Hello dear R help group. My question is statistical and not R specific, yet I hope some of you might be willing to help.
*Experiment settings*: We have a list of subjects. each of them went through two tests with the answer to each can be either 0 or 1. *Goal*: We want to know if the two experiments yielded different results in the subjects answers. *Statistical test (and why it won't work)*: Naturally we would turn to performing a mcnemar test. But here is the twist: we have missing values in our data. For our purpose, let's assume the missingnes is completely at random, and we also have no data to use for imputation. Also, we have much more missing data for experiment number 2 then in experiment number 1. So the question is, under these settings, how do we test for experiment effect on the outcome? So far I have thought of two options: 1) To perform the test only for subjects that has both values. But they are too scarce and will yield low power. 2) To treat the data as independent and do a pearson's chi square test (well, an exact fisher test that is) on all the non-missing data that we have. The problem with this is that our data is not fully independent (which is a prerequisite to chi test, if I understood it correctly). So I am not sure if that is a valid procedure or not. Any insights will be warmly welcomed. p.s: here is an example code producing this scenario. set.seed(102) x1 <- rbinom(100, 1, .5) x2 <- rbinom(100, 1, .3) X <- data.frame(x1,x2) tX <- table(X) margin.table(tX,1) margin.table(tX,2) mcnemar.test(tX) put.missings <- function(x.vector, na.percent) { turn.na <- rbinom(length(x.vector), 1, na.percent) x.vector[turn.na == 1] <- NA return(x.vector) } x1.m <- put.missings(x1, .3) x2.m <- put.missings(x2, .6) tX.m <- rbind(table(na.omit(x1.m)), table(na.omit(x2.m))) fisher.test(tX.m) With regards, Tal -- ---------------------------------------------- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.