Nicholas Negovetich
2018-Apr-24 17:49 UTC
[R] TukeyHSD and glht differ for models with a covariate
I have a question about TukeyHSD and the glht function because I'm getting different answers when a covariate is included in model for ANCOVA.? I'm using the cabbages dataset in the 'MASS' package for repeatability.? If I include HeadWt as a covariate, then I get different answers when performing multiple comparisons using TukeyHSD and the glht function. The difference appears related to the predicted means used in the Tukey posthoc test. The glht function uses the marginal means, which I can obtain using the effect function in the 'effects' package.? TukeyHSD generates the means using the model.tables function.? Per the help file, "the implementation is incomplete, and only simpler cases have been tested thoroughly". Does this mean that TukeyHSD shouldn't be used when covariates are included in the model? Could anyone elaborate on why the model.tables function is generating means that differ from the effect function?? Thanks... #-------------------------------- # Load libraries and data library(multcomp) library(effects) data(cabbages, package='MASS') #create the model mod1 <- lm(VitC~HeadWt+Cult+Date, data=cabbages) # Using TukeyHSD TukeyHSD(aov(mod1), which='Date') #? Tukey multiple comparisons of means # ? 95% family-wise confidence level # #Fit: aov(formula = mod1) # #$Date #????????????? diff??????? lwr????? upr???? p adj #d20-d16 -0.9216847 -5.5216345 3.678265 0.8797985 #d21-d16? 3.4237706 -1.1761792 8.023720 0.1814431 #d21-d20? 4.3454553 -0.2544945 8.945405 0.0678038 # Tukey contrasts in glht should generate the same difference in means, but it does not summary(glht(mod1, linfct=mcp(Date='Tukey'))) # #???? Simultaneous Tests for General Linear Hypotheses # #Multiple Comparisons of Means: Tukey Contrasts # # #Fit: lm(formula = VitC ~ HeadWt + Cult + Date, data = cabbages) # #Linear Hypotheses: #?????????????? Estimate Std. Error t value Pr(>|t|) #d20 - d16 == 0?? -1.213????? 1.926? -0.630?? 0.8042 #d21 - d16 == 0??? 4.186????? 2.018?? 2.074?? 0.1044 #d21 - d20 == 0??? 5.400????? 2.112?? 2.556?? 0.0351 * #--- #Signif. codes:? 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 #(Adjusted p values reported -- single-step method) # Differences used for glht could be obtained with the effect function effect('Date', mod1) # # Date effect #Date #???? d16????? d20????? d21 #56.95889 55.74578 61.14533 # model.tables() is used to generate the means for TukeyHSD model.tables(aov(mod1), type='means')$tables$Date #Date #???? d16????? d20????? d21 #57.11597 56.19429 60.53974 #Warning message: #In replications(paste("~", xx), data = mf) : non-factors ignored: HeadWt
Possibly Parallel Threads
- Help on R Coding
- Sweave recode(car) and Lyx, compiling but not executing on Mac
- RWin 1.2.1: Can't access sample datasets, e.g. MASS
- Fwd: Re: RWin 1.2.1: Can't access sample datasets, e.g. MASS
- [PATCH 3/5] resample: Add NEON optimized inner_product_single for fixed point