Hello Everyone, This is my first attempt to do something in R. As a precursor to a Willingness to Pay analysis, I want to conduct a Mixed Conditional Logit analysis but am unsure how to proceed because of some nesting within my data. Below is some data and code that illustrate what I’m trying to do. The data are based on responses to a conjoint survey obtained during pilot testing. In the survey, cancer patients are asked to complete several discrete choice tasks. In each task, the patient indicates whether they prefer treatment A or treatment B. The attributes of treatment A and treatment B generally vary from one task to the next. The data also contain some of the predictors that that are presumed to influence patient choices (chance of side effects, duration of side effects, severity of side effects). The mclogit package seems like a possible avenue for conducting my analysis. The code below appears to be properly specified and produces some intuitive results. Even with only 4 respondents, there appears to be a tendency for patients to prefer treatments with a low chance of side effects, a short duration of side effects, and a low severity of side effects. The only problem is that the current setup doesn't seem to address the fact that I have multiple discrete choice tasks within each respondent. It seems to me that knowing which option person 1 chose in task 1 might also indicate something about their responses in the other conjoint tasks and that my model doesn't account for this lack of statistical independence. So I'm wondering if there is any way to perform my analysis while taking this non-independence into account. Any assistance that people can render will be most appreciated. Thanks, Paul wtp_string <- "Subject,Task,Option,selected,chance_low,chance_medium,chance_high,duration_short,duration_medium,duration_long,severity_low,severity_medium,severity_high 1,1,A,1,0,0,1,1,0,0,1,0,0 1,1,B,0,0,1,0,0,0,1,0,0,1 1,2,A,1,1,0,0,1,0,0,0,0,1 1,2,B,0,0,1,0,0,1,0,0,1,0 1,3,A,0,0,0,1,0,1,0,1,0,0 1,3,B,1,1,0,0,0,0,1,0,1,0 1,4,A,1,0,0,1,0,1,0,1,0,0 1,4,B,0,0,1,0,0,0,1,0,0,1 1,5,A,1,0,1,0,1,0,0,1,0,0 1,5,B,0,1,0,0,0,1,0,0,1,0 1,6,A,1,1,0,0,1,0,0,0,0,1 1,6,B,0,0,0,1,0,0,1,0,1,0 1,7,A,1,1,0,0,0,0,1,1,0,0 1,7,B,0,0,1,0,0,1,0,0,0,1 1,8,A,1,0,0,1,1,0,0,0,1,0 1,8,B,0,0,1,0,0,1,0,0,0,1 1,9,A,1,0,1,0,1,0,0,1,0,0 1,9,B,0,0,0,1,0,1,0,0,1,0 1,10,A,1,1,0,0,1,0,0,0,1,0 1,10,B,0,0,0,1,0,0,1,1,0,0 1,11,A,1,0,1,0,0,1,0,1,0,0 1,11,B,0,0,0,1,1,0,0,0,0,1 1,12,A,1,1,0,0,0,1,0,1,0,0 1,12,B,0,0,1,0,0,0,1,0,1,0 1,13,A,0,0,0,1,0,0,1,0,1,0 1,13,B,1,1,0,0,0,1,0,0,0,1 1,14,A,0,0,0,1,0,0,1,0,0,1 1,14,B,1,0,1,0,1,0,0,1,0,0 1,15,A,1,1,0,0,1,0,0,0,1,0 1,15,B,0,0,0,1,0,1,0,0,0,1 1,16,A,1,1,0,0,0,0,1,1,0,0 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18,10,B,0,0,0,1,0,0,1,1,0,0 18,11,A,1,0,1,0,0,1,0,1,0,0 18,11,B,0,0,0,1,1,0,0,0,0,1 18,12,A,1,1,0,0,0,1,0,1,0,0 18,12,B,0,0,1,0,0,0,1,0,1,0 18,13,A,0,0,0,1,0,0,1,0,1,0 18,13,B,1,1,0,0,0,1,0,0,0,1 18,14,A,1,0,0,1,0,0,1,0,0,1 18,14,B,0,0,1,0,1,0,0,1,0,0 18,15,A,1,1,0,0,1,0,0,0,1,0 18,15,B,0,0,0,1,0,1,0,0,0,1 18,16,A,0,1,0,0,0,0,1,1,0,0 18,16,B,1,0,1,0,0,1,0,0,1,0 18,17,A,0,0,1,0,1,0,0,0,1,0 18,17,B,1,0,0,1,0,0,1,1,0,0 18,18,A,0,1,0,0,1,0,0,1,0,0 18,18,B,1,0,0,1,0,0,1,0,0,1 18,19,A,1,1,0,0,1,0,0,0,0,1 18,19,B,0,0,0,1,0,1,0,0,1,0 18,20,A,0,0,0,1,0,0,1,0,0,1 18,20,B,1,0,1,0,1,0,0,1,0,0 18,21,A,0,1,0,0,0,1,0,1,0,0 18,21,B,1,0,1,0,0,0,1,0,0,1 18,22,A,1,0,0,1,1,0,0,1,0,0 18,22,B,0,1,0,0,0,1,0,0,1,0 18,23,A,0,1,0,0,0,1,0,0,0,1 18,23,B,1,0,1,0,0,0,1,0,1,0 18,24,A,1,0,0,1,1,0,0,0,1,0 18,24,B,0,0,1,0,0,0,1,1,0,0 18,25,A,1,1,0,0,0,0,1,1,0,0 18,25,B,0,0,1,0,1,0,0,0,0,1 19,1,A,1,0,0,1,1,0,0,1,0,0 19,1,B,0,0,1,0,0,0,1,0,0,1 19,2,A,0,1,0,0,1,0,0,0,0,1 19,2,B,1,0,1,0,0,1,0,0,1,0 19,3,A,1,0,0,1,0,1,0,1,0,0 19,3,B,0,1,0,0,0,0,1,0,1,0 19,4,A,1,0,0,1,0,1,0,1,0,0 19,4,B,0,0,1,0,0,0,1,0,0,1 19,5,A,0,0,1,0,1,0,0,1,0,0 19,5,B,1,1,0,0,0,1,0,0,1,0 19,6,A,0,1,0,0,1,0,0,0,0,1 19,6,B,1,0,0,1,0,0,1,0,1,0 19,7,A,1,1,0,0,0,0,1,1,0,0 19,7,B,0,0,1,0,0,1,0,0,0,1 19,8,A,0,0,0,1,1,0,0,0,1,0 19,8,B,1,0,1,0,0,1,0,0,0,1 19,9,A,0,0,1,0,1,0,0,1,0,0 19,9,B,1,0,0,1,0,1,0,0,1,0 19,10,A,0,1,0,0,1,0,0,0,1,0 19,10,B,1,0,0,1,0,0,1,1,0,0 19,11,A,0,0,1,0,0,1,0,1,0,0 19,11,B,1,0,0,1,1,0,0,0,0,1 19,12,A,1,1,0,0,0,1,0,1,0,0 19,12,B,0,0,1,0,0,0,1,0,1,0 19,13,A,1,0,0,1,0,0,1,0,1,0 19,13,B,0,1,0,0,0,1,0,0,0,1 19,14,A,1,0,0,1,0,0,1,0,0,1 19,14,B,0,0,1,0,1,0,0,1,0,0 19,15,A,0,1,0,0,1,0,0,0,1,0 19,15,B,1,0,0,1,0,1,0,0,0,1 19,16,A,1,1,0,0,0,0,1,1,0,0 19,16,B,0,0,1,0,0,1,0,0,1,0 19,17,A,0,0,1,0,1,0,0,0,1,0 19,17,B,1,0,0,1,0,0,1,1,0,0 19,18,A,0,1,0,0,1,0,0,1,0,0 19,18,B,1,0,0,1,0,0,1,0,0,1 19,19,A,0,1,0,0,1,0,0,0,0,1 19,19,B,1,0,0,1,0,1,0,0,1,0 19,20,A,0,0,0,1,0,0,1,0,0,1 19,20,B,1,0,1,0,1,0,0,1,0,0 19,21,A,1,1,0,0,0,1,0,1,0,0 19,21,B,0,0,1,0,0,0,1,0,0,1 19,22,A,0,0,0,1,1,0,0,1,0,0 19,22,B,1,1,0,0,0,1,0,0,1,0 19,23,A,1,1,0,0,0,1,0,0,0,1 19,23,B,0,0,1,0,0,0,1,0,1,0 19,24,A,1,0,0,1,1,0,0,0,1,0 19,24,B,0,0,1,0,0,0,1,1,0,0 19,25,A,0,1,0,0,0,0,1,1,0,0 19,25,B,1,0,1,0,1,0,0,0,0,1 20,1,A,1,0,0,1,1,0,0,1,0,0 20,1,B,0,0,1,0,0,0,1,0,0,1 20,2,A,1,1,0,0,1,0,0,0,0,1 20,2,B,0,0,1,0,0,1,0,0,1,0 20,3,A,0,0,0,1,0,1,0,1,0,0 20,3,B,1,1,0,0,0,0,1,0,1,0 20,4,A,0,0,0,1,0,1,0,1,0,0 20,4,B,1,0,1,0,0,0,1,0,0,1 20,5,A,1,0,1,0,1,0,0,1,0,0 20,5,B,0,1,0,0,0,1,0,0,1,0 20,6,A,1,1,0,0,1,0,0,0,0,1 20,6,B,0,0,0,1,0,0,1,0,1,0 20,7,A,0,1,0,0,0,0,1,1,0,0 20,7,B,1,0,1,0,0,1,0,0,0,1 20,8,A,0,0,0,1,1,0,0,0,1,0 20,8,B,1,0,1,0,0,1,0,0,0,1 20,9,A,1,0,1,0,1,0,0,1,0,0 20,9,B,0,0,0,1,0,1,0,0,1,0 20,10,A,1,1,0,0,1,0,0,0,1,0 20,10,B,0,0,0,1,0,0,1,1,0,0 20,11,A,0,0,1,0,0,1,0,1,0,0 20,11,B,1,0,0,1,1,0,0,0,0,1 20,12,A,0,1,0,0,0,1,0,1,0,0 20,12,B,1,0,1,0,0,0,1,0,1,0 20,13,A,1,0,0,1,0,0,1,0,1,0 20,13,B,0,1,0,0,0,1,0,0,0,1 20,14,A,1,0,0,1,0,0,1,0,0,1 20,14,B,0,0,1,0,1,0,0,1,0,0 20,15,A,0,1,0,0,1,0,0,0,1,0 20,15,B,1,0,0,1,0,1,0,0,0,1 20,16,A,1,1,0,0,0,0,1,1,0,0 20,16,B,0,0,1,0,0,1,0,0,1,0 20,17,A,1,0,1,0,1,0,0,0,1,0 20,17,B,0,0,0,1,0,0,1,1,0,0 20,18,A,1,1,0,0,1,0,0,1,0,0 20,18,B,0,0,0,1,0,0,1,0,0,1 20,19,A,0,1,0,0,1,0,0,0,0,1 20,19,B,1,0,0,1,0,1,0,0,1,0 20,20,A,1,0,0,1,0,0,1,0,0,1 20,20,B,0,0,1,0,1,0,0,1,0,0 20,21,A,1,1,0,0,0,1,0,1,0,0 20,21,B,0,0,1,0,0,0,1,0,0,1 20,22,A,1,0,0,1,1,0,0,1,0,0 20,22,B,0,1,0,0,0,1,0,0,1,0 20,23,A,0,1,0,0,0,1,0,0,0,1 20,23,B,1,0,1,0,0,0,1,0,1,0 20,24,A,0,0,0,1,1,0,0,0,1,0 20,24,B,1,0,1,0,0,0,1,1,0,0 20,25,A,0,1,0,0,0,0,1,1,0,0 20,25,B,1,0,1,0,1,0,0,0,0,1" wtp <- read.table(textConnection(wtp_string), header=TRUE, sep=",") View(wtp) library(mclogit) summary(mclogit( cbind(selected,Task) ~ chance_medium + chance_high + duration_medium + duration_long + severity_medium + severity_high, data=wtp)) [[alternative HTML version deleted]]