.75, 22.2, 26.6, 21.15,
22, 15, 22.5, 30, 14.85, 27, 26.85, 19.55, 27.2, 27.2, 21.55,
18, 19.9), Leaf = c(95L, 95L, 95L, 90L, 80L, 90L, 95L, 95L, 90L,
80L, 80L, 80L, 95L, 90L, 95L, 95L, 95L, 100L, 100L, 95L, 5L,
80L, 80L, 80L, 80L, 90L, 95L, 95L, 95L, 85L, 90L), Prey = c(0.047,
0.051, 0.058, 0.057, 0.049, 0.046, 0.155, 0.108, 0.087, 0.093,
0.133, 0.095, 0.081, 0.104, 0.11, 0.086, 0.124, 0.134, 0.12,
0.139, 0.026, 0.045, 0.096, 0.035, 0.062, 0.065, 0.068, 0.068,
0.087, 0.052, 0.082), Abundance = c(0.141542817, 0.092071611,
0.077821012, 0.09906595, 0.113821138, 0.046202181, 0.641167367,
1.131059246, 0.346020761, 0.647748304, 1.424230915, 2.098280764,
0.23395382, 5.492325363, 1.713972302, 2.584891263, 1.049433858,
0.81246522, 1.895848332, 2.8125, 0.089866484, 0.15392509, 0.561643836,
0.400477763, 0.173869846, 1.158351129, 0.453206436, 0.50608052,
0.347007064, 0.461928178, 0.264333242)), .Names = c("Presence",
"Cover.size", "Ivy", "Overstory", "Moist", "Leaf", "Prey", "Abundance"
), row.names = 106:136, class = "data.frame")
xrange <- seq(from=min(dat$Overstory), to=max(dat$Overstory), length=100)
panelFunc <- function(x,y,data,...){
plot(x,y,...)
fit <- glm(y ~ x, data = dat, family = binomial(link = logit), na.action =
na.exclude)
lines(xrange, inv.logit(fit$coef[1]+ fit$coef[2]*xrange))
}
coplot(dat$Presence ~ dat$Overstory | dat$Ivy, number=3, panel=panelFunc,
rows=1)
Also, if you have a better alternative code, please share with me.
Thank you in advance for your time and help!
Sincerely,
Kiyoshi
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