Re: [R] Awk and Vilno

[Rogerio Porto]

Hey,

> What we should really compare is the four situations:
> R alone
> R + awk
> R + vilno
> R + awk + vilno
> and maybe "R + SAS Data step"
> and see what scripts are more  elegant (read 'short and understandable')

what do you guys think of creating a R-wiki page for syntax
comparisons among the various options to enhance R use?

I already have two sugestions:

1) syntax examples for using R and other tools to manipulate
and analyze large datasets (with a concise description of the
datasets);

2) syntax examples for using R and other tools (or R alone) to clean
and prepare datasets (simple and very small datasets, for didatic
purposes).

I think this could be interesting for R users and to promote other
software tools, since it seems there is a lot of R users that use
other tools also.

Besides that, questions on those two above subjects are prevalent
at this list. Thus a wiki page seems to be the right place to discuss
and teach this to other users.

What do you think?

Rogerio

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Re: [R] Spectral analysis

[Rogerio Porto]

David and Ted,

since David asked about wavelets, there are some examples
at the packages Wavethresh and Waveslim that could be useful.

Waveslim deals with time series that are or are not a power of 2,
but must be regularly spaced.

Wavethresh 3 (http://www.maths.bris.ac.uk/~wavethresh/)
has methods to analyze irregular time series, as suggested by Ted
but their length must be a power of 2.

Regards,

Rogerio

-- Cabeçalho original ---

De: [EMAIL PROTECTED]
Para: "David LEDU" [EMAIL PROTECTED]
Cópia: r-help@stat.math.ethz.ch
Data: Wed, 06 Jun 2007 22:34:21 +0100 (BST)
Assunto: Re: [R] Spectral analysis

> On 06-Jun-07 20:55:09, David LEDU wrote:
> > Hi all,
> > 
> > I am dealing with paleoceanographic data and I have a C14 time serie
> > and one other variable. I would like to perform a spectral analysis
> > (fft or wavelet) and plot it. Unfortunately I don't know the exact
> > script to do this. Does anybody could send me an example to perform my
> > spectral analysis ?
> > 
> > I Thank you
> > 
> > David
> 
> There are a lot of possible ramifications to your query,
> but for a basic spectral analysis of a series you can use
> the function spectrum() in the "stats" package.
> 
> What is the role of the "other variable"?
> 
> Best wishes,
> Ted.
> 
> 
> E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
> Fax-to-email: +44 (0)870 094 0861
> Date: 06-Jun-07   Time: 22:34:07
> -- XFMail --
> 
> __
> R-help@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.
>

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Re: [R] time series

[Rogerio Porto]

Jessica,

> I am working with a data file which is the record of precipitation
> measurement normaly done every 10 minutes. I would like to check if there
> are missing times in my data file.
> 
> Is there a function existing able to check for that in R ?

I'd use max(diff(time))==min(diff(time)).

HTH,

Rogerio

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Re: [R] sobre tutorial

[Rogerio Porto]

Danilo,

http://cran.r-project.org/other-docs.html#nenglish

Manuel Castejón Limas, Joaquín Ordieres Meré, Fco. Javier de Cos Juez, and 
Fco. Javier Martínez de Pisón Ascacibar. Control de Calidad. Metodologia para 
el 
analisis previo a la modelización de datos en procesos industriales. 
Fundamentos teóricos y aplicaciones con R. Servicio de Publicaciones de la 
Universidad de La Rioja, 2001. ISBN 84-95301-48-2.

[ ]s

Rogerio


-- Cabeçalho original ---

De: [EMAIL PROTECTED]
Para: [EMAIL PROTECTED]
Cópia: r-help@stat.math.ethz.ch
Data: Tue, 15 May 2007 18:20:04 +0100
Assunto: Re: [R] sobre tutorial

> Hello,
> 
> There are a number of resources (in Spanish) at the bottom of the page
> 
> http://es.wikipedia.org/wiki/Lenguaje_de_programación_R
> 
> Regards,
> 
> Carlos J. Gil Bellosta
> http://www.datanalytics.com
> 
> 
> On Tue, 2007-05-15 at 18:49 +0200, Danilo Ceschin wrote:
> > Estimado, te agradeceria me envies el tutorial en espaniol para R. Estoy
> > dando mis primeros pasos con esta aplicacion.
> > Desde ya muchas gracias
> > 
> > 
> > Danilo Ceschin Ph.D
> > IGBMC
> > 1 rue Laurent Fries
> > 67404 ILLKIRCH CEDEX - FRANCE
> > tel 33 3 88 65 3457
> > email [EMAIL PROTECTED]
> > 
> > __
> > R-help@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.
> 
> __
> R-help@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.
>

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Re: [R] Box Ljung Statistics

[Rogerio Porto]

Gaurav,

> I met with below mentioned statistics in paper "Stock Index Volatility 
> Forecasting with High Frequency Data"
> by Eugenie Hol, Siem Jan Koopman 
> http://ideas.repec.org/p/dgr/uvatin/20020068.html
> 
> I would like to ask that what is "Box-Ljung portmantacau statistic based 
> on N squared autocorrelation" ?
> Is it same as "Box-Ljung Statistics" of stats package ?

Yes, it seems the same. But note that the paper computes the
statistic for the raw data and also for the squared data.

> Further, please tell me how to compute it ?

If you mean R, use the Box.test() function. If you mean theory,
see any good book on time series like Brockwell and Davis'
Introduction to Time Series and Forecasting.

> I have a return series of an Index.
> Please help me in this i am not able to get the statistics what is given 
> in the paper for S & P 100:-)

I can't help you here since I don't have the 5-minute data used in
the paper.

Rogerio

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Re: [R] how to pick a value from AR equation

[Rogerio Porto]

Lorenzo,

in order to help you more, you should consider sending to the
list some relevant code with the functions and packages you
are using.

Rogerio.
- Original Message - 
From: "Lorenzo Bencivelli" <[EMAIL PROTECTED]>
To: 
Sent: Friday, May 26, 2006 1:21 PM
Subject: [R] how to pick a value from AR equation


>i need to compute several (hundreds) of regression AR and PP.test for
> untary roots.
> is there an easy way to pick the values of interest from the output of
> these operations?
> i would like to fill a matrix (in a for cycle) with all the values of
> coefficients, standard deviations, PP statistics and the relevant
> critical value for the series i have.
> thanks in advance L
>
> -- 
>
>
> 
> credo nella ragione umana,
> e nella liberta' e nella giustizia che dalla ragione scaturiscono. 
> (sciascia)
>
> __
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Re: [R] understanding DWT

[Rogerio Porto]

Tom,

I'm not sure I understood your question but I'll try to give some direction.

Those lines just plot the wavelet coefficients in a manner adequatelly to
visualize their magnitude in their respective location in time and scale 
(frequency).
In this way, those lines are not there because of some boudary condition.

The shifts you told are related to the location in time of those 
coefficients.
The various locations varies accordingly to the scales because of the very
nature of wavelets which are shifted and dilated functions. Since the dwt
function uses a fast diadic algorithm, the locations are proportional to 
2^j,
whre j is a scale.

HTH,

Rogerio.

- Original Message - 
From: "tom wright" <[EMAIL PROTECTED]>
To: "R-Stat Help" 
Sent: Thursday, May 25, 2006 1:02 PM
Subject: [R] understanding DWT


> Can someone please help me understand the examples given in the dwt
> function of the waveslim library
> library(waveslim)
> ?dwt
>
> I'm having a problem understanding these lines. I assume they are
> required because of how the algorythm deals with the signal bounderies.
> Am I correct in thinking that for wavelets of scale 1 and 2, the
> coefiecints need to be shifted by 2 places, for scale 3 and 4 shift by 3
> places, therefore for scales 5 and 6 do i require a 4 place shift,
> similarly for scales 7 and 8 a 5 place shift?
> ie more generally should the shift be ceiling(scale/2)+1
>
> Many thanks
> tom
>
> __
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Re: [R] Wavelet Functions

[Rogerio Porto]

Peter,

making wavelet analysis requires one of the packages
that you have to install:
wavethresh, waveslim, wavelets or rtw.

HTH,

Rogerio.
- Original Message - 
From: "Peter Lauren" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, May 25, 2006 1:23 PM
Subject: [R] Wavelet Functions


> Does R have any wavelet functions?  When I type
>> help.search("wavelet")
> I get
> " No help files found with alias or concept or title
> matching 'wavelet' using fuzzy matching."
>
> Thanks,
> Peter.
>
> __
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Re: [R] conditional replacement

[Rogerio Porto]

Sachin,

there's another slower but more flexible way than Gabor's solution:

ifelse(x<30,30,ifelse(x>60,60,x))

HTH,

Rogerio.
- Original Message - 
From: "Sachin J" <[EMAIL PROTECTED]>
To: 
Sent: Tuesday, May 23, 2006 3:40 PM
Subject: [R] conditional replacement


> Hi
>
>  How can do this in R.
>
>  >df
>
>  48
>  1
>  35
>  32
>  80
>
>  If df < 30  then replace it with 30 and else if df > 60 replace it with 
> 60. I have a large dataset so I cant afford to identify indexes and then 
> replace.
>  Desired o/p:
>
>  48
>  30
>  35
>  32
>  60
>
>  Thanx in advance.
>
> Sachin
> __
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@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
>

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Re: [R] Cross correlation/ bivariate/ mantel

[Rogerio Porto]

Sam,

maybe you'll like to read about some environmetrics packages at
http://cran.r-project.org/src/contrib/Views/Environmetrics.html
or about more specific spatial analysis packages at
http://cran.r-project.org/src/contrib/Views/Spatial.html

Have a good reading and... good luck!

Rogerio.
- Original Message - 
From: "McClatchie, Sam (PIRSA-SARDI)" <[EMAIL PROTECTED]>
To: 
Sent: Friday, May 19, 2006 12:16 AM
Subject: [R] Cross correlation/ bivariate/ mantel



> Background:
> OS: Linux Ubuntu Dapper
> release: R 2.3.0
> editor: GNU Emacs 21.4.1
> front-end: ESS 5.2.3
> -
> Colleagues
>
I have two spatial datasets (latitude, longitude, fish eggs) and (latitude, 
longitude, fish larvae) at the same 280 stations (i.e. 280 cases). I want to 
determine if the 2 datasets are spatially correlated. In other words, do 
high numbers of larvae occur where there are high numbers of eggs? I would 
like to calculate the cross correlation for these bivariate data and 
calculate a Mantel statistic as described on pg. 147 of Fortin and Dale 2005 
"Spatial analysis".

My search of R packages came up with acf and ccf functions but I don't think 
these are what I want. Does anyone know which spatial package I might find 
the appropriate test, please?

> Best fishes
>
> Sam
> 
> Sam McClatchie,
> Biological oceanography
> South Australian Aquatic Sciences Centre
> PO Box 120, Henley Beach 5022
> Adelaide, South Australia
> email <[EMAIL PROTECTED]>
> Cellular: 0431 304 497
> Telephone: (61-8) 8207 5448
> FAX: (61-8) 8207 5481
> Research home page 
>
>/\
>   ...>>
>  
><°)Xx><<
>   /  \\
> ><(((°>
>   >><(((°>   ...>>O<°)Xx><<
>

[[alternative HTML version deleted]]







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Re: [R] How can you buy R?

[Rogerio Porto]

While reading the various answers, I've remembered that
the juridic part can't be that so simple. If I'm not fogeting
something, there are some packages in R that has a more
restrictive licence than GPL.

HTH,

Rogerio.
- Original Message - 
From: "Damien Joly" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, May 18, 2006 6:51 PM
Subject: [R] How can you buy R?


> Hi all,
>
> This may seem like a dumb question, but I work for an entity that is soon
> converting to XP across the board, and I will lose the ability to install
> software on my own.  The entity has a policy of only using software that 
> has
> been purchased and "properly licensed" (whatever that means).
>
> This means I will soon lose the ability to use R at work - something I 
> can't
> do without at this point.
>
> HOWEVER, I might be able to work around this policy if I can find a 
> licensed
> software vendor, preferably in Canada, that sells R.
>
> I tried googling R vendors but was unsuccessful.
>
> Any ideas?
>
> Thanks,
>
> Damien
>
> [[alternative HTML version deleted]]
>
> __
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Re: [R] How can you buy R?

[Rogerio Porto]

Damien,

I think there isn't such a vendor. Maybe you can try to buy S-Plus.
Maybe you can look for donations to R foundation or reading the
licence term.

HTH,

Rogerio.
- Original Message - 
From: "Damien Joly" <[EMAIL PROTECTED]>
To: 
Sent: Thursday, May 18, 2006 6:51 PM
Subject: [R] How can you buy R?


> Hi all,
>
> This may seem like a dumb question, but I work for an entity that is soon
> converting to XP across the board, and I will lose the ability to install
> software on my own.  The entity has a policy of only using software that 
> has
> been purchased and "properly licensed" (whatever that means).
>
> This means I will soon lose the ability to use R at work - something I 
> can't
> do without at this point.
>
> HOWEVER, I might be able to work around this policy if I can find a 
> licensed
> software vendor, preferably in Canada, that sells R.
>
> I tried googling R vendors but was unsuccessful.
>
> Any ideas?
>
> Thanks,
>
> Damien
>
> [[alternative HTML version deleted]]
>
> __
> R-help@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
>

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Re: [R] Re : Large database help

[Rogerio Porto]

Thank you all for the discussion.

I'll try to summarize the suggestions and give some partial conclusions
for sake of completeness of this thread.

First, I had read the I/O manual but had forgotten the function read.fwf as
suggested by Roger Peng. I'm sorry. But, following manual orientation, this
function is not recommended for large files and I need to discover how to
read fixed-width-format files using scan function, since there isn't such an
example in that manual neither in ?scan. At a glance, it seems the function
read.fwf writes blank spaces among column pointers in order to read the
file using a simple scan() function.

I've also read the I/O manual, mainly chapter 4 about using Relational
Databases.
This suggestion was appointed by Uwe Ligges and Justin Bem who advocated
the use of MySQL with RMySQL package. I'm still installing MySQL to try
to convert my fixed-width-format file to that database but, from the I/O
manual, it seems I can only calculate five descriptive statistics (aggregate
functions). So I couldn't calculate medians or more advanced statistics
like a cluster analysis.
This point was one from Robert Citek and thus, I'm not sure that working
with MySQL will help to solve my problem. RMySQL has dbApply function
that apply R functions to groups (chunks) of database rows.

There was a suggestion to subset the file, by Roger Peng.
Almost all participants in this thread noted the need of lots of RAM to work
with a few variables as suggested by Prof. Brian Ripley.

The future looks promising through a collection *big* of packages specially
designed to handle big data files in almost any hardwarea and OS
configuration although time-demanding in some cases. It seems the first one
in this collection is the biglm package by Thomas Lumley cited by Greg Snow.
The obvious drawback is that one hat to re-write every package that can't
handle big data files or, al least, their most memory demanding operations.
This last point could be implemented by an option like big.file=TRUE to be
incorporated at some functions. This point of view is one of *scaling up*
the methods.

Another promising way is to *scale down* the dataset. Statisticians are
aware of these techniques from non-hierarquical cluster analysis and
principal component analysis among others (mainly sampling). Engineers
and signal processing people know them from data compression techniques. 
Computer scientists work with training sets and dataming wich use methods
to scale down datasets. An example was given by Richard M. Heiberger
who cites a paper from William DuMouchel et al. on Squashing Flat Files.
Maybe could be some R functions specialized in these methods that, using
DBMS, could retrieve significant data (records and variables) that could be
handled by R.

That's all, for a while!

Rogerio.

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[R] Large database help

[Rogerio Porto]

Hello all.

I have a large .txt file whose variables are fixed-columns, 
ie, variable V1 goes from columns 1 to 7, V2 from 8 to 23 etc.
This is a 60GB file with 90 variables and 60 million observations.

I'm working with a Pentium 4, 1GB RAM, Windows XP Pro.
I tried the following code just to see if I could work with 2 variables
but it seems not possible: 
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.1  (2005-12-20 r36812)
ISBN 3-900051-07-0
> gc()
 used (Mb) gc trigger (Mb) max used (Mb)
Ncells 169011  4.6 35  9.4   35  9.4
Vcells  62418  0.5 786432  6.0   289957  2.3
> memory.limit(size=4090)
NULL
> memory.limit()
[1] 4288675840
> system.time(a<-matrix(runif(1e6),nrow=1))
[1] 0.28 0.02 2.42   NA   NA
> gc()
  used (Mb) gc trigger (Mb) max used (Mb)
Ncells  171344  4.6 35  9.4   35  9.4
Vcells 1063212  8.23454398 26.4  4063230 31.0
> rm(a)
> ls()
character(0)
> system.time(a<-matrix(runif(60e6),nrow=1))
Error: not possible to alocate vector of size 468750 Kb
Timing stopped at: 7.32 1.95 83.55 NA NA 
> memory.limit(size=5000)
Erro em memory.size(size) : .4GB

So my questions are:
1) (newbie) how can I read fixed-columns text files like this?
2) is there a way I can analyze (statistics like correlations, cluster etc)
such a large database neither increasing RAM nor changing to 64bit
machine but still using R and not using a sample? How? 

Thanks in advance.

Rogerio.

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Re: [R] two relatively simple questions

[Rogerio Porto]

Mark,

1) search() is ok for R on my Windows XP: it shows all the loaded packages.
If you want to see all the intalled packages, try library().

2) try detach(package:nameofpackage) to remove it from seach list. To 
uninstall it,
simply delete its directory that you can see through searchpaths().

3) nothing to do with Perl or make...

HTH,

Rogerio.
- Original Message - 
From: "MARK LEEDS" <[EMAIL PROTECTED]>
To: 
Sent: Friday, May 12, 2006 4:19 PM
Subject: [R] two relatively simple questions


>I am using R on windows XP and I really tried to find the answers to below 
>but
> I haven't been succesful.
>
> the two questions are :
>
> 1) is there way of seeing what packages you have loaded ( search() gives 
> you
> the automatically included ones ).
>
> 2) is there a way of uninstalling packages that you have added by 
> accident.
> i found the command R CMD REMOVE "package name" and tried it.
>
> first it said it didn't understand perl so installed perl. But, now it
> saying that it doesn't understand make ? I think
> make is specific to linux but maybe not ?
>
>Thanks a lot.
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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[R] Wavelet ordenates

[Rogerio Porto]

Hello,

does someone knows how can I get the ordenates of a 
father wavelet using the package wavethresh?

And using other package? Any hints?

For example, I'd like knowing what's the value of
\phi{j,k}(t), that is, the value of a father wavelet
(from some family) at scale j, shift k, point t.

Thanks in advance,

Rogerio.

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Re: [R] Filters in waveslim

[Rogerio Porto]

Amir,

if you try the following code:

require(wavelslim)
data(doppler)
dwt(doppler, wf="la6")

you get:

Error in switch(name, haar = select.haar(), d4 = select.d4(), mb4 = 
select.mb4(),  :   Invalid selection for wave.filter

So, it seems that instead of "la8" (default) and "haar" you can choose also 
"d4" and "mb4" only.

HTH,

Rogerio.

>Message: 5
>Date: Sun, 8 Jan 2006 04:46:47 -0800 (PST)
>From: Amir Safari <[EMAIL PROTECTED]>
>Subject: [R] Filters in waveslim
>To: R-help@stat.math.ethz.ch
>Message-ID: ><[EMAIL PROTECTED]>
>Content-Type: text/plain
>
>
>
>  Dear R Users,
> For running  wavelet functions using dwt( ), modwt( ), and mra( ), a 
> wavelet >filter  algorithm is applied. For all these functions, default is 
> "la8" and  other >possibility is "haar". In related documents, another 
> possibilities like as symlet >and coiflet ... are not cited.
> Besides "la8" and "haar", which wavelet filters can be used?
>Thank you for any help,
>  Amir Safari

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