Lesson 6, Part 1: Linear Mixed Effects Models
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1 Lesson 6, Part 1: Linear Mixed Effects Models
2 This Lesson s Goals Learn about linear mixed effects models (LMEM) Make figures for data for LMEMs Run some preliminary LMEMs in R Summarise results in an R Markdown document
3 This Lesson s Goals Learn about linear mixed effects models (LMEM) Make figures for data for LMEMs Run some preliminary LMEMs in R Summarise results in an R Markdown document
4 End of Lesson 5 Questions But aren t percentages really just summarized count data? But we had to drop a bunch of Union states, isn t that a problem? But Alabama was missing one Democrat data point, isn t it not balanced? But what about the variance for year, shouldn t we try and account for that too? generalized linear mixed effects models
5 Math (Part 1)
6 yi = a + b1x1i + b2x2i + b3x1ix2i + ei How do I add factors for random variance? (i.e. things we re not directly testing)
7 yi = a + b1x1i + b2x2i + b3x1ix2i + ei yi = a + as + b1x1i + b2x2i + b3x1ix2i + ei random effect s = state
8 yi = a + b1x1i + b2x2i + b3x1ix2i + ei yi = a + as + b1x1i + b2x2i + b3x1ix2i + ei random intercept s = state
9 yi = a + b1x1i + b2x2i + b3x1ix2i + ei yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei random intercept #1 random intercept #2 s = state y = year
10 In this paper we tested the effect of time on weight. A total of 50 baby chicks were included in the study. ANOVA language LMEM language weight dependent variable dependent variable time independent variable fixed effect baby chick error variable random effect mixed effects
11 yi = a + as + ay + b1x1i + b2x2i +b3x1ix2i + ei yi = specific y value a = intercept as = random intercept #1 for specific level ay = random intercept #2 for specific level b1 = slope of first variable x1i = specific x value for first variable b2 = slope of second variable x2i = specific x value for second variable b3 = slope of third variable (interaction) ei = random variance or the residual
12 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
13 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
14 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
15 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
16 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Rhode Island Rhode Island Rhode Island Rhode Island 0 Union Confederacy Civil War country
17 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Kentucky Kentucky Kentucky Kentucky 0 Union Confederacy Civil War country
18 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
19 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Union Confederacy Civil War country
20 But, at the end of the last lesson we said this was bad, because it was a percentage of a count?
21 yi = a + as + ay + b1x1i + b2x2i +b3x1ix2i + ei log[p/(1-p)]i = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei logistic regression > generalized linear mixed effects model
22 R Code (Part 1)
23 lme4 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei lmer(perc_votes_incumbent ~ incumbent_party * civil_war + (1 state) + (1 year))
24 lme4 yi = a + as + ay + b1x1i + b2x2i + b3x1ix2i + ei lmer(perc_votes_incumbent ~ incumbent_party * civil_war + (1 state) + (1 year))
25 But, in the ANOVA we accounted for the fact that a variable could be within- or between-subject?
26 Math (Part 2)
27 yi = a + as + ay + b1x1i + b2x2i +b3x1ix2i + ei yi = a + as + ay + bs1+b1)x1i + (by1+b2)x2i + random slope s = state b3x1ix2i + ei random slope y = year
28 yi = a + as + ay + (bs1+b1)x1i + (by1+b2)x2i + yi = specific y value b3x1ix2i + ei x1i = x value for variable #1 a = intercept as = random intercept #1 ay = random intercept #2 bs1 = slope of r.e. #1 b1 = slope of variable #1 by1 = slope of r.e. #2 b2 = slope of variable #2 x2i = x value for variable #2 b3 = slope of variable #3 ei = random variance
29 yi = a + as + ay + (bs1+b1)x1i + (by1+b2)x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Rhode Island Rhode Island Rhode Island Rhode Island 0 Union Confederacy Civil War country
30 yi = a + as + ay + (bs1+b1)x1i + (by1+b2)x2i + b3x1ix2i + ei Percentage of Votes for Incumbent by Country in Civil War and Party of Incumbent Democrat Republican 100 Percentage of vote for incumbent Rhode Island Rhode Island Rhode Island Rhode Island Rhode Island Rhode Island Rhode Island Rhode Island 0 Union Confederacy Civil War country
31 R Code (Part 2)
32 lme4 yi = a + as + ay + (bs1+b1)x1i + (by1+b2)x2i + b3x1ix2i + ei lmer(perc_votes_incumbent ~ incumbent_party * civil_war + (1+incumbent_party state) + (1+civil_war year))
33 lme4 yi = a + as + ay + (bs1+b1)x1i + (by1+b2)x2i + b3x1ix2i + ei lmer(perc_votes_incumbent ~ incumbent_party * civil_war + (1+incumbent_party state) + (1+civil_war year))
34 LMEM with only random intercepts LMEM with only random intercepts and slopes
35 Lab
36 Data set: Stroop Task source: real students!
37 Say the color of the ink not the written word. blue
38 Say the color of the ink not the written word. blue
39 Say the color of the ink not the written word. blue blue word = ink color congruent trial word ink color incongruent trial
40 Data set: Stroop Task Congruency: Are responses to incongruent trials less accurate and slower than to congruent trials? Experiment half: Are responses more accurate and faster in the second half of the experiment than the first half of the experiment? Congruency x Experiment half: Is there an interaction between these variables? accuracy (logistic) logit pi = accuracy x1 = congruency x2 = experiment half r1 = subject r2 = item reaction times (linear) yi = reaction times x1 = congruency x2 = experiment half r1 = subject r2 = item source: real students!
41 dplyr data_clean = data_results
42 dplyr data_clean = data_results %>% rename(trial_number = SimpleRTBLock.TrialNr.) change variable name
43 dplyr data_clean = data_results %>% rename(trial_number = SimpleRTBLock.TrialNr.) %>% rename(congruency = Congruency) %>% rename(correct_response = StroopItem.CRESP.) %>% rename(given_response = StroopItem.RESP.) %>% rename(accuracy = StroopItem.ACC.) %>% rename(rt = StroopItem.RT.) %>% change variable name
44 dplyr data_clean = data_results %>% rename(trial_number = SimpleRTBLock.TrialNr.) %>% rename(congruency = Congruency) %>% rename(correct_response = StroopItem.CRESP.) %>% rename(given_response = StroopItem.RESP.) %>% rename(accuracy = StroopItem.ACC.) %>% rename(rt = StroopItem.RT.) %>% select(subject_id, block, item, trial_number, congruency, correct_response, given_response, accuracy, rt) change variable name choose subset of variables
45 RColorBrewer cols = brewer.pal(5, PuOr") call to make palette
46 RColorBrewer cols = brewer.pal(5, PuOr") call to make palette number of colors
47 RColorBrewer cols = brewer.pal(5, PuOr") call to make palette number of colors palette name
48 RColorBrewer cols = brewer.pal(5, PuOr") call to make palette number of colors palette name > cols [1] "#E66101" "#FDB863" "#F7F7F7" "#B2ABD2" "#5E3C99"
49 RColorBrewer cols = brewer.pal(5, PuOr") col_con = cols[1] call to make palette number of colors palette name > cols [1] "#E66101" "#FDB863" "#F7F7F7" "#B2ABD2" "#5E3C99"
50 RColorBrewer cols = brewer.pal(5, PuOr") col_con = cols[1] col_incon = cols[5] call to make palette number of colors palette name > cols [1] "#E66101" "#FDB863" "#F7F7F7" "#B2ABD2" "#5E3C99"
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