Hello Gavin, I am so sorry that I haven´t read your mail accurately.
Now I tried all and it works very well and is exactly what I need. Many thanks for your help. And also many thanks to all the other people helping me. Greetings Birgit Am 09.10.2007 um 17:38 schrieb Gavin Simpson: > On Tue, 2007-10-09 at 17:12 +0200, Birgit Lemcke wrote: >> Hello Gavin, >> >> thanks for your answer. >> >> Answering to your sort.list a data frame. I tried to convert it to a >> vector but it was also not successful: >> >> bract.awnMin<-as.vector(bract.awnMin) > > Why did you expect that to work? I guess you didn't check the result: > > ## using dat.fac from my earlier email: >> str(as.vector(dat.fac)) > 'data.frame': 10 obs. of 3 variables: > $ fac1: Factor w/ 4 levels "2","3","4","5": 4 1 3 4 3 3 4 2 2 3 > $ fac2: Factor w/ 6 levels "1","2","4","8",..: 6 5 5 3 1 1 6 4 2 6 > $ fac3: Factor w/ 4 levels "1","3","6","8": 4 3 3 2 4 1 4 4 3 3 >> class(as.vector(dat.fac)) > [1] "data.frame" > >> sort.list(bract.awnMin) >> Fehler in sort.list(bract.awnMin) : >> 'x' must be atomic for 'sort.list' >> Have you called 'sort' on a list? > > Whilst you are learning, you are going to get yourself in all sorts of > mess if you make assumptions about what certain functions do. Take > things step by step, and check the output of your commands as you go. > Here class() and str() are useful friends to have around. If you'd > used > them, as I have here, you'd have seen that you'd made a mistake very > early on and could then act to correct that, rather than get stuck > under > lots of permutations of things you think might work. > >> >> Now I will explain what I need. >> >> I have two datasets, each with two ordered multistate variables in >> columns. >> I would like to calculate the dissmiliarity using daisy(cluster). >> >> As I understood I have to order the values to be able to convert the >> variables into ordered factors? >> Is that right? > > No, you don't need to order then at all. The levels are what is > important. Below burried in your original email your example data > shows > something like I have here, that the levels go from low to high. > as.ordered treats these appropriately in this case. > > So the answer is in my email, you don't need order(): > >> dat.fac > fac1 fac2 fac3 > 1 5 10 8 > 2 2 9 6 > 3 4 9 6 > 4 5 4 3 > 5 4 1 8 > 6 4 1 1 > 7 5 10 8 > 8 3 8 8 > 9 3 2 6 > 10 4 10 6 >> dat.fac.ordered <- data.frame(lapply(dat.fac, as.ordered)) >> dat.fac.ordered > fac1 fac2 fac3 > 1 5 10 8 > 2 2 9 6 > 3 4 9 6 > 4 5 4 3 > 5 4 1 8 > 6 4 1 1 > 7 5 10 8 > 8 3 8 8 > 9 3 2 6 > 10 4 10 6 >> str(dat.fac.ordered) > 'data.frame': 10 obs. of 3 variables: > $ fac1: Ord.factor w/ 4 levels "2"<"3"<"4"<"5": 4 1 3 4 3 3 4 2 2 3 > $ fac2: Ord.factor w/ 6 levels "1"<"2"<"4"<"8"<..: 6 5 5 3 1 1 6 4 > 2 6 > $ fac3: Ord.factor w/ 4 levels "1"<"3"<"6"<"8": 4 3 3 2 4 1 4 4 3 3 > > Note this hasn't sorted the data frame in any way, R just now knows > that > each of the elements of the data frame are *ordered* factors - note > the > "<" in the levels info printed by str(). > > This of course assumes that all variables in your data frame are > factors, which they are in your case. > > Is this what you want? > > HTH > > G > >> >> But for me the problem here is, that the rows should stay together as >> they are in the original dataset what is not possible if I have to >> order each variable separately. >> >> Is there another way to classify variables as ordered factors? >> >> Thanks in advance and sorry for my surely sometimes stupid questions. >> >> Birgit >> >> Am 09.10.2007 um 16:23 schrieb Gavin Simpson: >> >>> Birgit, >>> >>> First things first, stop trying to sort.list a data frame. This >>> is why >>> you are getting the error. It is still a dataframe whether it has 1 >>> column or 100. ?sort.list clearly says argument 'x' is a vector, >>> and as >>> this shows, you are not passing it a vector >>> >>>> dat0 <- data.frame(var1 = runif(10)) >>>> class(dat0) >>> [1] "data.frame" >>>> sort.list(dat0) >>> Error in sort.list(dat0) : 'x' must be atomic for 'sort.list' >>> Have you called 'sort' on a list? >>> >>> This will work, >>> >>>> sort.list(dat$var1) >>> [1] 8 2 3 10 9 4 6 7 1 5 >>> >>> But returns the sorted *vector*, which is not what you want if I >>> understand you. >>> >>> Secondly, sort is not the correct tool for this job (again, if I've >>> understood what you are trying to achieve). Consider this example >>> with 3 >>> variables and I want to order them on the first two columns only: >>> >>>> dat <- data.frame(var1 = runif(10), var2 = runif(10), var3 = >>> runif(10)) >>>> dat >>> var1 var2 var3 >>> 1 0.6489870 0.0007092352 0.1577805 >>> 2 0.2248372 0.6350688518 0.5345221 >>> 3 0.3031260 0.9814894125 0.9830289 >>> 4 0.3512622 0.7134463033 0.3758332 >>> 5 0.9920157 0.0905250614 0.4813042 >>> 6 0.3578282 0.9150679281 0.3739445 >>> 7 0.4420517 0.2544773000 0.3243123 >>> 8 0.1610078 0.3951566671 0.5922013 >>> 9 0.3454540 0.7033491128 0.2121476 >>> 10 0.3224135 0.2658058712 0.9959194 >>>> ord <- order(dat$var1, dat$var2) >>>> ## if you need ordering on more columns, just add >>>> ## then in the line above >>>> dat.ord <- dat[ord, ] >>>> dat.ord >>> var1 var2 var3 >>> 8 0.1610078 0.3951566671 0.5922013 >>> 2 0.2248372 0.6350688518 0.5345221 >>> 3 0.3031260 0.9814894125 0.9830289 >>> 10 0.3224135 0.2658058712 0.9959194 >>> 9 0.3454540 0.7033491128 0.2121476 >>> 4 0.3512622 0.7134463033 0.3758332 >>> 6 0.3578282 0.9150679281 0.3739445 >>> 7 0.4420517 0.2544773000 0.3243123 >>> 1 0.6489870 0.0007092352 0.1577805 >>> 5 0.9920157 0.0905250614 0.4813042 >>> >>> Now I see that you have factors, so lets try that: >>> >>>> dat.fac <- data.frame(fac1 = as.factor(sample(1:5, 10, replace = >>>> TRUE)), >>> fac2 = as.factor(sample(1:10, 10, replace = >>> TRUE)), >>> fac3 = as.factor(sample(c(1,3,6,8), 10, >>> replace = TRUE))) >>>> dat.fac >>> fac1 fac2 fac3 >>> 1 5 10 8 >>> 2 2 9 6 >>> 3 4 9 6 >>> 4 5 4 3 >>> 5 4 1 8 >>> 6 4 1 1 >>> 7 5 10 8 >>> 8 3 8 8 >>> 9 3 2 6 >>> 10 4 10 6 >>>> ord <- order(dat.fac$fac1, dat.fac$fac2) >>>> ord [1] 2 9 8 5 6 3 10 4 1 7 >>>> dat.fac.ord <- dat.fac[ord, ] >>>> dat.fac.ord fac1 fac2 fac3 >>> 2 2 9 6 >>> 9 3 2 6 >>> 8 3 8 8 >>> 5 4 1 8 >>> 6 4 1 1 >>> 3 4 9 6 >>> 10 4 10 6 >>> 4 5 4 3 >>> 1 5 10 8 >>> 7 5 10 8 >>> >>> Read ?order, and see that it's first argument is ... and this is >>> supposed to be (quoting from ?order): >>> >>> Arguments: >>> >>> ...: a sequence of numeric, complex, character or logical >>> vectors, >>> all of the same length. >>> >>> Hence why my example works - assuming that is what you wanted of >>> course. >>> >>>> From now on though I'm less clear what you actually need. Is what >>>> I did >>> above sufficient? If you need to convert the factors to be >>> *ordered* in >>> the R sense, such that one level is treated higher or lower in value >>> than another, we need something else - perhaps in addition, which >>> applies as.ordered() to each element of the data frame in turn: >>> >>>> ## continue with the ordered data frame of factors from above >>>> ## but now convert each factor to an ordered factor >>>> new.fac.ord <- data.frame(lapply(dat.fac.ord, as.ordered)) >>>> new.fac.ord >>> fac1 fac2 fac3 >>> 1 2 9 6 >>> 2 3 2 6 >>> 3 3 8 8 >>> 4 4 1 8 >>> 5 4 1 1 >>> 6 4 9 6 >>> 7 4 10 6 >>> 8 5 4 3 >>> 9 5 10 8 >>> 10 5 10 8 >>>> str(new.fac.ord) >>> 'data.frame': 10 obs. of 3 variables: >>> $ fac1: Ord.factor w/ 4 levels "2"<"3"<"4"<"5": 1 2 2 3 3 3 3 4 4 4 >>> $ fac2: Ord.factor w/ 6 levels "1"<"2"<"4"<"8"<..: 5 2 4 1 1 5 6 3 >>> 6 6 >>> $ fac3: Ord.factor w/ 4 levels "1"<"3"<"6"<"8": 3 3 4 4 1 3 3 2 4 4 >>> >>> But I suspect this is not what you wanted as you use order() to >>> achieve >>> partly a solution but ordering on a single variable. >>> >>> HTH >>> >>> G >>> >>> On Tue, 2007-10-09 at 11:14 +0200, Birgit Lemcke wrote: >>>> Hello Friedrich, >>>> >>>> thanks for your help and it is really not important that the >>>> solution >>>> is elegant. Important is only that there is a solution. >>>> >>>> But I still have some problems with this topic. >>>> >>>> #I tried as you suggested to order the vectors separately. My first >>>> problem is that my data is a data.frame: >>>> >>>> data.frame': 348 obs. of 1 variable: >>>> $ bracts.length.relative.to.flower...............Min: Factor w/ 4 >>>> levels "1","2","3","4": 2 3 3 3 3 2 1 4 3 2 ... >>>> >>>> bracts.length.relative.to.flower...............Min >>>> 1 2 >>>> 2 3 >>>> 3 3 >>>> 4 3 >>>> 5 3 >>>> 6 2 >>>> >>>> >>>> #I tried to convert it to a vector using this: >>>> >>>> bract.awnMin<-as.vector(bract.awnMin) >>>> >>>> '#and then to use sort.list: >>>> >>>> sort.list(bract.awnMin) >>>> Fehler in sort.list(bract.awnMin) : >>>> 'x' must be atomic for 'sort.list' >>>> Have you called 'sort' on a list? >>>> >>>> #if I try to use the following for the data.frame with two >>>> variables, >>>> it works well. >>>> >>>> bract.awn[order(bract.awn[,1]),] >>>> >>>> #but I have tu order both variables an therefore I should do that >>>> separately and then use cbind. >>>> >>>> Can somebody help me with my problem please? >>>> >>>> Greetings >>>> >>>> Birgit >>>> >>>> >>>> >>>> >>>> >>>> >>>> Am 08.10.2007 um 20:46 schrieb Friedrich Schuster: >>>> >>>>> >>>>> Hello, >>>>> >>>>> (Warning. This might not be the most complete or elegant >>>>> solution ...) >>>>> >>>>> If you want a sorted dataframe: look here for example >>>>> http://tolstoy.newcastle.edu.au/R/help/05/02/12391.html >>>>> >>>>> To convert the factors from a data frame, you have to call >>>>> as.ordered for >>>>> each factor separately (not for the dataframe). >>>>> To convert two factors a and b and merge them into a new >>>>> dataframe: >>>>> newFrame <- as.data.frame(cbind(as.ordered(a),as.ordered(b))) >>>>> l >>>>> For a larger number of factors this can be done with a loop or >>>>> better one of >>>>> the "apply"-functions. >>>>> >>>>> Hope this helps, >>>>> Friedrich Schuster >>>>> >>>>> >>>>> Birgit Lemcke wrote: >>>>>> >>>>>> Hello Members, >>>>>> >>>>>> I try to convert variables in a data.frame (bract.awn) in the >>>>>> class >>>>>> ordered. >>>>>> >>>>>> str(bract.awn) >>>>>> 'data.frame': 348 obs. of 2 variables: >>>>>> $ bracts.length.relative.to.flower...............Min: Factor w/ 4 >>>>>> levels "1","2","3","4": 2 3 3 3 3 2 1 4 3 2 ... >>>>>> $ bract.awn.relative.to.body.................Max : Factor w/ 4 >>>>>> levels "1","2","3","4": 1 3 2 1 4 1 1 1 1 1 >>>>>> >>>>>> >>>>>> I tried this: >>>>>> >>>>>> bract.awn<-as.ordered(bract.awn) >>>>>> >>>>>> Fehler in sort.list(unique.default(x), na.last = TRUE) : >>>>>> 'x' must be atomic for 'sort.list' >>>>>> Have you called 'sort' on a list? >>>>>> >>>>>> What am I doing wrong? >>>>>> >>>>>> Thanks a lot in advance. >>>>>> >>>>>> Regards >>>>>> >>>>>> Birgit >>>>>> >>>>>> >>>>>> >>>>>> Birgit Lemcke >>>>>> Institut für Systematische Botanik >>>>>> Zollikerstrasse 107 >>>>>> CH-8008 Zürich >>>>>> Switzerland >>>>>> Ph: +41 (0)44 634 8351 >>>>>> [EMAIL PROTECTED] >>>>>> >>>>>> ______________________________________________ >>>>>> 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. >>>>>> >>>>>> >>>>> >>>>> -- >>>>> View this message in context: http://www.nabble.com/as.ordered- >>>>> tf4589454.html#a13102513 >>>>> Sent from the R help mailing list archive at Nabble.com. >>>>> >>>>> ______________________________________________ >>>>> 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. >>>> >>>> Birgit Lemcke >>>> Institut für Systematische Botanik >>>> Zollikerstrasse 107 >>>> CH-8008 Zürich >>>> Switzerland >>>> Ph: +41 (0)44 634 8351 >>>> [EMAIL PROTECTED] >>>> >>>> ______________________________________________ >>>> 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. >>> -- >>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ >>> %~% >>> Gavin Simpson [t] +44 (0)20 7679 0522 >>> ECRC, UCL Geography, [f] +44 (0)20 7679 0565 >>> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk >>> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ >>> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk >>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ >>> %~% >>> >> >> Birgit Lemcke >> Institut für Systematische Botanik >> Zollikerstrasse 107 >> CH-8008 Zürich >> Switzerland >> Ph: +41 (0)44 634 8351 >> [EMAIL PROTECTED] >> >> >> >> >> > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > Gavin Simpson [t] +44 (0)20 7679 0522 > ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] ______________________________________________ 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.
