[R] as.ordered
Gavin Simpson
gavin.simpson at ucl.ac.uk
Tue Oct 9 17:38:24 CEST 2007
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
> >>>> birgit.lemcke at systbot.uzh.ch
> >>>>
> >>>> ______________________________________________
> >>>> R-help at 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 at 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
> >> birgit.lemcke at systbot.uzh.ch
> >>
> >> ______________________________________________
> >> R-help at 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
> birgit.lemcke at systbot.uzh.ch
>
>
>
>
>
--
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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
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