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Mar 20th, 2019
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  1. library(emmeans)
  2. library(lme4)
  3.  
  4. # generate some sample data
  5. # condition (Placebo, Treatment)
  6. # type (some factor, e.g. two different medications)
  7. # value (outcome of interest)
  8. # subject
  9.  
  10. 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)))
  11.  
  12. # caluculate a mixed model
  13. fit_data <- lmer(value ~ condition*type + (1|subject), data = data)
  14.  
  15. # emmeans post-hoc test
  16. emmeans(fit_data, pairwise ~ condition | type)
  17.  
  18. # paired t-test
  19. t.test(data[data$condition==0 & data$type=="A","value"], data[data$condition==1 & data$type=="A","value"], paired = TRUE)
  20. t.test(data[data$condition==0 & data$type=="B","value"], data[data$condition==1 & data$type=="B","value"], paired = TRUE)
  21.  
  22. set.seed(12345)
  23. data <- data.frame(condition = as.factor(rep(c(0,1), times = 10)),
  24. value = rnorm(20), type = rep(c("A","B"), each = 10),
  25. subject = as.factor(rep(rep(1:5, each = 2), times = 2)))
  26.  
  27. > t.test(data[data$condition==0 & data$type=="A","value"],
  28. + data[data$condition==1 & data$type=="A","value"], paired = TRUE)
  29.  
  30. Paired t-test
  31.  
  32. data: data[data$condition == 0 & data$type == "A", "value"] and
  33. data[data$condition == 1 & data$type == "A", "value"]
  34. t = 1.9384, df = 4, p-value = 0.1246
  35. alternative hypothesis: true difference in means is not equal to 0
  36. 95 percent confidence interval:
  37. -0.3618957 2.0361137
  38. sample estimates:
  39. mean of the differences
  40. 0.837109
  41.  
  42. > library(lme4)
  43. > mod1 = lmer(value ~ condition*type + (1|subject), data = data)
  44. > pairs(emmeans(mod1, ~ condition | type))
  45.  
  46. type = A:
  47. contrast estimate SE df t.ratio p.value
  48. 0 - 1 0.837 0.475 12 1.764 0.1032
  49.  
  50. type = B:
  51. contrast estimate SE df t.ratio p.value
  52. 0 - 1 -0.677 0.475 12 -1.426 0.1795
  53.  
  54. > mod2 = lmer(value ~ condition + (1|subject), data = data,
  55. + subset = (type == "A"))
  56.  
  57. > pairs(emmeans(mod2, ~ condition))
  58. contrast estimate SE df t.ratio p.value
  59. 0 - 1 0.837 0.432 4 1.938 0.1246
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