[R] problem with read.table()

Hello R-User I have a table as tab-delimited textfile (291 rows, 83 columns). The first row are labels and the first line the variable names. I used the following code several times with different similar tables and it always worked. But now: setClass("of") setAs("character", "of", functi

Re: [R] problem with read.table()

I am sorry I just found the stupid mistake. I did not specify dec="," because I usually use . Anyway thanks for having the opportunity to get help in this list. B. Birgitle wrote: > > Hello R-User > > I have a table as tab-delimited textfile (291 rows, 83 columns

[R] glm error: factor levels

Hello R-Users, again me! I have a data.frame with 291 rows, 82 columns. Tha variables in the columns are factors, numerics and ordered factors. The response variable is a factor with two levels. I would like to find the best model by trying every possible variable combination using a logistic

[R] Sperman Correlation with rcorr (Hmisc)

Hello R-User! I have a data.frame with 82 variables (columns) and 290 rows. The variables are set to classes factor, ordered factor and numeric. I used the following code Matrix.My.data<-as.matrix(Df.My.Data[2:82]) Matrix.My.data.rcorr<-rcorr(Matrix.My.data, type="spearman") and got the foll

[R] Correlation dichotomous factor, continous (numerical) and ordered factor

Hello R-User! I appologise in advance if this should also go into statistics but I am presently puzzled. I have a data.frame (about 300 rows and about 80 variables) and my variables are dichotomous factors, continuous (numerical) and ordered factors. I would like to calculate the linear correlat

Re: [R] Correlation dichotomous factor, continous (numerical) and ordered factor

Many, many thanks that was fast and exactly what I was looking for. B. Mark Difford wrote: > > Hi Birgitle, > >>> ... my variables are dichotomous factors, continuous (numerical) and >>> ordered factors. ... >>> Now I am confused what I should use to cal

[R] Problems using hetcor (polycor)

Sorry if this post should be long but I tried to give you a piece of my data to reproduce my error message using hetcor: Fehler in result$rho : $ operator is invalid for atomic vectors Zusätzlich: Warning messages: 1: In polychor(x, y, ML = ML, std.err = std.err) : 1 row with zero marginal remo

Re: [R] Problems using hetcor (polycor)

eric",6), rep ("factor", 12)) TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1, na.strings="NA" ,colClasses = Classe72) library(polycor) TestPart.hetcor<-hetcor(TestPart, use="complete.obs") Mark Difford wrote: > > Hi Birgitle, >

Re: [R] Problems using hetcor (polycor)

t;of", 12)) TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1, na.strings="NA" ,colClasses = Classe72) library(polycor) TestPart.hetcor<-hetcor(TestPart, use="complete.obs") B. Birgitle wrote: > > Thanks Mark and I am sorry that I

Re: [R] Problems using hetcor (polycor)

Many Thanks Mark for your answer. It seems than, that it is not possible to use all variables without somehow imputing missing values. But I will try which variables I can finally use. Many thanks again. B. Mark Difford wrote: > > Hi Birgitle, > > It seems to be failing on t

Re: [R] Problems using hetcor (polycor)

: > > ## The first fails; the second works > hetcor(TestPart[,c(1:11,13:22,24:43,45:60)], pd=T, std.err=F) > hetcor(TestPart[,c(1:72)], pd=F, std.err=F) > > Mark Difford wrote: > > Hi Birgitle, > >>> It seems than, that it is not possible to use all variabl

Re: [R] Switch two rows in a matrix

sorry here the right thing a<-a[c(1,3,2,4),c(1,3,2,4)] B. Birgitle wrote: > > You could perhaps do it like that > > a<-a[c(1,2,4,3),] > > B. > > > Zhang Yanwei - Princeton-MRAm wrote: >> >> Hi all, >> I have a 4 by 4 matrix, and I w

Re: [R] Switch two rows in a matrix

You could perhaps do it like that a<-a[c(1,2,4,3),] B. Zhang Yanwei - Princeton-MRAm wrote: > > Hi all, > I have a 4 by 4 matrix, and I want to switch row 2 and row 3 first, then > switch column 2 and column 3. Is there an easy way to do it? > The following is a tedious way to get what I wa

[R] mob(party) formula question

I try tu use mob() with my data.frame ('data.frame':288 obs. of 81 variables; factors, numerics and ordered factors) My response is a binary variable and I should use for modelling a logistic regression (family=binomial). I read in the "MOB" Vignette that I could use a formula like this if I

Re: [R] mob(party) formula question (example)

= Classe72) then "party with the mob": library(party) Test.mob<-mob(X1~1|X34+X45+X73, data=DFExample, model=glinearModel, family=binomial()) Fehler in `[.data.frame`(x, r, vars, drop = drop) : undefined columns selected B. Birgitle wrote: > > I try tu use mob() with my

Re: [R] mob(party) formula question

ation would be should be used as partitioning variables. > ... > > What do you mean with "linear specification"? I would be very happy if you could explain. Thanks again B. Achim Zeileis wrote: > > On Wed, 13 Aug 2008, Birgitle wrote: > >> I try tu use

[R] Tiny help for tiny function

I just started to write tiny functions and therefore I appologise in advance if I am asking stupid question. I wrote a tiny function to give me back from the original matrix, a matrix showing only the values smaller -0.8 and bigger 0.8. y<-c(0.1,0.2,0.3,-0.8,-0.4,0.9) x<-c(0.5,0.3,0.9,-0.9,-0.7

Re: [R] Tiny help for tiny function

Many thanks. Much easier than my solution B. Birgitle wrote: > > I just started to write tiny functions and therefore I appologise in > advance if I am asking stupid question. > > I wrote a tiny function to give me back from the original matrix, a matrix > showing only

Re: [R] mob(party) formula question

Thanks again. Unfortunately I have always this missing values problem. But the missings have also a meaning and its impossible to code it differently or impute. Also thanks for the explanation. Now I understand. B. Achim Zeileis wrote: > > On Wed, 13 Aug 2008, Birgitle wrote: >

[R] No object with name: PDE

Hello R-User! When I plot my rpart-object: plot(data.rpart); text(data.rpart,cex=0.2, use.n=T) I get this error message No object with name: PDE Can somebody tell me why and what the meaning of the message is? Many thanks in advance B. - The art of living is more like wrestling tha

[R] cluster a distance(analogue)-object using agnes(cluster)

I try to perform a clustering using an existing dissimilarity matrix that I calculated using distance (analogue) I tried two different things. One of them worked and one not and I don`t understand why. Here the code: not working example library(cluster) library(analogue) iris2<-as.data.frame(ir

Re: [R] cluster a distance(analogue)-object using agnes(cluster)

agnes(cluster) to perform a clustering? Thanks again B. Birgitle wrote: > > I try to perform a clustering using an existing dissimilarity matrix that > I calculated using distance (analogue) > I tried two different things. One of them worked and one not and I don`t > understand

Re: [R] Swap variables in data.frame

Thanks Paul. I am not sure if I understood well, but when I do it then I have only two columns left: > L3 <- LETTERS[1:3] > (d <- data.frame(cbind(x=1, y=1:10, z=11:20), fac=sample(L3, 10, > replace=TRUE))) x y z fac 1 1 1 11 C 2 1 2 12 B 3 1 3 13 B 4 1 4 14 C 5 1 5 15 C

Re: [R] Swap variables in data.frame

That works perfect. Thanks a lot Paul! Greets Birgit Paul Smith wrote: > > On Mon, Jun 2, 2008 at 1:04 PM, Birgitle <[EMAIL PROTECTED]> > wrote: >> >> Thanks Paul. >> >> I am not sure if I understood well, but when I do it then I have only two &g

Re: [R] Swap variables in data.frame

Thanks might be easier in my case because I have so many variables. Could have found this solution on my own. Birgit Rogers, James A [PGRD Groton] wrote: > > > Birgit Lemcke wrote: > >> I have a dataframe and two of my variables are in the wrong position >> and I would like to swap those va

[R] missing data imputation - simulation

My dataset contains missing data and I would like to do something like an EM algorithm or a Markov Chain Monte Carlo approach to get rid of the missing data. Is there a function for imputation or simulation of missing data apart from those in the randomForest library? Thanks in advance Birgit

Re: [R] missing data imputation - simulation

Many thenks to both of you: Will have a look. Birgit Chuck Cleland wrote: > > On 6/4/2008 5:32 AM, Birgitle wrote: >> My dataset contains missing data and I would like to do something like an >> EM >> algorithm or a Markov Chain Monte Carlo approach to get rid o

Re: [R] bartlett.test()

I think you should specify your grouping factor: g a vector or factor object giving the group for the corresponding elements of x. Ignored if x is a list. batlett.test(xx, groupingfactor) Hope this helps. Birgit hanen wrote: > > i'm trying to test the homogeneity of variance of 92 samples

[R] Delete NA from a dist object

I have a dist object containing 1 row that is only NA (not very intelligent to have bas dataset with one NA speciesanyway). I would like to delete this row from this object. It may be not a difficult problem but I can not find a solution presently. So I would be very happy if somebody could

Re: [R] Delete NA from a dist object

Many thanks. Is there a way to give me the number of the row, if I have the row name? B. mel-10 wrote: > > Birgitle a écrit : > >> I have a dist object containing 1 row that is only NA (not very >> intelligent >> to have bas dataset with one NA speciesanyway)

Re: [R] Delete NA from a dist object

Additonally I got this error message TestDist = Dist.HalbDisGow88[-147,] Fehler in Dist.HalbDisGow88[-147, ] : falsche Anzahl von Dimensionen (Error in Dist.HalbDisGow88[-147, ] : wrong number of dimensions Birgit mel-10 wrote: > > Birgitle a écrit : > >> I have a dist obje

Re: [R] Delete NA from a dist object

n`t know what this means) operator Thanks Birgit mel-10 wrote: > > Birgitle a écrit : >> Many thanks. >> Is there a way to give me the number of the row, if I have the row name? >> B. > > a= object > 'w' = name > > > match('w', name

Re: [R] How to change the class of data?

I have an additional question concerning to this topic. I usually use something liek that: read.table(, colClasses=c("numeric", "factor", "character", "my.funny.class")) but why can I not implement "ordered.factor" in there? Birgit Kenn Konstabel wrote: > > Conversion to factor may hap

[R] randomForest outlier

I try to use ?randomForest to find variables that are the most important to divide my dataset (continuous, categorical variables) in two given groups. But when I plot the outliers: plot(outlier(FemMalSex_NAavoid88.rf33, cls=FemMalSex_NAavoid88$Sex), type="h",col=c("red","green")[as.numeric(FemMa

Re: [R] Cluster on both categorical and numerical data

You could have a look at library(analogue) , function ?distance and library (cluster), function ?agnes B. Chua Siang Li wrote: > > >Hello there. Is there any function in R that can do cluster on a set > of >data that has both categorical and numerical variables? thanks. >siangl

[R] ctree (party) plot meaning question

I tried to use ctree but am not sure about the meaning of the plot. My.data.cf<-ctree(Resp~., data=My.data) plot(FemMalSex_NAavoid88.ct) My data.frame contains 88 explanatory variables (continous,ordered/unordered multistate,count data) and one response with two groups. In the plot are only two

[R] problems using mice()

R 2.7.2 PPC Mac OS X 10.4.11 library mice 1.13.1 I try to use mice for multivariate data imputation. My variables are numeric, factors, count data, ordered factors. First I created a vector for the methods to use with each variable ImpMethMice<-c(rep("logreg", 62), rep("polyreg",1), rep("

[R] ace error because of missings?

Hello RUser! I try to use ace for an ancestral state reconstruction but got back an error message. ace(FacVar,Tree, type="discrete") Warning messages: 1: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) : NA/Inf durch größte positive Zahl ersetzt (NA/Inf repla

Re: [R] randomForest outlier

Still the same question: Birgitle wrote: > > I try to use ?randomForest to find variables that are the most important > to divide my dataset (continuous, categorical variables) in two given > groups. > > But when I plot the outlier: > > plot(outlier(rfObject, cls=grou

[R] rpart with only two small groups

Hello R-User! I try to do the following: New<-iris[c(1:7,90:97),1:5] New.rpart<-rpart(Species~., data=New, method="class") New.rpart n= 15 node), split, n, loss, yval, (yprob) * denotes terminal node 1) root 15 7 versicolor (0.467 0.533) * Does it mean it is not possible to fi

Re: [R] rpart with only two small groups

Thanks Gavin and sorry to all for this unnecessary question. B. Gavin Simpson wrote: > > On Tue, 2008-09-16 at 10:47 -0700, Birgitle wrote: >> Hello R-User! >> >> I try to do the following: >> >> New<-iris[c(1:7,90:97),1:5] >> New.rp

[R] contingency table, several variables from dataframe

Hello R-Users! I need a little help to build up a contingency table out of several variables. A<-c("F","M","M","F","F","F","F","M","F","M","F","F") B<-c(0,0,0,0,0,0,1,1,1,1,0,1) C<-c(0,1,1,1,1,1,1,1,1,0,0,0) ABC<-as.data.frame(cbind(A,B,C)) ABC A B C 1 F 0 0 2 M 0 1 3 M 0 1 4

Re: [R] contingency table, several variables from dataframe

e with 3 factor > variables due to the way cbind processes the input variables - which is > not intended I think. > > You can do sth like > > ABC<-data.frame(A,B,C) > aggregate(ABC[,2:3],by=list(A),sum) > > hth. > > Birgitle schrieb: >> Hello R

Re: [R] contingency table, several variables from dataframe

A),FUN=function(x)sum(x=='1')) # '1' is > here the level of the corresponding factor to be counted. > > will work. A more sophisticated version could include some "factor to > numeric" conversion, see FAQ 7.10. > hth. > > Birgitle schrieb: >

[R] problems using AFDM(FactoMineR)

Hello R-list members! I tried to do the following with my dataset that contains factor and numerics, (80columns,about 600 rows) Dataset.afdm<-AFDM(Dataset[282:595,], type=TypeVector, ncp=3) Fehler in svd(X) : infinite or missing values in 'x' TypeVector [1] "n" "n" "n" "n" "n" "n" "n" "n" "n"

[R] Problem installing ad administrating packages

Hello R-User! I am running R 2.8.1 on an Intel Mac. I just tried to install a package using the GUI and got the following error message: Fehler in if (14 + nchar(dcall, type = "w") + nchar(sm[1], type = "w") > : Fehlender Wert, wo TRUE/FALSE nötig ist Error in (14 + nchar(dcall, type = "w")

Re: [R] Problem installing ad administrating packages

where TRUE/FALSE is necessary Error in .readRDS(pfile) : unbekanntes Eingabeformat Fehler in if (!noCache && file.exists(dest) && file.info(dest)$mtime > : Fehlender Wert, wo TRUE/FALSE nötig ist Please could somebody give me an advice. I can not do anything because I need some packa

Re: [R] Problem installing ad administrating packages

Solved: I reinstalled R 2.8.1. B. Birgitle wrote: > > It is also not possible if I use this commands > > install.packages("analogue","/Library/Frameworks/R.framework/Versions/2.8/Resources/library",repos="http://R-Forge.R-project.org";)