使用multcomp设置三向交互的对比度

Question

我在2007年之前和2011年之后在三个地点进行了BACI实验。我很难设置对比度，所以我可以看看三个部位的治疗效果是否不同（对照组）。

我试图扩展小插曲中的例子，但没有成功。我也试过lsmeans包。

下面的示例df和代码，以及我想测试的明确对比。

library(nlme)
library(multcomp)
require(lsmeans)
# I have these versions:
# R version 3.2.4 Revised (2016-03-16 r70336)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 7 x64 (build 7601) Service Pack 1
# nlme_3.1-126
# multcomp_1.4-4 

exdf <- expand.grid(Site = c("Z",  "Y", "X"), 
                   Plot = 1:30,
                   Year = c("2007", "2011"), 
                   Treatment = c("Control", "A", "B", "A+B"))
exdf$Site <- factor(exdf$Site)
exdf$Plot <- factor(exdf$Plot)
exdf$Year <- factor(exdf$Year)
exdf$Treatment <- factor(exdf$Treatment)
exdf$Treatment <- relevel(exdf$Treatment, ref = "Control")
exdf$Response <- rnorm(mean = 1150, sd = 130, n = nrow(exdf))
mod1 <- lme(data = exdf,
            fixed =  Response ~ Year * Treatment * Site,
            random = ~1|Plot)

## would like to test (obviously that's not actual code)
## How do the treatments A, B, A+B differ in their interaction with 
## year, compared to the control treatment (ie do the slopes differ)
SiteX:Year:TreatmentControl - SiteX:Year:TreatmentA == 0
SiteX:Year:TreatmentControl - SiteX:Year:TreatmentB == 0
SiteX:Year:TreatmentControl - SiteX:Year:TreatmentA+B == 0
SiteY:Year:TreatmentControl - SiteY:Year:TreatmentA == 0
SiteY:Year:TreatmentControl - SiteY:Year:TreatmentB == 0
SiteY:Year:TreatmentControl - SiteY:Year:TreatmentA+B == 0
SiteZ:Year:TreatmentControl - SiteZ:Year:TreatmentA == 0
SiteZ:Year:TreatmentControl - SiteZ:Year:TreatmentB == 0
SiteZ:Year:TreatmentControl - SiteZ:Year:TreatmentA+B == 0
## Also potentially - does the interaction between site and year
## differ across sites? 
SiteX:Year:TreatmentA - SiteY:Year:TreatmentA == 0
SiteZ:Year:TreatmentA - SiteY:Year:TreatmentA == 0
SiteZ:Year:TreatmentA - SiteX:Year:TreatmentA == 0
SiteX:Year:TreatmentB - SiteY:Year:TreatmentB == 0
SiteZ:Year:TreatmentB - SiteY:Year:TreatmentB == 0
SiteZ:Year:TreatmentB - SiteX:Year:TreatmentB == 0
SiteX:Year:TreatmentA+B - SiteY:Year:TreatmentA+B == 0
SiteZ:Year:TreatmentA+B - SiteY:Year:TreatmentA+B == 0
SiteZ:Year:TreatmentA+B - SiteX:Year:TreatmentA+B == 0

## Started doing the example from 
#https://cran.r-project.org/web/packages/multcomp/vignettes/multcomp-examples.pdf
# Got a bit stuck
tmp <- expand.grid(Year = levels(exdf$Year),
                   Treatment = levels(exdf$Treatment),
                   Site = levels(exdf$Site))
X <- model.matrix(~ Year * Treatment * Site, data = tmp)
glht(mod1, linfct = X)

## Gives all the interactions not in the form I want..
tt <- lsmeans(mod1, specs = ~Year:Treatment|Site)
comps <- pairs(tt, interaction = TRUE)
summary(comps,  adjust = "holm")

Answer 1

让我们分步骤构建它。首先，你们想得到其他因素的每种组合的两年差异。这很容易在lsmeans中使用完成

tt = lsmeans(mod1, specs = ~ Year | Treatment:Site)
dd = pairs(tt, reverse = TRUE)   # (2011) - (2008) for each T*S comb
summary(dd, by = NULL)

您现在可以随心所欲地比较这些差异：

pairs(dd, by = "Site")
pairs(dd, by = "Treatment")

或者稍微比较一下：

pairs(lsmeans(dd, "Treatment"))
pairs(lsmeans(dd, "Site"))