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- library(emmeans)
- library(lme4)
- # generate some sample data
- # condition (Placebo, Treatment)
- # type (some factor, e.g. two different medications)
- # value (outcome of interest)
- # subject
- data <- data.frame(condition = as.factor(rep(c(0,1), times = 10)), value = rnorm(20), type = rep(c("A","B"), each = 10), subject = as.factor(rep(rep(1:5, each = 2), times = 2)))
- # caluculate a mixed model
- fit_data <- lmer(value ~ condition*type + (1|subject), data = data)
- # emmeans post-hoc test
- emmeans(fit_data, pairwise ~ condition | type)
- # paired t-test
- t.test(data[data$condition==0 & data$type=="A","value"], data[data$condition==1 & data$type=="A","value"], paired = TRUE)
- t.test(data[data$condition==0 & data$type=="B","value"], data[data$condition==1 & data$type=="B","value"], paired = TRUE)
- set.seed(12345)
- data <- data.frame(condition = as.factor(rep(c(0,1), times = 10)),
- value = rnorm(20), type = rep(c("A","B"), each = 10),
- subject = as.factor(rep(rep(1:5, each = 2), times = 2)))
- > t.test(data[data$condition==0 & data$type=="A","value"],
- + data[data$condition==1 & data$type=="A","value"], paired = TRUE)
- Paired t-test
- data: data[data$condition == 0 & data$type == "A", "value"] and
- data[data$condition == 1 & data$type == "A", "value"]
- t = 1.9384, df = 4, p-value = 0.1246
- alternative hypothesis: true difference in means is not equal to 0
- 95 percent confidence interval:
- -0.3618957 2.0361137
- sample estimates:
- mean of the differences
- 0.837109
- > library(lme4)
- > mod1 = lmer(value ~ condition*type + (1|subject), data = data)
- > pairs(emmeans(mod1, ~ condition | type))
- type = A:
- contrast estimate SE df t.ratio p.value
- 0 - 1 0.837 0.475 12 1.764 0.1032
- type = B:
- contrast estimate SE df t.ratio p.value
- 0 - 1 -0.677 0.475 12 -1.426 0.1795
- > mod2 = lmer(value ~ condition + (1|subject), data = data,
- + subset = (type == "A"))
- > pairs(emmeans(mod2, ~ condition))
- contrast estimate SE df t.ratio p.value
- 0 - 1 0.837 0.432 4 1.938 0.1246
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