Brilliant, David, thank you so much!
Cheers,
Rune
> 16. mai 2017 kl. 18.44 skrev David L Carlson <dcarl...@tamu.edu>:
>
> 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]]
>
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> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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