You found the HH package. That is a good start. Look at the ?MMC help page, and specifically at the entire maiz example.
For an example with two factors and a covariate and with multiple comparisons look at the apple example in file system.file("scripts/hh2", package="HH") The example is in chunks 18-32 The file is intended as support for the section in my book that provides the discussion. Heiberger, R. M. and Holland, B. (2004). Statistical Analysis and Data Display: An Intermediate Course with Examples in S-Plus, R, and SAS. Springer-Verlag, New York, first edition. Section 14.6 is the apple example. I am willing to provide specific support for your example, but to do so I will need "commented, minimal, self-contained, reproducible code." Fake data would be ok as long as the structure is the same as the real data. Rich On Wed, Jan 14, 2015 at 2:59 PM, lindsay hanford <lindsay.hanf...@gmail.com> wrote: > Hello R Community! > > I am an intermediate-level R user and I am trying to figure out how program > a two-way (Group and MCCB score) ANCOVA analysis and subsequent post-hoc > analysis. > My factors: > Group (2 levels) > Score (2 levels) > Covariates: > Age (continuous) > ICV (continuous) > Sex (M/F) > Y: > GMV(continuous) > > I am interested in looking at the interaction of these two factors and have > set up my ANCOVA as follows: > > *model1 <-aov(GMV~ GROUP*Score +Age +ICV +Sex, data=dataframe)* > *summary(model1) * > > which has given me some very exciting results... > > Analysis of Variance Table > Response: GMV > Df Sum Sq Mean Sq F value Pr(>F) > GROUP 1 104219614 104219614 25.119 1.739e-06 *** > Score 1 231825545 231825545 55.875 1.042e-11 *** > Sex 1 49112001 49112001 11.837 0.0007828 *** > Age 1 165812317 165812317 39.964 3.882e-09 *** > ICV 1 283849872 283849872 68.414 1.416e-13 *** > GROUP:Score 1 30802470 30802470 7.424 0.0073292 ** > Residuals 129 535224714 4149029 > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > I need to control for multiple comparisons as I will be trying other > variables in place of GMV. From the forum, TukeyHSD() will not work as I > have covariates. The glth() shows promise, however, I am not sure if the > resulting statistics are what I am looking for? > > *mc1<-mcalinfct(model1, "GROUP")* > *summary(glht(model1, linfct=mc1))* > > Simultaneous Tests for General Linear Hypotheses > Fit: aov(formula = GMV ~ GROUP * Score + Age + ICV +Sex, data =dataframe) > > Linear Hypotheses: > Estimate Std. Error t value Pr(>|t|) > 1 == 0 -844.9 392.2 -2.154 0.0331 * > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > (Adjusted p values reported -- single-step method) > > I believe this means that the difference in GMVs is statistical significant > between my groups (pcor = 0.03). Does this also mean that my interaction is > significant? If not, how do I test for that? My intention is to be able to > create a graphic of this interaction similar to the attached. > > I tried using previous posts from the help forum. I believe this post holds > the answer, but it is beyond my R programming ability. If someone could > help explain... > > http://r.789695.n4.nabble.com/Multiple-comparisons-for-a-two-factor-ANCOVA-td1593039.html > http://cran.r-project.org/web/packages/HH/HH.pdf > > Thanks! > > > Lindsay > > -- > Lindsay Hanford, BSc, PhD Candidate > McMaster Integrative Neuroscience Discovery & Study | *Department of > Psychology, Neuroscience & Behaviour * > McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* > Hamilton, ON, L8S 4L8 > 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.