Nabble - R

how use the results of rollapply in the previous row to the next row...

2009-11-24T20:38:34Z

Hi,

say I have a xts object x with data I want to apply a function f over row by
row (by.column=F)

x =
index c1 c2 c3
1 1 1 0
2 2 2 0
3 3 3 0
4 4 4 0
5 5 5 0

what i would like to do and i am not sure that that is possible is the
following

the result of operating on one row is put in the last column of x of that
same row
and is used in the operation on the next row, where f is some non-trivial
function of the columns

So for example the simple function summing over the row
and normalizing by the previous value of the last columns value in the
previous row
(first row does not normalize here)

x =
index c1 c2 c3
1 1 1 2 = 1+1
2 2 2 2 = 2/2+2/2 = 2
3 3 3 3 = 3/2+3/2 = 3
4 4 4 8/3 = 4/3+4/3
5 5 5 15/4 = 5/8*3+5/8*3

Is there some way to sneak this into rollapply?
Maybe I am asking too much, but if somebody
can enlighten it would be greatly appreciated
Thanks!
Jiri

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From forum: Rmetrics

Re: random effects correlation in lmer

2009-11-24T20:08:33Z

sorry, that escaped my attention. it was meant to be

y2=10+rand.int+tim+rand.int*tim+e

Daniel

-------------------------
cuncta stricte discussurus
-------------------------

_____

Von: Dennis Murphy [mailto:djmuser@...]
Gesendet: Tuesday, November 24, 2009 5:00 PM
An: Daniel Malter
Betreff: Re: [R] random effects correlation in lmer

HI Daniel:

I liked your explanation, but in the code snippet you provided, y1 and y2
are the
same. Did you mean to put

y2 <- 10 + rand.slop + time + e or y2 <- 10 + rand.int * rand.slop + tim
+ e?

Dennis

On Tue, Nov 24, 2009 at 12:17 PM, Daniel Malter <daniel@...> wrote:

It implies that the random intercept is perfectly collinear with the random
slope, as you suggested. I attach an example.

The data generating process of y1 has a random intercept, but no random
slope. When you fit a model with random intercept and random slope, the
correlation between the two is estimated at -1. However, note that the
variance of the random slope is almost zero. Thus, we fit the wrong model. A
random intercept only model would have sufficed.

The data generating process of y2 includes a random slope, but those with
the higher intercepts also have the greater slopes. Random intercept and
random slope estimates are perfectly collinear. This leads to the problem
you encounter. Models 2a and 2b provide random intercept only and random
slope only estimates for comparison. It would suffice in this case to fit a
random intercept model.

Finally, the data generating process for y3 has random intercept and slope,
but both are independent, so that the problem does not occur.

library(lme4)

tim=rep(10:19,10)
id=rep(1:10,each=10)
rand.int=rep(rnorm(10,0,1),each=10)
rand.slop=rep(rnorm(10,0,1),each=10)
e=rnorm(100,0,0.5)

y1=10+rand.int+tim+e
y2=10+rand.int+tim+e
y3=10+rand.int+tim+rand.slop*tim+e

reg1=lmer(y1~tim+(tim|id))
summary(reg1)

reg2=lmer(y2~tim+(tim|id))
summary(reg2)

reg2a=lmer(y2~tim+(1|id))
summary(reg2a)

reg2b=lmer(y2~tim+(-1+tim|id))
summary(reg2b)

reg3=lmer(y3~tim+(tim|id))
summary(reg3)

HTH,
Daniel

Kurt Smith-3 wrote:

>
> I am having an issue with lmer that I wonder if someone could explain.
>
> I am trying to fit a mixed effects model to a set of longitudinal data
> over a set of individual subjects:
> (fm1 <- lmer(x ~ time + (time|ID),aa))
>
>
> I quite often find that the correlation between the random effects is 1.0:
> Linear mixed model fit by REML
> Formula: x ~ time + (time | ID)
> Data: aa
> AIC BIC logLik deviance REMLdev
> 28574 28611 -14281 28561 28562
> Random effects:
> Groups Name Variance Std.Dev. Corr
> ID (Intercept) 77.035 8.7770
> time 10.817 3.2889 1.000
> Residual 112.151 10.5901
> Number of obs: 3539, groups: ID, 1000
>
> Fixed effects:
> Estimate Std. Error t value
> (Intercept) 98.7601 0.3894 253.64
> time 1.3671 0.2001 6.83
>
> Correlation of Fixed Effects:
> (Intr)
> time -0.045
>
>
> All other parameters seem to converge as I increase the size of the
> data set, or have a reasonable distribution over several bootstrap
> samples. This suggests to me there is a singularity or something in
> solving for the random effects correlation. Does anyone have any
> insight?
> Thanks,
> Kurt Smith
>
> ______________________________________________
> R-help@... 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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From forum: R help

interior and exterior colors of a map

2009-11-24T19:45:01Z

Hi useR's,
I have an image plot I want to overlay a map of the United States on, via map('usa'). The image is basically a large rectangular of various colors. When I overlay the United States map, the full rectangle of the image plot is visible, but I only want to display the image WITHIN the United States boundary.
Does anyone know a way to do this?
Thanks in advance,

dxc13

From forum: R help

which to trust...princomp() or prcomp() or neither?

2009-11-24T19:32:24Z

According to R help:
princomp() uses eigenvalues of covariance data.
prcomp() uses the SVD method.

yet when I run the (eg., USArrests) data example and compare with my own
"hand-written" versions of PCA I get what looks like the opposite.
Example:
comparing the variances I see:

Using prcomp(USArrests)
-------------------------------------
Standard deviations:
[1] 83.732400 14.212402 6.489426 2.482790

Using princomp(USArrests)
--------------------------------------
Comp.1 Comp.2 Comp.3 Comp.4
82.890847 14.069560 6.424204 2.457837

Using my custom pca_svd() --- (my PCA method using native R svd() function):
-----------------------------------------------
$stdev
[1] 82.890847 14.069560 6.424204 2.457837

Using my custom pca_cov() --- (my PCA method using native R cov() and eigen() functions):
-----------------------------------------------
$sdev
[1] 83.732400 14.212402 6.489426 2.482790

You see the problem: my SVD method yields results numerically similar to
the princomp() method which supposedly uses the eigenvector calculation.
Whereas my eigenvector calculation method yields results numerically
similar to the prcomp() method which supposedly is a SVD calculation!

Also, it surprised me that the two methods would differ so markedly (only 2 significant
figure agreement at best). Ultimately the question is which method to trust as most
accurate?

When I get time I'll just put in some data with KNOWN PC stdevs to see, but I'm
still curious to see if any of you reading this help list could explain in advance?

If any R gurus or the writers of either of the aforementioned routines can
enlighten me I'd be most grateful.

---
Dr Blair M. Smith
Industrial Research Limited
NZ
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From forum: R help

Re: reshape question

2009-11-24T19:06:31Z

What about the melt function in reshape package?

EX:

> x=sample(1:100,20,replace=T)

> x
[1] 48 94 32 96 81 99 10 64 64 94 57 60 16 64 32 76 63 1 64 8

> y=sample(1:100,20,replace=T)

> y
[1] 73 78 82 43 58 85 74 64 73 41 45 38 63 36 44 74 7 88 91 1

> xy=cbind(x,y)

> melt(xy)
X1 X2 value
1 1 x 48
2 2 x 94
3 3 x 32
4 4 x 96
5 5 x 81
6 6 x 99
7 7 x 10
8 8 x 64
9 9 x 64
10 10 x 94
11 11 x 57
12 12 x 60
13 13 x 16
14 14 x 64
15 15 x 32
16 16 x 76
17 17 x 63
18 18 x 1
19 19 x 64
20 20 x 8
21 1 y 73
22 2 y 78
23 3 y 82
24 4 y 43
25 5 y 58
26 6 y 85
27 7 y 74
28 8 y 64
29 9 y 73
30 10 y 41
31 11 y 45
32 12 y 38
33 13 y 63
34 14 y 36
35 15 y 44
36 16 y 74
37 17 y 7
38 18 y 88
39 19 y 91
40 20 y 1

>
Joe King
206-913-2912
jp@...
"Never throughout history has a man who lived a life of ease left a name
worth remembering." --Theodore Roosevelt

-----Original Message-----
From: r-help-bounces@... [mailto:r-help-bounces@...] On
Behalf Of David Winsemius
Sent: Tuesday, November 24, 2009 6:43 PM
To: AC Del Re
Cc: r-help@...
Subject: Re: [R] reshape question

On Nov 24, 2009, at 8:33 PM, AC Del Re wrote:

> Hi All,
>
> I am wanting to convert a data.frame from a wide format to a long
> format
> (with >1 variable) and am having difficulties. Any help is
> appreciated!
>
> #current wide format
>> head(data.out2)
> id rater.1 n.1 rater.2 n.2 rater.3 n.3 rater.4 n.4
> 11 11 0.1183333 79 NA NA NA NA NA NA
> 114 114 0.2478709 113 NA NA NA NA NA NA
> 12 12 0.3130655 54 0.3668242 54 NA NA NA NA
> 121 121 0.2400000 331 NA NA NA NA NA NA
> 122 122 0.3004164 25 0.1046278 25 0.2424871 25 0.2796937 25
> 125 125 0.1634865 190 NA NA NA NA NA NA
>
> #This is close but I would like the 'n' column to remain and for the
> '.1' to
> drop off

I don't really understand what you want and the example solution
throws away quite a lot of data, so consider this alternative:

data.out2 <- read.table(textConnection("id rater.1 n.1 rater.2 n.
2 rater.3 n.3 rater.4 n.4
11 11 0.1183333 79 NA NA NA NA NA NA
114 114 0.2478709 113 NA NA NA NA NA NA
12 12 0.3130655 54 0.3668242 54 NA NA NA NA
121 121 0.2400000 331 NA NA NA NA NA NA
122 122 0.3004164 25 0.1046278 25 0.2424871 25 0.2796937 25
125 125 0.1634865 190 NA NA NA NA NA NA"),
header=T, stringsAsFactors=F)

data.frame(id= data.out2$id, rater=stack(data.out2[,grep("rater",
names(data.out2))]),
n= stack(data.out2[,grep("n", names(data.out2))]) )

data.out2.id rater.values rater.ind n.values n.ind
1 11 0.1183333 rater.1 79 n.1
2 114 0.2478709 rater.1 113 n.1
3 12 0.3130655 rater.1 54 n.1
4 121 0.2400000 rater.1 331 n.1
5 122 0.3004164 rater.1 25 n.1
6 125 0.1634865 rater.1 190 n.1
7 11 NA rater.2 NA n.2
8 114 NA rater.2 NA n.2
9 12 0.3668242 rater.2 54 n.2
10 121 NA rater.2 NA n.2
11 122 0.1046278 rater.2 25 n.2
12 125 NA rater.2 NA n.2
13 11 NA rater.3 NA n.3
14 114 NA rater.3 NA n.3
15 12 NA rater.3 NA n.3
16 121 NA rater.3 NA n.3
17 122 0.2424871 rater.3 25 n.3
18 125 NA rater.3 NA n.3
19 11 NA rater.4 NA n.4
20 114 NA rater.4 NA n.4
21 12 NA rater.4 NA n.4
22 121 NA rater.4 NA n.4
23 122 0.2796937 rater.4 25 n.4
24 125 NA rater.4 NA n.4

You can take what you like from what I would consider a version that
has no loss of the original information.

>
>> data.out3<-reshape(data.out2,varying=list(names(data.out2)[-1]),
> + idvar='id',direction='long')
>> head(data.out3)
> id time rater.1
> 11.1 11 1 0.1183333
> 114.1 114 1 0.2478709
> 12.1 12 1 0.3130655
> 121.1 121 1 0.2400000
> 122.1 122 1 0.3004164
> 125.1 125 1 0.1634865
>
> Ideally I would like the columns to be set up in this manner:
>
> id time rater n

What is "time"?

>
>
> Thanks,
> html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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From forum: R help

Re: reshape question

2009-11-24T19:05:19Z

> I don't really understand what you want and the example solution throws away
> quite a lot of data, so consider this alternative:
>
> data.out2 <- read.table(textConnection("id rater.1 n.1 rater.2 n.2
> rater.3 n.3 rater.4 n.4
> 11 11 0.1183333 79 NA NA NA NA NA NA
> 114 114 0.2478709 113 NA NA NA NA NA NA
> 12 12 0.3130655 54 0.3668242 54 NA NA NA NA
> 121 121 0.2400000 331 NA NA NA NA NA NA
> 122 122 0.3004164 25 0.1046278 25 0.2424871 25 0.2796937 25
> 125 125 0.1634865 190 NA NA NA NA NA NA"), header=T,
> stringsAsFactors=F)
>

Or

library(reshape)
df <- melt(data.out2, na.rm = T, id = "id")
df <- cbind(df, colsplit(df$variable, "\\.", c("var", "time")))

cast(df, id + time ~ var)

See http://had.co.nz/reshape for more details.

Hadley

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From forum: R help

Re: reshape question

2009-11-24T18:42:37Z

On Nov 24, 2009, at 8:33 PM, AC Del Re wrote:

From forum: R help

XML package example code?

2009-11-24T17:49:31Z

I'm interested in parsing an html page. I should use XML, right? Could
you somebody show me some example code? Is there a tutorial for this
package?

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and provide commented, minimal, self-contained, reproducible code.

From forum: R help

reshape question

2009-11-24T17:33:35Z

Hi All,

I am wanting to convert a data.frame from a wide format to a long format
(with >1 variable) and am having difficulties. Any help is appreciated!

#current wide format
> head(data.out2)
id rater.1 n.1 rater.2 n.2 rater.3 n.3 rater.4 n.4
11 11 0.1183333 79 NA NA NA NA NA NA
114 114 0.2478709 113 NA NA NA NA NA NA
12 12 0.3130655 54 0.3668242 54 NA NA NA NA
121 121 0.2400000 331 NA NA NA NA NA NA
122 122 0.3004164 25 0.1046278 25 0.2424871 25 0.2796937 25
125 125 0.1634865 190 NA NA NA NA NA NA

#This is close but I would like the 'n' column to remain and for the '.1' to
drop off

> data.out3<-reshape(data.out2,varying=list(names(data.out2)[-1]),
+ idvar='id',direction='long')
> head(data.out3)
id time rater.1
11.1 11 1 0.1183333
114.1 114 1 0.2478709
12.1 12 1 0.3130655
121.1 121 1 0.2400000
122.1 122 1 0.3004164
125.1 125 1 0.1634865

Ideally I would like the columns to be set up in this manner:

id time rater n

Thanks,

AC

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From forum: R help

Re: Broken installer (PR#14083)

2009-11-24T17:31:49Z

On Nov 24, 2009, at 5:45 PM, robert.a.weller@... wrote:

> Full_Name: Robert A. Weller
> Version: current
> OS: Mac OS 10.6
> Submission from: (NULL) (129.59.140.86)
>
>
> The gfortran 4.2.4 installer in the Tools section that is supposed
> to install a
> Snow Leopard (10.6) version is actually installing version 4.2.1. I
> am finding
> that the 4.2.1 compiler installed as issues e.g. in interpreting the
> -fno-automatic command line switch and also -fdefault-real-8.
>
> We looked directly into the installer and saw that it was actually
> installing
> 4.2.1. Of course, gfortran --version confirmed this.
>

You are, of course, wrong because what you're looking at is the Apple
gcc version which is the version of the driver and the cc part (it is
the gcc-42 tree of Apple). The fortran merged unto the Apple gcc
branch is indeed 4.2.4.

Cheers,
Simon

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From forum: R devel

questions on the ff package

2009-11-24T17:28:44Z

Hi,

I have two questions on using the ff package and wonder if anyone who used
ff can share some thoughts.

I need to save a matrix as a memory-mapped file and load it back later. To
save the matrix, I use

mat = matrix(1:20, 4, 5)
matFF = ff(mat, dim=dim(mat), filename="~/a.mat", overwrite=TRUE, dimnames
= dimnames(mat))

To load it back, I use
matFF2 = ff(vmode = "double", dim= ???, filename="~/a.mat", overwrite=F)

However, I don't always know the dimension when loading the matrix back.
If I miss the dim attributes, ff will return it as vector. Is there a way
to load the matrix without specifying the dimension?

The second question is that the matrix may grow in terms of the number of
rows. I would like to synchronize the change to the memory-mapped file. Is
there an efficient way to do this?

Thanks

Jeff

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From forum: R help

problem in building an R package

2009-11-24T17:24:30Z

i am trying to build an R package and submit to CRAN.
i am using -
package.skeleton(name="xxzz", code_files = "H:\xxzz.R")
to build package xxzz.
---------------------------
The code above generates 'xxzz' folder.
It seems that I have to manually edit the files generated in xxzz folder (to
add titles, authors, etc)
--------------------------

But when I re-run -
package.skeleton(name="xxzz", code_files = "H:\xxzz.R")

All the edited information will be lost since the default files are
regenerated such as DESCRIPTION file.

---------------------------

I have found the process of building package is extremely troublesome.

Have anybody had a better approach?

Thanks.

From forum: R help

Re: Trellis Plot

2009-11-24T17:00:21Z

i was trying to do a for loop for plotting the histograms , but it doesnt work properly

> library(lattice)
> columns <- 8:153
> plots <- vector("list", length(columns))
> j <- 0
> for (i in columns)
+ {
+ plots[[ j <- j+1 ]] <- histogram( ~ data[,i] | data[,2],ylab = "Frequency",
+ xlab = "Score", xlim = c(1,5), ylim = c(0,100),layout=c(3,1),
+ main = c(colnames(data)[i],"index",j+1),mycolors = colors()[c(536,552,652,254,26)],
+ panel = function(..., col, mycolors) {
+ panel.histogram(..., col = mycolors[panel.number()])})
+ trellis.focus('strip', 1, 1, highlight=FALSE)
+ ltext(0.60, -0.25, 'PPM', col='blue', pos=3)
+ trellis.unfocus()
+ }
Error in grid.Call.graphics("L_downviewport", name$name, strict) :
Viewport 'plot1.strip.1.1.vp' was not found
>
> print(plots[[1]])

I am not sure what was happeneing. . . can anyone help me ?

ychu066 wrote:

anyone know how to add text in the Trellis plot panel ?? i want to add things eg: dot dot dot. in the headrer of the panel.

eg: hist1.png

From forum: R help

group generics

2009-11-24T16:34:25Z

I have classes A and B, where B contains A. In the implementation of
the group generic for B I would like to use the corresponding group
generic for A. Is there a way to do that?

I would also appreciate any comments if what I'm trying to do seems like
the wrong approach.

Here's a stripped down example:
setClass("A",
representation=representation(xa="numeric")
)

setMethod("Arith", signature(e1="numeric", e2="A"), function(e1, e2) {
new("A", ax=e1*e2@xa)
}
)

setClass("B",
representation=representation(xb="numeric"),
contains=c("A")
)

setMethod("Arith", signature(e1="numeric", e2="B"), function(e1, e2) {
# the next line does not work right
v <- selectMethod("callGeneric", signature=c("numeric", "A"))(e1, e2)
print(v)
new("B", v, xb=e1*e2@xb)
}
)

Results:
> t1 <- new("B", new("A", xa=4), xb=2)
> t1
An object of class “B”
Slot "xb":
[1] 2

Slot "xa":
[1] 4

> 3*t1
Error in getGeneric(f, !optional) :
no generic function found for "callGeneric"

Thanks.
Ross Boylan

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From forum: R devel

Re: Titles in plots overlap

2009-11-24T16:13:11Z

I did not get anything very interesting with that plot but
nonetheless, I suspect that you want to put your oma= parameter a bit
earlier.

On Nov 24, 2009, at 6:14 PM, Roslina Zakaria wrote:

> Hi,
>
> I use fCopulae package to draw different graphs of univariate and
> bivariate skew t. But the plots titles overlap. I tried using
> cex.main, font.main to adjust the size but they still overlaps.
> Here is my code:

#revised
opar <- par(mfrow = c(3, 1), oma=c(2,2,3,2) )
mu = 0
Omega = 1
alpha1 = 0
alpha2 = 1.5
alpha3 = 2
alpha4 = 0.5
Z1 = matrix(dmvst(x, 1, mu, Omega, alpha1, df = Inf), length(x))
Z2 = matrix(dmvst(x, 1, mu, Omega, alpha2, df = 5), length(x))
Z3 = matrix(dmvst(x, 1, mu, Omega, alpha3, df = 5), length(x))
Z4 = matrix(dmvst(x, 1, mu, Omega, alpha4, df = Inf), length(x))
plot(x,Z1, ylim=range(Z1,Z2), type='l')
points(x,Z2,type='l',col=2)
title(main = "Z1 (Skew=0, df=Inf) vs Z2 (Skew=1.5, df=5)",cex = 1.0)
plot(x,Z1, ylim=range(Z1,Z3), type='l')
points(x,Z3,type='l',col=3)
title(main = "Z1 (Skew=0, df=Inf) vs Z3 (Skew=2, df=5)",cex = 1.0)
plot(x,Z1, ylim=range(Z1,Z4), type='l')
points(x,Z4,type='l',col=4)
title(main = "Z1 (Skew=0, df=Inf) vs Z4 (Skew=0.5, df=Inf)",cex = 1.0)
#deleted
title("Different shapes of univariate skew-t distribution", outer =
TRUE, cex.main=2)
#added
par(opar)-

-

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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From forum: R help

Accessing remote data (ftp) over the net

2009-11-24T16:13:01Z

Hi,

Is there any way to access data remotely over the Internet? In
particular, I'm starting a project that will use data from the U.S.
Bureau of Labor Statistics. The Bureau regularly updates various data
series and publishes them as a series of flat files that can be
downloaded via ftp (e.g., cf. ftp://ftp.bls.gov/pub/time.series/sm/).
Since some of these files are rather large, I'd like to retrieve
selected elements by using sql queries. Since the files are often large
and updated frequently, I'd like to leave them on the server.

I'm thinking of trying something like: R -> RODBC -> MySQL -> query of
remote flat-file database and keeping the query as a view.

Has anyone been successful doing something like this? Is there a better
approach?

Thanks.

Marsh Feldman

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From forum: R help

Re: How to get the item in list that is a number?

2009-11-24T15:49:25Z

?unlist

if I understand you correctly.

On 24 Nov 2009, at 5:50PM, Peng Yu wrote:

> I have the following list. The second item in the list is a number.
> I'm wondering how to write R code to return this information for any
> list?
>
>
> $`1`
> integer(0)
>
> $`2`
> [1] 123
>
> $`3`
> integer(0)
>
> $`4`
> integer(0)
>
> $`5`
> integer(0)
>
> ______________________________________________
> R-help@... 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@... 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.

From forum: R help

Re: Split column

2009-11-24T15:34:00Z

I really appreciate your help. But if there is a big dataset, I need to write lots of code.

Lisa

David Winsemius wrote:

The solution I offered does exactly that. It also addresses your other
supplemental request.

--
David (Dangerfield?)

On Nov 24, 2009, at 5:57 PM, Lisaj wrote:

>
> I have a further question. If there is NA (missing data) in the
> original
> dataset, just like this:
>
> id var1 var2
> 1 1 3
> 2 3 1
> 3 NA 1
> 4 1 2
> 5 2 3
>
> how to deal with it? The converted dataset should be this:
>
> id var1.1 var1.2 var2.1 var2.2
> 1 1 1 2 2
> 2 2 2 1 1
> 3 NA NA 1 1
> 4 1 1 1 2
> 5 1 2 2 2
>
> Thanks.
>
> Lisa
>
> The
>
> Henrique Dallazuanna wrote:
>>
>> Try this:
>>
>> cbind(x$id, t(do.call(rbind, lapply(x[-1], sapply, switch, '1' =
>> c(1,1), '2' = c(1, 2), '3' = c(2, 2)))))
>>
>> On Tue, Nov 24, 2009 at 1:51 PM, Lisaj <lisajca@gmail.com> wrote:
>>>
>>> Hello, R users,
>>>
>>> I have a dataset that looks like this:
>>>
>>> id var1 var2
>>> 1 1 3
>>> 2 3 1
>>> 3 2 1
>>> 4 1 2
>>> 5 2 3
>>>
>>> I want to split one column to two columns with 1 = 1 and 1, 2 = 1
>>> and 2,
>>> 3 =
>>> 2 and 2:
>>>
>>> id var1.1 var1.2 var2.1 var2.2
>>> 1 1 1 2 2
>>> 2 2 2 1 1
>>> 3 1 2 1 1
>>> 4 1 1 1 2
>>> 5 1 2 2 2
>>>
>>> Can anyone please help how to get this done? Thanks a lot in advance
>>>
>>> Lisa
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Split-column-tp26498361p26498361.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.
>>>
>>
>>
>>
>> --
>> Henrique Dallazuanna
>> Curitiba-Paraná-Brasil
>> 25° 25' 40" S 49° 16' 22" O
>>
>> ______________________________________________
>> 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://old.nabble.com/Split-column-tp26498361p26504785.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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

______________________________________________
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.

From forum: R help

Re: 11 distinguishable colors

2009-11-24T15:27:14Z

Hi there,

I picked it up from r.colors' grass manual:

http://colorbrewer2.org/

The code bellow cold be usefull for you explore simbols and colors.

x11(900,500)
par(mfrow=c(1,2))
x<-runif(20)
y<-runif(20)
plot(y~x, type="n")
Number.of.symbols<-20
for (i in 1:Number.of.symbols)
{
points(y[i]~x[i], pch=i, cex=1.5)
text((x[i]+0.02),y[i], i)
}

colors.list<-colors()
Number.of.colors<-100
colors.list<-colors.list[1:Number.of.colors]
plot(0:1,0:1, type="n")
for (i in colors.list)
{
x<-runif(1)
y<-runif(1)
text(x,y, i, col=i)
}

cheers

miltinho

On Tue, Nov 24, 2009 at 6:01 PM, phoebe kong <sityeekong@...> wrote:

> It should be 11 different groups, not 8.
>
> On Tue, Nov 24, 2009 at 3:00 PM, phoebe kong <sityeekong@...> wrote:
>
> > Hi,
> >
> > I want to draw a plot where the data set has 8 different groups. Could
> you
> > suggest 8 combination of colors and symbols that are distinguishable? If
> the
> > colors are too close, it would be hard to differentiate from the plot.
> >
> > Thanks,
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

______________________________________________
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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.

From forum: R help

R Packages Crack the 3,000 Mark!

2009-11-24T15:26:54Z

Hi All,

I don't know if this has been reported before, but according to Henrique
Dallazuanna's program (below) the number of R packages has exceeded the
3,000 mark. The count today is 3,175. I ran this just a couple of months
ago & the number was still in the high 2,000s, so it must be fairly
recent. I think this represents about 50% growth in the last year. Not
bad!

Does anyone have a program that graphs the growth of R packages? I don't
know if that historical data is around.

Cheers,

Bob

http://RforSASandSPSSusers.com

Henrique's program:

> setRepositories()

> myPackageNames <- available.packages()

--- Please select a CRAN mirror for use in this session --- [I selected
them all]

> length(unique( rownames(myPackageNames) ))

[1] 3175

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Titles in plots overlap

2009-11-24T15:14:47Z

Hi,

I use fCopulae package to draw different graphs of univariate and bivariate skew t. But the plots titles overlap. I tried using cex.main, font.main to adjust the size but they still overlaps. Here is my code:
par(mfrow = c(3, 1))
mu = 0
Omega = 1
alpha1 = 0
alpha2 = 1.5
alpha3 = 2
alpha4 = 0.5
Z1 = matrix(dmvst(x, 1, mu, Omega, alpha1, df = Inf), length(x))
Z2 = matrix(dmvst(x, 1, mu, Omega, alpha2, df = 5), length(x))
Z3 = matrix(dmvst(x, 1, mu, Omega, alpha3, df = 5), length(x))
Z4 = matrix(dmvst(x, 1, mu, Omega, alpha4, df = Inf), length(x))
plot(x,Z1, ylim=range(Z1,Z2), type='l')
points(x,Z2,type='l',col=2)
title(main = "Z1 (Skew=0, df=Inf) vs Z2 (Skew=1.5, df=5)",cex = 1.0)
plot(x,Z1, ylim=range(Z1,Z3), type='l')
points(x,Z3,type='l',col=3)
title(main = "Z1 (Skew=0, df=Inf) vs Z3 (Skew=2, df=5)",cex = 1.0)
plot(x,Z1, ylim=range(Z1,Z4), type='l')
points(x,Z4,type='l',col=4)
title(main = "Z1 (Skew=0, df=Inf) vs Z4 (Skew=0.5, df=Inf)",cex = 1.0)
par(oma=c(2,2,3,2))
title("Different shapes of univariate skew-t distribution", outer = TRUE, cex.main=2)

Thank you so much for any help given.

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Re: Split column

2009-11-24T15:05:59Z

The solution I offered does exactly that. It also addresses your other
supplemental request.

--
David (Dangerfield?)

On Nov 24, 2009, at 5:57 PM, Lisaj wrote:

>
> I have a further question. If there is NA (missing data) in the
> original
> dataset, just like this:
>
> id var1 var2
> 1 1 3
> 2 3 1
> 3 NA 1
> 4 1 2
> 5 2 3
>
> how to deal with it? The converted dataset should be this:
>
> id var1.1 var1.2 var2.1 var2.2
> 1 1 1 2 2
> 2 2 2 1 1
> 3 NA NA 1 1
> 4 1 1 1 2
> 5 1 2 2 2
>
> Thanks.
>
> Lisa
>
> The
>
> Henrique Dallazuanna wrote:
>>
>> Try this:
>>
>> cbind(x$id, t(do.call(rbind, lapply(x[-1], sapply, switch, '1' =
>> c(1,1), '2' = c(1, 2), '3' = c(2, 2)))))
>>
>> On Tue, Nov 24, 2009 at 1:51 PM, Lisaj <lisajca@...> wrote:
>>>
>>> Hello, R users,
>>>
>>> I have a dataset that looks like this:
>>>
>>> id var1 var2
>>> 1 1 3
>>> 2 3 1
>>> 3 2 1
>>> 4 1 2
>>> 5 2 3
>>>
>>> I want to split one column to two columns with 1 = 1 and 1, 2 = 1
>>> and 2,
>>> 3 =
>>> 2 and 2:
>>>
>>> id var1.1 var1.2 var2.1 var2.2
>>> 1 1 1 2 2
>>> 2 2 2 1 1
>>> 3 1 2 1 1
>>> 4 1 1 1 2
>>> 5 1 2 2 2
>>>
>>> Can anyone please help how to get this done? Thanks a lot in advance
>>>
>>> Lisa
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Split-column-tp26498361p26498361.html
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> R-help@... 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.
>>>
>>
>>
>>
>> --
>> Henrique Dallazuanna
>> Curitiba-Paraná-Brasil
>> 25° 25' 40" S 49° 16' 22" O
>>
>> ______________________________________________
>> R-help@... 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://old.nabble.com/Split-column-tp26498361p26504785.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... 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@... 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.

From forum: R help

Re: 11 distinguishable colors

2009-11-24T15:01:41Z

It should be 11 different groups, not 8.

On Tue, Nov 24, 2009 at 3:00 PM, phoebe kong <sityeekong@...> wrote:

> Hi,
>
> I want to draw a plot where the data set has 8 different groups. Could you
> suggest 8 combination of colors and symbols that are distinguishable? If the
> colors are too close, it would be hard to differentiate from the plot.
>
> Thanks,
>

[[alternative HTML version deleted]]

______________________________________________
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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.

From forum: R help

11 distinguishable colors

2009-11-24T15:00:33Z

Hi,

I want to draw a plot where the data set has 8 different groups. Could you
suggest 8 combination of colors and symbols that are distinguishable? If the
colors are too close, it would be hard to differentiate from the plot.

Thanks,

[[alternative HTML version deleted]]

______________________________________________
R-help@... 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.

From forum: R help

Re: Split column

2009-11-24T14:57:06Z

I have a further question. If there is NA (missing data) in the original dataset, just like this:

id var1 var2
1 1 3
2 3 1
3 NA 1
4 1 2
5 2 3

how to deal with it? The converted dataset should be this:

id var1.1 var1.2 var2.1 var2.2
1 1 1 2 2
2 2 2 1 1
3 NA NA 1 1
4 1 1 1 2
5 1 2 2 2

Thanks.

Lisa

The

Henrique Dallazuanna wrote:

Try this:

cbind(x$id, t(do.call(rbind, lapply(x[-1], sapply, switch, '1' =
c(1,1), '2' = c(1, 2), '3' = c(2, 2)))))

On Tue, Nov 24, 2009 at 1:51 PM, Lisaj <lisajca@gmail.com> wrote:
>
> Hello, R users,
>
> I have a dataset that looks like this:
>
> id var1 var2
> 1 1 3
> 2 3 1
> 3 2 1
> 4 1 2
> 5 2 3
>
> I want to split one column to two columns with 1 = 1 and 1, 2 = 1 and 2, 3 =
> 2 and 2:
>
> id var1.1 var1.2 var2.1 var2.2
> 1 1 1 2 2
> 2 2 2 1 1
> 3 1 2 1 1
> 4 1 1 1 2
> 5 1 2 2 2
>
> Can anyone please help how to get this done? Thanks a lot in advance
>
> Lisa
>
> --
> View this message in context: http://old.nabble.com/Split-column-tp26498361p26498361.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.
>

--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

______________________________________________
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.

From forum: R help

How to get the item in list that is a number?

2009-11-24T14:50:14Z

I have the following list. The second item in the list is a number.
I'm wondering how to write R code to return this information for any
list?

$`1`
integer(0)

$`2`
[1] 123

$`3`
integer(0)

$`4`
integer(0)

$`5`
integer(0)

______________________________________________
R-help@... 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.

From forum: R help

Broken installer (PR#14083)

2009-11-24T14:45:12Z

Full_Name: Robert A. Weller
Version: current
OS: Mac OS 10.6
Submission from: (NULL) (129.59.140.86)

The gfortran 4.2.4 installer in the Tools section that is supposed to install a
Snow Leopard (10.6) version is actually installing version 4.2.1. I am finding
that the 4.2.1 compiler installed as issues e.g. in interpreting the
-fno-automatic command line switch and also -fdefault-real-8.

We looked directly into the installer and saw that it was actually installing
4.2.1. Of course, gfortran --version confirmed this.

R. Weller
Vanderbilt University

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From forum: R devel

Re: overdispersion and quasibinomial model

2009-11-24T14:36:11Z

On Nov 24, 2009, at 3:41 PM, djpren wrote:

>
> I am looking for the correct commands to do the following things:
>
> 1. I have a binomial logistic regression model and i want to test for
> overdispersion.

Under the teach a man to fish precept, ... try:

RSiteSearch("test over dispersion binomial models")

> 2. If I do indeed have overdispersion i need to then run a quasi-
> binomial
> model, but I'm not sure of the command.

?glm
# and follow the appropriate links

> 3. I can get the residuals of the model, but i need to then apply a
> shapiro
> wilk test to test them. Does anyone know the command for this?

RSiteSearch("shapiro-wilks") # not that people here recommend this
procedure

The overall flavor of these questions is "homework", so I'm
speculating that you may want to consult your instructors.

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

______________________________________________
R-help@... 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.

From forum: R help

Re: Link to pdf documentation from other package ?

2009-11-24T14:31:13Z

On Nov 24, 2009, at 10:58 , hadley wickham wrote:

>> But the help files are local. It would seem that this problem would
>> be addressed if the help files were not displayed using http://
>
> But then they couldn't be dynamic.
>
> One solution which would allow both would be to implement a proxy
> within the dynamic help that could point to any file on the file
> system.

That is already implemented but not allowed in unsafe directories for
security reasons (see previous discussion).

Cheers,
Simon

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From forum: R devel

Scatter plot with margin distributions

2009-11-24T14:28:27Z

Hi All,

My doub I think is very simple. I hope it is. So you can again help, guide
me.

I´m trying to make a graph (scatter graph) about two variables, imagine I
have a watter.txt file with two variables watter and hardness:

This code extracted from:
http://cran.r-project.org/web/packages/HSAUR/vignettes/Ch_simple_inference.pdf
would make a plot similar I want I mean to make an scatterplot with marginal
ditribution up and left...(in this case a boxplot on the left and also I
omitt the location).

layout(matrix(c(2, 0, 1, 3), 2, 2, byrow = TRUE),2 + c(2, 1), c(1, 2), TRUE)

plot(mortality ~ hardness, data = water, pch = psymb)

abline(lm(mortality ~ hardness, data = water))

legend("topright", legend = levels(water$location), 7 + pch = c(1,2), bty =
"n")

hist(water$hardness)

boxplot(water$mortality)

Can anyone explain what is the values in "layout" the inputs I mean, I have
read the help but because I´m a begginer I ´m not able to comprehed why they
put matrix c(2,0,1,3) and the other inputs?

I need if someone can help me an easy example....

Thanks a lot.

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

From forum: R help

Re: merge on non-identical names

2009-11-24T14:27:28Z

See agrep:

agrep("American Services", "Americam Services")

On Tue, Nov 24, 2009 at 7:11 PM, j daniel <jdlecy@...> wrote:

>
> Greetings,
>
> I need to conduct a merge on two databases containing information on
> organizations, but the organization names are often non-identical and there
> is no common unique identifier. Does anyone know a good way to calculate a
> similarity measure on two names, or even better is there a natural language
> matching function in an R package? I did some searches on this but must not
> know the right keywords to search.
>
> As an example, here are some possible non-identical names:
>
> Oxfam, Oxfam USA
> American Services, Americam Services - (just mis-spelled)
> Global Alliance for Action, Global Alliance for the Environment - (a
> non-match)
>
> Any suggestions are welcome!
>
>
> --
> View this message in context: http://old.nabble.com/merge-on-non-identical-names-tp26503346p26503346.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... 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.
>

--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

______________________________________________
R-help@... 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.

From forum: R help

Re: Re moving white space help

2009-11-24T14:26:17Z

If I understand, you can try this:

gsub("\\s+","",x)

On Tue, Nov 24, 2009 at 7:18 PM, Ramyathulasingam
<Ramya.Thulasingam@...> wrote:

>
> Hi there
>
> I am trying to remove the white space and replace it with nothing but didnt
> have any luck with that
>
> x <- and fgh-
>
> i can replace the comma using gsub
> gsub("\\-","",x)
> but i cant replace the white space with nothing.
>
> Ramya
> --
> View this message in context: http://old.nabble.com/Removing-white-space-help-tp26503431p26503431.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... 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.
>

From forum: R help

Re: Re moving white space help

2009-11-24T14:25:49Z

Is this what you want:

> x <- " and fgh- "
> gsub(" +", "", x)
[1] "andfgh-"

On Tue, Nov 24, 2009 at 4:18 PM, Ramyathulasingam
<Ramya.Thulasingam@...> wrote:

--
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

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From forum: R help

Aquamacs/emacs and color of echo in R console 2!

2009-11-24T14:13:45Z

Hi

Sorry, I forgot to state the version: GNU Emacs 22.3.1

I have been unable to find information on the following problem:

All the text in my *R* window is shown in light red, starting after the
echo "This is mgcv 1.5-6 . For overview type ", the following
`help("mgcv-package")' is already in the light red.

This color annoys me because I need more contrast, and it is even worse
for use with a beamer.

In the options menu I can open "Appearance" and then "Foreground color
for comint mode", but apart from the "[quit] in the upper left corner I
can see no hint how to make a choice, let alone make it permanent.

Or will I have to try "Appearance" > "Customize Aquamacs"?

M-x color-theme-select opens an empty frame with nothing to select from
(Hint given in http://www.emacswiki.org/emacs/AquamacsFAQ)

What am I missing?

Thanks for help.

C.Hoffmann

--
Dr. Christian W. Hoffmann,
Swiss Federal Research Institute WSL
Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
Tel +41-44-7392-277 (office), -111(exchange), -215 (fax)
christian.hoffmann@..., www.wsl.ch/personal_homepages/hoffmann/
"Jene, die grundlegende Freiheit aufgeben wuerden, um eine geringe
voruebergehende Sicherheit zu erwerben, verdienen weder Freiheit noch
Sicherheit." - Benjamin Franklin

______________________________________________
R-help@... 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.

From forum: R help

Aquamacs/emacs and color of echo in R console

2009-11-24T14:10:14Z

Hi

I have been unable to find information on the following problem:

All the text in my *R* window is shown in light red, starting after the
echo "This is mgcv 1.5-6 . For overview type ", the following
`help("mgcv-package")' is already in the light red.

This color annoys me because I need more contrast, and it is even worse
for use with a beamer.

In the options menu I can open "Appearance" and then "Foreground color
for comint mode", but apart from the "[quit] in the upper left corner I
can see no hint how to make a choice, let alone make it permanent.

Or will I have to try "Appearance" > "Customize Aquamacs"?

M-x color-theme-select opens an empty frame with nothing to select from
(Hint given in http://www.emacswiki.org/emacs/AquamacsFAQ)

What am I missing?

Thanks for help.

C.Hoffmann

--
Dr. Christian W. Hoffmann,
Swiss Federal Research Institute WSL
Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
Tel +41-44-7392-277 (office), -111(exchange), -215 (fax)
christian.hoffmann@..., www.wsl.ch/personal_homepages/hoffmann/
"Jene, die grundlegende Freiheit aufgeben wuerden, um eine geringe
voruebergehende Sicherheit zu erwerben, verdienen weder Freiheit noch
Sicherheit." - Benjamin Franklin

______________________________________________
R-help@... 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.

From forum: R help