On May 27, 2015, at 10:10 AM, Kengo Inagaki wrote: > I am currently working on a health care related project using R. I am > learning R while working on data analysis. > > Below is the part of the data in which i am encountering a problem. > > > Case# Sex Therapy1 Therapy2 Outcome > > 1 male no > no Alive >
snipped mangled data sent in HTML > > > "Outcome" is the response variable and "Sex", "Therapy1", "Therapy2" are > predictor variables. > > All of the predictors are significantly associated with the outcome by > univariate analysis. > > Logistic regression runs fine with most of the predictors when "Sex" and > "Therapy1" are not included at the same time (This is a part of table that > I cut out from a larger table for ease of > > presentation and there are more predictors that i tested). Please examine the data before reaching for ridge regression: What does this show: ... with(a, table(Sex, Therapy1) ) I predict you will see a zero cell entry. The read about "complete separation" and the so-called "Hauck-Donner effect". -- David. > > However, when "Sex" and "Therapy1" are included in logistic regression > model at the same time, standard error inflates and p value gets close to 1. > > The formula used is, > > > >> Model<-glm(Outcome~Sex+Therapy1,data=a,family=binomial) #I assigned a > vector "a" to represent above table. > > > > After doing some reading, I suspect this might be collinearity, as vif > values (using "vif()" function in car package) were sky high (8,875,841 for > both "Sex" and "Therapy1"). > > Learning that ridge regression may be a solution, I attempted using > logisticRidge {ridge} using the following formula, but i get the > accomapnying error message. > > > >> logisticRidge(a$Outcome~a$Sex+a$Therapy1) > > > > Error in ifelse(y, log(p), log(1 - p)) : > > invalid to change the storage mode of a factor > > > > At this point I do not have an idea how to solve this and would like to > seek help. > > I really really appreciate your input!!! > > [[alternative HTML version deleted]] > David Winsemius Alameda, CA, USA ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.