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Ramón Casero Cañas | 1 Oct 2005 02:39
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[R] update MASS


I'd like to update MASS from version 7.2-11 to version 7-2.19. I am
running R 2.0.1 on ubuntu, that installs MASS with the package r-cran-vr.

I have tried doing update.packages(), and I get a list of packages that
I could update, but none is called MASS.

I have tried the following too, right after launching emacs, but to no
avail.

<QUOTE>
> update.packages("MASS")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 65650 bytes
opened URL
==================================================
downloaded 64Kb

Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method
= method,  :
	no installed.packages for (invalid?) lib.loc=MASS
</QUOTE>

I have the package installed in /usr/lib/R/library/MASS. I can do

<QUOTE>
> library(MASS)
> search()
 [1] ".GlobalEnv"        "package:MASS"      "package:methods"
 [4] "package:stats"     "package:graphics"  "package:grDevices"
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David Hartley | 1 Oct 2005 03:40
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[R] Inverse autocorrelation function?

In time series analysis it is helpful to plot the
autocorrelation function (ACF), partial
autocorrelation function (PACF), and the inverse
autocorrelation function (IACF). The stats library
provides the ability to compute and plot the ACF and
PACF, but I cannot find an [R] procedure to compute
and plot the IACF. Is there one? 

Best regards, 

David Hartley, PhD

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rab45+ | 1 Oct 2005 06:26
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[R] R and Data Storage

Where I work a lot of people end up using Excel spreadsheets for storing
data. This has limitations and maybe some less than obvious problems. I'd
like to recommend a uniform way for storing and archiving data collected
in the department. Most of the data could be stored in simple csv type
files but it would be nice to have something that stores more information
about the variables and units. netcdf seems like overkill (and not easy
for casual users). Same for postgres and mysql databases. Could someone
recommend some system for storing relatively small data sets (50-100
variables, <1000 records) that would be reliable, safe, and easy for
people to view and edit their data that works nicely with R and is open
source? Am I asking for the moon?

Rick  B.

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Tobias Verbeke | 1 Oct 2005 10:36
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Re: [R] R and Data Storage

rab45+ <at> pitt.edu wrote:

>Where I work a lot of people end up using Excel spreadsheets for storing
>data. This has limitations and maybe some less than obvious problems. I'd
>like to recommend a uniform way for storing and archiving data collected
>in the department. Most of the data could be stored in simple csv type
>files but it would be nice to have something that stores more information
>about the variables and units. netcdf seems like overkill (and not easy
>for casual users). Same for postgres and mysql databases. Could someone
>recommend some system for storing relatively small data sets (50-100
>variables, <1000 records) that would be reliable, safe, and easy for
>people to view and edit their data that works nicely with R and is open
>source? Am I asking for the moon?
>  
>
Would the StatDataML format meet your needs ?
It is open, XML-based, stores variable
types and works nicely with R (as R wizards designed
StatDataML and the corresponding R package).

See
http://cran.r-project.org/src/contrib/Descriptions/StatDataML.html
or
http://www.omegahat.org/StatDataML/

HTH,
Tobias

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Ajay Narottam Shah | 1 Oct 2005 09:32

[R] Placing axes label strings closer to the graph?

Folks,

I have placed an example of a self-contained R program later in this
mail. It generates a file inflation.pdf. When I stare at the picture,
I see the "X label string" and "Y label string" sitting lonely and far
away from the axes. How can these distances be adjusted? I read ?par
and didn't find this directly.

I want to hang on to 2.8 x 2.8 inches as the overall size of graph,
but it will be nice if the inner square frame was bigger and thus the
axes were closer to the strings. I will be happy with (say)
par(mai=c(.6,.6,.2,.2)). But if I just do this, the "X label string"
and "Y label string" were lost.

Thanks,

        -ans.

D <- structure(list(dates = c(1983, 1984, 1985, 1986, 1987, 1988,
                      1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996,
                      1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
                      2005), inflation = c(7.6, 12.1, 6.3, 6.8, 8.7,
                               8.8, 9.4, 6.1, 11.6, 13.5, 9.6, 7.5, 10.1, 10.2,
                               9.3, 7, 13.1, 3.4, 3.7, 4.3, 4.1, 3.7, 4)),
               .Names = c("dates", "inflation"), row.names =
               c("1", "2", "3", "4", "5", "6", "7", "8", "9",
                 "10", "11", "12", "13", "14", "15", "16", "17",
                 "18", "19", "20", "21", "22", "23"), class =
               "data.frame")
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Prof Brian Ripley | 1 Oct 2005 12:01
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Re: [R] R-2.1.1 on AIX 5.*

Note your first error message is

> "connections.c", line 2580.18: 1506-052 (S) Duplicate case label for value 4.
> Labels must be unique.

and the relevant line is

#if SIZEOF_LONG == 8
             case sizeof(long):

so you have somehow got options to give you 4-byete longs although 
configure found 8-byte longs.  How you managed that is not clear from your 
output, and it has never been reported before.

Other people have succeeded on AIX 5.x, including with 2.2.0-beta.  Our 
advice would be to try the latter (since the 2.1.x branch is no longer 
under development), and to ask detailed programming questions in a 
suitable forum (an AIX forum, or R-devel where you are more likely to get 
a response).

On Thu, 29 Sep 2005, Raphael Bolze wrote:

> Hi,
>
> I need to install R-2.1.1 on a AIX machine. (i have tried several machine with
> different os version : 5.1, 5.2 and 5.3)
> I have tried several configuration which was advise on the R-install and admin
> section :
> but none goes to the end of compilation.
>
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Prof Brian Ripley | 1 Oct 2005 12:12
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Re: [R] update MASS

On Sat, 1 Oct 2005, Ramón Casero Cañas wrote:

> I'd like to update MASS from version 7.2-11 to version 7-2.19. I am
> running R 2.0.1 on ubuntu, that installs MASS with the package r-cran-vr.

First, MASS is part of VR, so it is VR you update.

Second, please do *READ THE HELP PAGE*.  The first argument of 
update.packages() is not a package name.

Third, check the CRAN information, here at

 	http://cran.r-project.org/src/contrib/Descriptions/VR.html

and note

Depends:	R (>= 2.1.0), graphics, stats
                       ^^^^^

and no VR update is currently available for your version of R.

Your R is seriously only of date.  You might want to wait a week and then 
install 2.2.0.

> I have tried doing update.packages(), and I get a list of packages that
> I could update, but none is called MASS.
>
> I have tried the following too, right after launching emacs, but to no
> avail.
>
(Continue reading)

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Prof Brian Ripley | 1 Oct 2005 12:28
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Re: [R] Placing axes label strings closer to the graph?

Use mtext() to put labels in the margin line you want.  title() writes 
xlab and ylab in line 3 AFAIR.  So you could use something like

par(mai=c(0.6,0.6,0.2,0.2))
plot(D$dates, D$inflation,
      type="l", lwd=2, col="cadetblue4", cex.axis=0.6)
mtext("X label string", 1, line=2, cex = 0.6)
mtext("Y label string", 2, line=2, cex = 0.6)

*However*, your error is to use cex to change the font size, not pointsize 
(which scales the lines suitably). Try instead

pdf(file="inflation.pdf", width=2.8, height=2.8, pointsize=6)
plot(D$dates, D$inflation, xlab="X label string", ylab="Y label string",
      type="l", lwd=2, col="cadetblue4")

On Sat, 1 Oct 2005, Ajay Narottam Shah wrote:

> Folks,
>
> I have placed an example of a self-contained R program later in this
> mail. It generates a file inflation.pdf. When I stare at the picture,
> I see the "X label string" and "Y label string" sitting lonely and far
> away from the axes. How can these distances be adjusted? I read ?par
> and didn't find this directly.
>
> I want to hang on to 2.8 x 2.8 inches as the overall size of graph,
> but it will be nice if the inner square frame was bigger and thus the
> axes were closer to the strings. I will be happy with (say)
> par(mai=c(.6,.6,.2,.2)). But if I just do this, the "X label string"
(Continue reading)

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John Maindonald | 1 Oct 2005 12:32
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[R] Multiple expressions, when using substitute()

expression() accepts multiple expressions as arguments, thus:

plot(1:2, 1:2)
legend("topleft",
               expression(y == a * x^b,
                                    "where "* paste(y=="wood; ",  
x=="dbh")))

Is there a way to do this when values are to be substituted
for a and b? i.e., the first element of the legend argument
to legend() becomes, effectively:
   substitute(y == a * x^b, list(a = B[1], b=B[2]))

John Maindonald             email: john.maindonald <at> anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Bioinformation Science, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.

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Paul Roebuck | 1 Oct 2005 13:07

[R] X-Axis Label Overwritten By TickMark Values

Can someone tell me how to fix the left margin of plot region
such that the tick values don't overwrite the x-axis label?
I haven't been able to set the correct par option to fix this...

TIA

------------
grdev <- function(...) {
    get(getOption("device"))(...)
}

plotFixMe <- function(spectrum, ...) {
    saved.par <- par(las = 1, tcl = 0.3)
    on.exit(par(saved.par))

    plot(spectrum,
         type = "l",
         col  = "blue",
         xlab = "",
         ylab = "",
         ...)
    title(main = "x-axis label overwritten by tick values",
          xlab = "Index",
          ylab = "Intensity")
}

grdev()
plotFixMe(rnorm(50)*20000, ylim = c(0, 50000))

----------------------------------------------------------
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Gmane