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Oct 12th, 2017
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  1. require(gsheet)
  2. data <- read.csv(text =
  3. gsheet2text('https://docs.google.com/spreadsheets/d/1QgtDcGJebyfW7TJsB8n6rAmsyAnlz1xkT3RuPFICTdk/edit?usp=sharing',
  4. format ='csv'))
  5.  
  6. > head(data)
  7. Subject Auditorium Education Time Emotion Caffeine Recall
  8. 1 Jim A HS 0 Negative 95 125.80
  9. 2 Jim A HS 0 Neutral 86 123.60
  10. 3 Jim A HS 0 Positive 180 204.00
  11. 4 Jim A HS 1 Negative 200 95.72
  12. 5 Jim A HS 1 Neutral 40 75.80
  13. 6 Jim A HS 1 Positive 30 84.56
  14.  
  15. library(ggplot2)
  16. p <- ggplot(data, aes(x = Caffeine, y = Recall, colour = Subject)) +
  17. geom_point(size=3) +
  18. geom_line(aes(y = predict(fit1)),size=1)
  19. print(p)
  20.  
  21. p <- ggplot(data, aes(x = Caffeine, y = Recall, colour = Subject)) +
  22. geom_point(size=3) +
  23. geom_line(aes(y = predict(fit2)),size=1)
  24. print(p)
  25.  
  26. > data$predict = predict(fit2)
  27. > head(data)
  28. Subject Auditorium Education Time Emotion Caffeine Recall predict
  29. 1 Jim A HS 0 Negative 95 125.80 132.45609
  30. 2 Jim A HS 0 Neutral 86 123.60 130.55145
  31. 3 Jim A HS 0 Positive 180 204.00 150.44439
  32. 4 Jim A HS 1 Negative 200 95.72 112.37045
  33. 5 Jim A HS 1 Neutral 40 75.80 78.51012
  34. 6 Jim A HS 1 Positive 30 84.56 76.39385
  35.  
  36. $`Time:Subject`
  37. (Intercept) Caffeine
  38. 0:Jason 75.03040 0.2116271
  39. 0:Jim 94.96442 0.2116271
  40. 0:Ron 58.72037 0.2116271
  41. 0:Tina 70.81225 0.2116271
  42. 0:Victor 86.31101 0.2116271
  43. 1:Jason 59.85016 0.2116271
  44. 1:Jim 52.65793 0.2116271
  45. 1:Ron 57.48987 0.2116271
  46. 1:Tina 68.43393 0.2116271
  47. 1:Victor 79.18386 0.2116271
  48. 2:Jason 43.71483 0.2116271
  49. 2:Jim 42.08250 0.2116271
  50. 2:Ron 58.44521 0.2116271
  51. 2:Tina 44.73748 0.2116271
  52. 2:Victor 36.33979 0.2116271
  53.  
  54. $Subject
  55. (Intercept) Caffeine
  56. Jason 30.40435 0.2116271
  57. Jim 79.30537 0.2116271
  58. Ron 13.06175 0.2116271
  59. Tina 54.12216 0.2116271
  60. Victor 132.69770 0.2116271
  61.  
  62. > coef(fit2)[[1]][2,1]
  63. [1] 94.96442
  64. > coef(fit2)[[2]][2,1]
  65. [1] 79.30537
  66. > coef(fit2)[[1]][2,2]
  67. [1] 0.2116271
  68. > data$Caffeine[1]
  69. [1] 95
  70. > coef(fit2)[[1]][2,1] + coef(fit2)[[2]][2,1] + coef(fit2)[[1]][2,2] * data$Caffeine[1]
  71. [1] 194.3744
  72.  
  73. > ranef(fit2)
  74. $`Time:Subject`
  75. (Intercept)
  76. 0:Jason 13.112130
  77. 0:Jim 33.046151
  78. 0:Ron -3.197895
  79. 0:Tina 8.893985
  80. 0:Victor 24.392738
  81. 1:Jason -2.068105
  82. 1:Jim -9.260334
  83. 1:Ron -4.428399
  84. 1:Tina 6.515667
  85. 1:Victor 17.265589
  86. 2:Jason -18.203436
  87. 2:Jim -19.835771
  88. 2:Ron -3.473053
  89. 2:Tina -17.180791
  90. 2:Victor -25.578477
  91.  
  92. $Subject
  93. (Intercept)
  94. Jason -31.513915
  95. Jim 17.387103
  96. Ron -48.856516
  97. Tina -7.796104
  98. Victor 70.779432
  99.  
  100. > summary(fit2)$coef[1]
  101. [1] 61.91827 # Overall intercept for Fixed Effects
  102. > ranef(fit2)[[1]][2,]
  103. [1] 33.04615 # Time:Subject random intercept for Jim
  104. > ranef(fit2)[[2]][2,]
  105. [1] 17.3871 # Subject random intercept for Jim
  106. > summary(fit2)$coef[2]
  107. [1] 0.2116271 # Fixed effect slope
  108. > data$Caffeine[1]
  109. [1] 95 # Value of caffeine
  110.  
  111. summary(fit2)$coef[1] + ranef(fit2)[[1]][2,] + ranef(fit2)[[2]][2,] +
  112. summary(fit2)$coef[2] * data$Caffeine[1]
  113. [1] 132.4561
  114.  
  115. > summary(fit2)
  116. Linear mixed model fit by REML ['lmerMod']
  117. Formula: Recall ~ (1 | Subject/Time) + Caffeine
  118. Data: data
  119.  
  120. REML criterion at convergence: 444.5
  121.  
  122. Scaled residuals:
  123. Min 1Q Median 3Q Max
  124. -1.88657 -0.46382 -0.06054 0.31430 2.16244
  125.  
  126. Random effects:
  127. Groups Name Variance Std.Dev.
  128. Time:Subject (Intercept) 558.4 23.63
  129. Subject (Intercept) 2458.0 49.58
  130. Residual 675.0 25.98
  131. Number of obs: 45, groups: Time:Subject, 15; Subject, 5
  132.  
  133. Fixed effects:
  134. Estimate Std. Error t value
  135. (Intercept) 61.91827 25.04930 2.472
  136. Caffeine 0.21163 0.07439 2.845
  137.  
  138. Correlation of Fixed Effects:
  139. (Intr)
  140. Caffeine -0.365
  141.  
  142. > ranef(fit2)
  143. $`Time:Subject`
  144. (Intercept)
  145. 0:Jason 13.112130
  146. 0:Jim 33.046151
  147. 0:Ron -3.197895
  148. 0:Tina 8.893985
  149. 0:Victor 24.392738
  150. 1:Jason -2.068105
  151. 1:Jim -9.260334
  152. 1:Ron -4.428399
  153. 1:Tina 6.515667
  154. 1:Victor 17.265589
  155. 2:Jason -18.203436
  156. 2:Jim -19.835771
  157. 2:Ron -3.473053
  158. 2:Tina -17.180791
  159. 2:Victor -25.578477
  160.  
  161. $Subject
  162. (Intercept)
  163. Jason -31.513915
  164. Jim 17.387103
  165. Ron -48.856516
  166. Tina -7.796104
  167. Victor 70.779432
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