Fixing a typo in the original, adding a simplification, and using dissimilarity instead of similarity:
set.seed(42) dta <- data.frame(ID=1:7, gender=sample(c("M", "F"), 7, replace=TRUE), age=sample.int(75, 7)) dsim <- dist(dta$age) # distance, already lower triangular dsim dta1 <- dta names(dta1) <- paste0(names(dta), "1") # generalizes to more than 3 columns dta2 <- dta names(dta2) <- paste0(names(dta), "2") dta12 <- merge(dta2, dta1) # order is important dta12 <- dta12[dta12$ID1 < dta12$ID2, ] # get rid of duplicates dta12 <- data.frame(dta12, dsim=as.vector(dsim)) # Typo was here dta12 <- dta12[, c("ID1", "ID2", "gender1", "gender2", "age1", "age2", "dsim")] dta12 David C -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of David L Carlson Sent: Tuesday, May 16, 2017 11:21 AM To: Rune Grønseth <nielsenr...@me.com>; r-help@r-project.org Subject: Re: [R] Extracting metadata information to corresponding dissimilarity matrix I think this is what you are trying to do. I've created a data set with 7 rows and a similarity matrix based on age: set.seed(42) dta <- data.frame(ID=1:7, gender=sample(c("M", "F"), 7, replace=TRUE), age=sample.int(75, 7)) sim <- max(dist(dta$age)) - dist(dta$age) # already lower triangular sim # 1 2 3 4 5 6 # 2 24 # 3 21 59 # 4 40 46 43 # 5 0 38 41 22 # 6 7 45 48 29 55 # 7 55 31 28 47 7 14 # Now duplicate dta: dta1 <- dta names(dta1) <- c("ID1", "gender1", "age1") dta2 <- dta names(dta2) <- c("ID2", "gender2", "age2") # Now merge and eliminate unneeded rows dta12 <- merge(dta2, dta1) # order is important dta12 <- dta12[dta12$ID1 < dta12$ID2, ] # Finally combine the similarities with the combined data and rearrange # the variable names dta12 <- data.frame(dta12mod, sim=as.vector(sim)) dta12 <- dta12[, c("ID1", "ID2", "gender1", "gender2", "age1", "age2", "sim")] dta12 # ID1 ID2 gender1 gender2 age1 age2 sim # 2 1 2 F F 11 49 24 # 3 1 3 F M 11 52 21 # 4 1 4 F F 11 33 40 # 5 1 5 F F 11 73 0 # 6 1 6 F F 11 66 7 # 7 1 7 F F 11 18 55 # 10 2 3 F M 49 52 59 # 11 2 4 F F 49 33 46 # 12 2 5 F F 49 73 38 # 13 2 6 F F 49 66 45 # 14 2 7 F F 49 18 31 # 18 3 4 M F 52 33 43 # 19 3 5 M F 52 73 41 # 20 3 6 M F 52 66 48 # 21 3 7 M F 52 18 28 # 26 4 5 F F 33 73 22 # 27 4 6 F F 33 66 29 # 28 4 7 F F 33 18 47 # 34 5 6 F F 73 66 55 # 35 5 7 F F 73 18 7 # 42 6 7 F F 66 18 14 ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Rune Grønseth Sent: Tuesday, May 16, 2017 4:31 AM To: r-help@r-project.org Subject: [R] Extracting metadata information to corresponding dissimilarity matrix Hi, I am R beginner. I've tried googling and reading, but this might be too simple to be found in the documentation. I have a dissimilarity index (symmetric matrix) from which I have extracted the unique values using the exodist package command "lower". There are 14 observations, so there are 91 unique comparisons. After this I'd like to extract corresponding metadata from a separate data frame (the 14 observations organized in rows identified by a samplenumber-vector, and other variables as gender, age, et cetera). The aim is to have a new data frame with 91 rows and metadata vectors giving me the value of the dissimilarity index, gender each of the two observations that are compared by the dissimilarity metric. So if I'm looking for gender differences, I need 5 vectors in the data frame: samplenumber1, samplenumber2, gender1, gender2 and dissimilarity metric. Does anyone have suggestions or experiences in reformatting data in this manner? This is just a test-dataset. My full data-set is for more than 100 observations, so I need a more general code, if that is possible. With great appreciation of any help. Rune Grønseth --- Rune Grønseth, MD, PhD, postdoctoral fellow Department of Thoracic Medicine Haukeland University Hospital N-5021 Bergen Norway [[alternative HTML version deleted]] ______________________________________________ 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. ______________________________________________ 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. ______________________________________________ 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.