Thanoon, You should still send the question to the R help list even when I helped you with the code you are currently using. I will not always know the best way or even how to proceed with some questions. As for to your question with the code below.
Firstly, there is no 'phi' method for cor in base R. If you are using it, you must have neglected to include a package you are using. However, given that the phi coefficient is equal to the pearson coefficient for dichotomous data, you can use the 'pearson' method. Secondly, with respect to your primary concern. In this case, we have randomly chosen variables to correlate between two INDEPENDENT DATASETS (i.e. different groups of samples). The idea with this code is that R1 and R2 are datasets of 1000 samples and 10 variables. It would be miraculous if they correlated when each had variables randomly assigned as correlated. The code work correctly, the question now becomes if you want to see correlations across variables for all samples (which this does for each DATASET) or if you want two DATASETS to be correlated. ords <- seq(0,1) p <- 10 N <- 1000 percent_change <- 0.9 R1 <- as.data.frame(replicate(p, sample(ords, N, replace = T))) R2 <- as.data.frame(replicate(p, sample(ords, N, replace = T))) # phi is more appropriate for dichotomous data cor(R1, method = "phi") cor(R2, method = "phi") # subset variable to have a stronger correlation v1 <- R1[,1, drop = FALSE] v1 <- R2[,1, drop = FALSE] # randomly choose which rows to retain keep <- sample(as.numeric(rownames(v1)), size = percent_change*nrow(v1)) change <- as.numeric(rownames(v1)[-keep]) # randomly choose new values for changing new.change <- sample(ords, ((1-percent_change)*N)+1, replace = T) # replace values in copy of original column v1.samp <- v1 v1.samp[change,] <- new.change # closer correlation cor(v1, v1.samp, method = "phi") # set correlated column as one of your other columns R1[,2] <- v1.samp R2[,2] <- v1.samp R1 R2 On Thu, Jul 31, 2014 at 7:29 AM, thanoon younis <thanoon.youni...@gmail.com> wrote: > dear Dr. Charles > i have a problem with the following R - program in simulation data with 2 > different samples and with high correlation between variables in each > sample so when i applied the program i got on a results but without > correlation between each sample. > i appreciate your help and your time > i did not send this code to R- help because you helped me before to write > it . > > many thanks to you > > Thanoon > -- Dr. Charles Determan, PhD Integrated Biosciences [[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.