[R] lsmeans in R
I need help with calculating lsmeans (adjusted means) of different terms in a linear model including the main effect and the interaction effect terms. I use lm to run the linear models...I previously noted from literature that that "effects" package can be used to generate lsmeans. But I tried to use it but could not figure out which option to use to get means. If anyone can give an example of how to get lsmeans using lm object, that will very helpful. Thanks, SUman [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting a dataframe to a matrix
Hi: Below works but it's extremely ugly and overly complicated. i'm sure
someone else will send you something better and I'll be waiting also.
Also, the way I named the rows and columns works for below but it won't
hold in the general case if you don't have nice ordered names like
you do below. So, use it until we something better.
DF <- read.table(textConnection("name color likes
1 sally red 0
2 sally blue 1
3 sally green 1
4 jake red 0
5 jake blue 1
6 jake green 1
7 tom red 1
8 tom blue 0
9 tom green 0"),header=TRUE,stringsAsFactors=FALSE)
mat <- matrix(sapply(1:nrow(DF),function(.row) {
DF[.row,3]
}),nrow=length(unique(DF$name)),byrow=TRUE,dimnames=list(c(unique(DF$name)),c(unique(DF$color
print(mat)
On Wed, Mar 11, 2009 at 12:42 AM, Jennifer Brea wrote:
If I have a dataframe which is organized like this:
name color likes?
1 sally red0
2 sally blue1
3 sally green1
4 jake red0
5 jake blue1
6 jake green1
7 tom red1
8 tom blue0
9 tom green0
And I want to create a matrix in the form:
red blue green
sally 01 1
jake01 1
tom 10 0
Are there any built-in commands that might help me do this? Also, I
can't assume that there is an observation for every person-color. In
other words, in the original dataset, there might be some colors for
which sally offered no opinion. In some cases, this may be
represented by NA, in others, it may mean that no row exists for sally
for that color.
Thank you!
__
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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.
__
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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.
Re: [R] Converting a dataframe to a matrix
xtabs is your friend: xtabs(likes ~ color + name, data=dat) color nameblue green red jake 1 1 0 sally1 1 0 tom 0 0 1 See ?xtabs for more info. Note that I changed the "likes?" column to just "likes". It is a bad idea to have question marks in variable names. Simon. On Wed, 2009-03-11 at 01:42 -0400, Jennifer Brea wrote: > If I have a dataframe which is organized like this: > >name color likes? > 1 sally red0 > 2 sally blue1 > 3 sally green1 > 4 jake red0 > 5 jake blue1 > 6 jake green1 > 7 tom red1 > 8 tom blue0 > 9 tom green0 > > > And I want to create a matrix in the form: > > red blue green > sally 01 1 > jake01 1 > tom 10 0 > > > Are there any built-in commands that might help me do this? Also, I > can't assume that there is an observation for every person-color. In > other words, in the original dataset, there might be some colors for > which sally offered no opinion. In some cases, this may be represented > by NA, in others, it may mean that no row exists for sally for that color. > > Thank you! > > __ > 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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ 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] prediction error for test set-cross validation
Hi, I have a database of 2211 rows with 31 entries each and I manually split my data into 10 folds for cross validation. I build logistic regression model as: >model <- glm(qual ~ AgGr + FaHx + PrHx + PrSr + PaLp + SvD + IndExam + Rad +BrDn + BRDS + PrinFin+ SkRtr + NpRtr + SkThck +TrThkc + SkLes + AxAdnp + ArcDst + MaDen + CaDt + MaMG + MaMrp + MaSh + SCTub + SCFoc + MaSz, family=binomial(link=logit)); Where the variables are taken from the trainSet of size 1989x31. The test set is sized 222x31. Now my question is when I try to predict on the test set it gives me the error: > predict.glm(model, testSet, type ="response") "Error in drop(X[, piv, drop = FALSE] %*% beta[piv]) : subscript out of bounds" It does fine on trainSet. so it is something about the testSet. On the other hand, I realized that some independent variables say "MaSz" takes 3 different values in the trainset vs. 4 different ones in the testSet. I am not sure if this is the cause.If so, what would be the remedy? Since I can retrieve the coefficients of the logistic regression, I could manually calculate response for each entry in the testSet. This could solve my problem although burdensome. But, I don't know an easy way of doing it as my logistic regression have 80+ coefficients. Could somebody advise? Thanks, M [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] North Arrow (.png file) on a Map
Is this "arrow" satisfactory for you?
north.arrow = function(x, y, h) {
polygon(c(x, x, x + h/2), c(y - h, y, y - (1 + sqrt(3)/2) * h),
col = "black", border = NA)
polygon(c(x, x + h/2, x, x - h/2), c(y - h, y - (1 + sqrt(3)/2) *
h, y, y - (1 + sqrt(3)/2) * h))
text(x, y, "N", adj = c(0.5, 0), cex = 4)
}
plot(1, type = "n", ylim = c(0, 1))
north.arrow(1, 0.8, 0.3)
Regards,
Yihui
--
Yihui Xie
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Tue, Mar 10, 2009 at 7:21 PM, Rodrigo Aluizio wrote:
> Hi list.
>
> I would like to know how do I insert a North arrow, stored as a png file in
> my computer, in a map? I found lots of post asking similar things, one of
> them mentioned the pixmap package. The map was done using map() and
> shapefiles (the code is below). I’m using the pixmap () and addlogo()
> functions. Well I can import the png with pixmap() function (I guess, once
> there’s no error message), but I can’t put It on the map, I got an error
> message telling me that:
>
>
>
> “Error at t(x...@index[nrow(x...@index):1, , drop = FALSE]) :
>
> index out of limits”
>
>
>
> Well I tried changing coordinates but I always got the same result. How do I
> do this correctly? Is there a better way?
>
>
>
> Thanks for the help and attention.
>
>
>
> Here is the complete map script:
>
>
>
> library(RODBC)
>
> library(maps)
>
> library(mapdata)
>
> library(maptools)
>
> library(pixmap)
>
> #Carregar Coordenadas e dados dos Pontos Amostrais
>
> Dados<-odbcConnectExcel('Campos.xls',readOnly=T)
>
> Coord<-sqlFetch(Dados,'CoordMed',colnames=F,rownames='Ponto')
>
> odbcClose(Dados)
>
> N<-pixmap('Norte.png',nrow=166,ncol=113)
>
> # Carregar pontos e shapes
>
> Batimetria<-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
> ogia/Campos/ShapeFiles/Batimetria_BC.shp')
>
> Estados<-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontologi
> a/Campos/ShapeFiles/Estados_Sudeste.shp')
>
> Faciologia<-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
> ogia/Campos/ShapeFiles/Faciologia_BC.shp')
>
> # Mapa com os Pontos da Bacia
>
> postscript('MapaCampos.eps',paper='special',onefile=F,horizontal=F,width=3.5
> ,height=4.5,bg='white',pointsize=3)
>
> par(mar=c(3,2,2,0))
>
> map('worldHires','brazil',ylim=c(23.9,20.3),xlim=c(42.1,39.2),type='n')
>
> plot(Faciologia,ylab='',xlab='',col=c('lightgreen','lightgreen','lightgreen'
> ,'lightgreen','lightgreen','lightgray','lightgray','lightgray','lightgray','
> lightgray','lightgray','lightgray','lightgray','lightgray','lightgray','ligh
> tgray','lightgray','lightgray','lightgray','lightgray','lightgray','lightyel
> low','lightyellow','lightyellow'),add=T,lwd=0.5,border=0)
>
> plot(Batimetria,ylab='',xlab='',col='darkgray',lty='solid',lwd=0.2,add=T)
>
> plot(Estados,ylab='',xlab='',lty='solid',add=T,lwd=0.8)
>
> text(Coord$Longitude[Coord$Réplicas=='1'],Coord$Latitude[Coord$Réplicas=='1'
> ],rownames(Coord)[Coord$Réplicas=='1'],col='red',cex=0.5,font=2)
>
> text(Coord$Longitude[Coord$Réplicas=='2'],Coord$Latitude[Coord$Réplicas=='2'
> ],rownames(Coord)[Coord$Réplicas=='2'],col='yellow',cex=0.5,font=2)
>
> text(Coord$Longitude[Coord$Réplicas=='3'],Coord$Latitude[Coord$Réplicas=='3'
> ],rownames(Coord)[Coord$Réplicas=='3'],col='blue',cex=0.5,font=2)
>
> points(Coord$Longitude,Coord$Latitude-0.045,pch=20,cex=0.7)
>
> text(c(41.5,41.3),c(21.7,20.6),c('RJ','ES'))
>
> axis(1,xaxp=c(42.1,39.2,2),cex.axis=1)
>
> axis(2,yaxp=c(23.9,20.3,4),cex.axis=1)
>
> title(main='Bacia')
>
> legend(40.2,23.5,c('Uma','Duas','Três'),pch=21,cex=1,pt.bg=c('red','yellow',
> 'blue'),bty='n',pt.cex=2,pt.lwd=0.6,title='Réplicas')
>
> legend(39.8,23.5,c('Areia','Calcário','Lama'),pch=21,cex=1,pt.bg=c('lightyel
> low','lightgray','lightgreen'),bty='n',pt.cex=2,pt.lwd=0.6,title='Faciologia
> ')
>
> addlogo(N,px=c(40,39.8),py=c(21,20.8))
>
> dev.off()
>
> q('no')
>
>
>
> -
>
> MSc. Rodrigo Aluizio
>
> Centro de Estudos do Mar/UFPR
> Laboratório de Micropaleontologia
>
>
> [[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.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
__
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] Converting a dataframe to a matrix
If I have a dataframe which is organized like this: name color likes? 1 sally red0 2 sally blue1 3 sally green1 4 jake red0 5 jake blue1 6 jake green1 7 tom red1 8 tom blue0 9 tom green0 And I want to create a matrix in the form: red blue green sally 01 1 jake01 1 tom 10 0 Are there any built-in commands that might help me do this? Also, I can't assume that there is an observation for every person-color. In other words, in the original dataset, there might be some colors for which sally offered no opinion. In some cases, this may be represented by NA, in others, it may mean that no row exists for sally for that color. Thank you! __ 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] Creating a directory for my data
Hi everyone,
I am currently working with a very large data set. It is data collected a
few times a day, so there are repeated titles in the data set. I want to
assign an id number to each different title and enter this information in a
directory that I can access whenever I am working with the data.
An example of a data I am workin with follows:
1 title A
2 title C
3 title B
1 title A
2 title B
3 title C
1 title D
2 title A
3 title C
1 title B
2 title A
3 title C
What I have tried thus far is for loops.
r<-matrix(x[,1])
t<-matrix(x[,2])
for(i in 1:length(t)) {
for(k in 1:length(r)) {
z = matrix(c(i,t))
A = "Article A"
for(j in 1:length(z)){
if(B=="Article A")
else{enter article in z}
}
}
This is of course giving me a lot of errors. I just have no idea where to go
with this. Does anyone have any ideas on where I can go from here to create
my directory?
I appreciate all your help.
Thank you in advance.
--
View this message in context:
http://www.nabble.com/Creating-a-directory-for-my-data-tp22448335p22448335.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
Re: [R] Cholesky Decomposition in R
A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) t(eigen(A)$vector) %*% A %*% eigen(A)$vector mat1 = t(eigen(A)$vector) mat2 = diag(eigen(A)$values)# this is your diagonal matrix Manli Yan wrote: > > Hi everyone: > I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I > only found how to decomposite A in to LL' by using chol(A),the function > Cholesky(A) doesnt work,any one know other command to decomposte A in to > LDL' > > My r code is: > library(Matrix) > A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > >> chol(A) > [,1] [,2] [,3] > [1,]111 > [2,]022 > [3,]003 > >> Cholesky(A) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Cholesky", for > signature > "matrix" > > whatz wrong??? > thanks~ > > [[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.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Cholesky-Decomposition-in-R-tp22444083p22448498.html 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.
Re: [R] Using napredict in prcomp
On Tue, 10 Mar 2009, Alain Paquette wrote: Hello all, I wish to compute site scores using PCA (prcomp) on a matrix with missing values, for example: DrainSlopeOrgL a41NA b2.5396 c6845 d3912 e3164 ... Where a,b... are sites. The command pca<-prcomp(~ Drain + Slope + OrgL, data = t, center = TRUE, scale = TRUE, na.action=na.exclude) works great, and from pca$x I can get site scores, e.g. PC1 PC2 PC3 a NA NA NA b -2.10475208 -2.315128625 -0.885197753 c 5.01177388 -1.778786252 -0.193285051 d 0.28638602 0.298315086 0.386113799 e -0.58861254 0.089498632 -0.434951813 ... Easy enough... But how do I use the "napredict" argument? Is it intended as an argument to be used in the prcomp line (as suggested in ?prcomp), or is it to be used by itself, to replace NAs in the above site score matrix (which is what I really want to do). I don't see an 'napredict' argument. The help says x: if 'retx' is true the value of the rotated data (the centred (and scaled if requested) data multiplied by the 'rotation' matrix) is returned. Hence, 'cov(x)' is the diagonal matrix 'diag(sdev^2)'. For the formula method, 'napredict' is applied to handle the treatment of values omitted by the 'na.action'. 'napredict' is a function (so please look up its help), and it says R applies it, not that you need to. It is napredict which gives you the NAs in the correct places. Thank you, Alain -- Alain Paquette, Ph.D. alain.paque...@gmail.com Centre d'étude de la forêt (CEF) Université du Québec à Montréal www.cef-cfr.ca Projet TRIADE www.projettriade.ca alain.paque...@projettriade.ca __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ 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] read.exp?
Dear Colleagues, The foreign library, ever-exceptionally useful, does not seem able to deal with this ancient SPSS ascii portable file I have with extension '.exp'. If anybody has familiarity with this filetype and could point me towards an R function that would allow me to get the data from this file, I would be much obliged! Or, even knowledge of the specification for these filetypes would be helpful, and I'll try my own hand at writing the import function. Cordially, Adam Kramer __ 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.
Re: [R] Question about datatypes/plotting issue
You need to convert W$Date into a real date variable. At the moment it
is just a character variable.
> str(W)
'data.frame': 265 obs. of 23 variables:
$ Date: Factor w/ 265 levels " ","April 1987",..: 1 90
68 156 2 178 134 ...
$ AZ.Phoenix : Factor w/ 236 levels "","100.00","100.43",..:
236 1 1 1 1 1 1 1 1 1 ...
$ CA.Los.Angeles : Factor w/ 260 levels "100.00","100.02",..: 260
113 114 115 116 ...
$ CA.San.Diego: Factor w/ 261 levels "100.00","101.07",..: 261
109 110 111 112 ...
$ CA.San.Francisco: Factor w/ 256 levels "100.00","102.70",..: 256
108 109 110 111 ...
.(output trimmed)
.
.
?Date # not the variable name, the R class name
?format.Date
?strptime
Unfortunately I seem to be at one of the many limits to my knowledge:
This code behaves in the manner I expected:
> format(Sys.time(), "%a %b %d %X %Y %Z")
[1] "Tue Mar 10 22:19:28 2009 EDT"
> strptime(format(Sys.time(), "%a %b %d %X %Y %Z"), format="%a %b %d
%X %Y %Z")
[1] "2009-03-10 22:20:04"
Whereas this code does not:
> format(Sys.Date(), "%B %Y")
[1] "March 2009"
> as.Date(format(Sys.Date(), "%B %Y"), "%B %Y")
# would have assumed one was the inverse of the other, but ...
[1] NA
For some reason I cannot get the space delimited Month- combo to
convert. I can getother space delimited formats to work for input or
output:
> as.Date("03 1998", "%M %Y")
[1] "1998-03-10"
> format(Sys.Date(), "%B %Y")
[1] "March 2009"
Puzzled;
--
David Winsemius
On Mar 10, 2009, at 9:15 PM, Oscar Bonilla wrote:
Hi,
I am trying to plot the Case-Shiller index found at:
http://www2.standardandpoors.com/spf/pdf/index/CSHomePrice_History_022445.xls
The way I'm importing it into R is as follows:
library(gdata)
W <- read.xls("http://www2.standardandpoors.com/spf/pdf/index/CSHomePrice_History_022445.xls
", header=TRUE)
attach(W)
To give you and idea of what the data looks like:
> head(W)
Date AZ.Phoenix CA.Los.Angeles CA.San.Diego CA.San.Francisco
1 PHXR LXXR SDXR
SFXR
2 January 1987 59.3354.67
46.61
3 February 1987 59.6554.89
46.87
4March 1987 59.9955.16
47.32
5April 1987 60.8155.85
47.69
6 May 1987 61.6756.35
48.31
CO.Denver DC.Washington FL.Miami FL.Tampa GA.Atlanta IL.Chicago
MA.Boston
1 DNXR WDXR MIXR TPXR ATXR
CHXR BOXR
2 50.20 64.1168.5077.33
53.55 70.04
3 49.96 64.7768.7677.93
54.64 70.08
4 50.15 65.7169.2377.76
54.80 70.00
5 50.55 66.4069.2077.56
54.88 70.70
6 50.63 67.2769.4677.85
55.43 71.51
MI.Detroit MN.Minneapolis NC.Charlotte NV.Las.Vegas NY.New.York
OH.Cleveland
1 DEXR MNXR CRXR LVXR
NYXR CEXR
2 63.3966.36
74.4253.53
3 63.9467.03
75.4353.50
4 64.1767.34
76.2553.68
5 64.8167.88
77.3453.75
6 65.1867.90
79.1654.71
OR.Portland TX.Dallas WA.Seattle Composite.10 Composite.20
1POXR DAXR SEXR CSXR SPCS20R
2 41.05 62.82
3 41.28 63.39
4 41.06 63.87
5 40.96 64.57
6 41.24 65.56
Now on to the problem... if I just run
plot(CA.San.Francisco ~ Date)
I get:
Which I suspect is a problem because the Date column is not really a
Date, it is a "factor"
> class(Date)
[1] "factor"
If I run:
plot(as.numeric(CA.San.Francisco), type="l")
I get:
which is wrong, as CA.San.Francisco has no such discontinuity.
> CA.San.Francisco
[1] SFXR 46.61 46.87 47.32 47.69 48.31 48.83 49.49 49.94
50.69
[11] 51.33 51.80 52.03 52.24 52.64 53.19 54.19 56.09 58.22
58.70
[21] 59.00 59.50 60.37 61.31 62.20 62.66 63.32 64.64 66.27
67.77
[31] 69.26 70.27 71.36 72.31 72.95 73.25 73.02 72.87 72.95
73.50
[41] 74.57 75.12 75.15 74.81 74.45 74.24 73.44 72.58 71.47
71.17
[51] 70.27 69.56 69.46 70.13 70.83 71.39 71.52 71.55 71.21
70.69
[61] 70.05 69.67 69.48 69.17 69.26 69.86 70.02 70.00 69.64
69.51
[71] 69.28 68.85 68.21 67.77 67.44 67.09 67.59 67.90 67.99
67.65
[81] 67.63 67.50 67.18 66.77 66.27 65.98 65.79 66.37 67.05
67.70
[91]
Re: [R] Nesting order for mixed models
On Tue, Mar 10, 2009 at 2:47 PM, Jon Zadra wrote:
> Hello,
> I am confused about the order of nesting in mixed models using functions
> like aov(), lme(), lmer().
> I have the following data:
> n subjects in either condition A or B
> each subject tested at each of 3 numerical values ("distance" = 40,50,60),
> repeated 4 times for each of the 3 numerical values ("trial" = 1,2,3,4)
> Variable summary:
> Condition: 2 level factor
> Distance: numerical (but only 3 values) in the same units as "y"
> Trial: 4 level factor
I don't think Trial is necessary. If I understand correctly it is not
really an experimental or observational factor in that you don't
expect that trial 1 for one subject/distance combination will be
related to trial 1 for another combination.
> I expect the subjects' data to differ due to condition and distance, and am
> doing repeated measurements to reduce any variability due to measurement
> error.
>
> Currently I'm using this model:
>
> lme(y ~ Condition + Distance, random = ...)
>
> the question is how do I organize the random statement? Is it:
> random = ~1 | Subject
I think that is all you need. In lmer the formula would be y ~
Condition + Distance + (1|Subject).
> random = ~1 | Subject/Trial
> random = ~1 | Trial/Subject
> random = ~1 | Condition/Distance/Subject/Trial
> ...etc, or something else entirely?
>
> Mostly I'm unclear about whether the Trials should be grouped under subject
> because I expect the trials to be more similar within a subject than across
> subjects, or whether subjects should be grouped under trials because the
> trials are going to differ depending on the subject. If trials should be
> grouped under subjects, then do the condition or distance belong as well,
> since the trials will be most similar within each distance within each
> subject?
In some ways of thinking of the model, Trial would be grouped under
the Subject:Distance combination but then it becomes unnecessary
because it is just another way of labeling the observations. A random
effect for Trial within Subject:Distance is confounded with the
"residual" or per-observation noise term.
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Re: [R] mean +/- SEM
?mean ?sd ?plot The request to plot mean has no context yet. What sort of problem are you working with? You will get better answers if you first read the Posting Guide and then provide example data. -- David Winsemius On Mar 10, 2009, at 6:39 PM, Stefo Ratino wrote: Hi all, I am looking for a R function which unables me to plot mean +/- SEM. Is there such a function in R? Many thanks, Stefo [[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.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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.
Re: [R] 2 Simple Lattice Plot Questions
Excellent, thank you very much :) Sundar Dorai-Raj-2 wrote: > > I don't believe Elena's suggestion will work. However, the following will: > > xyplot(..., scales = list(y = list(at = seq(5, 25, 5 > > though you may need to extend the limits a little as well: > > xyplot(..., ylim = lattice:::extend.limits(c(0, 30))) > > and add the scales argument from the first example to place explicit > tick marks rather than let xyplot do so. > > HTH, > > --sundar > > On Tue, Mar 10, 2009 at 7:04 PM, Elena Wilson > wrote: >> Have you tried specifying the levels of y's you want to display, e.g. >> ylim=c(0,5,10,15,20,30)? >> >> -Original Message- >> From: r-help-boun...@r-project.org >> [mailto:r-help-boun...@r-project.org] On Behalf Of jimdare >> Sent: Wednesday, 11 March 2009 12:50 PM >> To: r-help@r-project.org >> Subject: Re: [R] 2 Simple Lattice Plot Questions >> >> >> Thanks very much. One other thing... see how the Y axis begins before >> 0. >> At first glance it appears that the 0's are actually worth something. >> When >> I use ylim=c(0,30) I get the graph I want, but the tick marks show only >> 5,10,15,20,25. I want them to show 0,5,10,15,20,30. Does anyone know >> how >> to change this setting? >> >> Cheers, >> >> >> >> >> >> >> jimdare wrote: >>> >>> Hi, >>> >>> I have created the plot below and have a few questions about changes. >>> >>> 1) How do I change the "Year" title of each plot so it reads from the >>> top >>> "2006","2007","2008","2009". >>> 2) How do I get rid of those vertical grey bars in the title bar of each >>> plot? >>> >>> I apologise for my ignorance... one of those days :( >>> >>> James >>> >>> >>> http://www.nabble.com/file/p22445242/PLOT.jpg >>> >> >> -- >> View this message in context: >> http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22447415.html >> 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. >> -- >> Message protected by MailGuard: e-mail anti-virus, anti-spam and content >> filtering. >> http://www.mailguard.com.au/mg >> >> >> https://login.mailguard.com.au/report/1x1TEaABIw/4soNUVnBh04s1coMEHC4LA/7.998 >> >> __ >> 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-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/2-Simple-Lattice-Plot-Questions-tp22445242p22447866.html 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.
[R] mean +/- SEM
Hi all, I am looking for a R function which unables me to plot mean +/- SEM. Is there such a function in R? Many thanks, Stefo [[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.html and provide commented, minimal, self-contained, reproducible code.
[R] tcltk - insert scrollbar to window
Hello, I hava a problem with inserting a scrollbar into a tcltk toplevel.
The comand is as follows:
require(tcltk)
tt<-tktoplevel()
tkgrid(tklabel(tt,text="Choose path to the meteorology file used for CDM"))
OnOK2 <- function(){
wind.file<<-read.csv2(file.choose(),header=T,sep=";",dec=".")
wind<<-as.double(wind.file[,5])
uH<<-max(wind)
}
OK.but2 <-tkbutton(tt,text=" Search ",command=OnOK2)
tkbind(tkgrid, "",OnOK2)
tkgrid(OK.but2)
Because some more tkgrids with requestions to enter other parameters shall
follow within the same window the tcltk-window is to small to show all of
them. Therefore I would need a scrollbar for the whole window. How can I
create this?
Thanks! THoeb
-
Tamara Hoebinger
University of Vienna
--
View this message in context:
http://www.nabble.com/tcltk---insert-scrollbar-to-window-tp22443022p22443022.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] extracting dispersion parameter from quasipoisson lmer model
Hello, I have the exact same question: how to extract dispersion parameter from lmer() quasipoisson model? I did a search here and saw this post. However, I do not see answer. Could somebody please help? Thank you very much, Julia wayne hallstrom wrote: > > Hi, > I would like to obtain the dispersion parameter for a quasipoisson model > for later use in calculating QAIC values for model comparison.Can anyone > suggest a method of how to go about doing this? > > The idea I have now is that I could use the residual deviance divided by > the residual degrees of freedom to obtain the dispersion parameter. The > residual deviance is available in the summary output for the lmer model. > The problem with this idea is that the residual degrees of freedom is not > directly available. I have been assuming that the estimated/approximate DF > can be obtained through the formula listed below, and then subsequently > used to obtain the dispersion parameter as described above. Is this > correct? > > samp.m4 <- mcmcsamp(m4, n = 1000) > print(summary(samp.m4)) > (eDF <- mean(samp.m4[,"deviance"]) - deviance(m4, REML=FALSE)) > # potentially useful approximate DF? > > > However, rather than going through this roundabout, there appears to be > an easier way to obtain the dispersion parameter. I have noted that the > 'quasibinomial' produces a dispersion parameter in the model output, but > the 'quasipoisson' output does not contain this useful number. Given that > each of my models is fit by lmer with a quasipoisson distribution, the > program must be internally calculating the dispersion parameter as it > runs. Perhaps there is a way to obtain this number directly since I assume > it has already been calculated? Can somone who has experience with this > code provide some advice on whether this is possible and how I might > manage to do this? > > > Thank you for your time, > > Wayne Hallstrom > 403-370-3832 > > > > > - > > [[alternative HTML version deleted]] > > __ > r-h...@stat.math.ethz.ch 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/extracting-dispersion-parameter-from-quasipoisson-lmer-model-tp11992221p22441798.html 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.
[R] 2 dimension convolve
Anybody know how to do a fast 2 dimension convolve in R? I used a traditional method, but it's very slow, even can not stand it! -- View this message in context: http://www.nabble.com/2-dimension-convolve-tp22440837p22440837.html 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.
[R] removing daylight savings in R
Hello,
Thanks the Prof. Brian Ripley for his earlier response, however I still have
a few issues with the times in R.
I'd like to somehow set up R so it automatically has the timezone set to
Western Australian standard time when I open up a workspace instead of
Western Australian daylight savings time. Is this possible? I haven't had
much luck in trying to find this.
There are two main issues that I mentioned in my earlier email, in regards
to the Oracle database I'm using the RODBC package to extract the data into
R. I've tried using the newer version of RODBC (1.2-4) and the older version
(1.2-3) of this package and I still get the NA values for the 2am and 2:30am
datetime values for the start of daylight savings. However in R 2.6.2, I
can use either version of RODBC without getting the error.
The program is quite large, so I've just pickout the relevant bits of code
needed to extract the data from Oracle
>channel <<- odbcDriverConnect(paste("DSN=", dbdsn, ";UID=", dbuser,
";PWD=", dbpwd, sep=""), case="oracle")
>total_cnsmptn_summary_vw<-sqlQuery(channel, paste("select
INTERVAL_START_DATETIME, TOTAL_SMOOTHED_CNSMPTN_MWH+TOTAL_CHURN_MWH,
NON_VEST_CNSMPTN_MWH+NON_VEST_CHURN_MWH,
VEST_ISC_CNSMPTN_MWH+VEST_ISC_CHURN_MWH,
TOTAL_SMOOTHED_CNSMPTN_MWH-NON_VEST_CNSMPTN_MWH-VEST_ISC_CNSMPTN_MWH+VEST_VC
_CHURN_MWH from CONSUMPTION_SUMMARY where total_smoothed_cnsmptn_mwh > 0 and
vest_isc_cnsmptn_mwh > 0 order by INTERVAL_START_DATETIME"))
>names(total_cnsmptn_summary_vw)<-c('INTERVAL_START_DATETIME','TOTAL_SMOOTHE
D_CNSMPTN_MWH','NON_VEST_CNSMPTN_MWH',
'VEST_ISC_CNSMPTN_MWH','VEST_VC_CNSMPTN_MWH')
>total_cnsmptn_summary_vw[67735:67745,]
INTERVAL_START_DATETIMETOTAL_SMOOTHED_CNSMPTN_MWH
NON_VEST_CNSMPTN_MWH VEST_ISC_CNSMPTN_MWH VEST_VC_CNSMPTN_MWH
677352008-10-25 23:30:00 535.437
105.180 50.304 379.953
677362008-10-26 00:00:00 514.703
104.700 50.376 359.627
677372008-10-26 00:30:00 499.146
104.007 50.941 344.198
677382008-10-26 01:00:00 485.834
102.486 50.479 332.869
677392008-10-26 01:30:00 474.799
101.961 50.492 322.346
67740 469.783
102.070 50.755 316.958
67741 464.007
100.814 50.816 312.377
677422008-10-26 03:00:00 463.224
101.309 50.386 311.529
677432008-10-26 03:30:00 464.052
102.049 50.207 311.796
677442008-10-26 04:00:00 469.753
103.542 50.204 316.007
677452008-10-26 04:30:00 475.318
105.407 49.670 320.241
The second issue is the 2.8.1 version of R changing the times from a 2.6.2
workspace - this probably relates to the display setting, that mentioned
(I think if I can set this to always use Western Australian standard time
the problem will be fixed, but I am unsure as how to do this)
I create a datetime object in R 2.6.2 and then load that workspace into
2.8.1 the time changes,
In R 2.6.2 I've typed:
>date1<-ISOdatetime(2008,1,1,8,00,00)
>save.image("C:\\Data\\Profiles\\M063059\\Desktop\\test.RData")
> date1
[1] "2008-01-01 08:00:00 W. Australia Standard Time"
and then in R 2.8.1 I've typed
> load("C:\\Data\\Profiles\\M063059\\Desktop\\test.RData")
> date1
[1] "2008-01-01 09:00:00 WST"
Kind Regards
Rhiannon
Rhiannon Marchant
Forecasting Analyst
Wholesale
Synergy (ABN: 71 743 446 839), 228 Adelaide Tce, Perth, WA, 6000, Australia
phone: (08) 6212 1464 | fax: (08) 6212 1036 | email:
rhiannon.march...@synergy.net.au
business enquiries: 131354 | identification no.: 300794 | website:
[1]synergy.net.au
Please consider the environment before printing this email.
Prof Brian Ripley
27/02/2009 03:42 PM
To
Rhiannon Marchant
cc
r-help@r-project.org
Subject
Re: [R] removing daylight savings in R
What do you mean by 'standard time'? If you mean UTC, set TZ=UTC.
For anything else, see ?Sys.timezone (which explains the use of TZ).
I am guessing that
Re: [R] test two correlation coefficients against each other
Martin, See r.test in the psych package. This will probably do what you want to do. Bill At 1:29 AM +0100 3/11/09, Martin Batholdy wrote: hi, is there a function in R that calculates the probability that two correlation coefficients are from the same population? thanks! __ 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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r __ 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.
Re: [R] 2 Simple Lattice Plot Questions
I don't believe Elena's suggestion will work. However, the following will: xyplot(..., scales = list(y = list(at = seq(5, 25, 5 though you may need to extend the limits a little as well: xyplot(..., ylim = lattice:::extend.limits(c(0, 30))) and add the scales argument from the first example to place explicit tick marks rather than let xyplot do so. HTH, --sundar On Tue, Mar 10, 2009 at 7:04 PM, Elena Wilson wrote: > Have you tried specifying the levels of y's you want to display, e.g. > ylim=c(0,5,10,15,20,30)? > > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of jimdare > Sent: Wednesday, 11 March 2009 12:50 PM > To: r-help@r-project.org > Subject: Re: [R] 2 Simple Lattice Plot Questions > > > Thanks very much. One other thing... see how the Y axis begins before 0. > At first glance it appears that the 0's are actually worth something. When > I use ylim=c(0,30) I get the graph I want, but the tick marks show only > 5,10,15,20,25. I want them to show 0,5,10,15,20,30. Does anyone know how > to change this setting? > > Cheers, > > > > > > > jimdare wrote: >> >> Hi, >> >> I have created the plot below and have a few questions about changes. >> >> 1) How do I change the "Year" title of each plot so it reads from the top >> "2006","2007","2008","2009". >> 2) How do I get rid of those vertical grey bars in the title bar of each >> plot? >> >> I apologise for my ignorance... one of those days :( >> >> James >> >> >> http://www.nabble.com/file/p22445242/PLOT.jpg >> > > -- > View this message in context: > http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22447415.html > 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. > -- > Message protected by MailGuard: e-mail anti-virus, anti-spam and content > filtering. > http://www.mailguard.com.au/mg > > > https://login.mailguard.com.au/report/1x1TEaABIw/4soNUVnBh04s1coMEHC4LA/7.998 > > __ > 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-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.
Re: [R] 2 Simple Lattice Plot Questions
Yes, I have tried this. Unfortunately it doesn't seem to work i.e. it still shows 5,10,15,20,25. Elena Wilson-2 wrote: > > Have you tried specifying the levels of y's you want to display, e.g. > ylim=c(0,5,10,15,20,30)? > > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] > On Behalf Of jimdare > Sent: Wednesday, 11 March 2009 12:50 PM > To: r-help@r-project.org > Subject: Re: [R] 2 Simple Lattice Plot Questions > > > Thanks very much.One other thing... see how the Y axis begins before > 0. > At first glance it appears that the 0's are actually worth something. > When > I use ylim=c(0,30) I get the graph I want, but the tick marks show only > 5,10,15,20,25. I want them to show 0,5,10,15,20,30. Does anyone know how > to change this setting? > > Cheers, > > > > > > > jimdare wrote: >> >> Hi, >> >> I have created the plot below and have a few questions about changes. >> >> 1) How do I change the "Year" title of each plot so it reads from the top >> "2006","2007","2008","2009". >> 2) How do I get rid of those vertical grey bars in the title bar of each >> plot? >> >> I apologise for my ignorance... one of those days :( >> >> James >> >> >> http://www.nabble.com/file/p22445242/PLOT.jpg >> > > -- > View this message in context: > http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22447415.html > 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. > -- > Message protected by MailGuard: e-mail anti-virus, anti-spam and content > filtering. > http://www.mailguard.com.au/mg > > > https://login.mailguard.com.au/report/1x1TEaABIw/4soNUVnBh04s1coMEHC4LA/7.998 > > __ > 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/2-Simple-Lattice-Plot-Questions-tp22445242p22447626.html 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.
Re: [R] Cholesky Decomposition in R
On Tue, Mar 10, 2009 at 4:33 PM, Manli Yan wrote: > Hi everyone: > I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I > only found how to decomposite A in to LL' by using chol(A),the function > Cholesky(A) doesnt work,any one know other command to decomposte A in to > LDL' > > My r code is: > library(Matrix) > A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > >> chol(A) > [,1] [,2] [,3] > [1,] 1 1 1 > [2,] 0 2 2 > [3,] 0 0 3 > >> Cholesky(A) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Cholesky", for signature > "matrix" > > whatz wrong??? The answer, surprisingly, is in the documentation, accessible as ?Cholesky which says that the first argument has to be a sparse, symmetric matrix. Because the Cholesky function is intended for sparse matrices it is not the best approach. The object returned is rather obscure > Cholesky(as(A, "dsCMatrix"), LDL = TRUE) 'MatrixFactorization' of Formal class 'dCHMsimpl' [package "Matrix"] with 10 slots ..@ x : num [1:6] 1 1 1 4 1 9 ..@ p : int [1:4] 0 3 5 6 ..@ i : int [1:6] 0 1 2 1 2 2 ..@ nz : int [1:3] 3 2 1 ..@ nxt : int [1:5] 1 2 3 -1 0 ..@ prv : int [1:5] 4 0 1 2 -1 ..@ colcount: int [1:3] 3 2 1 ..@ perm: int [1:3] 0 1 2 ..@ type: int [1:4] 2 0 0 1 ..@ Dim : int [1:2] 3 3 It turns out that the factorization you want is encoded in the 'x' slot but not in an obvious way. Even if you ask for an expansion > expand(Cholesky(as(A, "dsCMatrix"), LDL = TRUE)) $P [1,] | . . [2,] . | . [3,] . . | $L [1,] 1 . . [2,] 1 2 . [3,] 1 2 3 the result is converted from the LDL' factor to the LL' factor. A better approach is to consider how the LDL' factorization is related to the R'R form of the factorization returned by chol() > ch <- chol(A) > dd <- diag(ch) > L <- t(ch/dd) > DD <- dd^2 > L [,1] [,2] [,3] [1,]100 [2,]110 [3,]111 > DD [1] 1 4 9 This is all rather backwards in that the whole purpose of the LDL' form of the factorization is to avoid taking square roots to get the diagonal elements and to contend with positive semidefinite matrices. In other words, the LDL' form avoids some of the possible problems of the LL' form but not if you go through the LL' form to get to it. I think the underlying reason that an LDL' form is not directly available in R is because there is no Lapack subroutine for it. Let me know what our grade on the homework is. __ 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.
Re: [R] 2 Simple Lattice Plot Questions
Have you tried specifying the levels of y's you want to display, e.g. ylim=c(0,5,10,15,20,30)? -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jimdare Sent: Wednesday, 11 March 2009 12:50 PM To: r-help@r-project.org Subject:Re: [R] 2 Simple Lattice Plot Questions Thanks very much.One other thing... see how the Y axis begins before 0. At first glance it appears that the 0's are actually worth something. When I use ylim=c(0,30) I get the graph I want, but the tick marks show only 5,10,15,20,25. I want them to show 0,5,10,15,20,30. Does anyone know how to change this setting? Cheers, jimdare wrote: > > Hi, > > I have created the plot below and have a few questions about changes. > > 1) How do I change the "Year" title of each plot so it reads from the top > "2006","2007","2008","2009". > 2) How do I get rid of those vertical grey bars in the title bar of each > plot? > > I apologise for my ignorance... one of those days :( > > James > > > http://www.nabble.com/file/p22445242/PLOT.jpg > -- View this message in context: http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22447415.html 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. -- Message protected by MailGuard: e-mail anti-virus, anti-spam and content filtering. http://www.mailguard.com.au/mg https://login.mailguard.com.au/report/1x1TEaABIw/4soNUVnBh04s1coMEHC4LA/7.998 __ 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.
Re: [R] Question about datatypes/plotting issue
There are two header lines which is confusing it. Use pattern= to
start at the second one.
See the three vignettes in zoo for info on the rest.
library(gdata)
W <-
read.xls("http://www2.standardandpoors.com/spf/pdf/index/CSHomePrice_History_022445.xls";,
pattern = "LXXR")
library(zoo)
w <- zooreg(as.matrix(W[-1]), start = as.yearmon("1987-01"), freq = 12)
plot(w[,1:2], col = 1:2, screen = 1, ylab = "")
On Tue, Mar 10, 2009 at 9:15 PM, Oscar Bonilla wrote:
> Hi,
>
> I am trying to plot the Case-Shiller index found at:
> http://www2.standardandpoors.com/spf/pdf/index/CSHomePrice_History_022445.xls
>
> The way I'm importing it into R is as follows:
>
> library(gdata)
> W <-
> read.xls("http://www2.standardandpoors.com/spf/pdf/index/CSHomePrice_History_022445.xls";,
> header=TRUE)
> attach(W)
>
> To give you and idea of what the data looks like:
>
>> head(W)
> Date AZ.Phoenix CA.Los.Angeles CA.San.Diego CA.San.Francisco
> 1 PHXR LXXR SDXR SFXR
> 2 January 1987 59.33 54.67 46.61
> 3 February 1987 59.65 54.89 46.87
> 4 March 1987 59.99 55.16 47.32
> 5 April 1987 60.81 55.85 47.69
> 6 May 1987 61.67 56.35 48.31
> CO.Denver DC.Washington FL.Miami FL.Tampa GA.Atlanta IL.Chicago MA.Boston
> 1 DNXR WDXR MIXR TPXR ATXR CHXR BOXR
> 2 50.20 64.11 68.50 77.33 53.55 70.04
> 3 49.96 64.77 68.76 77.93 54.64 70.08
> 4 50.15 65.71 69.23 77.76 54.80 70.00
> 5 50.55 66.40 69.20 77.56 54.88 70.70
> 6 50.63 67.27 69.46 77.85 55.43 71.51
> MI.Detroit MN.Minneapolis NC.Charlotte NV.Las.Vegas NY.New.York
> OH.Cleveland
> 1 DEXR MNXR CRXR LVXR NYXR
> CEXR
> 2 63.39 66.36 74.42
> 53.53
> 3 63.94 67.03 75.43
> 53.50
> 4 64.17 67.34 76.25
> 53.68
> 5 64.81 67.88 77.34
> 53.75
> 6 65.18 67.90 79.16
> 54.71
> OR.Portland TX.Dallas WA.Seattle Composite.10 Composite.20
> 1 POXR DAXR SEXR CSXR SPCS20R
> 2 41.05 62.82
> 3 41.28 63.39
> 4 41.06 63.87
> 5 40.96 64.57
> 6 41.24 65.56
>
>
> Now on to the problem... if I just run
>
> plot(CA.San.Francisco ~ Date)
>
> I get:
>
>
>
> Which I suspect is a problem because the Date column is not really a Date,
> it is a "factor"
>
> > class(Date)
> [1] "factor"
>
> If I run:
> plot(as.numeric(CA.San.Francisco), type="l")
>
> I get:
>
>
>
>
>
> which is wrong, as CA.San.Francisco has no such discontinuity.
>
>> CA.San.Francisco
> [1] SFXR 46.61 46.87 47.32 47.69 48.31 48.83 49.49 49.94 50.69
> [11] 51.33 51.80 52.03 52.24 52.64 53.19 54.19 56.09 58.22 58.70
> [21] 59.00 59.50 60.37 61.31 62.20 62.66 63.32 64.64 66.27 67.77
> [31] 69.26 70.27 71.36 72.31 72.95 73.25 73.02 72.87 72.95 73.50
> [41] 74.57 75.12 75.15 74.81 74.45 74.24 73.44 72.58 71.47 71.17
> [51] 70.27 69.56 69.46 70.13 70.83 71.39 71.52 71.55 71.21 70.69
> [61] 70.05 69.67 69.48 69.17 69.26 69.86 70.02 70.00 69.64 69.51
> [71] 69.28 68.85 68.21 67.77 67.44 67.09 67.59 67.90 67.99 67.65
> [81] 67.63 67.50 67.18 66.77 66.27 65.98 65.79 66.37 67.05 67.70
> [91] 68.15 68.38 68.40 68.21 68.17 68.04 67.93 67.73 67.40 66.79
> [101] 67.08 67.31 67.50 67.72 67.78 67.76 67.30 66.80 66.43 66.15
> [111] 65.97 65.92 66.44 67.05 67.67 68.02 68.35 68.43 68.53 68.72
> [121] 68.69 68.80 68.81 69.78 71.09 72.19 73.12 73.75 74.43 74.76
> [131] 75.22 75.31 75.81 76.19 76.53 77.48 79.08 80.82 82.41 83.52
> [141] 84.41 85.06 85.05 84.66 84.50 85.03 85.93 87.51 89.21 90.82
> [151] 92.52 94.20 95.14 96.15 96.72 97.87 98.90 100.00 102.70 106.56
> [161] 110.97 115.01 118.45 119.48 119.95 120.94 123.08 125.66 128.58 131.16
> [171] 133.27 134.10 134.38 134.09 132.64 130.95 129.15 128.60 128.01 126.99
> [181] 125.47 125.13 126.06 128.79 132.62 136.07 139.35 141.02 141.93 142.29
> [191] 142.74 143.06 142.40 141.90 142.19 143.00 144.69 145.53 146.53 147.75
> [201] 148.72 150.25 151.75 153.36 154.62 155.93 158.11 160.90 164.65 167.76
> [211] 171.51 173.85 175.89 178.15 180.75 183.15 185.72 189.35 193.50 198.30
> [
Re: [R] Matrices in R - Simple question?
I suspect you probably need to provide an example that illustrates why this seems difficult: > x <- 1:10 > f1 <- function(x) exp(x) > g1 <- function (x) log(x) > h1 <- function (x) x^(1/2) # any of these functions would return a 10 element vector if given x as an argument > f1(x)*g1(x)*h1(x) [1] 0.00e+00 7.243182e+00 3.821981e+01 1.513782e+02 5.34e+02 1.770607e+03 5.645900e+03 1.753265e+04 5.341289e+04 [10] 1.603838e+05 > sum( f1(x)*g1(x)*h1(x) ) [1] 239476.8 Examples might help -- David Winsemius On Mar 10, 2009, at 7:38 PM, Lars Bishop wrote: Hi, I'm a new R user and would appreciate your help regarding the following: Can I create a matrix whose elements are n functions of a vector x? In my problem I have 3 vectors (a,b,c) with elements a=[f1(x) f2(x)fn(x)]; b=[g1(x) g2(x)gn(x)]; c=[h1(x) h2(x)hn(x)]. I need to create a final function that looks like: f(x)=f1(x)*g1(x)*h1(x)+. +fn(x)*gn(x)*hn(x). (f(x) is my objective function of an optimization problem).Is this possible to create f(x) in the way I described? Many thanks in advance for your help! Lars. [[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.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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.
Re: [R] 2 Simple Lattice Plot Questions
Thanks very much.One other thing... see how the Y axis begins before 0. At first glance it appears that the 0's are actually worth something. When I use ylim=c(0,30) I get the graph I want, but the tick marks show only 5,10,15,20,25. I want them to show 0,5,10,15,20,30. Does anyone know how to change this setting? Cheers, jimdare wrote: > > Hi, > > I have created the plot below and have a few questions about changes. > > 1) How do I change the "Year" title of each plot so it reads from the top > "2006","2007","2008","2009". > 2) How do I get rid of those vertical grey bars in the title bar of each > plot? > > I apologise for my ignorance... one of those days :( > > James > > > http://www.nabble.com/file/p22445242/PLOT.jpg > -- View this message in context: http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22447415.html 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.
[R] anyone can help me with Cholesky Decomposition
Hi: what I want to do is decompose the a symmetric matrix A into this form A=LDL' hence TAT'=D,T is inverse of (L)and T is a lower trangular matrix,and D is dignoal matrix for one case A=1 1 1 1 5 5 1 5 14 T=inverse(L)= 1 0 0 -1 1 0 0 -1 1 D=(1,4,9) I tried to use chol(A),but it returns only trangular, anyone know the function can return both L and D? thank you very much~ [[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.html and provide commented, minimal, self-contained, reproducible code.
[R] test two correlation coefficients against each other
hi, is there a function in R that calculates the probability that two correlation coefficients are from the same population? thanks! __ 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.
Re: [R] Pseudo-random numbers between two numbers
I have modified my example to make it more convincing! See at end.
On 10-Mar-09 23:39:17, Ted Harding wrote:
> On 10-Mar-09 23:01:45, g...@ucalgary.ca wrote:
>> Please forget the last email I sent with the same subject.
>> =
>> I would like to generate pseudo-random numbers between two numbers
>> using R, up to a given distribution, for instance, norm. That is
>> something like
>> rnorm(HowMany,Min,Max,mean,sd)
>> over rnorm(HowMany,mean,sd).
>> I am wondering if
>>
>> qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)),
>> mean, sd)
>>
>> is good. Any idea? Thanks.
>> -james
>
> It would certainly work as intended! For instance:
>
> truncnorm<-function(HowMany,Min,Max,mean=0,sd=1){
> qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)),
> mean, sd)}
> Sample <- truncnorm(1000,-1,2.5)
> hist(Sample,breaks=100)
>
> Hoping this helps,
> Ted.
truncnorm<-function(HowMany,Min,Max,mean=0,sd=1){
qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)),
mean, sd)}
Sample <- truncnorm(10,-1,2.5)
hist(Sample,breaks=100)
u0<-(-0.975)+0.05*(0:69)
yy<-dnorm(u0)
du<-min(diff(H$breaks))
Y <- 10*yy*du/(pnorm(2.5)-pnorm(-1.0))
lines(u0,Y)
Ted.
E-Mail: (Ted Harding)
Fax-to-email: +44 (0)870 094 0861
Date: 11-Mar-09 Time: 00:05:23
-- XFMail --
__
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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.
[R] Centering multi-line strip text in lattice
I'm having trouble centering multi-line strip text in lattice. As the
code below demonstrates bounding box of the text is centered within
the strip, but the first line isn't centered in relation to the longer
second line. The "adj" argument to par.strip.text doesn't seem to do
much. Suggestions?
a=data.frame(
x=rep(1:10,2)
,y=rep(1:10,2)
,z=rep(c('First Line\nLonger Second Line (1)','First Line\nLonger
Second Line (2)'),each=10)
)
xyplot(
y~x|z
,data=a
,par.strip.text = list(cex = .75, lineheight=1, lines = 2, adj=.5),
)
--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
Looking to arrange a meeting? Check my public calendar:
http://tinyurl.com/mikes-public-calendar
~ Certainty is folly... I think. ~
__
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] Matrices in R - Simple question?
Hi, I'm a new R user and would appreciate your help regarding the following: Can I create a matrix whose elements are n functions of a vector x? In my problem I have 3 vectors (a,b,c) with elements a=[f1(x) f2(x)fn(x)]; b=[g1(x) g2(x)gn(x)]; c=[h1(x) h2(x)hn(x)]. I need to create a final function that looks like: f(x)=f1(x)*g1(x)*h1(x)+.+fn(x)*gn(x)*hn(x). (f(x) is my objective function of an optimization problem).Is this possible to create f(x) in the way I described? Many thanks in advance for your help! Lars. [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pseudo-random numbers between two numbers
On 10-Mar-09 23:01:45, g...@ucalgary.ca wrote:
> Please forget the last email I sent with the same subject.
> =
> I would like to generate pseudo-random numbers between two numbers
> using R, up to a given distribution, for instance, norm. That is
> something like
> rnorm(HowMany,Min,Max,mean,sd)
> over rnorm(HowMany,mean,sd).
> I am wondering if
>
> qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)),
> mean, sd)
>
> is good. Any idea? Thanks.
> -james
It would certainly work as intended! For instance:
truncnorm<-function(HowMany,Min,Max,mean=0,sd=1){
qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)),
mean, sd)}
Sample <- truncnorm(1000,-1,2.5)
hist(Sample,breaks=100)
Hoping this helps,
Ted.
E-Mail: (Ted Harding)
Fax-to-email: +44 (0)870 094 0861
Date: 10-Mar-09 Time: 23:39:13
-- XFMail --
__
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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.
Re: [R] 2 Simple Lattice Plot Questions
... but in general ?strip.default will explain these matters. In particular, note the style argument. Cheers, Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Elena Wilson Sent: Tuesday, March 10, 2009 3:56 PM To: jimdare; r-help@r-project.org Subject: Re: [R] 2 Simple Lattice Plot Questions With you first question, I had a similar problem when the year (in my case it was sample size) variable was numeric. Add as.factor in front of it and it should show you the actual levels... -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jimdare Sent: Wednesday, 11 March 2009 9:48 AM To: r-help@r-project.org Subject:[R] 2 Simple Lattice Plot Questions Hi, I have created the plot below and have a few questions about changes. 1) How do I change the "Year" title of each plot so it reads from the top "2006","2007","2008","2009". 2) How do I get rid of those vertical grey bars in the title bar of each plot? I apologise for my ignorance... one of those days :( James http://www.nabble.com/file/p22445242/PLOT.jpg -- View this message in context: http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22445242.ht ml 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. -- Message protected by MailGuard: e-mail anti-virus, anti-spam and content filtering. http://www.mailguard.com.au/mg https://login.mailguard.com.au/report/1x1QqLdh8M/3sazYwF0XpYQ6RvoZPBdoj/2.39 8 __ 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-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] Pseudo-random numbers between two numbers
Please forget the last email I sent with the same subject. = I would like to generate pseudo-random numbers between two numbers using R, up to a given distribution, for instance, norm. That is something like rnorm(HowMany,Min,Max,mean,sd) over rnorm(HowMany,mean,sd). I am wondering if qnorm(runif(HowMany, pnorm(Min,mean,sd), pnorm(Max,mean, sd)), mean, sd) is good. Any idea? Thanks. -james __ 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.
Re: [R] help structuring mixed model using lmer()
Mark Difford yahoo.co.uk> writes: > Briefly, y ~ x1 * x2 expands to y ~ x1 + x2 + x1:x2, where the last term > (interaction term) amounts to a test of slope. Normally you would read its > significance from F/chisq/p-value. Many practitioners consider the L.Ratio > test to be a better option. For the fixed effects part in lmer() do: > > mod1 <- y ~ x1 + x2 == y ~ x1 + x2 > mod2 <- y ~ x1 * x2 == y ~ x1 + x2 + x1:x2 > > anova(mod1, mod2) > > This will tell you if you need to worry about interaction or whether slopes > are parallel. ... except that you'd better hope that you have a large number of random units (years? I forget now), or the LR test will be unreliable -- see Pinheiro and Bates 2000, and refer further questions to the r-sig-mixed-models list ... cheers Ben Bolker __ 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.
Re: [R] 2 Simple Lattice Plot Questions
With you first question, I had a similar problem when the year (in my case it was sample size) variable was numeric. Add as.factor in front of it and it should show you the actual levels... -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jimdare Sent: Wednesday, 11 March 2009 9:48 AM To: r-help@r-project.org Subject:[R] 2 Simple Lattice Plot Questions Hi, I have created the plot below and have a few questions about changes. 1) How do I change the "Year" title of each plot so it reads from the top "2006","2007","2008","2009". 2) How do I get rid of those vertical grey bars in the title bar of each plot? I apologise for my ignorance... one of those days :( James http://www.nabble.com/file/p22445242/PLOT.jpg -- View this message in context: http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22445242.html 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. -- Message protected by MailGuard: e-mail anti-virus, anti-spam and content filtering. http://www.mailguard.com.au/mg https://login.mailguard.com.au/report/1x1QqLdh8M/3sazYwF0XpYQ6RvoZPBdoj/2.398 __ 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.
Re: [R] 2 Simple Lattice Plot Questions
Convert Year to a factor and both problems will be solved. --sundar On Tue, Mar 10, 2009 at 3:48 PM, jimdare wrote: > > Hi, > > I have created the plot below and have a few questions about changes. > > 1) How do I change the "Year" title of each plot so it reads from the top > "2006","2007","2008","2009". > 2) How do I get rid of those vertical grey bars in the title bar of each > plot? > > I apologise for my ignorance... one of those days :( > > James > > > http://www.nabble.com/file/p22445242/PLOT.jpg > -- > View this message in context: > http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22445242.html > 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. > __ 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] 2 Simple Lattice Plot Questions
Hi, I have created the plot below and have a few questions about changes. 1) How do I change the "Year" title of each plot so it reads from the top "2006","2007","2008","2009". 2) How do I get rid of those vertical grey bars in the title bar of each plot? I apologise for my ignorance... one of those days :( James http://www.nabble.com/file/p22445242/PLOT.jpg -- View this message in context: http://www.nabble.com/2-Simple-Lattice-Plot-Questions-tp22445242p22445242.html 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.
[R] Pseudo-random numbers between two numbers
I would like to generate pseudo-random numbers between two numbers using R, up to a given distribution, for instance, rnorm. That is something like rnorm(HowMany,Min,Max,mean,sd) over rnorm(HowMany,mean,sd). I am wondering if dnorm(runif(HowMany, Min, Max), mean, sd) is good. Any idea? Thanks. -james __ 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.
Re: [R] puzzled by math on date-time objects
Stavros Macrakis wrote: > I have documented some of these issues in my email "Semantics of > sequences in R" (22/02/2009 3:42 PM) and other emails, and I have > proposed to write code to resolve them, but have not received a warm > reception. > you said 'it *is* a mess', didn't you? warm reception? vQ __ 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.
Re: [R] puzzled by math on date-time objects
Stavros Macrakis wrote: > It does seem sensible that median and quantile would work for the > POSIXct, Date, and other classes for which they are logically > well-defined, but strangely enough, they do not (except for odd-length > input). The summary function has a special case (summary.POSIXct) > which does the straightforward, obvious thing here. I do not > understand why this is not done by median and quantile themselves. > > Conversely, for the complex class, median and quantile do not give an > error but instead produce meaningless results > median, but not quantile, seems to fail on complex: median(0i) # error, needs numeric quantile(0i) # fine the latter is a presumably a bug, because it doesn't follow the documentation, ?quantile: " quantile(x, ...) Arguments: x: numeric vectors whose sample quantiles are wanted. Missing values are ignored. " and complex is not numeric: is.numeric(0i) # FALSE > since the complexes do > not form an ordered field). well, in r complexes are not comparable, but they can be sorted: 0i < 1i # no go sort(c(0i, 1i)) # fine vQ __ 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.
Re: [R] Cholesky Decomposition in R
try Cholesky() in package Matrix. albyn On Tue, Mar 10, 2009 at 02:33:01PM -0700, Manli Yan wrote: > Hi everyone: > I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I > only found how to decomposite A in to LL' by using chol(A),the function > Cholesky(A) doesnt work,any one know other command to decomposte A in to > LDL' > > My r code is: > library(Matrix) > A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > > > chol(A) > [,1] [,2] [,3] > [1,]111 > [2,]022 > [3,]003 > > > Cholesky(A) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Cholesky", for signature > "matrix" > > whatz wrong??? > thanks~ > > [[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.html > and provide commented, minimal, self-contained, reproducible code. > __ 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.
Re: [R] R equivalent to MATLAB's "whos" Command?
Something similar in case anyone is interested, my own 'lls' command:
# This function performs a similar operation to the Unix command 'ls -l'
# It works like ls() in R except that it will also display object class,
# dimension/length, and object size.
# It can also take a class filter to view only objects of a certain type.
#
# Usage:
# lls() # list all objects
# lls(environmentName) # list all the objects in the specified environment
# lls(pattern="foo") # list all objects whose name matches pattern specified
# lls(classFilter="data.frame") # find all data frame objects
#
lls <- function(name, pos=-1, envir=as.environment(pos), all.names=FALSE,
pattern, classFilter)
{
if( !missing(name) )
{
envir = name
} else
{
envir = parent.frame()
}
lsList = ls(name, pos, envir, all.names, pattern)
cat("\nName: Class, Length, Size\n")
cat("-\n")
for( item in lsList )
{
realItem = eval(parse(text = item), envir)
itemClass = class(realItem)
itemSize = object.size(realItem)
itemDimension = paste(dim(realItem), collapse="x" )
if( itemDimension == "" )
{
itemDimension = length(realItem)
}
classFilterMatches = !missing(classFilter) && itemClass == classFilter
if( classFilterMatches || missing(classFilter) )
{
format(cat(item, ": ", itemClass, ", ", itemDimension, ", ", itemSize,
"\n",
sep=""), justify="centre")
}
}
cat("\n")
invisible(lsList)
}
# Overload the internal object.size function to return the size in B/KB/MB
#
object.size <-function(x)
{
size = .Internal(object.size(x))
if (size<1024)
{
size=paste(size, "B")
}
else if (size>=1024 & size < 1024*1024)
{
size=paste( round(size/1024, 1), "KB")
}
else
{
size=paste( round( size/1024/1024, 1 ),"MB")
}
return(size)
}
Creates output like:
Name: Class, Length, Size
-
calc: function, 1, 4.7 KB
data: data.frame, 175656x76, 100.9 MB
dollar: function, 1, 7.1 KB
file: character, 1, 120 B
fileList: character, 17, 1.9 KB
lls: function, 1, 17.6 KB
object.size: function, 1, 7.8 KB
changes: data.frame, 175656x70, 94.5 MB
columns: integer, 70, 304 B
value: numeric, 1, 32 B
Feel free to clean up & use as appropriate.
HTH,
John
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of andrew
Sent: Tuesday, March 10, 2009 5:46 PM
To: r-help@r-project.org
Subject: Re: [R] R equivalent to MATLAB's "whos" Command?
I saw this in
http://groups.google.com.au/group/r-help-archive/browse_thread/thread/7dca300a7fde5286/718dc5f1405618c9?lnk=gst&q=sort(+sapply(ls()%2Cfunction(x){object.size(get(x))}))#718dc5f1405618c9
The command is something like
sort( sapply(ls(),function(x){object.size(get(x))}))
very useful, so I have added it to my .First function
On Mar 11, 8:29 am, Jason Rupert wrote:
> Wow. Thank you for your quick response. However, I'm looking for an R
> command that lists what is currently in the R workspace.
>
> Here is a link to a description of the MATLAB "whos"
> command:http://www.math.carleton.ca/old/help/matlab/MathWorks_R13Doc/techdoc/...
> Essentially, it does the following:
> "who lists the variables currently in the workspace.
>
> whos lists the current variables and their sizes and types. It also reports
> the totals for sizes.
>
> who('global') and whos('global') list the variables in the global workspace
> "
>
> --- On Tue, 3/10/09, Jorge Ivan Velez wrote:
>
>
>
> > From: Jorge Ivan Velez
> > Subject: Re: [R] R equivalent to MATLAB's "whos" Command?
> > To: jasonkrup...@yahoo.com
> > Cc: r-h...@r-project.org
> > Date: Tuesday, March 10, 2009, 4:14 PM
> > Dear Jason,
> > How about this?
>
> > ?ls()
> > ls()
>
> > HTH,
>
> > Jorge
>
> > On Tue, Mar 10, 2009 at 5:05 PM, Jason Rupert
> > wrote:
>
> By any chance is there an R equivalent to MATLAB' "whos" command? I tried
> searching R and R-seek, but didn't really come up with anything. There are
> several items I would like to make sure are stored in the workspace and check
> their values. Thank you again for your help and any feedback.
>
>
>
> > > > ?workspace
> > > No documentation for 'workspace' in specified
> > packages and libraries:
> > > you could try '??workspace'
> > > > ??workspace
> > > No help files found with alias or concept or title
> > matching using fuzzy matching.
> > > > ??whos
> > > No help files found with alias or concept or title
> > matching using regular expression matching.
> > > > ??whos
> > > No help files found with alias or concept or title
> > matching using regular expression matching.
> > > > ?whos
> > > No documentation for 'whos' in specified
> > packages and libraries:
> > > you could try '??w
Re: [R] R equivalent to MATLAB's "whos" Command?
Learn to use R-search.
http://search.r-project.org/nmz.html
The obvious search strategy, ls size, seemed effective.
--
On Mar 10, 2009, at 5:29 PM, Jason Rupert wrote:
Wow. Thank you for your quick response. However, I'm looking for
an R command that lists what is currently in the R workspace.
Here is a link to a description of the MATLAB "whos" command:
http://www.math.carleton.ca/old/help/matlab/MathWorks_R13Doc/techdoc/ref/who.html
Essentially, it does the following:
"who lists the variables currently in the workspace.
whos lists the current variables and their sizes and types. It also
reports the totals for sizes.
who('global') and whos('global') list the variables in the global
workspace
"
--- On Tue, 3/10/09, Jorge Ivan Velez
wrote:
From: Jorge Ivan Velez
Subject: Re: [R] R equivalent to MATLAB's "whos" Command?
To: jasonkrup...@yahoo.com
Cc: R-help@r-project.org
Date: Tuesday, March 10, 2009, 4:14 PM
Dear Jason,
How about this?
?ls()
ls()
HTH,
Jorge
On Tue, Mar 10, 2009 at 5:05 PM, Jason Rupert
wrote:
By any chance is there an R equivalent to MATLAB' "whos" command? I
tried searching R and R-seek, but didn't really come up with
anything. There are several items I would like to make sure are
stored in the workspace and check their values. Thank you again for
your help and any feedback.
?workspace
No documentation for 'workspace' in specified
packages and libraries:
you could try '??workspace'
??workspace
No help files found with alias or concept or title
matching using fuzzy matching.
??whos
No help files found with alias or concept or title
matching using regular expression matching.
??whos
No help files found with alias or concept or title
matching using regular expression matching.
?whos
No documentation for 'whos' in specified
packages and libraries:
you could try '??whos'
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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.
Re: [R] puzzled by math on date-time objects
It does seem sensible that median and quantile would work for the
POSIXct, Date, and other classes for which they are logically
well-defined, but strangely enough, they do not (except for odd-length
input). The summary function has a special case (summary.POSIXct)
which does the straightforward, obvious thing here. I do not
understand why this is not done by median and quantile themselves.
Conversely, for the complex class, median and quantile do not give an
error but instead produce meaningless results (since the complexes do
not form an ordered field).
There are other operations as well that don't do the natural, useful
thing on a variety of classes, including POSIXct, Date, and difftime:
> dates <- c(as.Date('2000-01-01'), as.Date('2000-01-05'),
> as.Date('1990-08-09'), as.Date('2008-02-29'))
> median(dates)
Error in Summary.Date(c(10957, 10961), na.rm = FALSE) :
sum not defined for Date objects
> quantile(dates,.5)
Error in Ops.Date((1 - h), qs[i]) : * not defined for Date objects
> gaps <- diff(sort(dates))
> gaps
Time differences in days
[1] 34324 2977
> cumsum(gaps)
Error in Math.difftime(gaps) :
'cumsum' not defined for "difftime" objects
> rle(dates)
Error in rle(dates) : 'x' must be an atomic vector
> rle(gaps)
Error in rle(gaps) : 'x' must be an atomic vector
I have documented some of these issues in my email "Semantics of
sequences in R" (22/02/2009 3:42 PM) and other emails, and I have
proposed to write code to resolve them, but have not received a warm
reception.
All I can suggest at this point is that you write your own versions of
these functions. Or perhaps one of us will write a CRAN package,
though this really seems like core behavior.
-s
On Tue, Mar 10, 2009 at 11:44 AM, Denis Chabot wrote:
> I don't understand the following. When I create a small artificial set of
> date information in class POSIXct, I can calculate the mean and the median:
> ...But for real data (for this post, a short subset is in object c) that I
> have converted into a POSIXct object, I cannot calculate the median with
> median(), though I do get it with summary():
__
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] max-nsize, cons : what do they all mean?
Hello R users, I had recently run an R session where a particular function ran several thousand times, i think into the hundreds of thousands. I got this error related to cons cells, which I fixed by starting (actually Rserve) with the --max-nsize=1G option. I read the help page, but didn't quite understand it. What does the option do and why did I initially run into an error ? >From man R --max-nsize Set max number of cons cells to N Why should there be a maximum? Thanks for your time Saptarshi Guha __ 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.
Re: [R] R equivalent to MATLAB's "whos" Command?
I saw this in
http://groups.google.com.au/group/r-help-archive/browse_thread/thread/7dca300a7fde5286/718dc5f1405618c9?lnk=gst&q=sort(+sapply(ls()%2Cfunction(x){object.size(get(x))}))#718dc5f1405618c9
The command is something like
sort( sapply(ls(),function(x){object.size(get(x))}))
very useful, so I have added it to my .First function
On Mar 11, 8:29 am, Jason Rupert wrote:
> Wow. Thank you for your quick response. However, I'm looking for an R
> command that lists what is currently in the R workspace.
>
> Here is a link to a description of the MATLAB "whos"
> command:http://www.math.carleton.ca/old/help/matlab/MathWorks_R13Doc/techdoc/...
> Essentially, it does the following:
> "who lists the variables currently in the workspace.
>
> whos lists the current variables and their sizes and types. It also reports
> the totals for sizes.
>
> who('global') and whos('global') list the variables in the global workspace
> "
>
> --- On Tue, 3/10/09, Jorge Ivan Velez wrote:
>
>
>
> > From: Jorge Ivan Velez
> > Subject: Re: [R] R equivalent to MATLAB's "whos" Command?
> > To: jasonkrup...@yahoo.com
> > Cc: r-h...@r-project.org
> > Date: Tuesday, March 10, 2009, 4:14 PM
> > Dear Jason,
> > How about this?
>
> > ?ls()
> > ls()
>
> > HTH,
>
> > Jorge
>
> > On Tue, Mar 10, 2009 at 5:05 PM, Jason Rupert
> > wrote:
>
> By any chance is there an R equivalent to MATLAB' "whos" command? I tried
> searching R and R-seek, but didn't really come up with anything. There are
> several items I would like to make sure are stored in the workspace and check
> their values. Thank you again for your help and any feedback.
>
>
>
> > > > ?workspace
> > > No documentation for 'workspace' in specified
> > packages and libraries:
> > > you could try '??workspace'
> > > > ??workspace
> > > No help files found with alias or concept or title
> > matching using fuzzy matching.
> > > > ??whos
> > > No help files found with alias or concept or title
> > matching using regular expression matching.
> > > > ??whos
> > > No help files found with alias or concept or title
> > matching using regular expression matching.
> > > > ?whos
> > > No documentation for 'whos' in specified
> > packages and libraries:
> > > you could try '??whos'
>
> > > [[alternative HTML version deleted]]
>
> > > __
> > > r-h...@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-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
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.
Re: [R] Cholesky Decomposition in R
You can use singular value decomposition: ?svd > svd(A) $d [1] 16.3405917 2.8996176 0.7597907 # This is your diagonal matrix "D" $u [,1] [,2][,3] [1,] 0.08585595 -0.2420411 0.96645997 [2,] 0.40826313 -0.8763116 -0.25573252 [3,] 0.90881790 0.4165261 0.02357989 $v [,1] [,2][,3] [1,] 0.08585595 -0.2420411 0.96645997 [2,] 0.40826313 -0.8763116 -0.25573252 [3,] 0.90881790 0.4165261 0.02357989 > Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Manli Yan Sent: Tuesday, March 10, 2009 5:33 PM To: r-help@r-project.org Subject: [R] Cholesky Decomposition in R Hi everyone: I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I only found how to decomposite A in to LL' by using chol(A),the function Cholesky(A) doesnt work,any one know other command to decomposte A in to LDL' My r code is: library(Matrix) A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > chol(A) [,1] [,2] [,3] [1,]111 [2,]022 [3,]003 > Cholesky(A) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Cholesky", for signature "matrix" whatz wrong??? thanks~ [[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.html and provide commented, minimal, self-contained, reproducible code. __ 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] Cholesky Decomposition in R
Hi everyone: I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I only found how to decomposite A in to LL' by using chol(A),the function Cholesky(A) doesnt work,any one know other command to decomposte A in to LDL' My r code is: library(Matrix) A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > chol(A) [,1] [,2] [,3] [1,]111 [2,]022 [3,]003 > Cholesky(A) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Cholesky", for signature "matrix" whatz wrong??? thanks~ [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R equivalent to MATLAB's "whos" Command?
Jason Rupert wrote: > Â > By any chance is there an R equivalent to MATLAB's "whos" command? > whos = function(envir=parent.frame()) print(sapply(ls(envir=envir), USE.NAMES=TRUE, get, envir=envir)) or simply whos = ls.str and x = 1 y = 2 whos() vQ __ 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.
Re: [R] R equivalent to MATLAB's "whos" Command?
Wow. Thank you for your quick response. However, I'm looking for an R command
that lists what is currently in the R workspace.
Here is a link to a description of the MATLAB "whos" command:
http://www.math.carleton.ca/old/help/matlab/MathWorks_R13Doc/techdoc/ref/who.html
Essentially, it does the following:
"who lists the variables currently in the workspace.
whos lists the current variables and their sizes and types. It also reports the
totals for sizes.
who('global') and whos('global') list the variables in the global workspace
"
--- On Tue, 3/10/09, Jorge Ivan Velez wrote:
> From: Jorge Ivan Velez
> Subject: Re: [R] R equivalent to MATLAB's "whos" Command?
> To: jasonkrup...@yahoo.com
> Cc: R-help@r-project.org
> Date: Tuesday, March 10, 2009, 4:14 PM
> Dear Jason,
> How about this?
>
> ?ls()
> ls()
>
> HTH,
>
> Jorge
>
>
> On Tue, Mar 10, 2009 at 5:05 PM, Jason Rupert
> wrote:
>
>
By any chance is there an R equivalent to MATLAB' "whos" command? I tried
searching R and R-seek, but didn't really come up with anything. There are
several items I would like to make sure are stored in the workspace and check
their values. Thank you again for your help and any feedback.
> > > ?workspace
> > No documentation for 'workspace' in specified
> packages and libraries:
> > you could try '??workspace'
> > > ??workspace
> > No help files found with alias or concept or title
> matching using fuzzy matching.
> > > ??whos
> > No help files found with alias or concept or title
> matching using regular expression matching.
> > > ??whos
> > No help files found with alias or concept or title
> matching using regular expression matching.
> > > ?whos
> > No documentation for 'whos' in specified
> packages and libraries:
> > you could try '??whos'
> >
> >
> >
> >
> >[[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.html
> > and provide commented, minimal, self-contained,
> reproducible code.
> >
> >
__
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] Using napredict in prcomp
Hello all, I wish to compute site scores using PCA (prcomp) on a matrix with missing values, for example: DrainSlopeOrgL a41NA b2.5396 c6845 d3912 e3164 ... Where a,b... are sites. The command > pca<-prcomp(~ Drain + Slope + OrgL, data = t, center = TRUE, scale = TRUE, na.action=na.exclude) works great, and from > pca$x I can get site scores, e.g. PC1 PC2 PC3 a NA NA NA b -2.10475208 -2.315128625 -0.885197753 c 5.01177388 -1.778786252 -0.193285051 d 0.28638602 0.298315086 0.386113799 e -0.58861254 0.089498632 -0.434951813 ... Easy enough... But how do I use the "napredict" argument? Is it intended as an argument to be used in the prcomp line (as suggested in ?prcomp), or is it to be used by itself, to replace NAs in the above site score matrix (which is what I really want to do). Thank you, Alain -- Alain Paquette, Ph.D. alain.paque...@gmail.com Centre d'étude de la forêt (CEF) Université du Québec à Montréal www.cef-cfr.ca Projet TRIADE www.projettriade.ca alain.paque...@projettriade.ca __ 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.
Re: [R] R equivalent to MATLAB's "whos" Command?
Dear Jason, How about this? ?ls() ls() HTH, Jorge On Tue, Mar 10, 2009 at 5:05 PM, Jason Rupert wrote: >  > By any chance is there an R equivalent to MATLAB's "whos" command? >  > I tried searching R and R-seek, but didn't really come up with anything. >  > There are several items I would like to make sure are stored in the > workspace and check their values. >  > Thank you again for your help and any feedback. >  >  > > ?workspace > No documentation for 'workspace' in specified packages and libraries: > you could try '??workspace' > > ??workspace > No help files found with alias or concept or title matching âworkspaceâ > using fuzzy matching. > > ??whos > No help files found with alias or concept or title matching âwhosâ > using regular expression matching. > > ??whos > No help files found with alias or concept or title matching âwhosâ > using regular expression matching. > > ?whos > No documentation for 'whos' in specified packages and libraries: > you could try '??whos' > > > > >[[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.html > and provide commented, minimal, self-contained, reproducible code. > > [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] popular R packages
s...@xlsolutions-corp.com wrote:
Hi Spencer,
XLSolutions is currently analyzing r-help archived questions to rank
packages for the upcoming R-PLUS 3.3 Professional version and we will be
happy to share the outcome with interested parties. Please email
d...@xlsolutions-corp.com
I would expect that the correlation between popularity on the one hand
and usefulness as well as quality to be relatively low. If it was
possible to rate the downloaders in respect to "seriousness" and whether
they actually use the package for some sensible purpose I would be more
interested. Consider a highly specialized and good quality package used
by a relatively small group of distinguished reseachers. Would that
have a high rank? No. But important? Possibly yes.
Tom
Regards -
Sue Turner
Senior Account Manager
XLSolutions Corporation
North American Division
1700 7th Ave
Suite 2100
Seattle, WA 98101
Phone: 206-686-1578
Email: s...@xlsolutions-corp.com
web: www.xlsolutions-corp.com
--- On Sat, 3/7/09, Spencer Graves wrote:
From: Spencer Graves
Subject: Re: [R] popular R packages
To: "Wacek Kusnierczyk"
Cc: r-help@r-project.org, "Jeroen Ooms" , "Thomas Adams"
Date: Saturday, March 7, 2009, 5:22 PM
I just did RSiteSearch("library(xxx)") with xxx =
the names of 6 packages familiar to me, with the following
numbers of hits:
hits package
169 lme4
165 nlme
6 fda
4 maps
2 FinTS
2 DierckxSpline
Software could be written to (1) extract the names of
current packages from CRAN then (2) perform queries similar
to this on all such packages and summarize the results. I
don't have the time now to write code for this, but
I've written similar code before for step (1); it can
be found in "scripts/TsayFiles.R" in the
"FinTS" package on CRAN. For step (2), Sundar
Dorai-Raj wrote code that is is included in the preliminary
"RSiteSearch" package available from R-Forge via
install.'packages("RSiteSearch",repos="http://r-forge.r-project.org";)'.
Code to do this could probably be written (a) in a
matter of seconds by many of those in the R Core team or (b)
in a matter of hours by virtually any reader of this list
using the examples I just cited. And it could provide
numbers without a need to convince others to keep download
statistics and make them available later.
Hope this helps. Spencer Graves
Wacek Kusnierczyk wrote:
i have kept r installed on more than ten computers
during the past few
years, some of them running win + more than one linux
distro, all of
them having r, most often installed from a separate
download.
i know of many cases where students download r for the
purpose of a
course in statistics -- often an introductory course
for students who
otherwise have little to do with stats. some of them
do it more than
once during the semester, and many of them never use r
again.
taking into account that basic statistics courses are
taught to most
university students and that r is surely the most
popular free
statistical computing environment, download-based
usage estimates may be
a bit optimistic, unless 'usage' is taken to
include 'learn-pass-forget'.
vQ
Tal Galili wrote:
I agree with Thomas, over the years I have
installed R on at least 5
computers.
BTW: does any one knows how the website statistics
of r-project are
being analyzed?
Since I can't see any "google
analytics" or other tracking code in the main
website, I am guessing someone might be running
some log-file analyzer - but
I'd rather hear that then assume.
On Sun, Mar 8, 2009 at 12:45 AM, Thomas Adams
wrote:
I don't think "At least one of the
participants in the 2004 thread
suggested that it would be a "good
thing" to track the numbers of downloads
by package." is reasonable because I
download R packages for 2 home
computers (laptop & desktop) and 2 at work
(1 Linux & 1 Mac). There must be
many such cases…
Tom
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--
++
| Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology |
| University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY |
| Tel : +
[R] R equivalent to MATLAB's "whos" Command?
 By any chance is there an R equivalent to MATLAB's "whos" command?  I tried searching R and R-seek, but didn't really come up with anything.  There are several items I would like to make sure are stored in the workspace and check their values.  Thank you again for your help and any feedback.   > ?workspace No documentation for 'workspace' in specified packages and libraries: you could try '??workspace' > ??workspace No help files found with alias or concept or title matching âworkspaceâ using fuzzy matching. > ??whos No help files found with alias or concept or title matching âwhosâ using regular expression matching. > ??whos No help files found with alias or concept or title matching âwhosâ using regular expression matching. > ?whos No documentation for 'whos' in specified packages and libraries: you could try '??whos' [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] require() is not giving TRUE / FALSE statements ?
Duncan Murdoch wrote: > On 10/03/2009 4:40 PM, Wacek Kusnierczyk wrote: >> Duncan Murdoch wrote: >>> On 10/03/2009 4:15 PM, Wolfgang Raffelsberger wrote: Dear list, ?require says : "... |require| is designed for use inside other functions; it returns |FALSE| and gives a warning (rather than an error as |library()| does by default) if the package does not exist ..." However when I run the following code I don't get any TRUE / FALSE statements (but the warning only). >>> You never printed the value, so you didn't see it. (It was returned >>> marked invisible, i.e. not for printing.) >>> >> >> maybe it would help if the man page said 'returns invisibly' instead of >> 'returns'. > > It does. indeed, though not where wolfgang quotes it above, hence my suggestion. sorry, my fault, should have checked. vQ __ 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.
Re: [R] require() is not giving TRUE / FALSE statements ?
On 10/03/2009 4:40 PM, Wacek Kusnierczyk wrote: Duncan Murdoch wrote: On 10/03/2009 4:15 PM, Wolfgang Raffelsberger wrote: Dear list, ?require says : "... |require| is designed for use inside other functions; it returns |FALSE| and gives a warning (rather than an error as |library()| does by default) if the package does not exist ..." However when I run the following code I don't get any TRUE / FALSE statements (but the warning only). You never printed the value, so you didn't see it. (It was returned marked invisible, i.e. not for printing.) maybe it would help if the man page said 'returns invisibly' instead of 'returns'. It does. Duncan Murdoch __ 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.
Re: [R] system() not accepting strings from cat()
On 11/03/2009, at 9:34 AM, culpritNr1 wrote:
I meant charm, not sharm!
(how embarrasing...)
If you're embarrassed by ***that*** you need to watch more Monty
Python! :-)
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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Re: [R] require() is not giving TRUE / FALSE statements ?
Duncan Murdoch wrote: > On 10/03/2009 4:15 PM, Wolfgang Raffelsberger wrote: >> Dear list, >> >> ?require says : >> "... |require| is designed for use inside other functions; it returns >> |FALSE| and gives a warning (rather than an error as |library()| does >> by default) if the package does not exist ..." >> >> However when I run the following code I don't get any TRUE / FALSE >> statements (but the warning only). > > You never printed the value, so you didn't see it. (It was returned > marked invisible, i.e. not for printing.) > maybe it would help if the man page said 'returns invisibly' instead of 'returns'. vQ __ 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.
Re: [R] system() not accepting strings from cat()
embarrasSing, not embarrasing.
You see how I became culpritNr1?
culpritNr1 wrote:
>
> I meant charm, not sharm!
>
> (how embarrasing...)
>
>
>
>
> culpritNr1 wrote:
>>
>> OH! The joy!
>>
>> It worked like a sharm.
>>
>> Thank you.
>>
>> culpritNr1
>>
>>
>>
>>
>>
>> baptiste auguie-2 wrote:
>>>
>>>
>>> try
>>> ?paste
>>>
>>>
>>> baptiste
>>>
>>> On 10 Mar 2009, at 20:01, ig2ar-s...@yahoo.co.uk wrote:
>>>
Hi again R-ists,
How do you construct a string that you can pass to system()?
For instance. Say I do
> system("echo Hello!")
Hello!
That works. Now the alternative: I need to construct the string like
this
> a <- "echo"
> b <- "Hello!"
> c <- "\n"
> cat(a, b, c)
echo Hello!
Looks nice... but see what happens when I try to use it
> system(cat(a, b, c))
echo Hello!
Error in system(command, intern) : non-empty character argument
expected
I have googled extensively in and out of r-lists but I can't find a
solution.
Can anybody help?
__
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.
>>>
>>> _
>>>
>>> Baptiste Auguié
>>>
>>> School of Physics
>>> University of Exeter
>>> Stocker Road,
>>> Exeter, Devon,
>>> EX4 4QL, UK
>>>
>>> Phone: +44 1392 264187
>>>
>>> http://newton.ex.ac.uk/research/emag
>>>
>>> __
>>> 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/system%28%29-not-accepting-strings-from-cat%28%29-tp22442414p22443051.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
Re: [R] system() not accepting strings from cat()
I meant charm, not sharm!
(how embarrasing...)
culpritNr1 wrote:
>
> OH! The joy!
>
> It worked like a sharm.
>
> Thank you.
>
> culpritNr1
>
>
>
>
>
> baptiste auguie-2 wrote:
>>
>>
>> try
>> ?paste
>>
>>
>> baptiste
>>
>> On 10 Mar 2009, at 20:01, ig2ar-s...@yahoo.co.uk wrote:
>>
>>>
>>> Hi again R-ists,
>>>
>>> How do you construct a string that you can pass to system()?
>>>
>>> For instance. Say I do
>>>
system("echo Hello!")
>>> Hello!
>>>
>>> That works. Now the alternative: I need to construct the string like
>>> this
>>>
a <- "echo"
b <- "Hello!"
c <- "\n"
cat(a, b, c)
>>> echo Hello!
>>>
>>> Looks nice... but see what happens when I try to use it
>>>
system(cat(a, b, c))
>>> echo Hello!
>>> Error in system(command, intern) : non-empty character argument
>>> expected
>>>
>>> I have googled extensively in and out of r-lists but I can't find a
>>> solution.
>>>
>>> Can anybody help?
>>>
>>>
>>>
>>>
>>> __
>>> 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.
>>
>> _
>>
>> Baptiste Auguié
>>
>> School of Physics
>> University of Exeter
>> Stocker Road,
>> Exeter, Devon,
>> EX4 4QL, UK
>>
>> Phone: +44 1392 264187
>>
>> http://newton.ex.ac.uk/research/emag
>>
>> __
>> 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/system%28%29-not-accepting-strings-from-cat%28%29-tp22442414p22443015.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
Re: [R] system() not accepting strings from cat()
OH! The joy!
It worked like a sharm.
Thank you.
culpritNr1
baptiste auguie-2 wrote:
>
>
> try
> ?paste
>
>
> baptiste
>
> On 10 Mar 2009, at 20:01, ig2ar-s...@yahoo.co.uk wrote:
>
>>
>> Hi again R-ists,
>>
>> How do you construct a string that you can pass to system()?
>>
>> For instance. Say I do
>>
>>> system("echo Hello!")
>> Hello!
>>
>> That works. Now the alternative: I need to construct the string like
>> this
>>
>>> a <- "echo"
>>> b <- "Hello!"
>>> c <- "\n"
>>> cat(a, b, c)
>> echo Hello!
>>
>> Looks nice... but see what happens when I try to use it
>>
>>> system(cat(a, b, c))
>> echo Hello!
>> Error in system(command, intern) : non-empty character argument
>> expected
>>
>> I have googled extensively in and out of r-lists but I can't find a
>> solution.
>>
>> Can anybody help?
>>
>>
>>
>>
>> __
>> 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.
>
> _
>
> Baptiste Auguié
>
> School of Physics
> University of Exeter
> Stocker Road,
> Exeter, Devon,
> EX4 4QL, UK
>
> Phone: +44 1392 264187
>
> http://newton.ex.ac.uk/research/emag
>
> __
> 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/system%28%29-not-accepting-strings-from-cat%28%29-tp22442414p22442991.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
Re: [R] require() is not giving TRUE / FALSE statements ?
On 10/03/2009 4:15 PM, Wolfgang Raffelsberger wrote: Dear list, ?require says : "... |require| is designed for use inside other functions; it returns |FALSE| and gives a warning (rather than an error as |library()| does by default) if the package does not exist ..." However when I run the following code I don't get any TRUE / FALSE statements (but the warning only). You never printed the value, so you didn't see it. (It was returned marked invisible, i.e. not for printing.) Just save the value to a variable, or use it in a test, or explicitly print it: > print(require(stats)) [1] TRUE > print(require(doesNotExist)) Loading required package: doesNotExist [1] FALSE Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'doesNotExist' Duncan Murdoch Since I want to test from inside of a function if a given package is installed (and do some specific actions like eg trying to install if the answer is negative), I need the FALSE statement for use with if(). I found a work-around (see below), but I wanted to bring to your attention that require() doesn't give the message(s) it's supposed to return. Wolfgang > require(stats) > require(doesNotExist)# example for library that's not existing on my system Loading required package: doesNotExist Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'doesNotExist' >## After all I found a work-around with : >library(doesNotExist,logical.return=T) [1] FALSE Warning message: In library(doesNotExist, logical.return = T) : there is no package called 'doesNotExist' >## for completeness : > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] RODBC_1.2-4svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5 svIDE_0.9-5 loaded via a namespace (and not attached): [1] tools_2.8.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et Génomique Intégratives CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr __ 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-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.
Re: [R] popular R packages
Bioconductor already provides download stats for all packages... http://bioconductor.org/packages/stats/bioc/affy.html -Christos > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Max Kuhn > Sent: Tuesday, March 10, 2009 12:25 PM > To: r-help@r-project.org > Subject: Re: [R] popular R packages > > If is easy to get the download numbers, we should do it and > deal with the interpretation issues. I'd like to know the > numbers so I can understand which (of my) packages have the > most usage. > > One other compication about # downloads: I suspect that a > package being on teh depends/suggests/imports list of another > package might be a big driver with respect to how many times > that it was downloaded. > > If I remember correctly, about 5 years ago Bioconductor asked > for volunteers to review packages to get detailed, specific > feedback by people who use the package (and should be fairly > R proficient). I think that this is pretty important and > something like Crantastic is a good interface. I personally > got a lot out of the comments the a JSS reviewer had for a package. > > -- > > Max > > __ > 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-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] require() is not giving TRUE / FALSE statements ?
Dear list, ?require says : "... |require| is designed for use inside other functions; it returns |FALSE| and gives a warning (rather than an error as |library()| does by default) if the package does not exist ..." However when I run the following code I don't get any TRUE / FALSE statements (but the warning only). Since I want to test from inside of a function if a given package is installed (and do some specific actions like eg trying to install if the answer is negative), I need the FALSE statement for use with if(). I found a work-around (see below), but I wanted to bring to your attention that require() doesn't give the message(s) it's supposed to return. Wolfgang > require(stats) > require(doesNotExist)# example for library that's not existing on my system Loading required package: doesNotExist Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'doesNotExist' >## After all I found a work-around with : >library(doesNotExist,logical.return=T) [1] FALSE Warning message: In library(doesNotExist, logical.return = T) : there is no package called 'doesNotExist' >## for completeness : > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] RODBC_1.2-4svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5 svIDE_0.9-5 loaded via a namespace (and not attached): [1] tools_2.8.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et Génomique Intégratives CNRS UMR7104, IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr __ 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.
Re: [R] system() not accepting strings from cat()
try
?paste
baptiste
On 10 Mar 2009, at 20:01, ig2ar-s...@yahoo.co.uk wrote:
Hi again R-ists,
How do you construct a string that you can pass to system()?
For instance. Say I do
system("echo Hello!")
Hello!
That works. Now the alternative: I need to construct the string like
this
a <- "echo"
b <- "Hello!"
c <- "\n"
cat(a, b, c)
echo Hello!
Looks nice... but see what happens when I try to use it
system(cat(a, b, c))
echo Hello!
Error in system(command, intern) : non-empty character argument
expected
I have googled extensively in and out of r-lists but I can't find a
solution.
Can anybody help?
__
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.
_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
__
R-help@r-project.org mailing list
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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.
Re: [R] help structuring mixed model using lmer()
Hi Simon, Have a look at Chap. 11 of "An Introduction to R" (one of R's manuals), which explains the different ways of specifying models using formulae. Briefly, y ~ x1 * x2 expands to y ~ x1 + x2 + x1:x2, where the last term (interaction term) amounts to a test of slope. Normally you would read its significance from F/chisq/p-value. Many practitioners consider the L.Ratio test to be a better option. For the fixed effects part in lmer() do: mod1 <- y ~ x1 + x2 == y ~ x1 + x2 mod2 <- y ~ x1 * x2 == y ~ x1 + x2 + x1:x2 anova(mod1, mod2) This will tell you if you need to worry about interaction or whether slopes are parallel. Regards, Mark. Simon Pickett-4 wrote: > > Cheers, > > Actually I was using quasipoisson for my models, but for the puposes of my > example, it doesnt really matter. > > I am trying to work out a way of quantifying whether the slopes (for > years) > are covary with habitat scores. > > The more I think about it, the more I am convinced that it isnt possible > do > to that using a glm approach. I think I have to run separate models for > each > site, calculate the gradient, then do a lm with gradient explained by > habitat score > > Thanks, Simon. > > > > >> On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett >> wrote: >> >>> This is partly a statistical question as well as a question about R, but >>> I am stumped! >> >>> I have count data from various sites across years. (Not all of the sites >>> in the study appear in all years). Each site has its own habitat score >>> "habitat" that remains constant across all years. >> >>> I want to know if counts declined faster on sites with high "habitat" >>> scores. >> >>> I can construct a model that tests for the effect of habitat as a main >>> effect, controlling for year >> >>> model1<-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) >>> model2<-lmer(count~yr+(1|site), family=quasibinomial,data=m) >>> anova(model1,model2) >> >> I'm curious as to why you use the quasibinomial family for count data. >> When you say "count data" do you mean just presence/absence or an >> actual count of the number present? Generally the binomial and >> quasibinomial families are used when you have a binary response, and >> the poisson or quasipoisson family are used for responses that are >> counts. >> > > __ > 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/help-structuring-mixed-model-using-lmer%28%29-tp22436596p22442012.html 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.
Re: [R] help structuring mixed model using lmer()
Hi Simon, Have a look at Chap. 11 of "An Introduction to R" (one of R's manuals), which explains the different ways of specifying models using formulae. Briefly, y ~ x1 * x2 expands to y ~ x1 + x2 + x1:x2, where the last term (interaction term) amounts to a test of slope. Normally you would read its significance from F/chisq/p-value. Many practitioners consider the L.Ratio test to be a better option. For the fixed effects part in lmer() do: mod1 <- y ~ x1 + x2 == y ~ x1 + x2 mod2 <- y ~ x1 * x2 == y ~ x1 + x2 + x1:x2 anova(mod1, mod2) This will tell you if you need to worry about interaction or whether slopes are parallel. Regards, Mark. Simon Pickett-4 wrote: > > Cheers, > > Actually I was using quasipoisson for my models, but for the puposes of my > example, it doesnt really matter. > > I am trying to work out a way of quantifying whether the slopes (for > years) > are covary with habitat scores. > > The more I think about it, the more I am convinced that it isnt possible > do > to that using a glm approach. I think I have to run separate models for > each > site, calculate the gradient, then do a lm with gradient explained by > habitat score > > Thanks, Simon. > > > > >> On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett >> wrote: >> >>> This is partly a statistical question as well as a question about R, but >>> I am stumped! >> >>> I have count data from various sites across years. (Not all of the sites >>> in the study appear in all years). Each site has its own habitat score >>> "habitat" that remains constant across all years. >> >>> I want to know if counts declined faster on sites with high "habitat" >>> scores. >> >>> I can construct a model that tests for the effect of habitat as a main >>> effect, controlling for year >> >>> model1<-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) >>> model2<-lmer(count~yr+(1|site), family=quasibinomial,data=m) >>> anova(model1,model2) >> >> I'm curious as to why you use the quasibinomial family for count data. >> When you say "count data" do you mean just presence/absence or an >> actual count of the number present? Generally the binomial and >> quasibinomial families are used when you have a binary response, and >> the poisson or quasipoisson family are used for responses that are >> counts. >> > > __ > 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/help-structuring-mixed-model-using-lmer%28%29-tp22436596p22441985.html 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.
[R] system() not accepting strings from cat()
Hi again R-ists,
How do you construct a string that you can pass to system()?
For instance. Say I do
> system("echo Hello!")
Hello!
That works. Now the alternative: I need to construct the string like this
> a <- "echo"
> b <- "Hello!"
> c <- "\n"
> cat(a, b, c)
echo Hello!
Looks nice... but see what happens when I try to use it
> system(cat(a, b, c))
echo Hello!
Error in system(command, intern) : non-empty character argument expected
I have googled extensively in and out of r-lists but I can't find a solution.
Can anybody help?
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Re: [R] Sparse PCA in R
Take a look at the elasticnet package. -Christos > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of joris meys > Sent: Tuesday, March 10, 2009 3:43 PM > To: R-help Mailing List > Subject: [R] Sparse PCA in R > > Dear all, > > I would like to perform a sparse PCA, but I didn't find any > library offering me this in R. Is there one available, or do > I have to write the functions myself? > > Kind regards > Joris Meys > > [[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.html > and provide commented, minimal, self-contained, reproducible code. > > __ 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.
Re: [R] How to color certain area under curve
Just a small typo. I forgot a ) in the polygon function. The code must be: polygon(x = c(qrv[1], drv$x[select], qrv[2]), y = c(0, drv$y[select], 0), col='blue') __ 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] Nesting order for mixed models
Hello,
I am confused about the order of nesting in mixed models using functions
like aov(), lme(), lmer().
I have the following data:
n subjects in either condition A or B
each subject tested at each of 3 numerical values ("distance" =
40,50,60), repeated 4 times for each of the 3 numerical values ("trial"
= 1,2,3,4)
Variable summary:
Condition: 2 level factor
Distance: numerical (but only 3 values) in the same units as "y"
Trial: 4 level factor
I expect the subjects' data to differ due to condition and distance, and
am doing repeated measurements to reduce any variability due to
measurement error.
Currently I'm using this model:
lme(y ~ Condition + Distance, random = ...)
the question is how do I organize the random statement? Is it:
random = ~1 | Subject
random = ~1 | Subject/Trial
random = ~1 | Trial/Subject
random = ~1 | Condition/Distance/Subject/Trial
...etc, or something else entirely?
Mostly I'm unclear about whether the Trials should be grouped under
subject because I expect the trials to be more similar within a subject
than across subjects, or whether subjects should be grouped under trials
because the trials are going to differ depending on the subject. If
trials should be grouped under subjects, then do the condition or
distance belong as well, since the trials will be most similar within
each distance within each subject?
Thanks in advance!
- Jon
--
Jon Zadra
Department of Psychology
University of Virginia
P.O. Box 400400
Charlottesville VA 22904
(434) 982-4744
email: za...@virginia.edu
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Re: [R] ordering
Thanks Peter, that did the trick. I'll modify my function so that the numeric conversion is done automatically thus saving me the extra step of converting later on. Aaron Wells > Subject: RE: [R] ordering > Date: Wed, 11 Mar 2009 08:41:50 +1300 > From: palsp...@hortresearch.co.nz > To: awell...@hotmail.com; r-help@r-project.org > > Kia ora Aaron > > As you have identified, test[,2] is not numeric - it is probably factor. > Your function must have made the conversion, so you may want to modify > that. Alternative, try: > > test[order(as.numeric(as.character(test[,2]))),] > > BTW, str(test) is a good way to find out more about the structure of > your object. > > HTH > > Peter Alspach > > > > > > -Original Message- > > From: r-help-boun...@r-project.org > > [mailto:r-help-boun...@r-project.org] On Behalf Of aaron wells > > Sent: Wednesday, 11 March 2009 8:30 a.m. > > To: r-help@r-project.org > > Subject: [R] ordering > > > > > > Hello, I would like to order a matrix by a specific column. > > For instance: > > > > > > > > > test > > [,1] [,2] [,3] > > [1,] 1 100 21 > > [2,] 2 3 22 > > [3,] 3 100 23 > > [4,] 4 60 24 > > [5,] 5 55 25 > > [6,] 6 45 26 > > [7,] 7 75 27 > > [8,] 8 12 28 > > [9,] 9 10 29 > > [10,] 10 22 30 > > > > > > > test[order(test[,2]),] > > [,1] [,2] [,3] > > [1,] 2 3 22 > > [2,] 9 10 29 > > [3,] 8 12 28 > > [4,] 10 22 30 > > [5,] 6 45 26 > > [6,] 5 55 25 > > [7,] 4 60 24 > > [8,] 7 75 27 > > [9,] 1 100 21 > > [10,] 3 100 23 > > > > > > This works well and good in the above example matrix. > > However in the matrix that I actually want to sort (derived > > from a function that I wrote) I get something like this: > > > > > > > > > test[order(as.numeric(test[,2])),] ### First column is row.names > > > > > > f con f.1 cov f.2 minimum f.3 maximum f.4 cl > > asahi * 100 * 1 * 0.1 * 2 * test > > castet * 100 * 2 * 0.1 * 5 * test > > clado * 100 * 1 * 0.7 * 2 * test > > aulac * 33 * 0 * 0.1 * 0.1 * test > > buell * 33 * 0 * 0.1 * 0.1 * test > > camlas * 33 * 0 * 0.1 * 0.1 * test > > carbig * 33 * 1 * 1 * 1 * test > > poaarc * 67 * 0 * 0.1 * 0.1 * test > > polviv * 67 * 0 * 0.1 * 0.1 * test > > > > > > > > > > where R interprets 100 to be the lowest value and orders > > increasing from there. > > > > > > > > > is.numeric(test[,2]) > > [1] FALSE > > > is.double(test[,2]) > > [1] FALSE > > > is.integer(test[,2]) > > [1] FALSE > > > is.real(test[,2]) > > [1] FALSE > > > > > > > > > > My questions are: Why is this happening? and How do I fix it? > > > > > > > > Thanks in advance! > > > > > > > > Aaron Wells > > > > _ > > > > > > cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 > > [[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.html > > and provide commented, minimal, self-contained, reproducible code. > > > > The contents of this e-mail are confidential and may be subject to legal > privilege. > If you are not the intended recipient you must not use, disseminate, > distribute or > reproduce all or any part of this e-mail or attachments. If you have received > this > e-mail in error, please notify the sender and delete all material pertaining > to this > e-mail. Any opinion or views expressed in this e-mail are those of the > individual > sender and may not represent those of The New Zealand Institute for Plant and > Food Research Limited. _ [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ordering
A) I predict that if you apply the str function to the second test that you will find that "con" is not numeric but rather of class character or factor. And the second test is probably not a matrix but rather a dataframe. Matrices in R need to have all their elements of the same class. B) Read the FAQ ... find the one that tells you how to convert factors to numeric. -- David Winsemius On Mar 10, 2009, at 3:29 PM, aaron wells wrote: Hello, I would like to order a matrix by a specific column. For instance: test [,1] [,2] [,3] [1,]1 100 21 [2,]23 22 [3,]3 100 23 [4,]4 60 24 [5,]5 55 25 [6,]6 45 26 [7,]7 75 27 [8,]8 12 28 [9,]9 10 29 [10,] 10 22 30 test[order(test[,2]),] [,1] [,2] [,3] [1,]23 22 [2,]9 10 29 [3,]8 12 28 [4,] 10 22 30 [5,]6 45 26 [6,]5 55 25 [7,]4 60 24 [8,]7 75 27 [9,]1 100 21 [10,]3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi* 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado* 100 * 1 * 0.7 * 2 * test aulac* 33 * 0 * 0.1 * 0.1 * test buell* 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. is.numeric(test[,2]) [1] FALSE is.double(test[,2]) [1] FALSE is.integer(test[,2]) [1] FALSE is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[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.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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.
Re: [R] How to color certain area under curve
ucalgary.ca> writes: > > For a given random variable rv, for instance, rv = rnorm(1000), > I plot its density curve and calculate some quantiles: > plot(density(rv)) > P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) > I would like to color the area between P10 and P90 and under the curve > and mark the P50 on the curve. > > > rv = rnorm(1000) > > plot(density(rv)) > > P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) > > Could you please teach me how to do these using R? > Thanks, > -james > see ?polygon Here after is an example of the use of polygon to solve your problem: rv <- rnorm(1000) drv <- density(rv) plot(drv) # further steps: # 1. compute quantiles # 2. determine the x and y of the area that must be drawn # 3. drawn # 4. add q.5 info qrv <- quantile(rv, prob=c(0.1, 0.9)) select <- qrv[1] <= drv$x & drv$x <= qrv[2] polygon(x = c(qrv[1], drv$x[select], qrv[2]), y = c(0, drv$y[select], 0, col='blue') abline(v= quantile(rv, p=0.5), lty=2) Hope this will help. Matthieu __ 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] Sparse PCA in R
Dear all, I would like to perform a sparse PCA, but I didn't find any library offering me this in R. Is there one available, or do I have to write the functions myself? Kind regards Joris Meys [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ordering
Kia ora Aaron As you have identified, test[,2] is not numeric - it is probably factor. Your function must have made the conversion, so you may want to modify that. Alternative, try: test[order(as.numeric(as.character(test[,2]))),] BTW, str(test) is a good way to find out more about the structure of your object. HTH Peter Alspach > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of aaron wells > Sent: Wednesday, 11 March 2009 8:30 a.m. > To: r-help@r-project.org > Subject: [R] ordering > > > Hello, I would like to order a matrix by a specific column. > For instance: > > > > > test > [,1] [,2] [,3] > [1,]1 100 21 > [2,]23 22 > [3,]3 100 23 > [4,]4 60 24 > [5,]5 55 25 > [6,]6 45 26 > [7,]7 75 27 > [8,]8 12 28 > [9,]9 10 29 > [10,] 10 22 30 > > > > test[order(test[,2]),] > [,1] [,2] [,3] > [1,]23 22 > [2,]9 10 29 > [3,]8 12 28 > [4,] 10 22 30 > [5,]6 45 26 > [6,]5 55 25 > [7,]4 60 24 > [8,]7 75 27 > [9,]1 100 21 > [10,]3 100 23 > > > This works well and good in the above example matrix. > However in the matrix that I actually want to sort (derived > from a function that I wrote) I get something like this: > > > > > test[order(as.numeric(test[,2])),] ### First column is row.names > > > f con f.1 cov f.2 minimum f.3 maximum f.4 cl > asahi* 100 * 1 * 0.1 * 2 * test > castet * 100 * 2 * 0.1 * 5 * test > clado* 100 * 1 * 0.7 * 2 * test > aulac* 33 * 0 * 0.1 * 0.1 * test > buell* 33 * 0 * 0.1 * 0.1 * test > camlas * 33 * 0 * 0.1 * 0.1 * test > carbig * 33 * 1 * 1 * 1 * test > poaarc * 67 * 0 * 0.1 * 0.1 * test > polviv * 67 * 0 * 0.1 * 0.1 * test > > > > > where R interprets 100 to be the lowest value and orders > increasing from there. > > > > > is.numeric(test[,2]) > [1] FALSE > > is.double(test[,2]) > [1] FALSE > > is.integer(test[,2]) > [1] FALSE > > is.real(test[,2]) > [1] FALSE > > > > > My questions are: Why is this happening? and How do I fix it? > > > > Thanks in advance! > > > > Aaron Wells > > _ > > > cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 > [[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.html > and provide commented, minimal, self-contained, reproducible code. > The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. __ 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] ordering
Hello, I would like to order a matrix by a specific column. For instance: > test [,1] [,2] [,3] [1,]1 100 21 [2,]23 22 [3,]3 100 23 [4,]4 60 24 [5,]5 55 25 [6,]6 45 26 [7,]7 75 27 [8,]8 12 28 [9,]9 10 29 [10,] 10 22 30 > test[order(test[,2]),] [,1] [,2] [,3] [1,]23 22 [2,]9 10 29 [3,]8 12 28 [4,] 10 22 30 [5,]6 45 26 [6,]5 55 25 [7,]4 60 24 [8,]7 75 27 [9,]1 100 21 [10,]3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: > test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi* 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado* 100 * 1 * 0.7 * 2 * test aulac* 33 * 0 * 0.1 * 0.1 * test buell* 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. > is.numeric(test[,2]) [1] FALSE > is.double(test[,2]) [1] FALSE > is.integer(test[,2]) [1] FALSE > is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help structuring mixed model using lmer()
Cheers, Actually I was using quasipoisson for my models, but for the puposes of my example, it doesnt really matter. I am trying to work out a way of quantifying whether the slopes (for years) are covary with habitat scores. The more I think about it, the more I am convinced that it isnt possible do to that using a glm approach. I think I have to run separate models for each site, calculate the gradient, then do a lm with gradient explained by habitat score Thanks, Simon. On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett wrote: This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score "habitat" that remains constant across all years. I want to know if counts declined faster on sites with high "habitat" scores. I can construct a model that tests for the effect of habitat as a main effect, controlling for year model1<-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) model2<-lmer(count~yr+(1|site), family=quasibinomial,data=m) anova(model1,model2) I'm curious as to why you use the quasibinomial family for count data. When you say "count data" do you mean just presence/absence or an actual count of the number present? Generally the binomial and quasibinomial families are used when you have a binary response, and the poisson or quasipoisson family are used for responses that are counts. __ 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.
Re: [R] puzzled by math on date-time objects
median.default was changed between 2.7.1 and 2.8.1 to
call sum(...)/2 instead of mean(...) and that causes
the problem for POSIXct objects (sum fails but mean
works for them).
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
> -Original Message-
> From: William Dunlap
> Sent: Tuesday, March 10, 2009 11:37 AM
> To: 'r-help@r-project.org'
> Subject: Re: [R] puzzled by math on date-time objects
>
> Your problem arises in R 2.8.1 (and 2.9.0-devel, but not 2.7.0) when
> length(POSIXct object) is even, because median(POSIXct object)
> passes a POSIXct object to median.default, which calls
> sum() in the even length case.
>
> > median( as.POSIXct(Sys.time()))
> [1] "2009-03-10 10:28:46 PDT"
> > median( as.POSIXct(rep(Sys.time(),2)))
> Error in Summary.POSIXct(c(1236706132.54740,
> 1236706132.54740), na.rm = FALSE) :
> 'sum' not defined for "POSIXt" objects
> > traceback()
> 4: stop(gettextf("'%s' not defined for \"POSIXt\" objects", .Generic),
>domain = NA)
> 3: Summary.POSIXct(c(1236706132.54740, 1236706132.54740),
> na.rm = FALSE)
> 2: median.default(as.POSIXct(rep(Sys.time(), 2)))
> 1: median(as.POSIXct(rep(Sys.time(), 2)))
> > version
>_
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 2
> minor 8.1
> year 2008
> month 12
> day22
> svn rev47281
> language R
> version.string R version 2.8.1 (2008-12-22)
>
> Bill Dunlap
> TIBCO Software Inc - Spotfire Division
> wdunlap tibco.com
>
>
> [R] puzzled by math on date-time objects
>
> Denis Chabot chabotd at globetrotter.net
> Tue Mar 10 16:44:07 CET 2009
> Previous message: [R] nonmetric clustering
> Next message: [R] perform subgroup meta-analysis and create
> forest plot displaying subgroups
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> Hi,
>
> I don't understand the following. When I create a small
> artificial set
> of date information in class POSIXct, I can calculate the
> mean and the
> median:
>
> a = as.POSIXct(Sys.time())
> a = a + 60*0:10; a
>
> [1] "2009-03-10 11:30:16 EDT" "2009-03-10 11:31:16 EDT"
> "2009-03-10
> 11:32:16 EDT"
> [4] "2009-03-10 11:33:16 EDT" "2009-03-10 11:34:16 EDT"
> "2009-03-10
> 11:35:16 EDT"
> [7] "2009-03-10 11:36:16 EDT" "2009-03-10 11:37:16 EDT"
> "2009-03-10
> 11:38:16 EDT"
> [10] "2009-03-10 11:39:16 EDT" "2009-03-10 11:40:16 EDT"
>
> median(a)
> [1] "2009-03-10 11:35:16 EDT"
> mean(a)
> [1] "2009-03-10 11:35:16 EDT"
>
>
> But for real data (for this post, a short subset is in object
> c) that
> I have converted into a POSIXct object, I cannot calculate
> the median
> with median(), though I do get it with summary():
>
> c
> [1] "2009-02-24 14:51:18 EST" "2009-02-24 14:51:19 EST"
> "2009-02-24
> 14:51:19 EST"
> [4] "2009-02-24 14:51:20 EST" "2009-02-24 14:51:20 EST"
> "2009-02-24
> 14:51:21 EST"
> [7] "2009-02-24 14:51:21 EST" "2009-02-24 14:51:22 EST"
> "2009-02-24
> 14:51:22 EST"
> [10] "2009-02-24 14:51:22 EST"
>
> class(c)
> [1] "POSIXt" "POSIXct"
>
> median(c)
> Erreur dans Summary.POSIXct(c(1235505080.6, 1235505081.1), na.rm =
> FALSE) :
>'sum' not defined for "POSIXt" objects
>
> One difference is that in my own date-time series, some events are
> repeated (the original data contained fractions of seconds).
> But then,
> why can I get a median through summary()?
>
> summary(c)
> Min. 1st
> Qu.Median
> "2009-02-24 14:51:18 EST" "2009-02-24 14:51:19 EST" "2009-02-24
> 14:51:20 EST"
> Mean 3rd
> Qu. Max.
> "2009-02-24 14:51:20 EST" "2009-02-24 14:51:21 EST" "2009-02-24
> 14:51:22 EST"
>
> Thanks in advance,
>
>
> Denis Chabot
>
> sessionInfo()
> R version 2.8.1 Patched (2009-01-19 r47650)
> i386-apple-darwin9.6.0
>
> locale:
> fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] doBy_3.7 chron_2.3-30
>
> loaded via a namespace (and not attached):
> [1] Hmisc_3.5-2 cluster_1.11.12 grid_2.8.1 lattice_0.17-20
> tools_2.8.1
>
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Re: [R] puzzled by math on date-time objects
Your problem arises in R 2.8.1 (and 2.9.0-devel, but not 2.7.0) when
length(POSIXct object) is even, because median(POSIXct object)
passes a POSIXct object to median.default, which calls
sum() in the even length case.
> median( as.POSIXct(Sys.time()))
[1] "2009-03-10 10:28:46 PDT"
> median( as.POSIXct(rep(Sys.time(),2)))
Error in Summary.POSIXct(c(1236706132.54740, 1236706132.54740), na.rm =
FALSE) :
'sum' not defined for "POSIXt" objects
> traceback()
4: stop(gettextf("'%s' not defined for \"POSIXt\" objects", .Generic),
domain = NA)
3: Summary.POSIXct(c(1236706132.54740, 1236706132.54740), na.rm = FALSE)
2: median.default(as.POSIXct(rep(Sys.time(), 2)))
1: median(as.POSIXct(rep(Sys.time(), 2)))
> version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 8.1
year 2008
month 12
day22
svn rev47281
language R
version.string R version 2.8.1 (2008-12-22)
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
[R] puzzled by math on date-time objects
Denis Chabot chabotd at globetrotter.net
Tue Mar 10 16:44:07 CET 2009
Previous message: [R] nonmetric clustering
Next message: [R] perform subgroup meta-analysis and create forest plot
displaying subgroups
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi,
I don't understand the following. When I create a small artificial set
of date information in class POSIXct, I can calculate the mean and the
median:
a = as.POSIXct(Sys.time())
a = a + 60*0:10; a
[1] "2009-03-10 11:30:16 EDT" "2009-03-10 11:31:16 EDT" "2009-03-10
11:32:16 EDT"
[4] "2009-03-10 11:33:16 EDT" "2009-03-10 11:34:16 EDT" "2009-03-10
11:35:16 EDT"
[7] "2009-03-10 11:36:16 EDT" "2009-03-10 11:37:16 EDT" "2009-03-10
11:38:16 EDT"
[10] "2009-03-10 11:39:16 EDT" "2009-03-10 11:40:16 EDT"
median(a)
[1] "2009-03-10 11:35:16 EDT"
mean(a)
[1] "2009-03-10 11:35:16 EDT"
But for real data (for this post, a short subset is in object c) that
I have converted into a POSIXct object, I cannot calculate the median
with median(), though I do get it with summary():
c
[1] "2009-02-24 14:51:18 EST" "2009-02-24 14:51:19 EST" "2009-02-24
14:51:19 EST"
[4] "2009-02-24 14:51:20 EST" "2009-02-24 14:51:20 EST" "2009-02-24
14:51:21 EST"
[7] "2009-02-24 14:51:21 EST" "2009-02-24 14:51:22 EST" "2009-02-24
14:51:22 EST"
[10] "2009-02-24 14:51:22 EST"
class(c)
[1] "POSIXt" "POSIXct"
median(c)
Erreur dans Summary.POSIXct(c(1235505080.6, 1235505081.1), na.rm =
FALSE) :
'sum' not defined for "POSIXt" objects
One difference is that in my own date-time series, some events are
repeated (the original data contained fractions of seconds). But then,
why can I get a median through summary()?
summary(c)
Min. 1st
Qu.Median
"2009-02-24 14:51:18 EST" "2009-02-24 14:51:19 EST" "2009-02-24
14:51:20 EST"
Mean 3rd
Qu. Max.
"2009-02-24 14:51:20 EST" "2009-02-24 14:51:21 EST" "2009-02-24
14:51:22 EST"
Thanks in advance,
Denis Chabot
sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650)
i386-apple-darwin9.6.0
locale:
fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doBy_3.7 chron_2.3-30
loaded via a namespace (and not attached):
[1] Hmisc_3.5-2 cluster_1.11.12 grid_2.8.1 lattice_0.17-20
tools_2.8.1
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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.
Re: [R] a general question
Hello Bogdan, Put in those terms, option b looks more defensible. It sounds like a test of two proportions, sometimes called z-test. The problem is that, for that test to be used, you must be sampling from large population. You know that under regular ChIP-seq sequencing we are lucky if we get 10 reads in a particuar region of interest. So, we get a population and that population itself is small. So, z-test does not look applicable. Google for z-test and you'll see the conditions. What to do then? Well, forget comparing signal to backgroung and, instead, compare directly number of reads in the experiment versus number of reads in the control. Actually, you simplify your algorithm by not having to define (and defend) an arbitrary area to call "background". An example? Sure! Check out "PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls", Joel Rozowsky1, Ghia Euskirchen2, Raymond K Auerbach3, Zhengdong D Zhang1, Theodore Gibson1, Robert Bjornson4, Nicholas Carriero4, Michael Snyder1,2 & Mark B Gerstein1,3,4. Nature Biotechnology, 2009. Take a look at it and let us know what you think. Your culpritNr1 PS: next time, please go for a more descriptive subject such as ChIP-seq. That would help in the future when we need to over old messages. Don't you think? Bogdan Tanasa wrote: > > Hi everyone, > > Although this question is more related to ChIP and ChIP-seq, it could be > probably anchored in a more general statistical context. > > The question is : what method is better to assess the significance of the > change in a signal (the signal can be DNA binding, for instance) given > the > background and 2 conditions. > > <. condition1 (eg no treatment) : background = 1; > signal = 5; > > <. condition2 (eg hormonal treatment) : background = 3; >signal = 6. > > The methods can be : > > a. substract the background : i.e. (signal_treatment - > background_treatment) > / (signal_no_treatment - background_no_treatment) > > b. calculate the fold change: i.e. (signal_treatment / > background_treatment) > / (signal_no_treatment / background_no_treatment) > > c. any other method ? i.e. (signal_treatment - signal_no_treatment) / ( > background_treatment - background_no_treatment) > > Thank you very much. > > Bogdan > > [[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.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/a-general-question-tp22382289p22440722.html 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.
Re: [R] Changing factor to numeric
By the way, it could be that one of your numbers has "space" in them. in which case, R tends to turn the entire vector into a factor. try opening the file in a spreadsheet like excel, and do "search replace" on " " with "". and see how many it catches. Tal On Tue, Mar 10, 2009 at 7:25 AM, ojal john owino < ojal.johnow...@googlemail.com> wrote: > Dear Users, > I have a variable in my dataset which is of type factor. But it actually > contains numeric entries which like 5.735 4.759 . This is because the > data was read from a CSV file into R and this variable contained other > charaters which were not numeric. I have now dropped the records with the > characters which are not numeric for this variable and want to change it to > numeric srotage type. > > I have tried using as.numeric() function but it changes the values in the > variable to what I think are the ranks of the individual values of the > varible in the dataset. For example if 5.735 is the current content in the > field, then the new object created by as.numeric will contain a value like > 680 if the 5.735 was the highest value for the varible and the dataset had > 680 records. > > > How can I change the storage type without changing the contents of this > variable in this case? > > Thanks for your consideration. > > > > -- > Ojal John Owino > P.O Box 230-80108 > Kilifi, Kenya. > Mobile:+254 728 095 710 > >[[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.html > and provide commented, minimal, self-contained, reproducible code. > -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: www.talgalili.com www.biostatistics.co.il [[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.html and provide commented, minimal, self-contained, reproducible code.
[R] Alternative to interp.surface() offered
I wanted a simple function for bilinear interpolation on a 2-D grid, and
interp.surface() in the fields package didn't quite suit my needs. In
particular, it requires uniform spacing between grid points. It also
didn't have the "visual" reference frame I was looking for. Here is an
alternative function, followed by an example.
# A function for bilinear interpolation on a 2-d grid, based on the
# interp.surface() from the fields package and code by Steve Koehler.
# The points of the grid do not have to be uniformly spaced. Looking at
the 2-d
# grid in plan view, the origin is at upper left, so y (row) index
increases
# downward. findInterval() is used to locate the new coordinates on the
grid.
#
# Scott Waichler, scott.waich...@pnl.gov, 03/10/09.
my.interp.surface <- function (obj, loc) {
# obj is a surface object like the list for contour or image.
# loc is a matrix of (x, y) locations
x <- obj$x
y <- obj$y
x.new <- loc[,1]
y.new <- loc[,2]
z <- obj$z
ind.x <- findInterval(x.new, x, all.inside=T)
ind.y <- findInterval(y.new, y, all.inside=T)
ex <- (x.new - x[ind.x]) / (x[ind.x + 1] - x[ind.x])
ey <- (y.new - y[ind.y]) / (y[ind.y + 1] - y[ind.y])
# set weights for out-of-bounds locations to NA
ex[ex < 0 | ex > 1] <- NA
ey[ey < 0 | ey > 1] <- NA
return(
z[cbind(ind.y, ind.x)] * (1 - ex) * (1 - ey) + # upper
left
z[cbind(ind.y + 1, ind.x)] * (1 - ex) * ey + # lower
left
z[cbind(ind.y + 1, ind.x + 1)] * ex * ey + # lower
right
z[cbind(ind.y, ind.x + 1)] * ex * (1 - ey)# upper
right
)
}
## # An example.
## # z matrix, y index increasing downwards
## # 4 5 6 7 8
## # 3 4 5 6 7
## # 2 3 4 5 6
## # 1 2 3 4 5
## z.vec <- c(4,5,6,7,8,3,4,5,6,7,2,3,4,5,6,1,2,3,4,5) # "read in" the
data for the matrix
## x.mat <- 1:5# x coordinates of the z values
## y.mat <- seq(100, 400, by=100) # y coordinates of the z values
## obj <- list(x = x.mat, y = y.mat, z = matrix(z.vec, ncol=5, byrow=T))
# grid you want to interpolate on
## x.out <- round(runif(6, min = min(x.mat), max = max(x.mat)), 2) # x
for points you want interpolate to
## y.out <- round(runif(6, min = min(y.mat), max = max(y.mat)), 2) # y
for points you want interpolate to
## loc <- cbind(x.out, y.out)
## z.out <- my.interp.surface(obj, loc)
## cat(file="", "x.out = ", loc[,1], "\n", "y.out = ", loc[,2], "\n",
"z.out = ", round(z.out, 2), "\n")
Regards,
Scott Waichler
Pacific Northwest National Laboratory
Richland, WA 99352USA
scott.waich...@pnl.gov
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[R] (no subject)
Dear Members, I have a question about using R2WinBUGS to obtain the WinBUGS results. By default, when R2WinBUGS returns summary stats, I got mean, sd, 2.5%, 25%, median, 75% and 97.5%. Could anyone tell me how to modify the code to obtain 5% and 95% summary results? Many thanks Alice _ [[elided Hotmail spam]] [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help structuring mixed model using lmer()
On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett wrote: > This is partly a statistical question as well as a question about R, but I am > stumped! > I have count data from various sites across years. (Not all of the sites in > the study appear in all years). Each site has its own habitat score "habitat" > that remains constant across all years. > I want to know if counts declined faster on sites with high "habitat" scores. > I can construct a model that tests for the effect of habitat as a main > effect, controlling for year > model1<-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) > model2<-lmer(count~yr+(1|site), family=quasibinomial,data=m) > anova(model1,model2) I'm curious as to why you use the quasibinomial family for count data. When you say "count data" do you mean just presence/absence or an actual count of the number present? Generally the binomial and quasibinomial families are used when you have a binary response, and the poisson or quasipoisson family are used for responses that are counts. __ 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] How to color certain area under curve
For a given random variable rv, for instance, rv = rnorm(1000), I plot its density curve and calculate some quantiles: plot(density(rv)) P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) I would like to color the area between P10 and P90 and under the curve and mark the P50 on the curve. > rv = rnorm(1000) > plot(density(rv)) > P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) Could you please teach me how to do these using R? Thanks, -james __ 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.
Re: [R] popular R packages
Pricing each download at 99 cents ( the same as a song from I Tunes) can measure users more accurately. Thats my 2 cents anyways. On Tue, Mar 10, 2009 at 9:54 PM, Max Kuhn wrote: > If is easy to get the download numbers, we should do it and deal with > the interpretation issues. I'd like to know the numbers so I can > understand which (of my) packages have the most usage. > > One other compication about # downloads: I suspect that a package > being on teh depends/suggests/imports list of another package might be > a big driver with respect to how many times that it was downloaded. > > If I remember correctly, about 5 years ago Bioconductor asked for > volunteers to review packages to get detailed, specific feedback by > people who use the package (and should be fairly R proficient). I > think that this is pretty important and something like Crantastic is a > good interface. I personally got a lot out of the comments the a JSS > reviewer had for a package. > > -- > > Max > > __ > 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. > [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] popular R packages
On Tuesday 10 March 2009, Frank E Harrell Jr wrote: > Gabor Grothendieck wrote: > > On Tue, Mar 10, 2009 at 6:14 AM, Jim Lemon wrote: > >> Gabor Grothendieck wrote: > >>> R-Forge already has this but I don't think its used much. R-Forge > >>> does allow authors to opt out which seems sensible lest it deter > >>> potential authors from submitting packages. > >>> > >>> I think objective quality metrics are better than ratings, e.g. does > >>> package > >>> have a vignette, has package had a release within the last year, > >>> does package have free software license, etc. That would have > >>> the advantage that authors might react to increase their package's > >>> quality assessment resulting in an overall improvement in quality on > >>> CRAN that would result in more of a pro-active cycle whereas ratings > >>> are reactive > >>> and don't really encourage improvement. > >> > >> I beg to offer an alternative assessment of quality. Do users download > >> the package and find it useful? If so, they are likely to download it > >> again when it is updated. > > > > I was referring to motivating authors, not users, so that CRAN improves. > > > >> Much as I appreciate the convenience of vignettes, regular > >> updates and the absolute latest GPL license, a perfectly dud package can > >> have all of these things. If a package is downloaded upon first release > >> and > > > > These are nothing but the usual FUD against quality improvement, i.e. > > the quality metrics are not measuring what you want but the fact is that > > quality metrics can work and have had huge successes. Also I think > > objective measures would be more accepted by authors than ratings. No one > > is going to be put off that their package has no vignette when obviously > > it doesn't and the authors are free to add one and instantly improve > > their package's rating. > > > >> not much thereafter, the maintainer might be motivated to attend to its > >> shortcomings of utility rather than incrementing the version number > >> every month or so. Downloads, as many have pointed out, are not a direct > >> assessment of quality, but if I saw a package that just kept getting > >> downloaded, version after version, I would be much more likely to check > >> it out myself and perhaps even write a review for Hadley's neat site. > >> Which I will try to do tonight. > > > > I was arguing for objective metrics rather than ratings. Downloading is > > not a rating but is objective although there are measurement problems as > > has been pointed out. Also, the worst feature is that it does not react > > to changes in quality very quickly making it anti-motivating. > > Gabor I think your approach will have more payoff in the long run. I > would suggest one other metric: the number of lines of code in the > 'examples' section of all the package's help files. > > Frank Absolutely. From the perspective of a user, not an expert, packages with a good vignette and lots of examples are by far my favorite and most used. Dylan -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 __ 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] Plots of different aspect ratios on one page, base aligned(trellis.print)
Hello,
I have an example of a 2 paneled plot, with two different aspect
ratios displayed on one page.
An example would help
n=20
x1 <- cumsum(runif(n))
x2 <- cumsum(runif(n))
d <- data.frame(val=c(x1,x2),id=c(1:n,1:n), nt=c(rep("A",n),rep("B",n)))
u1 <- xyplot(val~id | nt, data=d,aspect=1,layout=c(1,2))
u2 <- xyplot(val~id|nt, data=d,aspect=0.5,layout=c(1,2))
postscript("~/k.ps",colormodel="rgb",paper="letter",horiz=T)
print(u1,position=c(0,0,1/3,1),more=T,newpage=T)
print(u2,position=c(1/3,0,1,1),more=F,newpage=F)
dev.off()
The two figures are not base aligned. I would like them share the same
the baseline and same height, if necessary the paper width and height
can be adjusted
( i tried setting the paper width and height to no avail).
Is the way to base align the two figures? Do I have to get down the grid level?
Regards
Saptarshi Guha
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] File permissions
Great. I tried chmod (which does not exist) but I didn't know that there was sys.chmod. Thank you. Prof Brian Ripley wrote: > > On Tue, 10 Mar 2009, ig2ar-s...@yahoo.co.uk wrote: > >> >> Hello fellow R-ists, >> >> How do I change file permissions? >> >> I know that file.access can display permission information but how >> do I SET those permissions? > > Well, file.info is better are displaying permission information, and > Sys.chmod set them in the format used by file.info. > >> Thank you >> >> Your culpritNr1 > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UKFax: +44 1865 272595 > > __ > 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/File-permissions-tp22437684p22439004.html 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.
[R] How to stop loop inside status ? ( haplo.stats package )
How to stop loop inside status ?
require(haplo.stats)
## normal status
y=rep(c(0,1),each=50)
geno=as.data.frame(matrix(sample(c("A","G","T","C"),600,replace=T),100,6))
hs<- haplo.score(y, geno, trait.type="binomial", offset = NA, x.adj = NA,
min.count=5,
locus.label=NA, miss.val=c(0,NA), haplo.effect="additive",
eps.svd=1e-5, simulate=TRUE,
sim.control=score.sim.control(min.sim=200,max.sim=500))
hs$score.global.p.sim
## find loop inside ,and I can't stop it!
geno=as.data.frame(matrix("G",100,6))
hs<- haplo.score(y, geno, trait.type="binomial", offset = NA, x.adj = NA,
min.count=5,
locus.label=NA, miss.val=c(0,NA), haplo.effect="additive",
eps.svd=1e-5, simulate=TRUE,
sim.control=score.sim.control(min.sim=200,max.sim=500))
hs$score.global.p.sim
How to stop loop inside status ?
--
Nash - morri...@ibms.sinica.edu.tw
__
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Re: [R] Lattice: Customizing point-sizes with groups
Yup, that would be my work-around.
I was hoping for a cleaner way of doing this, though, because I am
calculating cex based on other properties of the data-points, so that it
becomes a continuous variable.
-Original Message-
From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com]
Sent: Tuesday, March 10, 2009 12:01 PM
To: Paul C. Boutros
Cc: r-help@r-project.org
Subject: Re: [R] Lattice: Customizing point-sizes with groups
Sorry, I missed your point the first time. Why not create a group for
each subset then?
xyplot(y ~ x, temp, groups = interaction(cex, groups),
par.settings = list(
superpose.symbol = list(
cex = c(1, 2, 3, 4),
pch = 19,
col = c("blue", "red", "green", "purple"
On Tue, Mar 10, 2009 at 8:11 AM, Paul C. Boutros
wrote:
> Hi Sundar,
>
> Thanks for your help! Unfortunately your code seems to give the same
> result. Compare this:
>
> temp <- data.frame(
> x = 1:10,
> y = 1:10,
> cex = rep( c(1,3), 5),
> col = c( rep("blue", 5), rep("red", 5) ),
> groups = c( rep("A", 5), rep("B", 5) )
> );
>
> xyplot(y ~ x, temp, groups = groups,
> par.settings = list(
> superpose.symbol = list(
> cex = c(1, 3),
> pch = 19,
> col = c("blue", "red"
>
> And this:
> xyplot(y ~ x, temp, cex = temp$cex, col = temp$col, pch = 19);
>
> Once I introduce groups, I lose the ability to customize individual
> data-points and seem only to be able to customize entire groups.
>
> Paul
>
> -Original Message-
> From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com]
> Sent: Tuesday, March 10, 2009 5:49 AM
> To: paul.bout...@utoronto.ca
> Cc: r-help@r-project.org
> Subject: Re: [R] Lattice: Customizing point-sizes with groups
>
> Try this:
>
> xyplot(y ~ x, temp, groups = groups,
> par.settings = list(
> superpose.symbol = list(
> cex = c(1, 3),
> pch = 19,
> col = c("blue", "red"
>
> See:
>
> str(trellis.par.get())
>
> for other settings you might want to change.
>
> Also, you should drop the ";" from all your scripts.
>
> HTH,
>
> --sundar
>
> On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros
> wrote:
>> Hello,
>>
>> I am creating a scatter-plot in lattice, and I would like to customize
the
>> size of each point so that some points are larger and others smaller.
>> Here's a toy example:
>>
>> library(lattice);
>>
>> temp <- data.frame(
>>x = 1:10,
>>y = 1:10,
>>cex = rep( c(1,3), 5),
>>groups = c( rep("A", 5), rep("B", 5) )
>>);
>>
>> xyplot(y ~ x, temp, cex = temp$cex, pch = 19);
>>
>> This works just fine if I create a straight xy-plot, without groups.
>> However when I introduce groupings the cex argument specifies the
>> point-size for the entire group. For example:
>>
>> xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups);
>>
>> Is it possible to combine per-spot sizing with groups in some way? One
>> work-around is to manually specify all graphical parameters, but I
thought
>> there might be a better way than this:
>>
>> temp$col <- rep("blue", 10);
>> temp$col[temp$groups == "B"] <- "red";
>> xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col);
>>
>> Any suggestions/advice is much appreciated!
>> Paul
>>
>> __
>> 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.
>>
>
>
__
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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.
Re: [R] reliability, scale scores in the psych package
Ista, As you figured out, psych reverses items by subtracting from the maximimum + minimum possible for each item. (i.e., for items going from 1 to 4, it reverses items by subtracting from 5). If all of the items have the same potential range then you can just let it figure out the range by itself. If they differ in their ranges (some items are 0 - 1 items, some are 1-9 items, etc., then you need to give it the maximum and minimum vectors to use. The min and max are figured out from all the items used in an inventory, rather than just the items used in a particular scale. This makes particular sense when you are scoring multiple scales from the same inventory. In answer to your first question (what packages do I tend to use for scale construction?), the answer is that I tend to use the psych package for basic analysis, and then the sem package for structural equation analysis. Bill At 10:45 AM -0400 3/10/09, Ista Zahn wrote: Second question: I spent some time with the psych package trying to figure out how to use the score.items() function, and it's become clear to me that I don't understand what it's doing. I assumed that setting a key equal to -1 would result in the item being reverse scored, but I get weird results, as shown below. When I try to reverse score (by setting a value of -1 in the key), I get scale scores that don't add up (e.g., the mean score is reported as being larger than the maximum item score). How is the score.items() function intended to be used? Do I need to reverse score items before using score.items()? I did it again--it seems like I always figure out the answer just after I ask for help. The score.items() function needs to know the maximum of the scale in order to reverse score. For some reason, the maximum appears to be calculated from all the scores, not just scores that have a 1 or a -1 in the key. On a hunch I set the max argument to a vector of scale maxima, and it worked. I'm still interested in responses to question 1 though. Thanks again, Ista -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r __ 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] Help installing Kernlab: cannot find -lgfortran
I am trying to install a package kernlab on Linux machine. After downloading and unpacking, installation goes through a number of C code compiles which ends with code linking, where error is generated as follows: g++ -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -L/usr/lib64/R/lib -lRblas -lgfortran -lm -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lR /usr/bin/ld: cannot find -lgfortran collect2: ld returned 1 exit status I suppose compiler cannot find libgfortran, which is in /usr/lib64/ in my case. Does anyone know where I specify or how I pass this info to R. I suppose there must be some UNIX environment variable or argument to install.packages Thanks, Andre __ 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] nonmetric clustering
Hi all, does anybody know where it is possible to find the "Riffle" package? Thank you R [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice: Customizing point-sizes with groups
Hi Sundar,
Thanks for your help! Unfortunately your code seems to give the same
result. Compare this:
temp <- data.frame(
x = 1:10,
y = 1:10,
cex = rep( c(1,3), 5),
col = c( rep("blue", 5), rep("red", 5) ),
groups = c( rep("A", 5), rep("B", 5) )
);
xyplot(y ~ x, temp, groups = groups,
par.settings = list(
superpose.symbol = list(
cex = c(1, 3),
pch = 19,
col = c("blue", "red"
And this:
xyplot(y ~ x, temp, cex = temp$cex, col = temp$col, pch = 19);
Once I introduce groups, I lose the ability to customize individual
data-points and seem only to be able to customize entire groups.
Paul
-Original Message-
From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com]
Sent: Tuesday, March 10, 2009 5:49 AM
To: paul.bout...@utoronto.ca
Cc: r-help@r-project.org
Subject: Re: [R] Lattice: Customizing point-sizes with groups
Try this:
xyplot(y ~ x, temp, groups = groups,
par.settings = list(
superpose.symbol = list(
cex = c(1, 3),
pch = 19,
col = c("blue", "red"
See:
str(trellis.par.get())
for other settings you might want to change.
Also, you should drop the ";" from all your scripts.
HTH,
--sundar
On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros
wrote:
> Hello,
>
> I am creating a scatter-plot in lattice, and I would like to customize the
> size of each point so that some points are larger and others smaller.
> Here's a toy example:
>
> library(lattice);
>
> temp <- data.frame(
> x = 1:10,
> y = 1:10,
> cex = rep( c(1,3), 5),
> groups = c( rep("A", 5), rep("B", 5) )
> );
>
> xyplot(y ~ x, temp, cex = temp$cex, pch = 19);
>
> This works just fine if I create a straight xy-plot, without groups.
> However when I introduce groupings the cex argument specifies the
> point-size for the entire group. For example:
>
> xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups);
>
> Is it possible to combine per-spot sizing with groups in some way? One
> work-around is to manually specify all graphical parameters, but I thought
> there might be a better way than this:
>
> temp$col <- rep("blue", 10);
> temp$col[temp$groups == "B"] <- "red";
> xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col);
>
> Any suggestions/advice is much appreciated!
> Paul
>
> __
> 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-help@r-project.org mailing list
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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.
[R] Re : (no subject)
see ?unique Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 De : "arnaud_mosn...@uqar.qc.ca" À : r-help@r-project.org Envoyé le : Mardi, 10 Mars 2009, 17h15mn 57s Objet : [R] (no subject) Dear R users, I have a table with the following form STATION X Y 1-7030 1-7030 1-7030 2-7229 2-7229 2-7229 2-7229 How want to extract unique value for those columns ... I am sure it is very[[elided Yahoo spam]] I want to obtain something like STATIONX Y 1-7030 2-7229 Thanks !!! [[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.html and provide commented, minimal, self-contained, reproducible code. [[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.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (no subject)
Hi Arnaud, is very simple: > unique( datos) Regards 2009/3/10 > > Dear R users, > > I have a table with the following form > > STATION X Y > 1-7030 > 1-7030 > 1-7030 > 2-7229 > 2-7229 > 2-7229 > 2-7229 > > How want to extract unique value for those columns ... I am sure it is very > simple, but I can not achieve to find the correct way ! > > I want to obtain something like > > STATIONX Y > 1-7030 > 2-7229 > > Thanks !!! > >[[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.html > and provide commented, minimal, self-contained, reproducible code. > [[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.html and provide commented, minimal, self-contained, reproducible code.
