date:20110918



On Sep 17, 2011, at 10:45 PM, Sandy Mitchell wrote:



Hello,


I have downloaded  graph package  from 
http://www.bioconductor.org/packages/release/bioc/html/graph.html

Is there anyone who can teach me how to install graph into R?



What happens when you follow the instructions on that page? (They are  
right at the top.)


--

David Winsemius, MD
West Hartford, CT

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Re: [R] calculating VAR of a (Gumbel) copula



On Sep 18, 2011, at 5:51 AM, Iva wrote:


Hello,

I am a new user of R (2.13.1), my operational system is Windows Vista.

I have a problem with the attached file SFEVaRHAC.r, calculating the  
VAR of
a Gumbel copula, based on the attached  
GumHAC_VaR_PL_w250_n1000_s2500.txt


1.  I had a Error in file(file, rt) : cannot open the connection  
message.
I solved it by reading a post in nabble to use setwd(choose.dir())   
and
read.table(file.choose()) and point the location of each file  
directly.


2. However, there is some other error - as I run the code now I get an
output:* Null Devise 1*

I am 100 % sure I have installed the used packages correctly and I  
don't

have any idea what is wrong.


Maybe nothing?



Could somebody help me with this issue?



Perhaps the procedure succeeded and you are misinterpreting the  
console message about the current active device (in your case the NULL  
device) and in my case R says this:

 dev.off()
quartz
 2

Have you checked you working directory to see what PL_VaR_Gumbel  
3D_0.05.pdf file looks like?


--
David.



Best,
Iva
http://r.789695.n4.nabble.com/file/n3821566/SFEVaRHAC.r SFEVaRHAC.r
http://r.789695.n4.nabble.com/file/n3821566/GumHAC_VaR_PL_w250_n1000_s2500.txt
GumHAC_VaR_PL_w250_n1000_s2500.txt


--
View this message in context: 
http://r.789695.n4.nabble.com/calculating-VAR-of-a-Gumbel-copula-tp3821566p3821566.html
Sent from the R help mailing list archive at Nabble.com.

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


David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
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Re: [R] Replacing matching values by related values



On Sep 18, 2011, at 3:56 AM, Janssen, K.J.M. wrote:


Thanks Michael.
I tested it and it works for numeric values, but not for the 'text'  
values that I am comparing, thus comparing a with a,b, etc.

Any advice how I can solve it?


Solve what? You never posted full working code and an explicit  
example. Unless there were actually objects named a, b, c, etc.  
in your workspace then the code that started out: v -  
c(f,a,e,d,m,  would not have been meaningful except to hint at the  
possibility that you might be comparing character vectors. I assumed  
that d[,2] was actually letters[1:17] rather than what you wrote. It's  
especially important to indicate whehte ryou have attached any objects.


Post dput(head(d)) and dput(v) for the example part and include any  
code use to construct them.


--
david.



Thanks!


-Oorspronkelijk bericht-
Van: R. Michael Weylandt michael.weyla...@gmail.com [mailto:michael.weyla...@gmail.com 
]

Verzonden: zo 18-9-2011 2:27
Aan: Janssen, K.J.M.
CC: r-help@r-project.org
Onderwerp: Re: [R] Replacing matching values by related values

Try playing with match(). Something like

d[match(v,d[,1]),2]

Should work (untested bc I'm writing from my phone though)

Michael Weylandt

On Sep 17, 2011, at 4:33 PM, Janssen, K.J.M. k.j.m.jans...@umcutrecht.nl 
 wrote:




I am trying to replace values of a vector (consisting of 15 values)  
by a value that is related to a matching value in a dataset  
(consisting of 17 rows).

Here's an example
The vector:
v - c(f,a,e,d,m,o,e,f,i,n,e,i,b,a,o)

The dataset's columns consist of the following values
d[,1] - c(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q)
d[,2] - 1:17

So I want to end up with a vector that consists of the values of  
the second colomn, when the value of the vector matches the value  
of the first colomn.

Thus, I aim to end up with a vector with the following values
c(6,1,5,4,13,15,5,6,9,14,5,9,2,1,15)

Help is appreciated!

--

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht  
onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de  
afzender direct
te informeren door het bericht te retourneren. Het Universitair  
Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin  
van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat  
geregistreerd bij

de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

--

This message may contain confidential information and is... 
{{dropped:12}}


__
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.


__
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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.


David Winsemius, MD
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.

[R] Removing a single element from an array

2011-09-18 Thread Dennis Fisher

R 2.13.1
OS X

Colleagues

I frequently encounter a situation in which I want to remove a single element 
of an array.  For example, if I am reading in a bunch of CSV files, I create 
the list of files to be read with:
LIST- dir()
However, sometimes I want to exclude one or more files.  I can accomplish this 
with a second command:
LIST- LIST[LIST != filename.to.be.excluded]
This is cumbersome -- is there some more efficient code to accomplish this?

Dennis


Dennis Fisher MD
P  (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com


[[alternative HTML version deleted]]

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

Re: [R] Replacing matching values by related values

2011-09-18 Thread Janssen, K.J.M.

Apologies, I wanted to make life easier by shortly describing my problem.
Indeed, it is better to post the full code.
I am not familiar with the dput, but I have pasted the code that I have used 
below.


d - matrix(NA,15,5)   
d - as.data.frame(d)  

colnames(d) - c(studynumber,t1,t2,t[,1],t[,2])

d$studynumber - c(1:15)# add study numbers to select studies 
in scenarios
d$t1 
-c(car_pac,car_pac,cis_vin,car_pac,cis_doc,cis_gem,cis_gem,cis_vin,car_pac,car_doc,car_pac,car_pac,car_doc.pac,cis_vin,cis_iri)
d$t2 
-c(gef,bev_car_pac,cet_cis_vin,gef,gef,bev_cis_gem,cis_pem,cet_cis_vin,car_gem_pac,car_pem,erl,cis_pac,cet_car_doc.pac,cis_doc,car_pac)

# Link treatment to relating treatment number: make vector of all unique 
treatment options
t1 - duplicated(c(d$t1,d$t2)) # returns TRUE and False, implying that we can 
need it so select
t2 - c(d$t1,d$t2) # combine both vectors, as treatments can be both reference 
as index treatment
t3 - na.omit(ifelse(t1==FALSE,c(d$t1,d$t2),NA))[1:nt] # omit double treatment

#make dataset with first colomn all possible treatments, and second colomn 
their respective numbers 
t.n - matrix(NA,17,2)  # list possible treatments (here 17), and link 
them to numbers
t.n - as.data.frame(t.n)
colnames(t.n) - c(treatment,numbers)
t.n$treatment - t3
t.n$numbers - 1:17

# link treatments in d with treatment numbers in dataset t.n

Here is where I aim to fill d$t[,1] and d$t[,2] with the corresrponding 
numbers from t.n

Thanks.

Kristel




-Oorspronkelijk bericht-
Van: David Winsemius [mailto:dwinsem...@comcast.net]
Verzonden: zo 18-9-2011 15:20
Aan: Janssen, K.J.M.
CC: michael.weyla...@gmail.com; r-help@r-project.org
Onderwerp: Re: [R] Replacing matching values by related values
 

On Sep 18, 2011, at 3:56 AM, Janssen, K.J.M. wrote:

 Thanks Michael.
 I tested it and it works for numeric values, but not for the 'text'  
 values that I am comparing, thus comparing a with a,b, etc.
 Any advice how I can solve it?

Solve what? You never posted full working code and an explicit  
example. Unless there were actually objects named a, b, c, etc.  
in your workspace then the code that started out: v -  
c(f,a,e,d,m,  would not have been meaningful except to hint at the  
possibility that you might be comparing character vectors. I assumed  
that d[,2] was actually letters[1:17] rather than what you wrote. It's  
especially important to indicate whehte ryou have attached any objects.

Post dput(head(d)) and dput(v) for the example part and include any  
code use to construct them.

-- 
david.


 Thanks!


 -Oorspronkelijk bericht-
 Van: R. Michael Weylandt michael.weyla...@gmail.com 
 [mailto:michael.weyla...@gmail.com 
 ]
 Verzonden: zo 18-9-2011 2:27
 Aan: Janssen, K.J.M.
 CC: r-help@r-project.org
 Onderwerp: Re: [R] Replacing matching values by related values

 Try playing with match(). Something like

 d[match(v,d[,1]),2]

 Should work (untested bc I'm writing from my phone though)

 Michael Weylandt

 On Sep 17, 2011, at 4:33 PM, Janssen, K.J.M. k.j.m.jans...@umcutrecht.nl 
  wrote:


 I am trying to replace values of a vector (consisting of 15 values)  
 by a value that is related to a matching value in a dataset  
 (consisting of 17 rows).
 Here's an example
 The vector:
 v - c(f,a,e,d,m,o,e,f,i,n,e,i,b,a,o)

 The dataset's columns consist of the following values
 d[,1] - c(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q)
 d[,2] - 1:17

 So I want to end up with a vector that consists of the values of  
 the second colomn, when the value of the vector matches the value  
 of the first colomn.
 Thus, I aim to end up with a vector with the following values
 c(6,1,5,4,13,15,5,6,9,14,5,9,2,1,15)

 Help is appreciated!

 --

 De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
 uitsluitend bestemd voor de geadresseerde. Indien u dit bericht  
 onterecht
 ontvangt, wordt u verzocht de inhoud niet te gebruiken en de  
 afzender direct
 te informeren door het bericht te retourneren. Het Universitair  
 Medisch
 Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin  
 van de W.H.W.
 (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat  
 geregistreerd bij
 de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

 Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

 --

 This message may contain confidential information and is... 
 {{dropped:12}}

 __
 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

Re: [R] Removing a single element from an array



On Sep 18, 2011, at 10:47 AM, Dennis Fisher wrote:


R 2.13.1
OS X

Colleagues

I frequently encounter a situation in which I want to remove a  
single element of an array.  For example, if I am reading in a bunch  
of CSV files, I create the list of files to be read with:

LIST- dir()
However, sometimes I want to exclude one or more files.  I can  
accomplish this with a second command:

LIST- LIST[LIST != filename.to.be.excluded]
This is cumbersome -- is there some more efficient code to  
accomplish this?


Doesn't negative indexing provide this?

?Extract

--

David Winsemius, MD
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] Alternatives to integrate?

2011-09-18 Thread . .

Hello all,

Returning to this question, I would like to ask for help on how to
integrate the PMF of a discrete distribution - Michael's guess about
the most immediate problem (Sep 01, 2011; 2:44pm).

I was thinking in two ways to do this: First is numerically integrate
the function but sampling it only at integer values. For this, I've
used the rectangle method of integration:

leftrect - function(f, from, to, n, ...) {
h - (to - from) / n
sum - 0
d - list(...)
for(i in seq(from, to-h, h)) {
dots - c(list(i), d)
sum - sum + do.call(f, dots)
}
return(h * sum)
}

Second option in my mind is to, find and replace the discrete function
by a continuous version, but I've no idea how to do this.

First option don't gave results as good. May another method ... ? Is
it possible to specify the sampling points in Integrate?

Any comments are welcome.

Thanks in advanve.


On Wed, Sep 7, 2011 at 4:47 AM, Berend Hasselman b...@xs4all.nl wrote:

 . wrote:

 Hi, continuing the improvements...

 I've prepared a new code:

 ddae - function(individuals, frac, sad, samp=pois, trunc=0, ...) {
   dots - list(...)
   Compound - function(individuals, frac, n.species, sad, samp, dots) {
     print(c(Size:, length(individuals), Compound individuals:,
 individuals, End.))
     RegDist - function(n.species, sad, dots) {  # RegDist may be
 Exponential, Gamma, etc.
       dcom - paste(d, as.name(sad), sep=)
       dots - as.list(c(n.species, dots))
       ans - do.call(dcom, dots)
       return(ans)
     }
     SampDist - function(individuals, frac, n.species, samp) {  #
 SampDist may be Poisson or Negative Binomial
       dcom - paste(d, samp, sep=)
       lambda - frac * n.species
       dots - as.list(c(individuals, lambda))
       ans - do.call(dcom, dots)
       return(ans)
     }
     ans - RegDist(n.species, sad, dots) * SampDist(individuals, frac,
 n.species, samp)
     return(ans)
   }
   IntegrateScheme - function(Compound, individuals, frac, sad, samp,
 dots) {
     print(c(Size:, length(individuals), Integrate individuals:,
 individuals))
     ans - integrate(Compound, 0, 2000, individuals, frac, sad, samp,
 dots)$value
     return(ans)
   }
   ans - IntegrateScheme(Compound, individuals, frac, sad, samp, dots)
   return(ans)
 }

 ddae(2, 0.05, exp)

 Now I can't understand what happen to individuals, why is it
 changing in value and size? I've tried to traceback() and debug(),
 but I was not smart enough to understand what is going on.

 Could you, please, give some more help?


 From the help for integrate argument f :

 an R function taking a numeric first argument and returning a numeric vector
 of the same length. .

 Function Compound is passed to integrate. First argument is individuals
 and integrate is integrating over individuals. That is why it is changing in
 value and size: integrate is only doing what you asked it do.

 The code is too uncommented and convoluted to supply further comments.
 You really should simplify this

 Berend


 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Alternatives-to-integrate-tp3783624p3795491.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.

Re: [R] Removing a single element from an array



On Sep 18, 2011, at 11:10 AM, David Winsemius wrote:



On Sep 18, 2011, at 10:47 AM, Dennis Fisher wrote:


R 2.13.1
OS X

Colleagues

I frequently encounter a situation in which I want to remove a  
single element of an array.  For example, if I am reading in a  
bunch of CSV files, I create the list of files to be read with:

LIST- dir()
However, sometimes I want to exclude one or more files.  I can  
accomplish this with a second command:

LIST- LIST[LIST != filename.to.be.excluded]
This is cumbersome -- is there some more efficient code to  
accomplish this?


Doesn't negative indexing provide this?

?Extract


The most general way to convert character vectors to numbers for this  
purpose is with grep which therefore supports regex patterns:


LIST - dir(path=~/)
 length(LIST)
[1] 551
 LIST[1]
[1] _train_1.dat

 LIST - LIST[ -grep(_train_1.dat, LIST) ]

 length(LIST)
[1] 550

Patterns can also be used in the dir() call.

--

David Winsemius, MD
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.

Re: [R] Replacing matching values by related values

2011-09-18 Thread Justin Haynes

in your assignment for t3 you use nt which is undefined.  thus t.n$treatment
is NAs

but:

df-data.frame(num=1:10,let=letters[1:10])
dat-data.frame(let=sample(letters[1:10],20,replace=T))

dat$matched-df$num[match(dat$let,df$let)]

should get you started


On Sun, Sep 18, 2011 at 7:56 AM, Janssen, K.J.M. 
k.j.m.jans...@umcutrecht.nl wrote:

 Apologies, I wanted to make life easier by shortly describing my problem.
 Indeed, it is better to post the full code.
 I am not familiar with the dput, but I have pasted the code that I have
 used below.


 d - matrix(NA,15,5)
 d - as.data.frame(d)

 colnames(d) - c(studynumber,t1,t2,t[,1],t[,2])

 d$studynumber - c(1:15)# add study numbers to select
 studies in scenarios
 d$t1
 -c(car_pac,car_pac,cis_vin,car_pac,cis_doc,cis_gem,cis_gem,cis_vin,car_pac,car_doc,car_pac,car_pac,car_doc.pac,cis_vin,cis_iri)
 d$t2
 -c(gef,bev_car_pac,cet_cis_vin,gef,gef,bev_cis_gem,cis_pem,cet_cis_vin,car_gem_pac,car_pem,erl,cis_pac,cet_car_doc.pac,cis_doc,car_pac)

 # Link treatment to relating treatment number: make vector of all unique
 treatment options
 t1 - duplicated(c(d$t1,d$t2)) # returns TRUE and False, implying that we
 can need it so select
 t2 - c(d$t1,d$t2) # combine both vectors, as treatments can be both
 reference as index treatment
 t3 - na.omit(ifelse(t1==FALSE,c(d$t1,d$t2),NA))[1:nt] # omit double
 treatment

 #make dataset with first colomn all possible treatments, and second colomn
 their respective numbers
 t.n - matrix(NA,17,2)  # list possible treatments (here 17), and
 link them to numbers
 t.n - as.data.frame(t.n)
 colnames(t.n) - c(treatment,numbers)
 t.n$treatment - t3
 t.n$numbers - 1:17

 # link treatments in d with treatment numbers in dataset t.n

 Here is where I aim to fill d$t[,1] and d$t[,2] with the corresrponding
 numbers from t.n

 Thanks.

 Kristel




 -Oorspronkelijk bericht-
 Van: David Winsemius [mailto:dwinsem...@comcast.net]
 Verzonden: zo 18-9-2011 15:20
 Aan: Janssen, K.J.M.
 CC: michael.weyla...@gmail.com; r-help@r-project.org
 Onderwerp: Re: [R] Replacing matching values by related values


 On Sep 18, 2011, at 3:56 AM, Janssen, K.J.M. wrote:

  Thanks Michael.
  I tested it and it works for numeric values, but not for the 'text'
  values that I am comparing, thus comparing a with a,b, etc.
  Any advice how I can solve it?

 Solve what? You never posted full working code and an explicit
 example. Unless there were actually objects named a, b, c, etc.
 in your workspace then the code that started out: v -
 c(f,a,e,d,m,  would not have been meaningful except to hint at the
 possibility that you might be comparing character vectors. I assumed
 that d[,2] was actually letters[1:17] rather than what you wrote. It's
 especially important to indicate whehte ryou have attached any objects.

 Post dput(head(d)) and dput(v) for the example part and include any
 code use to construct them.

 --
 david.

 
  Thanks!
 
 
  -Oorspronkelijk bericht-
  Van: R. Michael Weylandt michael.weyla...@gmail.com [mailto:
 michael.weyla...@gmail.com
  ]
  Verzonden: zo 18-9-2011 2:27
  Aan: Janssen, K.J.M.
  CC: r-help@r-project.org
  Onderwerp: Re: [R] Replacing matching values by related values
 
  Try playing with match(). Something like
 
  d[match(v,d[,1]),2]
 
  Should work (untested bc I'm writing from my phone though)
 
  Michael Weylandt
 
  On Sep 17, 2011, at 4:33 PM, Janssen, K.J.M. 
 k.j.m.jans...@umcutrecht.nl
   wrote:
 
 
  I am trying to replace values of a vector (consisting of 15 values)
  by a value that is related to a matching value in a dataset
  (consisting of 17 rows).
  Here's an example
  The vector:
  v - c(f,a,e,d,m,o,e,f,i,n,e,i,b,a,o)
 
  The dataset's columns consist of the following values
  d[,1] - c(a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q)
  d[,2] - 1:17
 
  So I want to end up with a vector that consists of the values of
  the second colomn, when the value of the vector matches the value
  of the first colomn.
  Thus, I aim to end up with a vector with the following values
  c(6,1,5,4,13,15,5,6,9,14,5,9,2,1,15)
 
  Help is appreciated!
 
 
 --
 
  De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
  uitsluitend bestemd voor de geadresseerde. Indien u dit bericht
  onterecht
  ontvangt, wordt u verzocht de inhoud niet te gebruiken en de
  afzender direct
  te informeren door het bericht te retourneren. Het Universitair
  Medisch
  Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin
  van de W.H.W.
  (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat
  geregistreerd bij
  de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
 
  Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
 
 
 --
 
  This message may contain confidential information and is...
  {{dropped:12}}

Re: [R] Extracting a a chunk of text from a pdf file

2011-09-18 Thread Victor

Unfortunately pdf2text doesn't seem to exist either in linux or mac osx.
Ciao Vittorio

Il giorno 17/set/2011, alle ore 21:00, Jeff Newmiller ha scritto:

 Doesn't seen like an R task, but see pdf2text? (From pdftools, UNIX command 
 line tools)
 ---
 Jeff Newmiller The . . Go Live...
 DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
 Live: OO#.. Dead: OO#.. Playing
 Research Engineer (Solar/Batteries O.O#. #.O#. with
 /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
 --- 
 Sent from my phone. Please excuse my brevity.
 
 Victor vdem...@gmail.com wrote:
 In an R script I need to extract some  figures from  many web pages in pdf 
 format. As an example see 
 http://www.terna.it/LinkClick.aspx?fileticket=TTQuOPUf%2fs0%3damp;tabid=435amp;mid=3072
  from which I would like to extract the Totale: 1,025,823).
 Is there any solution?
 Ciao
 Vittorio
 
 
 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]]

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

[R] troubles with a for loop

2011-09-18 Thread Francesco Sarracino

Dear all,

I am a stata user and I am moving my first steps in R.
I am dealing with a silly issue concerning looping over variables. I read
previous posts on similar topics in the R help archive, but I did not find a
solution.
Here is my case:

I run a simple bivariate linear regression saving the output in objects
called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3

pd.memb.0 - lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
pd.memb.1 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb =
quantile(M.fs.memb, .25)  tag2 == 1))
pd.memb.2 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb 
quantile(M.fs.memb, .25)  M.fs.memb = quantile(M.fs.memb, .75)  tag2 ==
1))
pd.memb.3 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb 
quantile(M.fs.memb, .75)  tag2 == 1))

Subsequently, I wish to plot my data superimposing a different line for each
regression model. Here I am trying to apply my loop. Looking at the info I
found around, the following code sound to me as correct, but I am wrong.

plot(M.fs.memb , E.fs.memb)
for(i =  1:3){
  curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100, col =
red)
}

The plot is plotted, but the curves are not printed and  I get the following
error message:


Error in coef(pd.memb.i) :
  error in evaluating the argument 'object' in selecting a method for
function 'coef' }Error: unexpected '}' in }


What am I doing wrong?
Thanks a lot for your help,
f.

[[alternative HTML version deleted]]

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

Re: [R] Extracting a a chunk of text from a pdf file

2011-09-18 Thread Joshua Wiley

On Sun, Sep 18, 2011 at 7:44 AM, Victor vdem...@gmail.com wrote:
 Unfortunately pdf2text doesn't seem to exist either in linux or mac osx.

I think Jeff's main point was to search for software specific for your
task (convert a pdf to text).  Formatting will be lost so once you get
your text files, I would look at regular expressions to try to find
the right part of text to grab.  Some general functions that seem like
they might be relevant:

## for getting the text into R
?readLines
?scan
## for finding the part you need
?regexp
?grep

Cheers,

Josh


 Ciao Vittorio

 Il giorno 17/set/2011, alle ore 21:00, Jeff Newmiller ha scritto:

 Doesn't seen like an R task, but see pdf2text? (From pdftools, UNIX command 
 line tools)
 ---
 Jeff Newmiller The . . Go Live...
 DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
 Live: OO#.. Dead: OO#.. Playing
 Research Engineer (Solar/Batteries O.O#. #.O#. with
 /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
 ---
 Sent from my phone. Please excuse my brevity.

 Victor vdem...@gmail.com wrote:
 In an R script I need to extract some  figures from  many web pages in pdf 
 format. As an example see 
 http://www.terna.it/LinkClick.aspx?fileticket=TTQuOPUf%2fs0%3damp;tabid=435amp;mid=3072
  from which I would like to extract the Totale: 1,025,823).
 Is there any solution?
 Ciao
 Vittorio


 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.




-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.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] troubles with a for loop

2011-09-18 Thread Sarah Goslee

You don't have a variable named pd.memb.i

Instead, you need something like:
get(paste(pd.memb., i, sep=))

The error message you're getting, though, is because your
loop syntax is wrong:
for(i in 1:3) {
 do something
}

Sarah

On Sun, Sep 18, 2011 at 12:05 PM, Francesco Sarracino
f.sarrac...@gmail.com wrote:
 Dear all,

 I am a stata user and I am moving my first steps in R.
 I am dealing with a silly issue concerning looping over variables. I read
 previous posts on similar topics in the R help archive, but I did not find a
 solution.
 Here is my case:

 I run a simple bivariate linear regression saving the output in objects
 called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3

 pd.memb.0 - lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
 pd.memb.1 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb =
 quantile(M.fs.memb, .25)  tag2 == 1))
 pd.memb.2 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb 
 quantile(M.fs.memb, .25)  M.fs.memb = quantile(M.fs.memb, .75)  tag2 ==
 1))
 pd.memb.3 - lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb 
 quantile(M.fs.memb, .75)  tag2 == 1))

 Subsequently, I wish to plot my data superimposing a different line for each
 regression model. Here I am trying to apply my loop. Looking at the info I
 found around, the following code sound to me as correct, but I am wrong.

 plot(M.fs.memb , E.fs.memb)
 for(i =  1:3){
  curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100, col =
 red)
 }

 The plot is plotted, but the curves are not printed and  I get the following
 error message:


 Error in coef(pd.memb.i) :
  error in evaluating the argument 'object' in selecting a method for
 function 'coef' }Error: unexpected '}' in }


 What am I doing wrong?
 Thanks a lot for your help,
 f.

        [[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.




-- 
Sarah Goslee
http://www.functionaldiversity.org

__
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] Tobit Fixed Effects

2011-09-18 Thread Felipe Nunes

Thanks!

*Felipe Nunes*
CAPES/Fulbright Fellow
PhD Student Political Science - UCLA
Web: felipenunes.bol.ucla.edu



On Sun, Sep 18, 2011 at 2:19 AM, Arne Henningsen 
arne.henning...@googlemail.com wrote:

 Hi Felipe

 On 18 September 2011 09:09, Felipe Nunes felipnu...@gmail.com wrote:
  Thanks, Arne!
  But I'm having another problem now. When I transform my data into a
  pdata.frame form and try to run a tobit model with random effects I get
 an
  error. Below I provide the head of my data, the code I used and the error
  message. Any help?
  head(pdata)
 X   X.1 year mun.cod uf.cod uf.name
   mun.name   uf.mun
  ACACRELANDIA-2003  ACACRELANDIA-2003 1 2003 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
  ACACRELANDIA-2004CEIBIAPINA-2003  5561 2004 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
  ACACRELANDIA-2005 MGARACUAI-2007 11121 2005 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
  ACACRELANDIA-2006 MGSAO GERALDO-2006 16681 2006 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
  ACACRELANDIA-2007 PBSERTAOZINHO-2005 22241 2007 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
  ACACRELANDIA-2008PRPIEN-2008 27801 2008 1200013 12  AC
  ACRELANDIA  ACACRELANDIA
transfers populat agric.pib indust.pib servic.pib
  apu.pib
   tax.pib   pib
  ACACRELANDIA-2003   9208695  31744.92   5292.439   26942.19
 15955.14
  4527.178  68506.73
  ACACRELANDIA-2004 0   10668  48947.97   9353.529   33134.56
 19922.54
  5825.801  97261.86
  ACACRELANDIA-2005 49287   11451  56291.90  11214.051   39326.32
 23340.46
  7661.003 114493.30
  ACACRELANDIA-2006385000   11786  55290.26  11976.119   46405.99
 27401.64
  7730.059 121402.40
  ACACRELANDIA-2007   1599730   11520  68478.03  15526.679   54555.67
 31382.93
  7550.055 146110.40
  ACACRELANDIA-2008   1295000   11987  61736.50  12812.245   63688.96
 37518.87
  7824.615 146062.30
bol.fam  ifdm mayor.party mayor.num
mayor.name mayor.vot
  ACACRELANDIA-2003   0 0.4225000PSDB45 SEBASTI\xeaO
  BOCALOM RODRIGUES  2394
  ACACRELANDIA-2004 402 0.3943083PSDB45 SEBASTI\xeaO
  BOCALOM RODRIGUES  2394
  ACACRELANDIA-2005 742 0.5401000PSDB45 SEBASTI\xcdO
  BOCALOM RODRIGUES  2173
  ACACRELANDIA-2006 779 0.5138000PSDB45 SEBASTI\xcdO
  BOCALOM RODRIGUES  2173
  ACACRELANDIA-2007 932 0.5109000PSDB45 SEBASTI\xcdO
  BOCALOM RODRIGUES  2173
  ACACRELANDIA-2008 968 0.5593250PSDB45 SEBASTI\xcdO
  BOCALOM RODRIGUES  2173
mayor.vot.per
   mayor.coalt voters.able
  ACACRELANDIA-20030.5901 PSDB / PT / PC do B / PV / PMN / PSB /
 PPS /
  PDT6422
  ACACRELANDIA-20040.5901 PSDB / PT / PC do B / PV / PMN / PSB /
 PPS /
  PDT6422
  ACACRELANDIA-20050.4082   PP / PDT / PMDB / PPS / PFL
 /
  PSDB6422
  ACACRELANDIA-20060.4082   PP / PDT / PMDB / PPS / PFL
 /
  PSDB6422
  ACACRELANDIA-20070.4082   PP / PDT / PMDB / PPS / PFL
 /
  PSDB7548
  ACACRELANDIA-20080.4082   PP / PDT / PMDB / PPS / PFL
 /
  PSDB7548
presd.turnout lula.vot lula.vot.per transfers.cap
 pt.dummy
  pres.turnout.cap
  ACACRELANDIA-2003  4282 2202  0.51425 0.1058079
  0
 0.4924669
  ACACRELANDIA-2004  4282 2202  0.51425 0.000
  0
 0.4013873
  ACACRELANDIA-2005  4282 2202  0.51425 4.3041656
  0
 0.3739411
  ACACRELANDIA-2006  4282 2202  0.5142532.6658748
  0
 0.3633124
  ACACRELANDIA-2007  5461 2422  0.44400   138.8654514
  0
 0.4740451
  ACACRELANDIA-2008  5461 2422  0.44400   108.0337032
  0
 0.4555769
  pib.cap mun.vote mun.vote2 mun.vote3 mayor.party.r
  mayor.party.r2 lula.vot.weight
  ACACRELANDIA-2003  7.8788651PT  0.PT 0
  2.Opposition5.084315e-06
  ACACRELANDIA-2004  9.1171601PT  0.PT 0
  2.Opposition5.084315e-06
  ACACRELANDIA-2005  9.9985421PT  0.PT 0
  2.Opposition5.084315e-06
  ACACRELANDIA-2006 10.3005601PT  0.PT 0
  2.Opposition5.084315e-06
  ACACRELANDIA-2007 12.6831940  PSDB1.PSDB 0
  2.Opposition5.592285e-06
  ACACRELANDIA-2008 12.1850590  PSDB1.PSDB 0
  2.Opposition5.592285e-06
trans.dummy transfers.cap.lag year2 district term
  pt.pt pt.coa pt.opp psdb.pt
  ACACRELANDIA-2003   1NA 2003-2004   PT/Opo0
  0  0  1   0
  ACACRELANDIA-2004   0NA 2003-2004   PT/Opo0
  0  0

Re: [R] troubles with a for loop

2011-09-18 Thread Patrick Burns


Sarah has told you how to get from where
you are to where you want to be.

However, it is easier to start somewhere
else.  The more R way to do what you are
doing is to use a list to put the results
of your regressions into.  It is then very
easy to use that list, and it is easier to
keep track of.

The two documents mentioned in my signature
may help you get up and running in R.  Since
you are coming from Stata, you should also
look at http://r4stats.com

On 18/09/2011 17:05, Francesco Sarracino wrote:

Dear all,

I am a stata user and I am moving my first steps in R.
I am dealing with a silly issue concerning looping over variables. I read
previous posts on similar topics in the R help archive, but I did not find a
solution.
Here is my case:

I run a simple bivariate linear regression saving the output in objects
called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3

pd.memb.0- lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
pd.memb.1- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb=
quantile(M.fs.memb, .25)  tag2 == 1))
pd.memb.2- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
quantile(M.fs.memb, .25)  M.fs.memb= quantile(M.fs.memb, .75)  tag2 ==
1))
pd.memb.3- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
quantile(M.fs.memb, .75)  tag2 == 1))

Subsequently, I wish to plot my data superimposing a different line for each
regression model. Here I am trying to apply my loop. Looking at the info I
found around, the following code sound to me as correct, but I am wrong.

plot(M.fs.memb , E.fs.memb)
for(i =  1:3){
   curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100, col =
red)
}

The plot is plotted, but the curves are not printed and  I get the following
error message:


Error in coef(pd.memb.i) :
   error in evaluating the argument 'object' in selecting a method for
function 'coef'  }Error: unexpected '}' in }


What am I doing wrong?
Thanks a lot for your help,
f.

[[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.



--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')

__
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] troubles with a for loop

2011-09-18 Thread R. Michael Weylandt

Furthermore, if you want to add lines to a plot, I'd advise against the
curve() function, rather use lines() to add lines (or points() for, well,
points) on a plot.

E.g.,

x - seq(0,10,by=0.025)
y - sin(x)
y2 - cos(x)

plot(x,y,type=l,col=red4,lwd=3)
lines(x,y2)

curve() wouldn't work for this

Michael

On Sun, Sep 18, 2011 at 1:23 PM, Patrick Burns pbu...@pburns.seanet.comwrote:

 Sarah has told you how to get from where
 you are to where you want to be.

 However, it is easier to start somewhere
 else.  The more R way to do what you are
 doing is to use a list to put the results
 of your regressions into.  It is then very
 easy to use that list, and it is easier to
 keep track of.

 The two documents mentioned in my signature
 may help you get up and running in R.  Since
 you are coming from Stata, you should also
 look at http://r4stats.com


 On 18/09/2011 17:05, Francesco Sarracino wrote:

 Dear all,

 I am a stata user and I am moving my first steps in R.
 I am dealing with a silly issue concerning looping over variables. I read
 previous posts on similar topics in the R help archive, but I did not find
 a
 solution.
 Here is my case:

 I run a simple bivariate linear regression saving the output in objects
 called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3

 pd.memb.0- lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
 pd.memb.1- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb=
 quantile(M.fs.memb, .25)  tag2 == 1))
 pd.memb.2- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
 quantile(M.fs.memb, .25)  M.fs.memb= quantile(M.fs.memb, .75)  tag2 ==
 1))
 pd.memb.3- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
 quantile(M.fs.memb, .75)  tag2 == 1))

 Subsequently, I wish to plot my data superimposing a different line for
 each
 regression model. Here I am trying to apply my loop. Looking at the info I
 found around, the following code sound to me as correct, but I am wrong.

 plot(M.fs.memb , E.fs.memb)
 for(i =  1:3){
   curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100, col
 =
 red)
 }

 The plot is plotted, but the curves are not printed and  I get the
 following
 error message:


 Error in coef(pd.memb.i) :
   error in evaluating the argument 'object' in selecting a method for
 function 'coef'  }Error: unexpected '}' in }


 What am I doing wrong?
 Thanks a lot for your help,
 f.

[[alternative HTML version deleted]]

 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://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.


 --
 Patrick Burns
 pbu...@pburns.seanet.com
 twitter: @portfolioprobe
 http://www.portfolioprobe.com/**blog http://www.portfolioprobe.com/blog
 http://www.burns-stat.com
 (home of 'Some hints for the R beginner'
 and 'The R Inferno')


 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://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.

Re: [R] calculating VAR of a (Gumbel) copula

2011-09-18 Thread Ivette

Yes, David, you are right - I have misinterpreted the result. The.pdf is the
exact output and the algorithm is working.

Many thanks!

Ivette

--
View this message in context: 
http://r.789695.n4.nabble.com/calculating-VAR-of-a-Gumbel-copula-tp3821566p3822196.html
Sent from the R help mailing list archive at Nabble.com.

__
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] Extracting a a chunk of text from a pdf file

2011-09-18 Thread Victor

That's exactly the way I work. Here you are a chunk of text of my script. 
To put it in a nutshell I'm  already  extracting - by means of grep and gsub 
from indweb (luckily an html file)  - the web addresses 
like  
http://www.terna.it/LinkClick.aspx?fileticket=TTQuOPUf%2fs0%3damp;tabid=435amp;mid=3072
 and the likes, pdf files (unfortunately for me).
That's why I need to translate the pdf into a txt file.
 
Ciao
Vittorio

==
indweb-http://www.terna.it/default/Home/SISTEMA_ELETTRICO/dispacciamento/dati_esercizio/dati_giornalieri/confronto.aspx;
testo-readLines(indweb)


k-grep(^(.)+dnn_ctr3072_DocumentTerna_grdDocuments_(.)+CategoryCell\(\\d\\d)/(\\d\\d)/201(\\d),testo)
n-length(k)
# Poichè le date sono in ordine decrescente, ordina in ordine crescente
k-k[order(k,decreasing=TRUE)]

for (i in 1:length(k) ) {


data-gsub(^(.)+dnn_ctr3072_DocumentTerna_grdDocuments_(.)+CategoryCell\,,testo[k[1]])
data-paste(substr(data,7,10), substr(data,4,5), substr(data,1,2), 
sep=-)
mysel-paste(select count(*) from richiesta where 
data=\,data,\;,sep=)
dataesiste-as.integer(dbGetQuery(con,mysel))

if (dataesiste == 0) {

rif-gsub(\Confronto Giornaliero(.)+,,testo[k[30]])
rif-gsub(^(.)+href=\,,rif)
pag-paste(http://www.terna.it,rif,sep=;)
pagina-readLines(pag)
……….
……….
……….

Il giorno 18/set/2011, alle ore 18:25, Joshua Wiley ha scritto:

 On Sun, Sep 18, 2011 at 7:44 AM, Victor vdem...@gmail.com wrote:
 Unfortunately pdf2text doesn't seem to exist either in linux or mac osx.
 
 I think Jeff's main point was to search for software specific for your
 task (convert a pdf to text).  Formatting will be lost so once you get
 your text files, I would look at regular expressions to try to find
 the right part of text to grab.  Some general functions that seem like
 they might be relevant:
 
 ## for getting the text into R
 ?readLines
 ?scan
 ## for finding the part you need
 ?regexp
 ?grep
 
 Cheers,
 
 Josh
 
 
 Ciao Vittorio
 
 Il giorno 17/set/2011, alle ore 21:00, Jeff Newmiller ha scritto:
 
 Doesn't seen like an R task, but see pdf2text? (From pdftools, UNIX command 
 line tools)
 ---
 Jeff Newmiller The . . Go Live...
 DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
 Live: OO#.. Dead: OO#.. Playing
 Research Engineer (Solar/Batteries O.O#. #.O#. with
 /Software/Embedded Controllers) .OO#. .OO#. rocks...1k
 ---
 Sent from my phone. Please excuse my brevity.
 
 Victor vdem...@gmail.com wrote:
 In an R script I need to extract some  figures from  many web pages in pdf 
 format. As an example see 
 http://www.terna.it/LinkClick.aspx?fileticket=TTQuOPUf%2fs0%3damp;tabid=435amp;mid=3072
  from which I would like to extract the Totale: 1,025,823).
 Is there any solution?
 Ciao
 Vittorio
 
 
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 Programmer Analyst II, ATS Statistical Consulting Group
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[R] R-Help

2011-09-18 Thread Gastón

Hi, my name is Gastón. I just read a question, made by Walter Durka, about a
nonparametric discriminant analysis. It wasn´t any answer, and I was
wondering if at this moment there is one. I have the same problem as W.
Durka.  I´m trying to classify and to cross-validate samples of three
tunicates species based on morphometric data and to identify the variables
that best discriminate between species.
Thanks for help.

Kind regards!

Gaston Alurralde
-- 
*[ GASTÓN ]*
*
*

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Re: [R] R-Help

2011-09-18 Thread Bert Gunter

Gaston:

There are many ways to do this, but I think this is mostly a question about
statistics, not about R. Once you have decided *what* you want to do, then
you can search in R for tools to do it. So I would suggest you post your
question on a statistics site, like http://stats.stackexchange.com/  .
Better yet by far is to collaborate with a local statistician.

Cheers,
Bert

On Sun, Sep 18, 2011 at 11:25 AM, Gastón mitocondriareve...@gmail.comwrote:

 Hi, my name is Gastón. I just read a question, made by Walter Durka, about
 a
 nonparametric discriminant analysis. It wasn´t any answer, and I was
 wondering if at this moment there is one. I have the same problem as W.
 Durka.  I´m trying to classify and to cross-validate samples of three
 tunicates species based on morphometric data and to identify the variables
 that best discriminate between species.
 Thanks for help.

 Kind regards!

 Gaston Alurralde
 --
 *[ GASTÓN ]*
 *
 *

[[alternative HTML version deleted]]


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-- 
Men by nature long to get on to the ultimate truths, and will often be
impatient with elementary studies or fight shy of them. If it were possible
to reach the ultimate truths without the elementary studies usually prefixed
to them, these would not be preparatory studies but superfluous diversions.

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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Re: [R] troubles with a for loop

2011-09-18 Thread Jorge I Velez

Why wouldn't?  It does for me ;-)

curve(sin(x), 0, 10, col = 4, lwd = 2, las = 1)
curve(cos(x), 0, 10, add = TRUE)

Best,
Jorge


On Sun, Sep 18, 2011 at 2:07 PM, R. Michael Weylandt  wrote:

 Furthermore, if you want to add lines to a plot, I'd advise against the
 curve() function, rather use lines() to add lines (or points() for, well,
 points) on a plot.

 E.g.,

 x - seq(0,10,by=0.025)
 y - sin(x)
 y2 - cos(x)

 plot(x,y,type=l,col=red4,lwd=3)
 lines(x,y2)

 curve() wouldn't work for this

 Michael

 On Sun, Sep 18, 2011 at 1:23 PM, Patrick Burns wrote:

  Sarah has told you how to get from where
  you are to where you want to be.
 
  However, it is easier to start somewhere
  else.  The more R way to do what you are
  doing is to use a list to put the results
  of your regressions into.  It is then very
  easy to use that list, and it is easier to
  keep track of.
 
  The two documents mentioned in my signature
  may help you get up and running in R.  Since
  you are coming from Stata, you should also
  look at http://r4stats.com
 
 
  On 18/09/2011 17:05, Francesco Sarracino wrote:
 
  Dear all,
 
  I am a stata user and I am moving my first steps in R.
  I am dealing with a silly issue concerning looping over variables. I
 read
  previous posts on similar topics in the R help archive, but I did not
 find
  a
  solution.
  Here is my case:
 
  I run a simple bivariate linear regression saving the output in objects
  called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3
 
  pd.memb.0- lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
  pd.memb.1- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb=
  quantile(M.fs.memb, .25)  tag2 == 1))
  pd.memb.2- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
  quantile(M.fs.memb, .25)  M.fs.memb= quantile(M.fs.memb, .75)  tag2
 ==
  1))
  pd.memb.3- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
  quantile(M.fs.memb, .75)  tag2 == 1))
 
  Subsequently, I wish to plot my data superimposing a different line for
  each
  regression model. Here I am trying to apply my loop. Looking at the info
 I
  found around, the following code sound to me as correct, but I am wrong.
 
  plot(M.fs.memb , E.fs.memb)
  for(i =  1:3){
curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100,
 col
  =
  red)
  }
 
  The plot is plotted, but the curves are not printed and  I get the
  following
  error message:
 
 
  Error in coef(pd.memb.i) :
error in evaluating the argument 'object' in selecting a method for
  function 'coef'  }Error: unexpected '}' in }
 
 
  What am I doing wrong?
  Thanks a lot for your help,
  f.
 
 [[alternative HTML version deleted]]
 
  __**
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  https://stat.ethz.ch/mailman/**listinfo/r-help
 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.
 
 
  --
  Patrick Burns
  pbu...@pburns.seanet.com
  twitter: @portfolioprobe
  http://www.portfolioprobe.com/**blog http://www.portfolioprobe.com/blog
 
  http://www.burns-stat.com
  (home of 'Some hints for the R beginner'
  and 'The R Inferno')
 
 
  __**
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  https://stat.ethz.ch/mailman/**listinfo/r-help
 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.
 

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Re: [R] Could R run Cox proportional hazard model with multiple failure time data

2011-09-18 Thread Frank Harrell

You sent that question to me individually as well as posting to the group. 
Kindly pick the most appropriate place and send to only that.
Frank

-
Frank Harrell
Department of Biostatistics, Vanderbilt University
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Re: [R] troubles with a for loop

2011-09-18 Thread Francesco Sarracino

Wow,
thanks a lot for your quick replies and useful comments.
Indeed, Sarah's advice does the job perfectly.
I wish to thank you all also for your advices on how to shift from a Stata
mindset to  an R one (which is currently my main obstacle).
Best,
f.

On 18 September 2011 20:07, R. Michael Weylandt
michael.weyla...@gmail.comwrote:

 Furthermore, if you want to add lines to a plot, I'd advise against the
 curve() function, rather use lines() to add lines (or points() for, well,
 points) on a plot.

 E.g.,

 x - seq(0,10,by=0.025)
 y - sin(x)
 y2 - cos(x)

 plot(x,y,type=l,col=red4,lwd=3)
 lines(x,y2)

 curve() wouldn't work for this

 Michael

 On Sun, Sep 18, 2011 at 1:23 PM, Patrick Burns 
 pbu...@pburns.seanet.comwrote:

 Sarah has told you how to get from where
 you are to where you want to be.

 However, it is easier to start somewhere
 else.  The more R way to do what you are
 doing is to use a list to put the results
 of your regressions into.  It is then very
 easy to use that list, and it is easier to
 keep track of.

 The two documents mentioned in my signature
 may help you get up and running in R.  Since
 you are coming from Stata, you should also
 look at http://r4stats.com


 On 18/09/2011 17:05, Francesco Sarracino wrote:

 Dear all,

 I am a stata user and I am moving my first steps in R.
 I am dealing with a silly issue concerning looping over variables. I read
 previous posts on similar topics in the R help archive, but I did not
 find a
 solution.
 Here is my case:

 I run a simple bivariate linear regression saving the output in objects
 called: pd.memb.0, pd.memb.1, pd.memb.2, pd.memb.3

 pd.memb.0- lm(E.fs.memb ~ M.fs.memb, data, subset = (tag2 == 1))
 pd.memb.1- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb=
 quantile(M.fs.memb, .25)  tag2 == 1))
 pd.memb.2- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
 quantile(M.fs.memb, .25)  M.fs.memb= quantile(M.fs.memb, .75)  tag2 ==
 1))
 pd.memb.3- lm(E.fs.memb ~ M.fs.memb, data, subset = (M.fs.memb
 quantile(M.fs.memb, .75)  tag2 == 1))

 Subsequently, I wish to plot my data superimposing a different line for
 each
 regression model. Here I am trying to apply my loop. Looking at the info
 I
 found around, the following code sound to me as correct, but I am wrong.

 plot(M.fs.memb , E.fs.memb)
 for(i =  1:3){
   curve(coef(pd.memb.i)[1] + coef(pd.memb.i)[2]*x, add = T, cex = 100,
 col =
 red)
 }

 The plot is plotted, but the curves are not printed and  I get the
 following
 error message:


 Error in coef(pd.memb.i) :
   error in evaluating the argument 'object' in selecting a method for
 function 'coef'  }Error: unexpected '}' in }


 What am I doing wrong?
 Thanks a lot for your help,
 f.

[[alternative HTML version deleted]]

 __**
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 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.


 --
 Patrick Burns
 pbu...@pburns.seanet.com
 twitter: @portfolioprobe
 http://www.portfolioprobe.com/**blog http://www.portfolioprobe.com/blog
 http://www.burns-stat.com
 (home of 'Some hints for the R beginner'
 and 'The R Inferno')


 __**
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 posting-guide.html http://www.R-project.org/posting-guide.html
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[[alternative HTML version deleted]]

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Re: [R] Referring to an object by a variable containing its name: 6 failures

2011-09-18 Thread andrewH

Thanks Josh Duncan! That was very clear and helpful. After going back and
reviewing documentation for { and $ I am realizing that R the pattern in
R documentation is simply to tell you the truth, and not to give much effort
to distinguishing confusable choices. Once again, things that seemed crazy
to me become perfectly sensible once understood. I think I need to read
function documentation more the way one reads concept definitions in a math
book.

Josh, one question: Your reasons to avoid attach() seem cogent. However,
Venables, Smith et al. say in “An Introduction to R”
:
A useful convention that allows you to work with many different problems
comfortably together
in the same working directory is
gather together all variables for any well defined and separate problem in
a data frame
under a suitably informative name;
when working with a problem attach the appropriate data frame at position
2, and use the
working directory at level 1 for operational quantities and temporary
variables;
before leaving a problem, add any variables you wish to keep for future
reference to the
data frame using the $ form of assignment, and then detach();
finally remove all unwanted variables from the working directory

I'm still at the point that I am doing things just because Authority says
so, but unfortunately, everyone is Authority, relative to me. Still, I
wonder if you have any thoughts about why such a venerable authority as
Venables et al. would recomend a programming practice if that practice
should always be avoided. For cognative dissonance form authority conflicts,
that's up there with the Google R stylesheet saying to avoid using S4
classes.

Again, my thanks.
andrewH

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Re: [R] R-Help



On Sep 18, 2011, at 2:25 PM, Gastón wrote:

Hi, my name is Gastón. I just read a question, made by Walter Durka,  
about a

nonparametric discriminant analysis. It wasn´t any answer, and I was
wondering if at this moment there is one. I have the same problem as  
W.

Durka.  I´m trying to classify and to cross-validate samples of three
tunicates species based on morphometric data and to identify the  
variables

that best discriminate between species.
Thanks for help.


http://cran.r-project.org/web/views/Cluster.html


--
David Winsemius, MD
West Hartford, CT

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[R] graph bugs using R on MAC

This is has been bugging me for a long time. Nobody around me seems to  
have this problem. I hope someone on the forum could help me.


When I generate a R graph and want to bring the image into Word. I  
cannot copy and paste it like many of my classmates can do. The  
Select in Edit menu have all options grayed out. So what I ended up  
doing is to save it as pdf file and bring it into Word. But if I use  
Identify in the Plot statement, there will be values labels on the  
graph when you click on the observation. For some reason, these labels  
don't show up in the pdf file.


So the last resort I have is prinscreen, which always have irrelevant  
things showing.


I've tried updating R/OS and all softwares on my MAC, but nothing  
seems to do anything. I have OX 10.6.8. Does this problem sound  
familiar to anyone?


Thanks in advance!

Bonnie Yuan

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Re: [R] graph bugs using R on MAC



On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:

This is has been bugging me for a long time. Nobody around me seems  
to have this problem. I hope someone on the forum could help me.


When I generate a R graph and want to bring the image into Word. I  
cannot copy and paste it like many of my classmates can do. The  
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.

So what I ended up doing is to save it as pdf file and bring it  
into Word. But if I use Identify in the Plot statement, there  
will be values labels on the graph when you click on the  
observation. For some reason, these labels don't show up in the pdf  
file.


So the last resort I have is prinscreen, which always have  
irrelevant things showing.


I've tried updating R/OS and all softwares on my MAC, but nothing  
seems to do anything. I have OX 10.6.8. Does this problem sound  
familiar to anyone?


Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

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Re: [R] graph bugs using R on MAC

Copy paste doesn't work. So I tried to Select and then copy paste, but  
it doesn't work either.


Quoting Don McKenzie d...@u.washington.edu:



On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:

This is has been bugging me for a long time. Nobody around me seems  
 to have this problem. I hope someone on the forum could help me.


When I generate a R graph and want to bring the image into Word. I   
cannot copy and paste it like many of my classmates can do. The   
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.

So what I ended up doing is to save it as pdf file and bring it   
into Word. But if I use Identify in the Plot statement, there   
will be values labels on the graph when you click on the   
observation. For some reason, these labels don't show up in the pdf  
 file.


So the last resort I have is prinscreen, which always have   
irrelevant things showing.


I've tried updating R/OS and all softwares on my MAC, but nothing   
seems to do anything. I have OX 10.6.8. Does this problem sound   
familiar to anyone?


Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu


__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] graph bugs using R on MAC

2011-09-18 Thread B77S

Have you been shown how to save a graph as a JPEG or PNG?

try this:

png(myGraph.png)
plot(your_data)
dev.off()

A png will appear in your working directory, which can be imported into the
Word document.
You can do the same with a JPEG

see ?jpeg or ?png and ?dev.off

HTH
 


bonnieyuan wrote:
 
 This is has been bugging me for a long time. Nobody around me seems to  
 have this problem. I hope someone on the forum could help me.
 
 When I generate a R graph and want to bring the image into Word. I  
 cannot copy and paste it like many of my classmates can do. The  
 Select in Edit menu have all options grayed out. So what I ended up  
 doing is to save it as pdf file and bring it into Word. But if I use  
 Identify in the Plot statement, there will be values labels on the  
 graph when you click on the observation. For some reason, these labels  
 don't show up in the pdf file.
 
 So the last resort I have is prinscreen, which always have irrelevant  
 things showing.
 
 I've tried updating R/OS and all softwares on my MAC, but nothing  
 seems to do anything. I have OX 10.6.8. Does this problem sound  
 familiar to anyone?
 
 Thanks in advance!
 
 Bonnie Yuan
 
 __
 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
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Re: [R] graph bugs using R on MAC


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.


That doesn't work for me with OpenOffice (I don't have Word). 
copy2eps(file=some.eps) does work, along with Insert | Picture | From 
file...





So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my copy of 
OpenOffice doesn't recognize .pdf as a picture type.


But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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] graph bugs using R on MAC



On 18-Sep-11, at 12:59 PM, Duncan Murdoch wrote:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.


That doesn't work for me with OpenOffice (I don't have Word).  
copy2eps(file=some.eps) does work, along with Insert | Picture |  
From file...


Odd -- I was using OpenOffice when trying to duplicate the problem.   
Well NeoOffice, the mac twin.





So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my copy  
of OpenOffice doesn't recognize .pdf as a picture type.


But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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.







Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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] graph bugs using R on MAC

Yes, I'm positive I had the right window highlighted, and I have shown  
this problem to lots of people including tech staff, to get no  
answers. So I suspect it's probably a somewhat obscure problem.


Duncan, thanks for the lead on the new group. I will follow up on  
that. What is the copy2eps? Is it to Excel? Do you get that option in R?


Bonnie Yuan.

Quoting Duncan Murdoch murdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture | From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
 quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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] Add png image outside plot borders

2011-09-18 Thread Amelia McNamara

I am trying to add a copyright disclaimer outside the plot borders of
some images I have created. I can use mtext() to add the written
portion, but I would like to have the Creative Commons license image
(http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
text. I've found that I can plot a .png image inside the plot
boundaries using rasterImage() but I can't figure out how to do it
outside the boundaries.

Any help would be great. If you know unicode or Adobe Symbol encoding
for the CC logo, that might work too.

~Amelia McNamara
Statistics PhD student, UCLA

__
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] Add png image outside plot borders

2011-09-18 Thread Joshua Wiley

Hi Amelia,

Can you give an example (using text where you want the CC is fine)?
Two angles I would try would be A) changing the regions or related but
more flexible (and hence complex) B) use grid of course if you're
making these with, say, ggplot2, you're already in grid (but then
mtext probably would not work, though I have not tried it offhand).
Anyway, an example (code please, not just the picture), will clear up
all these questions and we can offer a solution tailored to what you
are doing.

Cheers,

Josh

On Sun, Sep 18, 2011 at 1:18 PM, Amelia McNamara
amelia.mcnam...@stat.ucla.edu wrote:
 I am trying to add a copyright disclaimer outside the plot borders of
 some images I have created. I can use mtext() to add the written
 portion, but I would like to have the Creative Commons license image
 (http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
 text. I've found that I can plot a .png image inside the plot
 boundaries using rasterImage() but I can't figure out how to do it
 outside the boundaries.

 Any help would be great. If you know unicode or Adobe Symbol encoding
 for the CC logo, that might work too.

 ~Amelia McNamara
 Statistics PhD student, UCLA

 __
 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.




-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.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] graph bugs using R on MAC


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:

Yes, I'm positive I had the right window highlighted, and I have shown
this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture | From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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] graph bugs using R on MAC


I think it's actually dev.copy2eps()

or at least that one works.


On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:
Yes, I'm positive I had the right window highlighted, and I have  
shown

this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option  
in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:

This is has been bugging me for a long time. Nobody around me  
seems

to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word  
processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture  
| From

file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the  
pdf

file.


They did show up with copy2eps().  I didn't try copy2pdf(); my  
copy of

OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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.










Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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] graph bugs using R on MAC


On 11-09-18 4:53 PM, Don McKenzie wrote:

I think it's actually dev.copy2eps()

or at least that one works.


Right, sorry.

Duncan Murdoch




On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:

Yes, I'm positive I had the right window highlighted, and I have
shown
this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option
in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me
seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word
processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture
| From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the
pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my
copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
   quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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.










Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu






__
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] Add png image outside plot borders

2011-09-18 Thread Amelia McNamara

If you run this, you'll see that I have some text at the bottom, but
the logo is within the plot borders.

plot(c(1.1, 2.3, 4.6), c(2.0, 1.6, 3.2), ylab=, xlab=)
mtext(X axis label, side=1, line=3)
mtext(Copyright statement, side=1, line=4, adj=0, cex=0.7)
library(png)
z - readPNG(Cc.logo.circle.png)
rasterImage(z, 1, 1.6, 1.2, 1.7)

I've tried doing things like

rasterImage(z, 1, 0.5, 1.2, 1)

but nothing shows up. The documentation for rasterImage() says that
the corner values have to be within the plot region. As I said before,
I want the logo to be down on the level of my copyright text, outside
the plot region.

Thanks!


On Sun, Sep 18, 2011 at 1:26 PM, Joshua Wiley jwiley.ps...@gmail.com wrote:
 Hi Amelia,

 Can you give an example (using text where you want the CC is fine)?
 Two angles I would try would be A) changing the regions or related but
 more flexible (and hence complex) B) use grid of course if you're
 making these with, say, ggplot2, you're already in grid (but then
 mtext probably would not work, though I have not tried it offhand).
 Anyway, an example (code please, not just the picture), will clear up
 all these questions and we can offer a solution tailored to what you
 are doing.

 Cheers,

 Josh

 On Sun, Sep 18, 2011 at 1:18 PM, Amelia McNamara
 amelia.mcnam...@stat.ucla.edu wrote:
 I am trying to add a copyright disclaimer outside the plot borders of
 some images I have created. I can use mtext() to add the written
 portion, but I would like to have the Creative Commons license image
 (http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
 text. I've found that I can plot a .png image inside the plot
 boundaries using rasterImage() but I can't figure out how to do it
 outside the boundaries.

 Any help would be great. If you know unicode or Adobe Symbol encoding
 for the CC logo, that might work too.

 ~Amelia McNamara
 Statistics PhD student, UCLA

 __
 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.




 --
 Joshua Wiley
 Ph.D. Student, Health Psychology
 Programmer Analyst II, ATS Statistical Consulting Group
 University of California, Los Angeles
 https://joshuawiley.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] randomForest2Rules

2011-09-18 Thread saskay

Hi,
I'm trying to extract the rules from every tree in the random forest model
that I've created. I've used randomForest2Rules function from rattle
package however I get an error Error in if (var.class == character |
var.class == factor) { : 
  argument is of length zero 

Sample code:
library(rattle)
library(randomForest)
iris.10tree - randomForest(Species ~ ., data=iris, ntree=10)
iris.10tree
printRandomForests(iris.10tree) #this prints the rules as described in the
vignette
ruleset-randomForest2Rules(iris.10tree) # this does not work and gives the
error I mentioned above.

Rattle package: http://cran.r-project.org/web/packages/rattle/rattle.pdf

Please can someone tell me where I'm going wrong.

--
View this message in context: 
http://r.789695.n4.nabble.com/randomForest2Rules-tp3822530p3822530.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] graph bugs using R on MAC


Don and Duncan,

That function works, up to the same point where I can save pdf into  
Word using the menu. But when I use Identify function together with  
plot function, the Quartz window has to be closed before I can go back  
the console to execute copy2eps function. But by then, I don't have  
an active device anymore. So it beats the purpose.


Dan,

I'm using Word 2004. Upgrading Word is an idea. I will definitely look  
into it, although I didn't think those who didn't have this problem  
necessarily had a higher version of Word.


Bonnie Yuan

Quoting Duncan Murdoch murdoch.dun...@gmail.com:


On 11-09-18 4:53 PM, Don McKenzie wrote:

I think it's actually dev.copy2eps()

or at least that one works.


Right, sorry.

Duncan Murdoch




On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:

Yes, I'm positive I had the right window highlighted, and I have
shown
this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option
in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me
seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word
processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture
| From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the
pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my
copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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.










Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu






__
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] graph bugs using R on MAC


On Sep 18, 2011, at 2:15 PM, bby2...@columbia.edu wrote:

 Don and Duncan,
 
 That function works, up to the same point where I can save pdf into Word 
 using the menu. But when I use Identify function together with plot function, 
 the Quartz window has to be closed before I can go back the console to 
 execute copy2eps function.
   **
This is indeed strange.  Running R 2.13.0 on mac SnowLeopard, with quartz 
window manager

 plot(1,1)
 identify(1,1)
warning: no point within 0.25 inches
[1] 1
 dev.copy2eps(file=test.eps)
quartz 
 2 

The eps file shows up in my working directory just as it should.  There should 
be no need to close the quartz window, 
or even look at it for that matter.  Can you show us your session info?

 But by then, I don't have an active device anymore. So it beats the purpose.
 
 Dan,
 
 I'm using Word 2004. Upgrading Word is an idea. I will definitely look into 
 it, although I didn't think those who didn't have this problem necessarily 
 had a higher version of Word.
 
 Bonnie Yuan
 
 Quoting Duncan Murdoch murdoch.dun...@gmail.com:
 
 On 11-09-18 4:53 PM, Don McKenzie wrote:
 I think it's actually dev.copy2eps()
 
 or at least that one works.
 
 Right, sorry.
 
 Duncan Murdoch
 
 
 
 On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:
 
 On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:
 Yes, I'm positive I had the right window highlighted, and I have
 shown
 this problem to lots of people including tech staff, to get no
 answers. So I suspect it's probably a somewhat obscure problem.
 
 Duncan, thanks for the lead on the new group. I will follow up on
 that. What is the copy2eps? Is it to Excel? Do you get that option
 in R?
 
 copy2eps() is a function in R.  Try ?copy2eps for details.
 
 Duncan Murdoch
 
 
 Bonnie Yuan.
 
 Quoting Duncan Murdochmurdoch.dun...@gmail.com:
 
 On 11-09-18 3:48 PM, Don McKenzie wrote:
 
 On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:
 
 This is has been bugging me for a long time. Nobody around me
 seems
 to have this problem. I hope someone on the forum could help me.
 
 When I generate a R graph and want to bring the image into Word. I
 cannot copy and paste it like many of my classmates can do. The
 Select in Edit menu have all options grayed out.
 
 You want Copy, not Select.  Then Paste into your word
 processor.
 
 That doesn't work for me with OpenOffice (I don't have Word).
 copy2eps(file=some.eps) does work, along with Insert | Picture
 | From
 file...
 
 
 So what I ended up doing is to save it as pdf file and bring it
 into Word. But if I use Identify in the Plot statement, there
 will be values labels on the graph when you click on the
 observation. For some reason, these labels don't show up in the
 pdf
 file.
 
 They did show up with copy2eps().  I didn't try copy2pdf(); my
 copy of
 OpenOffice doesn't recognize .pdf as a picture type.
 
 But Bonnie will probably get a better answer on the R-sig-mac list.
 
 Duncan Murdoch
 
 
 So the last resort I have is prinscreen, which always have
 irrelevant things showing.
 
 I've tried updating R/OS and all softwares on my MAC, but nothing
 seems to do anything. I have OX 10.6.8. Does this problem sound
 familiar to anyone?
 
 Thanks in advance!
 
 Bonnie Yuan
 
 __
 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.
 
 When we look at the wings of the eagle
 To the left, closest to the heart, is the spirit
 To the right, far away from the heart, is the science
 No bird can ever lift off with wings that are not equal
 
 -- Greenland First Nations elder
  quoted in EOS Transactions
 
 
 Don McKenzie, Research Ecologist
 Pacific WIldland Fire Sciences Lab
 US Forest Service
 
 Affiliate Professor
 School of Forest Resources, College of the Environment
 CSES Climate Impacts Group
 University of Washington
 
 phone: 206-732-7824
 d...@uw.edu
 
 __
 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.
 
 
 
 
 
 
 
 Don McKenzie, Research Ecologist
 Pacific WIldland Fire Sciences Lab
 US Forest Service
 
 Affiliate Professor
 School of Forest Resources, College of the Environment
 CSES Climate Impacts Group
 University of Washington
 
 phone: 206-732-7824
 d...@uw.edu
 
 
 
 
 
 

Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu




[[alternative HTML version deleted]]

Re: [R] graph bugs using R on MAC

Sorry -- you do have to highlight the quartz window to use identify(), but that 
shouldn't matter either.

On Sep 18, 2011, at 2:41 PM, Don McKenzie wrote:

 
 On Sep 18, 2011, at 2:15 PM, bby2...@columbia.edu wrote:
 
 Don and Duncan,
 
 That function works, up to the same point where I can save pdf into Word 
 using the menu. But when I use Identify function together with plot 
 function, the Quartz window has to be closed before I can go back the 
 console to execute copy2eps function.
**
 This is indeed strange.  Running R 2.13.0 on mac SnowLeopard, with quartz 
 window manager
 
  plot(1,1)
  identify(1,1)
 warning: no point within 0.25 inches
 [1] 1
  dev.copy2eps(file=test.eps)
 quartz 
  2 
 
 The eps file shows up in my working directory just as it should.  There 
 should be no need to close the quartz window, 
 or even look at it for that matter.  Can you show us your session info?
 
 But by then, I don't have an active device anymore. So it beats the purpose.
 
 Dan,
 
 I'm using Word 2004. Upgrading Word is an idea. I will definitely look into 
 it, although I didn't think those who didn't have this problem necessarily 
 had a higher version of Word.
 
 Bonnie Yuan
 
 Quoting Duncan Murdoch murdoch.dun...@gmail.com:
 
 On 11-09-18 4:53 PM, Don McKenzie wrote:
 I think it's actually dev.copy2eps()
 
 or at least that one works.
 
 Right, sorry.
 
 Duncan Murdoch
 
 
 
 On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:
 
 On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:
 Yes, I'm positive I had the right window highlighted, and I have
 shown
 this problem to lots of people including tech staff, to get no
 answers. So I suspect it's probably a somewhat obscure problem.
 
 Duncan, thanks for the lead on the new group. I will follow up on
 that. What is the copy2eps? Is it to Excel? Do you get that option
 in R?
 
 copy2eps() is a function in R.  Try ?copy2eps for details.
 
 Duncan Murdoch
 
 
 Bonnie Yuan.
 
 Quoting Duncan Murdochmurdoch.dun...@gmail.com:
 
 On 11-09-18 3:48 PM, Don McKenzie wrote:
 
 On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:
 
 This is has been bugging me for a long time. Nobody around me
 seems
 to have this problem. I hope someone on the forum could help me.
 
 When I generate a R graph and want to bring the image into Word. I
 cannot copy and paste it like many of my classmates can do. The
 Select in Edit menu have all options grayed out.
 
 You want Copy, not Select.  Then Paste into your word
 processor.
 
 That doesn't work for me with OpenOffice (I don't have Word).
 copy2eps(file=some.eps) does work, along with Insert | Picture
 | From
 file...
 
 
 So what I ended up doing is to save it as pdf file and bring it
 into Word. But if I use Identify in the Plot statement, there
 will be values labels on the graph when you click on the
 observation. For some reason, these labels don't show up in the
 pdf
 file.
 
 They did show up with copy2eps().  I didn't try copy2pdf(); my
 copy of
 OpenOffice doesn't recognize .pdf as a picture type.
 
 But Bonnie will probably get a better answer on the R-sig-mac list.
 
 Duncan Murdoch
 
 
 So the last resort I have is prinscreen, which always have
 irrelevant things showing.
 
 I've tried updating R/OS and all softwares on my MAC, but nothing
 seems to do anything. I have OX 10.6.8. Does this problem sound
 familiar to anyone?
 
 Thanks in advance!
 
 Bonnie Yuan
 
 __
 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.
 
 When we look at the wings of the eagle
 To the left, closest to the heart, is the spirit
 To the right, far away from the heart, is the science
 No bird can ever lift off with wings that are not equal
 
 -- Greenland First Nations elder
  quoted in EOS Transactions
 
 
 Don McKenzie, Research Ecologist
 Pacific WIldland Fire Sciences Lab
 US Forest Service
 
 Affiliate Professor
 School of Forest Resources, College of the Environment
 CSES Climate Impacts Group
 University of Washington
 
 phone: 206-732-7824
 d...@uw.edu
 
 __
 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.
 
 
 
 
 
 
 
 Don McKenzie, Research Ecologist
 Pacific WIldland Fire Sciences Lab
 US Forest Service
 
 Affiliate Professor
 School of Forest Resources, College of the Environment
 CSES Climate Impacts Group
 University of Washington
 
 phone: 206-732-7824
 d...@uw.edu
 
 
 
 
 
 
 
 Don McKenzie, Research Ecologist
 Pacific WIldland Fire Sciences Lab
 US Forest Service
 
 Affiliate Professor
 School of Forest Resources,

Re: [R] Add png image outside plot borders

2011-09-18 Thread Duncan Temple Lang


Amelia

  You can persuade rasterImage() (and other functions) to draw
outside of the data region using xpd = NA or xpd = TRUE.
See the help for the par function.

D.

On 9/18/11 1:59 PM, Amelia McNamara wrote:
 If you run this, you'll see that I have some text at the bottom, but
 the logo is within the plot borders.
 
 plot(c(1.1, 2.3, 4.6), c(2.0, 1.6, 3.2), ylab=, xlab=)
 mtext(X axis label, side=1, line=3)
 mtext(Copyright statement, side=1, line=4, adj=0, cex=0.7)
 library(png)
 z - readPNG(Cc.logo.circle.png)
 rasterImage(z, 1, 1.6, 1.2, 1.7)
 
 I've tried doing things like
 
 rasterImage(z, 1, 0.5, 1.2, 1)
 
 but nothing shows up. The documentation for rasterImage() says that
 the corner values have to be within the plot region. As I said before,
 I want the logo to be down on the level of my copyright text, outside
 the plot region.
 
 Thanks!
 
 
 On Sun, Sep 18, 2011 at 1:26 PM, Joshua Wiley jwiley.ps...@gmail.com wrote:
 Hi Amelia,

 Can you give an example (using text where you want the CC is fine)?
 Two angles I would try would be A) changing the regions or related but
 more flexible (and hence complex) B) use grid of course if you're
 making these with, say, ggplot2, you're already in grid (but then
 mtext probably would not work, though I have not tried it offhand).
 Anyway, an example (code please, not just the picture), will clear up
 all these questions and we can offer a solution tailored to what you
 are doing.

 Cheers,

 Josh

 On Sun, Sep 18, 2011 at 1:18 PM, Amelia McNamara
 amelia.mcnam...@stat.ucla.edu wrote:
 I am trying to add a copyright disclaimer outside the plot borders of
 some images I have created. I can use mtext() to add the written
 portion, but I would like to have the Creative Commons license image
 (http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
 text. I've found that I can plot a .png image inside the plot
 boundaries using rasterImage() but I can't figure out how to do it
 outside the boundaries.

 Any help would be great. If you know unicode or Adobe Symbol encoding
 for the CC logo, that might work too.

 ~Amelia McNamara
 Statistics PhD student, UCLA

 __
 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.




 --
 Joshua Wiley
 Ph.D. Student, Health Psychology
 Programmer Analyst II, ATS Statistical Consulting Group
 University of California, Los Angeles
 https://joshuawiley.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.

Re: [R] AIC

2011-09-18 Thread B77S

This isn't a question about R; more appropriate for stackexchange.

Here is one string that might interest you:

http://stats.stackexchange.com/questions/4997/can-aic-compare-across-different-types-of-model






Tania Sav wrote:
 
 Hello,
 
 I'm using AIC() to choose a better model. I have 3 options: 
 1) y=ax+b 
 2) y=ax^2 +bx + c
 3) y=a(1-exp(-x/b)) + c
 
 Is it ok to use AIC() for determine wich is the better equation to use for
 fit to my data?
 
 Thanks
 Tania
 

Tania Sav wrote:
 
 Hello,
 
 I'm using AIC() to choose a better model. I have 3 options: 
 1) y=ax+b 
 2) y=ax^2 +bx + c
 3) y=a(1-exp(-x/b)) + c
 
 Is it ok to use AIC() for determine wich is the better equation to use for
 fit to my data?
 
 Thanks
 Tania
 


--
View this message in context: 
http://r.789695.n4.nabble.com/AIC-tp3820732p3822647.html
Sent from the R help mailing list archive at Nabble.com.

__
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] Add png image outside plot borders

2011-09-18 Thread baptiste auguie

Hi,

if your logo is in vector format you should probably try the grImport
package; see its vignette for examples, also below,


library(grImport)
## http://creativecommons.org/about/downloads/
PostScriptTrace(cc.logo.eps)
cc - readPicture(cc.logo.eps.xml)


logo - pictureGrob(cc[16:18], x=unit(1, npc), y=unit(0, npc),
 width=unit(2,cm),
 height=unit(2,cm),
 just= c(right, bottom), use.gc = FALSE,
 gp = gpar(fill = grey40, col = grey50))


plot(1:10, rnorm(10),
 panel.first = grid.draw(logo))

HTH,

baptiste


On 19 September 2011 08:18, Amelia McNamara
amelia.mcnam...@stat.ucla.edu wrote:
 I am trying to add a copyright disclaimer outside the plot borders of
 some images I have created. I can use mtext() to add the written
 portion, but I would like to have the Creative Commons license image
 (http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
 text. I've found that I can plot a .png image inside the plot
 boundaries using rasterImage() but I can't figure out how to do it
 outside the boundaries.

 Any help would be great. If you know unicode or Adobe Symbol encoding
 for the CC logo, that might work too.

 ~Amelia McNamara
 Statistics PhD student, UCLA

 __
 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] Add png image outside plot borders

2011-09-18 Thread Joshua Wiley

Great, thanks Amelia.  Here is what I would do:

require(png)
require(grid)

## select the PNG file
z - readPNG(file.choose())

## Function to draw your statement
copyright.draw - function(label, image, x, y, size, ...) {
  lab - textGrob(label = label,
x = unit(x, npc), y = unit(y, npc),
just = c(left, centre), gp = gpar(...))
  logo - rasterGrob(image = image,
x = unit(x, npc) + unit(1, grobwidth, lab), y = unit(y, npc),
width = unit(size, cm), height = unit(size, cm),
just = c(left, centre), gp = gpar(...))
  grid.draw(lab)
  grid.draw(logo)
}

plot(1:10, 1:10)
copyright.draw(Copyright statement , z, .02, .04, .5, fontsize = 8)

Seems reasonably aesthetically pleasing to me (don't forget the space
after your copyright statement if you want there to be a space there
before the CC logo).

I kind like Baptiste's idea to use the SVG file directly, but you
asked for PNG.  Also, the function is not strictly necessary, what is
nice about it is that it handles positioning the logo based on the
text.  You don't want to be in a position where you are trying to
manually line the two up.  You can pass additional arguments as you
like to gpar (though note it will affect botht he text and raster
grobs.

Cheers,

Josh

On Sun, Sep 18, 2011 at 1:59 PM, Amelia McNamara
amelia.mcnam...@stat.ucla.edu wrote:
 If you run this, you'll see that I have some text at the bottom, but
 the logo is within the plot borders.

 plot(c(1.1, 2.3, 4.6), c(2.0, 1.6, 3.2), ylab=, xlab=)
 mtext(X axis label, side=1, line=3)
 mtext(Copyright statement, side=1, line=4, adj=0, cex=0.7)
 library(png)
 z - readPNG(Cc.logo.circle.png)
 rasterImage(z, 1, 1.6, 1.2, 1.7)

 I've tried doing things like

 rasterImage(z, 1, 0.5, 1.2, 1)

 but nothing shows up. The documentation for rasterImage() says that
 the corner values have to be within the plot region. As I said before,
 I want the logo to be down on the level of my copyright text, outside
 the plot region.

 Thanks!


 On Sun, Sep 18, 2011 at 1:26 PM, Joshua Wiley jwiley.ps...@gmail.com wrote:
 Hi Amelia,

 Can you give an example (using text where you want the CC is fine)?
 Two angles I would try would be A) changing the regions or related but
 more flexible (and hence complex) B) use grid of course if you're
 making these with, say, ggplot2, you're already in grid (but then
 mtext probably would not work, though I have not tried it offhand).
 Anyway, an example (code please, not just the picture), will clear up
 all these questions and we can offer a solution tailored to what you
 are doing.

 Cheers,

 Josh

 On Sun, Sep 18, 2011 at 1:18 PM, Amelia McNamara
 amelia.mcnam...@stat.ucla.edu wrote:
 I am trying to add a copyright disclaimer outside the plot borders of
 some images I have created. I can use mtext() to add the written
 portion, but I would like to have the Creative Commons license image
 (http://en.wikipedia.org/wiki/File:Cc.logo.circle.svg) before the
 text. I've found that I can plot a .png image inside the plot
 boundaries using rasterImage() but I can't figure out how to do it
 outside the boundaries.

 Any help would be great. If you know unicode or Adobe Symbol encoding
 for the CC logo, that might work too.

 ~Amelia McNamara
 Statistics PhD student, UCLA

 __
 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.




 --
 Joshua Wiley
 Ph.D. Student, Health Psychology
 Programmer Analyst II, ATS Statistical Consulting Group
 University of California, Los Angeles
 https://joshuawiley.com/





-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.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] perm.test()

2011-09-18 Thread song_gpqg

Hi!
I am doing a two sample permutation test and trying to find confidence
interval. perm.test() seems can do that but when the vector contains
negative numbers it occurs an error. And for perm.test(x,y), elements in x
can't be more than in y. I am wondering how I can fix these two problems?
Thanks a lot.


--
View this message in context: 
http://r.789695.n4.nabble.com/perm-test-tp3822738p3822738.html
Sent from the R help mailing list archive at Nabble.com.

__
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] graph bugs using R on MAC


On 11-09-18 5:15 PM, bby2...@columbia.edu wrote:

Don and Duncan,

That function works, up to the same point where I can save pdf into
Word using the menu. But when I use Identify function together with
plot function, the Quartz window has to be closed before I can go back
the console to execute copy2eps function. But by then, I don't have
an active device anymore. So it beats the purpose.


You stop the identify function by right-clicking in the graphics window. 
I have my one-button Mac set up to do this with a two-finger tap, you 
may have it set some other way.  (I think Mac calls this a secondary 
tap.)  After that dev.copy2eps should copy the identifiers too.


Duncan Murdoch




Dan,

I'm using Word 2004. Upgrading Word is an idea. I will definitely look
into it, although I didn't think those who didn't have this problem
necessarily had a higher version of Word.

Bonnie Yuan

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 4:53 PM, Don McKenzie wrote:

I think it's actually dev.copy2eps()

or at least that one works.


Right, sorry.

Duncan Murdoch




On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:

Yes, I'm positive I had the right window highlighted, and I have
shown
this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option
in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me
seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word
processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture
| From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the
pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my
copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

__
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.


When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
   quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

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










Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu









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[R] Linear regression interaction terms

2011-09-18 Thread Andrey A

Hello I performed a linear regression, my equation is Y = âo+ â1A + â2B +
â3AB.
Is there a way to separate interaction terms, say â3AB and plot it against a
certain variable?
Thanks, Andrew

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Re: [R] graph bugs using R on MAC

Cool! Don showed me another trick--use (n= ) in Identify. The active  
window will come back to console after the specified amount of clicks,  
you will be able to execute more commands in console.


Thank you!

Quoting Duncan Murdoch murdoch.dun...@gmail.com:


On 11-09-18 5:15 PM, bby2...@columbia.edu wrote:

Don and Duncan,

That function works, up to the same point where I can save pdf into
Word using the menu. But when I use Identify function together with
plot function, the Quartz window has to be closed before I can go back
the console to execute copy2eps function. But by then, I don't have
an active device anymore. So it beats the purpose.


You stop the identify function by right-clicking in the graphics
window. I have my one-button Mac set up to do this with a two-finger
tap, you may have it set some other way.  (I think Mac calls this a
secondary tap.)  After that dev.copy2eps should copy the identifiers
too.

Duncan Murdoch




Dan,

I'm using Word 2004. Upgrading Word is an idea. I will definitely look
into it, although I didn't think those who didn't have this problem
necessarily had a higher version of Word.

Bonnie Yuan

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 4:53 PM, Don McKenzie wrote:

I think it's actually dev.copy2eps()

or at least that one works.


Right, sorry.

Duncan Murdoch




On 18-Sep-11, at 1:51 PM, Duncan Murdoch wrote:


On 11-09-18 4:11 PM, bby2...@columbia.edu wrote:

Yes, I'm positive I had the right window highlighted, and I have
shown
this problem to lots of people including tech staff, to get no
answers. So I suspect it's probably a somewhat obscure problem.

Duncan, thanks for the lead on the new group. I will follow up on
that. What is the copy2eps? Is it to Excel? Do you get that option
in R?


copy2eps() is a function in R.  Try ?copy2eps for details.

Duncan Murdoch



Bonnie Yuan.

Quoting Duncan Murdochmurdoch.dun...@gmail.com:


On 11-09-18 3:48 PM, Don McKenzie wrote:


On 18-Sep-11, at 12:38 PM, bby2...@columbia.edu wrote:


This is has been bugging me for a long time. Nobody around me
seems
to have this problem. I hope someone on the forum could help me.

When I generate a R graph and want to bring the image into Word. I
cannot copy and paste it like many of my classmates can do. The
Select in Edit menu have all options grayed out.


You want Copy, not Select.  Then Paste into your word
processor.


That doesn't work for me with OpenOffice (I don't have Word).
copy2eps(file=some.eps) does work, along with Insert | Picture
| From
file...




So what I ended up doing is to save it as pdf file and bring it
into Word. But if I use Identify in the Plot statement, there
will be values labels on the graph when you click on the
observation. For some reason, these labels don't show up in the
pdf
file.


They did show up with copy2eps().  I didn't try copy2pdf(); my
copy of
OpenOffice doesn't recognize .pdf as a picture type.

But Bonnie will probably get a better answer on the R-sig-mac list.

Duncan Murdoch



So the last resort I have is prinscreen, which always have
irrelevant things showing.

I've tried updating R/OS and all softwares on my MAC, but nothing
seems to do anything. I have OX 10.6.8. Does this problem sound
familiar to anyone?

Thanks in advance!

Bonnie Yuan

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PLEASE do read the posting guide http://www.R-project.org/posting-
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When we look at the wings of the eagle
To the left, closest to the heart, is the spirit
To the right, far away from the heart, is the science
No bird can ever lift off with wings that are not equal

-- Greenland First Nations elder
  quoted in EOS Transactions


Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu

__
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.










Don McKenzie, Research Ecologist
Pacific WIldland Fire Sciences Lab
US Forest Service

Affiliate Professor
School of Forest Resources, College of the Environment
CSES Climate Impacts Group
University of Washington

phone: 206-732-7824
d...@uw.edu









__
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[R] regression summary results pvalues and coefficients into a excel

2011-09-18 Thread Donald Price

Hi All,

I have run many regression analyses (14000 +) and want to collect the
coefficients and pvalues into an excel file.  I can get the statements below
to work up to step 4.  I can printout the regressionresults (sample output
below).

So my hope is to run something like step 5 and 6 and put the pvalues (and
then coefficients) into an excel file.  Can anyone suggest what I am doing
wrong or a better way :0

Thanks

Don





1) sdata - read.table(gene.csv, row.names=1, sep=',')

2)  headshape - c(0.575818, 0.573874, 0.525701, 0.548490, 0.685111,
0.592502, 0.566001, 0.563605, 0.637906, 0.578099, 0.588142, 0.383393,
0.561732, 0.456134, 0.430472, 0.603143, 0.514315, 0.53328, 0.482734,
0.637906)

3) morphtrait - headshape aof-function(x){m-data.frame(morphtrait,x);
summary(lm(morphtrait~x, m))}

4) regressionresults -apply(sdata, 1, aof)

5) regpvalues - data.frame(lapply(regressionresults,
function(x){x[Pr(|t|)][1:2,]}))

6) write.table(t(regpvalues), file = regression-resultsheadshape.txt,
quote = F, sep ='\t')





 regressionresults

$CUST_54_PI410671829

Call:
lm(formula = morphtrait ~ x, data = m)

Residuals:
 Min   1Q   Median   3Q  Max
-0.23217 -0.08980 -0.04592 -0.00947  1.07688

Coefficients:
 Estimate Std. Error t value Pr(|t|)
(Intercept) 0.5985797  0.0364510  16.421   2e-16 ***
x   0.0005372  0.0011161   0.4810.632
---
Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1

Residual standard error: 0.2379 on 76 degrees of freedom
Multiple R-squared: 0.003039,   Adjusted R-squared: -0.01008
F-statistic: 0.2316 on 1 and 76 DF,  p-value: 0.6317


$CUST_13662_PI410671829

Call:
lm(formula = morphtrait ~ x, data = m)

Residuals:
 Min   1Q   Median   3Q  Max
-0.23434 -0.09000 -0.05062 -0.01427  1.06208

Coefficients:
 Estimate Std. Error t value Pr(|t|)
(Intercept)  0.626368   0.030173  20.759   2e-16 ***
x   -0.003815   0.003337  -1.1430.256
---
Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1

Residual standard error: 0.2362 on 76 degrees of freedom
Multiple R-squared: 0.01691,Adjusted R-squared: 0.003976
F-statistic: 1.307 on 1 and 76 DF,  p-value: 0.2565


$CUST_8938_PI410671829

Call:
lm(formula = morphtrait ~ x, data = m)

Residuals:
 Min   1Q   Median   3Q  Max
-0.23424 -0.09051 -0.04721 -0.01216  1.07195

Coefficients:
 Estimate Std. Error t value Pr(|t|)
(Intercept) 0.6056038  0.0368423  16.438   2e-16 ***
x   0.0004091  0.0021406   0.1910.849
---
Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1

Residual standard error: 0.2382 on 76 degrees of freedom
Multiple R-squared: 0.0004803,  Adjusted R-squared: -0.01267
F-statistic: 0.03652 on 1 and 76 DF,  p-value: 0.849


$CUST_5773_PI410671829

Call:
lm(formula = morphtrait ~ x, data = m)

Residuals:
 Min   1Q   Median   3Q  Max
-0.23587 -0.09139 -0.04895 -0.01037  1.07437

Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 0.598110   0.038504  15.534   2e-16 ***
x   0.001818   0.004070   0.4470.656
---
Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1

Residual standard error: 0.2379 on 76 degrees of freedom
Multiple R-squared: 0.002619,   Adjusted R-squared: -0.0105
F-statistic: 0.1996 on 1 and 76 DF,  p-value: 0.6563

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Re: [R] regression summary results pvalues and coefficients into a excel