date:20120420

Re: [R] symmetric matrix on both diagonals

2012-04-20 Thread Petr Savicky

On Fri, Apr 20, 2012 at 10:52:47AM -0400, David Winsemius wrote:
> 
> On Apr 20, 2012, at 7:05 AM, Petr Savicky wrote:
> 
> >On Fri, Apr 20, 2012 at 03:03:40AM -0700, juliane0212 wrote:
> >>
> >>I'm  having some problems computing a matrix being symmetric on both
> >>diagonals.
> >>
> >>Does anyone know a way to get from this matrix
> >>
> >>
> >>M <- matrix(c(1,0,0,0,2,7,0,0,3,4,0,0,6,0,0,0), ncol=4)
> >>
> >>to this one
> >>
> >>  M_final <- matrix(c(1,2,3,6,2,7,4,3,3,4,7,2,6,3,2,1),  
> >>ncol=4)
> >
> >Hi.
> >
> >Try the following.
> >
> > M[row(M) > col(M)] <- t(M)[row(M) > col(M)]
> > n <- nrow(M)
> > M[row(M) + col(M) > n + 1] <- M[n:1, n:1][row(M) + col(M) > n + 1]
> > all(M == M_final)
> >
> > [1] TRUE
> 
> How about?
> 
> > M[3:4, ] <- rev(M[1:2,])
> > M
>  [,1] [,2] [,3] [,4]
> [1,]1236
> [2,]2743
> [3,]3472
> [4,]6321

Hi.

I am not sure, which matrix did you start from. If we start
from the original matrix, then we get

  M <- matrix(c(1,0,0,0,2,7,0,0,3,4,0,0,6,0,0,0), ncol=4)
  M[3:4, ] <- rev(M[1:2,])
  M

   [,1] [,2] [,3] [,4]
  [1,]1236
  [2,]0740
  [3,]0470
  [4,]6321

where the components 2 and 3 have two and not four copies.

Petr.

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Re: [R] Fwd: User defined panel functions in lattice

2012-04-20 Thread Bert Gunter

A comment...

On Fri, Apr 20, 2012 at 8:32 PM, Duncan Mackay  wrote:
> Hi David, ilai
>
> The root cause of the problem is the passing of arguments to panel functions
> to me and my colleagues.
> Just going through the archives there seems to be different ways for very
> similar/same outcomes and
> trying to get a pattern is hard to discern.

Bad strategy!  Trying to infer the rules from examples in complex
cases -- and as you said, different equivalent ways -- is nuts. You
need to read the docs carefully (including Deepayan's book, possibly)
and use the examples for understanding what is explained there.

Finally, I don't know if this is relevant or helpful but:

## this code works fine
 xyplot(rnorm(5) ~ 1:5, type="l",
  panel = function(...)panel.xyplot(...,lwd=2))

## This code throws an error about repeat lwd arguments. Is it obvious why?
 xyplot(rnorm(5) ~ 1:5,  lwd=1,type="l",
  panel = function(...) panel.xyplot(...,lwd=2))

-- Bert

> I frequently have to use the subscripts or group.number to access other
> data.
> I thought I had things sorted out in my head with the panel.groups and
> group.number but this has shattered it.
>
> Thanks
>
> Duncan
>
> At 12:15 21/04/2012, you wrote:
>
>> On Apr 20, 2012, at 9:14 PM, ilai wrote:
>>
>>> Oops - that is "reply all"
>>> On Fri, Apr 20, 2012 at 5:29 PM, David Winsemius >> > wrote:


 I'm a bit puzzled by this exchange. I know there is a
 'panel.locfit', but
 you two are spelling it differently. Can you explain why you are
 doing so?
>>>
>>>
>>> Hi David,
>>> Thanks for stepping in. panel.Locfit is the OP's local function (or
>>> just a wrapper ?) which I believe is here
>>> http://www.mail-archive.com/r-help@r-project.org/msg167164.html
>>>
>>> Note the two errors OP encountered (solved down the thread) were
>>> caused by the way he called the function in xyplot, not by
>>> panel.Locfit itself, which I did not modify. I guess now the issue is
>>> how to generalize panel.Locfit somehow, but I am not sure how. I
>>> suspect the problem is not my understanding but that there really
>>> isn't any one specific problem here for the list to solve, though,
>>> again, I am known for misinterpreting OP requests... :)
>>>
> ?panel.locfit
>>>
>>>
>>> As I said, I am unfamiliar with the package - but this doesn't
>>> surprise me. Thank you for pointing it out, wish you've noticed the
>>> exchange sooner...
>>
>>
>> Another puzzle. In the original posting there was this segment:
>> ---
>> but gives an error message without par.settings if i want to add
>>                       panel.Locfit(x,y,nn= 0.9,lwd = c(1,2,3), ...)
>>
>> Error using packet 1
>> formal argument "Iwd" matched by multiple actual arguments
>> ---
>>
>> On my mailer that formal argument starts with a capital "I" but the
>> code seemed to be attempting a lowercase "l".
>>
>> I could never see reason offered for defining a new panel.locfit, but
>> I'm wondering if the sometimes similar representation of those two
>> different letters could be causing an obscure conflict?
>>
>> --
>> David.
>>>
>>>
>>> Cheers
>>>
>>>
> ?panel.Locfit

 No documentation for 'panel.Locfit' in specified packages and
 libraries:
 you could try '??panel.Locfit'

> ?panel.locfit


 {locfit}        R Documentation
 Locfit panel function

 Description

 This panel function can be used to add locfit fits to plots
 generated by
 trellis.



> I am trying to construct a function/s to cover as many of the normal
> situations as possible.
> Usually I have to amend colours lines etc to distinguish the data.
>
> I want to cover a number of situations
> 1 Conditioned by panel no groups
> 2 Conditioned by panel and groups.
> 3 Multiple values for above - to show colleagues (EDA)
> 4 Conditioned by panel and groups + an overall fit for all the
> data within
> a panel
> 5 Several y values in a panel eg Y1+Y2 and outer = FALSE with a
> fit for
> each of Y1 and Y2
>
> I am trying to cover as many of the above situations in 1 function
> before
> resulting to trellis.focus or
> overlaying. The graphs that I normally create are not simple,
> generally
> involving useOuterStrips
> which may have different y scales for panel rows (combindeLimits/
> manual)
> and different panel row heights.
>
> locfit is like loess but 2 arguments for smoothing; the degree of
> smoothing produced by the defaults
> is approximately that of loess but I normally need less smoothing
> (the
> same would be apply for loess).
>
> Most of the questions to Rhelp are for 1 with just a small number
> for 5
> and they are not applicable here
> and understanding the requirements for passing arguments in these
> different situations I find difficult.
> I would like to reduce the number of panel functions to the
> minimu

Re: [R] multi-machine parallel setup?

2012-04-20 Thread ivo welch

the vignette to the library(parallel) mentions snow repeatedly (esp
differences in its implementation in parallel from the original).
unfortunately, it doesn't give an example or tutorial for
multi-machine use with sockets.

could someone please point me to a simple working example, where a
master just has both itself and a 4-core slave on a second machine
(IP), and wants to execute an mclapply on a list on both machines,
like

   master.ip <- "localhost"
   slave.ip <- "Rfriend@192.168.2.10"  ## has key ssh access
   mclapply( 1:100, function(x) { cat(x); Sys.sleep(1); x } )  # on both, please

iaw

On Wed, Apr 18, 2012 at 1:01 PM, ivo welch  wrote:
> Dear R experts:
>
> could someone please point me to a page that explains how to set up
> more than 1 machine for library parallel (which is quickly becoming my
> favorite!)
...

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Re: [R] Fwd: User defined panel functions in lattice

2012-04-20 Thread ilai

On Fri, Apr 20, 2012 at 8:15 PM, David Winsemius  wrote:
>
> Another puzzle. In the original posting there was this segment:
> ---
>
> but gives an error message without par.settings if i want to add
>                       panel.Locfit(x,y,nn= 0.9,lwd = c(1,2,3), ...)
>
> Error using packet 1
> formal argument "Iwd" matched by multiple actual arguments
> ---
>
> On my mailer that formal argument starts with a capital "I" but the code
> seemed to be attempting a lowercase "l".
>
> I could never see reason offered for defining a new panel.locfit, but I'm
> wondering if the sometimes similar representation of those two different
> letters could be causing an obscure conflict?
>

If that is indeed what's happening, it will be the first time for me.
My mailer shows upper case "L" too, I assume that this is correct and
the OP's intention is exactly that - not redefine panel.locfit but
create his own (if that is good use of his/our time is another matter
altogether). Seems to me the source of this error was, as the error
message suggested, simply the "default" formals:

 panel.Locfit <-
 function(x,y, nn, h, col, col.line, lwd = lwd, lty = lty, ...){
...
}

Which is why this solved it:

  xyplot(y ~x,xx,
   groups = Farm,
   auto.key=TRUE,lwd=1:3,
   panel = panel.superpose,panel.groups=function(x,y,nn,...){
  panel.Locfit(x,y,nn=.9,...)
  panel.xyplot(x,y,...)
}
   )

With my new found understanding of the OP's real intentions, maybe a
call to trellis.par.get('superpose.line') inside panel.Locfit is the
answer?

Cheers

> --
> David.
>
>>
>> Cheers
>>
>>
 ?panel.Locfit
>>>
>>> No documentation for ‘panel.Locfit’ in specified packages and libraries:
>>> you could try ‘??panel.Locfit’
>>>
 ?panel.locfit
>>>
>>>
>>> {locfit}        R Documentation
>>> Locfit panel function
>>>
>>> Description
>>>
>>> This panel function can be used to add locfit fits to plots generated by
>>> trellis.
>>>
>>>
>>>
 I am trying to construct a function/s to cover as many of the normal
 situations as possible.
 Usually I have to amend colours lines etc to distinguish the data.

 I want to cover a number of situations
 1 Conditioned by panel no groups
 2 Conditioned by panel and groups.
 3 Multiple values for above - to show colleagues (EDA)
 4 Conditioned by panel and groups + an overall fit for all the data
 within
 a panel
 5 Several y values in a panel eg Y1+Y2 and outer = FALSE with a fit for
 each of Y1 and Y2

 I am trying to cover as many of the above situations in 1 function
 before
 resulting to trellis.focus or
 overlaying. The graphs that I normally create are not simple, generally
 involving useOuterStrips
 which may have different y scales for panel rows (combindeLimits/manual)
 and different panel row heights.

 locfit is like loess but 2 arguments for smoothing; the degree of
 smoothing produced by the defaults
 is approximately that of loess but I normally need less smoothing (the
 same would be apply for loess).

 Most of the questions to Rhelp are for 1 with just a small number for 5
 and they are not applicable here
 and understanding the requirements for passing arguments in these
 different situations I find difficult.
 I would like to reduce the number of panel functions to the minimum to
 cover the general situaltions because
 my graphs are usually not normal and then add to them for a particular
 situation.

 Regards

 Duncan

 At 01:38 21/04/2012, you wrote:
>
>
> Duncan,
> First off, I admit it is not clear to me what you are trying to
> achieve and more importantly, why? by "why" I mean 1) I don't see the
> advantage of writing one general panel function for completely
> different situations (one/multiple smoothers, grouping levels etc.) 2)
> your intended result as I understand it seems rather cluttered, google
> . 3) I am unfamiliar with locfit package, but are we
> reinventing the wheel here ? i.e. will modifying settings in xyplot(y
> ~x, xx, groups = Farm, type=c('p','smooth')) achieve the same ?
>
> With your initial reproducible example (thank you) it was easy to
> eliminate the errors, but clearly the resulting plots are not what you
> intended (continue inline):
>
> On Thu, Apr 19, 2012 at 4:23 PM, Duncan Mackay 
> wrote:
> 
>>
>> 3. What I want to be able to add in the above is extra lines with
>> different
>> values of nn.
>>  I think I will have to modify panel.Locfit so that it goes through
>> different values of nn in each of the panels and groups if I want
>> different
>> colours for extra lines with different nn values
>
>
> Yes you could. There are several options:
> add group.number to the arguments of panel.locfit and u

Re: [R] Splitting a dataframe by character vector

2012-04-20 Thread Rolf Turner

On 21/04/12 13:52, Ben Neal wrote:

I am just trying to split a dataframe of 750 observations of 29 variables by
"Site", which is a vector in the dataframe with five text names (ex.
PtaCaracol). I just want to generate summary statistics for my other variables for each
site individually.

I know this should be simple, and I did read up on options, choosing to use "subset", but
I am honestly confounded that this does not result in a new dataframe split by this factor. I tried
"subset" with an argument based on my various other numeric vectors, and it worked just
fine. My very simple code is below, and thank you for any responses. I apologize for asking such a
simple question, but I wrote this out exactly as found it in an exactly similar question, which
indicated this should work. Now I am confused! Thank you for any assistance. Ben Neal

# Load data from CSV file
Cover = read.csv ("/Users/benjaminneal/Documents/1110_Panama/Transect series
/1210_BocasTransectSummary.csv",
header=T)
# Divide dataframe by Site names
Site1<- subset(Cover, Site = "PtaCaracol")

PS The csv loads fine, gives normal summary stats, and does not seem to be the issue. I
thought about just renaming by hand all the sites in the file (i.e.
"PtaCaracol"=1 . . but this seems like a weak solution).

What about a ***reproducible*** example?

What isn't working? What (if any) error message did you get?

I am at least 99% confident that numeric versus character values in
Cover$Site

is completely irrelevant.

My ***guess*** (and it can only be a guess, given the vagueness and
lack of detail in your question) is that you need a double ("logical")
equals sign. I.e. I suspect that

Site1<- subset(Cover, Site == "PtaCaracol")

will work.

That being said --- since you want to *split* your data frame by "Site" ---
why the don't you use split()???

E.g.:

Splitz <- split(Cover,Cover$Site)

cheers,

Rolf Turner

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