Re: [R] randomForest outlier

immediately by reply e-mail and then delete it from your system. === Birgit Lemcke Institut of Systematic Botany University of Zurich Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 mail: [EMAIL PROTECTED] === _

Re: [R] randomForest outlier

e a bit unusual as a similarity measure. -Original Message- From: Birgit Lemcke [mailto:[EMAIL PROTECTED] Sent: Wednesday, July 16, 2008 8:55 AM To: Liaw, Andy Cc: R Hilfe Subject: Re: [R] randomForest outlier Thanks anyway for your answer. That was also an option that I took into account (no pot

[R] calculate glm slope

Hello list-members! Is there a function that automatically calculates the slope and the confidence intervals for the different explanatory variables from the glm output? Many thanks in advance for every hint. B. = Birgit Lemcke Institut of Systematic Botany

[R] boxplot with text and symbols on x

the easiest way to implement the text and it was kind of fiddling around to find the right position for the text. I would be glad if somebody would have an easier solution. My second question is about adding symbols (usual male and female symbol) to the x-axis to label the boxes. I would

Re: [R] boxplot with text and symbols on x

ition 1 und 2 , lab=expression( "\u2642", "\u2640")) #zeichne dort Mann/Frau Symbole dev.off() But the symbols do not appear in the pdf. What is the reason for that and how can I create a pdf with the symbols. Thanks again Birgit Am 29.05.2008 um 13:13 schrieb Gabor Groth

[R] Swap variables in data.frame

swap those variables. It is easier to handle the dataset if the variables have a certain order. I will be grateful for a hint to solve this. Greets Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED

Re: [R] boxplot with text and symbols on x

] On Behalf Of Birgit Lemcke Sent: Thursday, May 29, 2008 6:05 AM To: Gabor Grothendieck Cc: R Hilfe Subject: Re: [R] boxplot with text and symbols on x Thanks that was a huge help. Now I am using this: pdf("InfLengMaxVarHomogeneity.pdf") plot(inflorescence_length_Max~Sex,xaxt="n

[R] ANCOVA

Error message. I thought the function should use with my dataset. What am I doing wrong? Thanks in advance for your help. Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH

Re: [R] ANCOVA

nt family=binomial in > the call to glm(). > > Had you included the commands that you used as well as the error that > was produced, it wouldn't be necessary to guess. > > I hope this helps, > John > > On Mon, 21 Apr 2008 14:23:13 +0200 > Birgit Lemcke <[EMAIL PRO

Re: [R] ANCOVA error again

; > Had you included the commands that you used as well as the error that > was produced, it wouldn't be necessary to guess. > > I hope this helps, > John > > On Mon, 21 Apr 2008 14:23:13 +0200 > Birgit Lemcke <[EMAIL PROTECTED]> wrote: >> R version 2.6.2

Re: [R] ANCOVA error again

l not very good in statistics. Presently I still have the same error message and don`t know how to fix this. Greets B. Am 21.04.2008 um 16:52 schrieb Gavin Simpson: > On Mon, 2008-04-21 at 15:43 +0200, Birgit Lemcke wrote: >> Hello R users! >> >> I got again an error messag

[R] randomForest and ordered factors

nce=TRUE, proximity=TRUE, ntree=1, do.trace=1000, keep.forest=FALSE) My dataset contains also ordered factors classified as such. Is randomForest able to deal with it, does it change anything or is there no difference in using factors or ordered factors? Many thanks in advance B. Bir

Re: [R] randomForest and ordered factors

ally treated as numerics in RF: trees only make use of ranks for numeric variables, so there's basically no difference between ordered factors and numeric variables as predictors.) Andy From: Birgit Lemcke Hello R-user! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and sta

[R] randomForest weighting of variables and count data

different weights to the explaining variables and additonally if it makes a difference using count data? Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH

[R] Count data in random Forest

difference because only the ranks are used in the trees? Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF

[R] Problems using rfImpute

rsely_paniculate: Factor w/ 3 levels "0","1","NA": 1 1 1 3 1 1 1 1 1 1 ... But there are still NA`s in the data frame. Sorry if this reason is only ma stupididty and thanks for answering in advance. B. Birgit Lemcke Institut für Systematische Botanik

Re: [R] Problems using rfImpute

t;NA" are different. The first is treated as missing; the second is not. For example, > table(factor(c(NA,"0","1","NA","NA"))) 0 1 NA 1 1 2 I suspect you have "NA" where you want NA, and this is causing your problem. James --

[R] How many random numbers needed?

. Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008

Re: [R] How many random numbers needed?

:21 +0200, Birgit Lemcke wrote: Hello R-People! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Perhaps this is another stupid question of me, but I was wondering how I know the needed random (set.seed) numbers, when running randomForest (library randomForest

[R] metaMDS using Dissimilarity matrix

hat causes a problem in isoMDS (vegan) Test<-isoMDS(Dist.GowerTest) Fehler in isoMDS(Dist.GowerTest) : zero or negative distance between objects 240 and 241 Sorry might be that I am just to stupid to understand the documentation, but could somebody help me anyway. Than

Re: [R] metaMDS using Dissimilarity matrix

= foo, weights=vectorname) Thanks again for help. Birgit And again Am 15.05.2008 um 13:41 schrieb Gavin Simpson: On Thu, 2008-05-15 at 13:13 +0200, Birgit Lemcke wrote: Hello R-user community! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Presently I try to

[R] glm model syntax

Hello R users! What is the difference between glm(A~N+M) glm(A~N:M) glm(A~N*M) Thanks in advance. Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen

Re: [R] glm model syntax

~ as.numeric(N)*as.numeric(M), dat) lm(y ~ as.numeric(N):as.numeric(M), dat) Then the latter two are different, but only under the coercion to numeric. -Original Message- From: Berwin A Turlach [mailto:[EMAIL PROTECTED] Sent: Friday, May 16, 2008 12:27 PM To: Doran, Harold Cc: Birgit Lemcke; R

Re: [R] PCA with NA

Birgit Am 23.11.2007 um 17:26 schrieb Thibaut Jombart: > Birgit Lemcke wrote: > >> Dear all, >> (Mac OS X 10.4.11, R 2.6.0) >> I have a quantitative dataset with a lot of Na´s in it. So many, >> that it is not possible to delete all rows with NA´s and also &

[R] PCA with NA

many NA´s. Thanks in advance 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

Re: [R] Clustering

quot;) > > > Thank you very much, > Eleni > > [[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.h

Re: [R] PCA with NA

>> 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. >>

[R] Discriminant function analysis

. Is there another function that is able to handle this? Thank you all in advance. Greetings Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft

Re: [R] Discriminant function analysis

Am 06.02.2008 um 21:00 schrieb Tyler Smith: > On 2008-02-06, Birgit Lemcke <[EMAIL PROTECTED]> wrote: >> >> I am using R 2.6.1 on a PowerBook G4. >> I would like to perform a discriminant function analysis. I found lda >> in MASS but as far as I understood, is it

Re: [R] Discriminant function analysis

e] gavin.simpsonATNOSPAMucl.ac.uk > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > __

[R] create library for own datasets

ere an easier way to do that? Thanks in advance for your help. B. Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent

[R] ChiSquare-Test

question is now: how can I say to R that these numbers have to be treated separately? In the example as a 1, a 2 and a 9 and not as 129) I really hope you understand what I mean. If not please ask me. I would be very pleased, if somebody could help me. Greetings Birgit Birgit Lemcke Institut

[R] Ambiguities in vector

.. Greetings Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org mailing

Re: [R] Ambiguities in vector

bbolker: > > > > Birgit Lemcke wrote: >> >> >> Perhaps you haven´t understood my question in the mail yesterday. So >> I will try to describe my problem in a different way >> >> You see the tables. I would like to test the variables between the >>

Re: [R] Ambiguities in vector

} > > Hope this helps, > James > -- > James Reilly > Department of Statistics, University of Auckland > Private Bag 92019, Auckland, New Zealand > > On 21/9/07 7:14 AM, Birgit Lemcke wrote: >> First thanks for your answer. >> Now I try to explain better: >> I have

[R] save 3dplot to file

I think it is an easy question but i haven´t found a solution since I am r beginner. I did this plot3d(PCoA, type="p", col=rainbow(1000),size=5) text3d(PCoA, text=Nam) How can I save it including the labels to a jpg-file? Thanks in advance. Birgit Birgit Lemck

[R] simple matching with R

How can i do that? Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project

Re: [R] simple matching with R

SEs in a given object (tRow). Variable dissimilarity is > then the application of this dissimilar function for each row of > comparison. In this example, 0 means all of the entries in a row > matche, 9 means none of them matched. You can see the solution here > in recipe form: http:

Re: [R] simple matching with R

he lists and using lengths (but the speed increase will only be > noticeable on very, very, very long lists). > > --Jeff. > > On Sep 28, 2007, at 12:47 PM, Birgit Lemcke wrote: > >> Thanks a lot for both solutions of my problem. >> >> I tried it immediately and I un

Re: [R] Ambiguities in vector

<- c("13", "2", "13", "123", "1", "23") > Then colSums will give you frequency counts for each attribute. > > I think you would need greatly simplify the multiple response data > to apply anything like a paired t-test. Have you

[R] Error loading DCluster

ng message) Zusätzlich: Warning message: (There is no package spdep in:.) es gibt kein Paket 'spdep' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) Can somebody tell me why I get this error and what I can do against it? Thanks in advance. Regards Birgit Bi

Re: [R] Ambiguities in vector

of plant species, which you > are trying to generalise about? > > If so, is the population much larger than your sample? And was your > sample of species selected randomly, i.e. with equal selection > probabilities? If not, standard tests probably won't apply. > >

[R] as.ordered

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] __

Re: [R] as.ordered

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

[R] problem with lower, upper triangles and diagonal

stupid to find the solution by myself. Thanks a lot. 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

Re: [R] as.ordered

) >> 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. >>

Re: [R] problem with lower, upper triangles and diagonal

his problem. I appologise in advance, because I was to stupid to find the solution by myself. Thanks a lot. Regards Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] ___

Re: [R] as.ordered

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.vecto

[R] as.dist with diagonal unequal zero

s a vector within as.dist? I would be glad if somebody could help me. Greetings Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] __ R-help@r-pro

Re: [R] as.dist with diagonal unequal zero

vik: > On 10/10/07, Birgit Lemcke <[EMAIL PROTECTED]> wrote: >> Hello and sorry that I still haven´t found a solution for my problem. >> >> I need to extract the lower and upper triangle from a square matrix >> including the diagonal. This diagonal is not zero i

[R] hist () x-axis

mean) of the xaxis, so that it shows not only 0.3 and 0.4 but also 0.35? Thanks in advance for your help. Regards Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED

[R] plot3d with more than 8 colors

ors, size=0.5) but I get only different colors for the numbers 1 to 8 and after that it starts again with the first colour black. How can get more different colours? And two further questions: how can I ad a legend to the 3d-plot and is there now a possibility to export movable 3d files? Thank

Re: [R] plot3d with more than 8 colors

Am 22.10.2007 um 17:19 schrieb Duncan Murdoch: > On 10/22/2007 9:54 AM, Birgit Lemcke wrote: >> Hello R user and helper! >> I would like to get a 3d plot with coloured points. >> I did that: >> colors<-c(rep("2",7), rep("3",12), rep("4"

[R] (no subject)

enclos) : objekt ".__M__coerce" nicht gefunden What am I doing wrong? Thanks in advance for your help. B Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] ___

[R] t.test() with missing values

lly need two know if may two vectors are significantly different. (If this results are then reliable is an other question) By the way is there a better possibility (and I guess there is) to save or export the t.test() results as textfile? Thanks in advance for your help. Greetings

Re: [R] t.test() with missing values

ce. Birgit Am 13.09.2007 um 18:50 schrieb Peter Dalgaard: > Birgit Lemcke wrote: >> Hello! >> >> I am using R 2.5.1 on a Apple Power Book G4 with Mac OS X 10.4.10 >> and I am still R beginner. >> >> I try to calculate a t.test() using this code: >&g

Re: [R] t.test() with missing values

Am 14.09.2007 um 10:26 schrieb Peter Dalgaard: > Birgit Lemcke wrote: >> Thanks for your answer. >> >> First I will show you both vectors: >> [...] >> >> I tried this (complete.cases(Fem66, Mal66)) and you are right, it >> gives me back: >&g

Re: [R] t.test() with missing values

o you mean with mu1-mu2 and what are s.e.´s? Once again thank you for your help. Birgit > > -- >O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B > c/ /'_ --- De

Re: [R] t.test() with missing values

Am 14.09.2007 um 14:12 schrieb Petr PIKAL: > Hi > > [EMAIL PROTECTED] napsal dne 14.09.2007 13:50:58: > >> Birgit Lemcke wrote: >>> >>> Am 14.09.2007 um 12:05 schrieb Peter Dalgaard: >>> >>>> S Ellison wrote: >>>>> &g

Re: [R] t.test() with missing values

Am 14.09.2007 um 14:27 schrieb Peter Dalgaard: > Petr PIKAL wrote: >> Hi >> >> [EMAIL PROTECTED] napsal dne 14.09.2007 13:50:58: >> >> >>> Birgit Lemcke wrote: >>> >>>> Am 14.09.2007 um 12:05 schrieb Peter Dalgaard: >>

Re: [R] t.test() with missing values

Am 14.09.2007 um 15:54 schrieb Petr PIKAL: >> Petr PIKAL wrote: >>> Hi >>> >>> [EMAIL PROTECTED] napsal dne 14.09.2007 13:50:58: >>> >>> >>>> Birgit Lemcke wrote: >>>> >>>>> Am 14.09.2007 um 12:05 sc