Hi,
The problem is that I would like to do an interaction plot with
intervals based on Tukey's honestly significant difference (HSD)
procedure, but I do not know how to do it in R.
I have 3 factors "A", "B" and "C" and a response variable "response".
I would like to study a model where there are main effects and second
order interaction effects.
For instance, for factors B and C, I would like to plot a line for each
level of C connecting the least square means for every level of B.
Additionally, I would like to include the 95,0% HSD intervals for
the means in such a way that any two intervals which do not overlap
correspond to a
pair of means which have a statistically significant difference.
For comparison, in STATGRAPHICS Plus, I choose Analysis of Variance ->
Multifactor ANOVA...
Then I plot the second order interactions and I have the option to plot
intervals. I choose to plot Tukey HSD intervals at 95% and I obtain an
interaction plot like using interaction.plot on R, but addittionally an
interval is plotted on every point.
How can I do this on R?
I have already looked in Google, in the mail archive and in some books,
but I didn´t find the answer.
I tried to calculate the intervals using:
|tk <- TukeyHSD(aov(X$response ~ (factor(X$A) + factor(X$B) +
factor(X$C))^2, data=X) , conf.level=0.95)
HSDfactor1 <-
max(abs(tk$"factor(X$A):factor(X$B)"[,2]-tk$"factor(X$A):factor(X$B)"[,3]))
HSDfactor2 <-
max(abs(tk$"factor(X$A):factor(X$C)"[,2]-tk$"factor(X$A):factor(X$C)"[,3]))
HSDfactor3 <-
max(abs(tk$"factor(X$B):factor(X$C)"[,2]-tk$"factor(X$B):factor(X$C)"[,3]))
And I modified the function interaction.plot() adding the following
lines of code:
...................................................................................
*++ ylim <- c(min(cells)-(HSDfactor*0.5), max(cells)+(HSDfactor*0.5))*
matplot(xvals, cells, ..., type = type, xlim = xlim, ylim = ylim,
xlab = xlab, ylab = ylab, axes = axes, xaxt = "n",
col = col, lty = lty, pch = pch)
*++ ly <- cells[,1]+(HSDfactor*0.5)
++ uy <- cells[,1]-(HSDfactor*0.5)*
*++ errbar(xvals,cells[,1],ly,uy,add=TRUE, lty=3, cap=0, lwd=2)
++ ly <- cells[,2]+(HSDfactor*0.5)
++ uy <- cells[,2]-(HSDfactor*0.5)
++ errbar(xvals,cells[,2],ly,uy,add=TRUE, lty=3, cap=0, lwd=2)*
if(legend) {
yrng <- diff(ylim)
yleg <- ylim[2] - 0.1 * yrng
.....................................................................
|Finally, I call this modified function as:
|interaction.plot2( factor(X$A), factor(X$B), response,las=3, type="b",
HSDfactor = HSDfactor1, lwd=3)
|However, the resulting intervals are much bigger than the ones
calculated by STATGRAPHICS, thus I think I did something wrong.
I am not an expert in Statistics nor in R, thus if anyone has any
suggestion...
Thank you very much,
Manuel.
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