[R] How can I read the "text" or "character string" from a txt file?

[jpm miao]

Hello,

   I have a large number of time series, which needs to be transformed by
log or difference. Some of them are just processed by "level" (LV) without
any transformation. For that purpose, I produce a text file (.csv or .xls)
as follows:

DLN DLNDLN LV LV LV...

How can I read the preceding strings so that I can easily access them,
i.e., S[1]=DLN, S[2]=DLN, S[3]=DLN, S[4]=LV,S[5]=LV,S[6]=LV? I tried
read.csv and read.table, but they don't work well. If I can access the
string, then I will be able to write an "if" statement so that

   If the string is DLN, then take log and then difference.
   If the string is LV, then just keep it as it is.

   Thanks,

miao

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[R] Combined grouped and stacked bargraph

[Nicola Van Wilgen]

Dear R-list

 

I am having some trouble drawing a bar-graph with two groups, both of
which are stacked.

 

Here are my data in the dput format:

 

cs.not.log.bp <- (

structure(c(168, 69, 16, 69, 41, 6, 148, 6, 5, 4, 7, 4, 4, 2, 7, 2, 4,
2, 4, 2, 1, 0, 2, 0), .Dim = c(4L, 6L), .Dimnames = list(

c("IUCN.Terrestrial", "IUCN.Marine", "National.CS.Terrestrial", 

"National.CS.Marine"), c("NE", "LC", "NT", "VU", "EN", "CR"

))) )

 

The database format is shown below, where columns represent conservation
status and the rows are two classification methods each split into
marine and terrestrial:

 

 NE  LC NT VU EN CR

IUCN.Terrestrial168  41  5  4  4  1

IUCN.Marine  69   6  4  2  2  0

National.CS.Terrestrial  16 148  7  7  4  2

National.CS.Marine   69   6  4  2  2  0

 

I would like to plot the conservation status according to two
classifications (i.e. my groups - IUCN status and national status), and
for each of those groups I would like data for the marine and
terrestrial species to be stacked. 

 

I have tried the following code (where cs.not.log.bp is my data), but it
does not work:

 

barplot(cs.not.log.bp[c(1:2),], xlab = "Conservation status", ylab =
"Number of species", col = c("grey90","grey80"), ylim = c(0,250), space
= 2)

 

barplot(cs.not.log.bp[c(3:4),], col = c("grey60","grey30"), beside =
T,add = T,names.arg = NA)

 

legend("topright",c("IUCN Terrestrial","IUCN Marine","National CS
Terrestrial","National CS Marine"),  col =
c("grey90","grey80","grey60","grey30"), pch = 15)

 

What happens is that some of the data in the second group stacks onto
the first group and then the remainder forms a second group. I would
like only "like" data (i.e. from the same database row) to stack within
a group.

 

There was one other similar post on the R-list
(http://r.789695.n4.nabble.com/barplot-question-td3670861.html ) where
the user had the same problem as I did, but it does not seem that this
was resolved.

 

Please let me know if you have any suggestions.

 

Thanks and best wishes,

 

Nicola

 


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Re: [R] returning value from source() in R .Net

[Jeff Newmiller]

I am mystified as to why you think you can source a snippet of one interpreted 
language into a different compiled language.

Fortunately this is not the correct forum for your question, so I can punt. 
Google suggests that you look at rdotnet.codeplex.com, and perhaps read their 
documentation, and if that doesn't help then post your question on their 
discussion forum.
---
Jeff NewmillerThe .   .  Go Live...
DCN:Basics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

paul.rusto...@csiro.au wrote:

>Hello
>I would like to source an R script from within a C# .Net application
>equivalent to:
>
>source("my_r_code.r")
>
>I can get this to run but am not sure how to retrieve R objects defined
>with script my_r_code.r at runtime.
>
>For example, if "my_r_code.r" contains
>
>#-- contents of my_r_code.r-
>x <- 1:10
>xmean <- mean(x)
>#--
>
>My question is how to return the value of xmean to the .Net
>application?
>
>Paul
>
>
>
>
>
>   [[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.

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Re: [R] Equivalent of Nothing (in VBA) or [] in Matlab in R

[ruipbarradas]

Hello, I'm glad it worked.

You could have posted it in r-help, this may be of use to others...

 

Rui Barradas

Citando sb kr :
> Hi Rui Barradas, as you guessed the second option worked 
> 
>Thanks again
> 
>lm
> 
>> Date: Sun, 29 Apr 2012 16:52:45 -0700
>  > From: ruipbarra...@sapo.pt
>  > To: r-help@r-project.org
>  > Subject: Re: [R] Equivalent of Nothing (in VBA) or [] in Matlab in R
>  >
>  > Hello,
>  >
>  > There are other types of "empty" objects in R (zero length or
> dimension).
>  > Maybe some of these
>  >
>  > x <- list()
>  > length(x)
>  >
>  > x <- matrix(list())
>  > dim(x) <- c(0, 0)
>  > x
>  >
>  > Matlab's [] is the empty matrix so maybe the second works.
>  > Other possibilities could be x <- numeric(0) (or integer(0) or
>  > character(0)).
>  > Trial and error might get you there...
>  >
>  > Hope this helps,
>  >
>  > Rui Barradas
>  >
>  >
>  > --
>  > View this message in context:
> http://r.789695.n4.nabble.com/Equivalent-of-Nothing-in-VBA-or-in-Matlab-in-R-tp4595385p4597157.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.
>
>
>

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[R] returning value from source() in R .Net

[Paul.Rustomji]

Hello
I would like to source an R script from within a C# .Net application equivalent 
to:

source("my_r_code.r")

I can get this to run but am not sure how to retrieve R objects defined with 
script my_r_code.r at runtime.

For example, if "my_r_code.r" contains

#-- contents of my_r_code.r-
x <- 1:10
xmean <- mean(x)
#--

My question is how to return the value of xmean to the .Net application?

Paul





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Re: [R] Numeric data not numeric in .csv file

[Jeff Newmiller]

Sounds like you have some text in your csv file. Open it with a text editor and 
look at it. Some common problems are: alphabetic or symbol characters, spaces, 
quotes around numbers. Also watch out for blank rows or columns.

Read the Posting Guide (mentioned at the bottom of every post). Tips: The dput 
function is useful for generating an unambiguous representation of your data, 
which is key in getting correct advice around here. The head function can be 
used to chop off a short amount of data if you have a lot. The str function is 
good for troubleshooting your own issues.
---
Jeff NewmillerThe .   .  Go Live...
DCN:Basics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Eve Proper  wrote:

>I am a raw novice to R, playing around with a mini .csv dataset created
>in
>Excel. I can read it in and the data looks OK in Excel and upon initial
>inspection in R:
>
>hikes <- read.csv("/Users/eproper/Desktop/hikes.csv", header=TRUE)
>print(hikes)
>
>does exactly what it is supposed to do.
>
>Two of the variables are genuine strings, but the others ought to be
>numeric, and R will calculate their min, max etc. However, is.numeric
>returns FALSE for all of them; storage.mode returns "language."
>as.numeric
>returns "Error: 'pairlist' object cannot be coerced to type 'double'."
>In
>what I suspect is a related problem, any command that calls for a
>variable
>name requires an initial ~ to work. That is, instead of plot(miles) I
>have
>to use plot(~miles).
>
>No doubt there is some very elementary mistake I am making, but I can't
>figure it out. Any help would be appreciated.
>
>
>
>   [[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.

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Re: [R] error bars for a barchart

[ilai]

Thank you for your example. I only skimmed it, but since both
solutions use nlevels and box.ratio it is no surprise we end up at the
same place (although I do think your g-median is nicer than my 3/4).

Thing is, I wouldn't call either of these "simple"... would be nice if
one could just query the "new" centers, but I don't know if there is a
way without hacking panel.barchart itself ?

Cheers

On Tue, May 1, 2012 at 1:34 PM, Walmes Zeviani  wrote:
> I have a repoducibe example here
>
> http://ridiculas.wordpress.com/2011/11/23/media-e-desvio-padrao-de-muitas-variaveis-separado-por-grupos/
>
> Sorry for it be in Portuguese.
>
> Walmes.
>
> ==
> Walmes Marques Zeviani
> LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
> Departamento de Estatística - Universidade Federal do Paraná
> fone: (+55) 41 3361 3573
> VoIP: (3361 3600) 1053 1173
> e-mail: wal...@ufpr.br
> twitter: @walmeszeviani
> homepage: http://www.leg.ufpr.br/~walmes
> linux user number: 531218
> ==

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[R] MCMCglmm priors including phylogeny

[Stott, Iain]

Hi all,

I'm hoping I might be able to get some help with some issues specifying priors 
for MCMCglmm.

I'm trying to fit a gaussian glmm using MCMCglmm to a data set with two 
(correlated) response variables.  The response variables are both 
logit-transformed proportions (there are a few reasons why I've chosen these 
with gaussian error over binomal glmm, which I won't  go into).  Each 
probability represents a response for a single plant species (c.150 species), 
and I want to incorporate the phylogeny (almost fully resolved with only 2 
polytomies, including branch lengths) in the error structure.  There is only 1 
explanatory variable, a 5-level factor.  I'm using uninformative priors for 
fixed parameters (i.e. not specifying any priors).

Here's my code:

#prior model1
prior1<-list(R = list(V = diag(2)*x, n=2),
 G = list(G1=list(V = diag(2)*x, n=2)))

#model1
m1<-MCMCglmm(cbind(y1.logit,y2.logit) ~ trait:Ecotype - 1, 
 random=~us(trait):animal, rcov=~us(trait):units, 
family=c("gaussian","gaussian"),
 prior=prior1, data=meandata, pedigree=meantree, nodes="TIPS",
 thin=100, nitt=15, burnin=3, verbose=F)

#prior model2
prior2<-list(R = list(V = diag(2)*x, n=2))

#model2
m2<-MCMCglmm(cbind(reac.prob.logit,inert.prob.logit) ~ trait:Ecotype - 1, 
 rcov=~us(trait):units, family=c("gaussian","gaussian"),
 prior=prior2, data=meandata, 
 thin=100, nitt=15, burnin=3, verbose=F)

I've tried prior variance values of 5, 10, 50, 100, 500, 1000, 5000 and 1 
(by varying x in the code above), and I've used a large thinning interval (100) 
to deal with autocorrelation arising from the correlated responses. Chains seem 
to mix well as long as I use enough iterations (over 10 seems to be best).  
Posterior distributions from plot(model) are normal-distributed for fixed 
effects and residuals in every case.  However, posteriors for errors don't 
behave as nicely:
- Lower prior values (superficially <100) result in positively-skewed 
distributions for trait:animal whereas higher prior values (superficially >100) 
are much more normal.  With the logit data running from ~-3.5 to ~10, it seems 
that the prior values that result in well-fitting models are higher than the 
variance of the data itself.  
- Fixed parameter values vary (but not considerably) with choice of prior, but 
error parameters seem to be more sensitive to prior choice.  
- Posterior means for errors and residuals are larger and more variable for 
y1:y1 and y2:y2 combinations (in the hundreds) but smaller for y1:y2 and y2:y1 
combinations (in the tens).

Considering this, my first question is: what are appropriate priors for G and R?

I'm aware that my priors assume a priori independence between the two 
responses, and I know that they will covary, but my understanding is that 
specifying us(trait) in my errors and residuals in my residuals should estimate 
covariance anyway.  But, my second question is this: what are the merits in 
using a multi-response model?  The phylogenetic models are taking a fair amount 
of time to run, and I hope that without the need to estimate covariances, they 
might be a bit speedier.

At some point, I will want to incorporate replication within species in the 
analysis (populations nested within species), but for now I'm really just 
interested in looking at mean response per species.  I'm assuming that priors 
will probably be of similar value (but more of them) once I include 
within-species replication... or will I have to go through this again??


Any help appreciated, thanks in advance

Iain



Iain Stott
Centre for Ecology and Conservation
University of Exeter, Cornwall Campus
Tremough
Treliever Road
Penryn
Cornwall
TR10 9EZ
Tel: 01326 371852
http://biosciences.exeter.ac.uk/cec/staff/postgradresearch/iainstott/

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[R] Numeric data not numeric in .csv file

[Eve Proper]

I am a raw novice to R, playing around with a mini .csv dataset created in
Excel. I can read it in and the data looks OK in Excel and upon initial
inspection in R:

hikes <- read.csv("/Users/eproper/Desktop/hikes.csv", header=TRUE)
print(hikes)

does exactly what it is supposed to do.

Two of the variables are genuine strings, but the others ought to be
numeric, and R will calculate their min, max etc. However, is.numeric
returns FALSE for all of them; storage.mode returns "language." as.numeric
returns "Error: 'pairlist' object cannot be coerced to type 'double'." In
what I suspect is a related problem, any command that calls for a variable
name requires an initial ~ to work. That is, instead of plot(miles) I have
to use plot(~miles).

No doubt there is some very elementary mistake I am making, but I can't
figure it out. Any help would be appreciated.



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[R] Robust estimation of a geometric random variable

[List User]

Hi,

I have a bunch of data which is assumed to be instances of a geometric random 
variable with outliers. How can I do a robust estimation of the parameter p so 
that the effect of outliers is minimized?
As a part of the estimation process, I also need to know which are the outliers 
in the data. I found glmrob which does robust estimation of Poisson and 
binomial random variables but not geometric random variable.

I understand that the maximum likelihood estimate of p of geometric random 
variable is the mean of the instance values. So if we do robust estimate of 
mean of the instance values, can we say that we are doing robust estimation of 
the underlying geometric random variable? If so, which method is most suitable 
for doing the robust mean estimation. (I am a newbie in statistics and R).


Thanks
suresh
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[R] coxph reference hazard rate

[Georges Dupret]

Hi,

In the following results I interpret exp(coef) as the factor that multiplies
the base hazard rate if the corresponding variable is TRUE. For example,
when the bucket is ks008 and fidelity <= 3, then the rate, compared to the
base rate h_0(t), is h(t) = 0.200 h_0(t). My question is then, to what case
does the base hazard rate correspond to? I would expect the reference to be
the first factor value, i.e. bucket jpc001 with fidelity <= 3, but its
exp(coef) is not one. I verified the contrasts, and the row corresponding to
the first factor value is zero everywhere; moreover, I didn't change the
default, so a bad setting of the contrasts doesn't seem to be the issue.

Best,

ge

Call:
coxph(formula = Surv(time, event = (censored == 
FALSE)) ~ bucket:factor(fidelity > 3), data = week.15)


 coef exp(coef) se(coef)  z  p
bucketjpc001:factor(fidelity > 3)FALSE -1.606 0.201  0.00624 -257.5  0
bucketks006:factor(fidelity > 3)FALSE  -1.613 0.199  0.00627 -257.5  0
bucketks007:factor(fidelity > 3)FALSE  -1.620 0.198  0.00626 -258.8  0
bucketks008:factor(fidelity > 3)FALSE  -1.611 0.200  0.00625 -257.6  0
bucketks009:factor(fidelity > 3)FALSE  -1.620 0.198  0.00626 -258.9  0
bucketks010:factor(fidelity > 3)FALSE  -1.619 0.198  0.00626 -258.6  0
bucketjpc001:factor(fidelity > 3)TRUE  -0.156 0.856  0.00596  -26.2  0
bucketks006:factor(fidelity > 3)TRUE   -0.171 0.842  0.00600  -28.6  0
bucketks007:factor(fidelity > 3)TRUE   -0.168 0.845  0.00602  -28.0  0
bucketks008:factor(fidelity > 3)TRUE   -0.167 0.846  0.00600  -27.8  0
bucketks009:factor(fidelity > 3)TRUE   -0.170 0.844  0.00599  -28.4  0
bucketks010:factor(fidelity > 3)TRUE   NANA  0.0 NA NA

Likelihood ratio test=294562  on 11 df, p=0  n= 1173838, number of events=
629383 

--
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[R] please help me

[Ulfa Hasanah]

hi all,can you help me? index moran is very difficut for me, i have data n 
neighbor as enclosure:
please help me to make the program for find index moran value each 
variabel,...thank very much
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Re: [R] VarCorr procedure from lme4

[David Stevens]

That was it - detaching 'nlme' was the trick. Thanks Walmes and the rest.

David

On 5/1/2012 7:47 PM, David Stevens wrote:
> Yes - I also have nlme.  Bad juju?
>
> David
>
> On 5/1/2012 1:32 PM, Walmes Zeviani wrote:
>> It could be a bad coexistence between packages in the same R session. Are
>> you using nlme and/or doBy packages too?
>>
>> Bests.
>> Walmes.
>>
>> ==
>> Walmes Marques Zeviani
>> LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
>> Departamento de Estatística - Universidade Federal do Paraná
>> fone: (+55) 41 3361 3573
>> VoIP: (3361 3600) 1053 1173
>> e-mail: wal...@ufpr.br
>> twitter: @walmeszeviani
>> homepage: http://www.leg.ufpr.br/~walmes
>> linux user number: 531218
>> ==
>>
>>  [[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.
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
David K Stevens, P.E., Ph.D., Professor
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT  84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stev...@usu.edu




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Re: [R] VarCorr procedure from lme4

[David Stevens]

Yes - I also have nlme.  Bad juju?

David

On 5/1/2012 1:32 PM, Walmes Zeviani wrote:
> It could be a bad coexistence between packages in the same R session. Are
> you using nlme and/or doBy packages too?
>
> Bests.
> Walmes.
>
> ==
> Walmes Marques Zeviani
> LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
> Departamento de Estatística - Universidade Federal do Paraná
> fone: (+55) 41 3361 3573
> VoIP: (3361 3600) 1053 1173
> e-mail: wal...@ufpr.br
> twitter: @walmeszeviani
> homepage: http://www.leg.ufpr.br/~walmes
> linux user number: 531218
> ==
>
>   [[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.

-- 
David K Stevens, P.E., Ph.D., Professor
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT  84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stev...@usu.edu




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

Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

[Ben Bolker]

  wlandres.net> writes:

> 
> On 01-May-2012 19:58:41 Arnaud Mosnier wrote:
> > Dear UseRs,
> > 
> > Is there a way to define the lower-upper bounds for parameters
> > fitted by optim using the Nelder-Mead method ?
> > 
> > Thanks,
> > Arnaud
> 
> The Nelder-Mead method does not provide built-in capability
> to set bounds on the range of paramaters. However, you can
> achieve it "by hand" by re-defining the function being
> minimised, so that it tests whether an out-of-range parameter
> parameter value is being used.
> 
> If not out-of-range, then return the standard value of the function.
> If out-of range, then return a very large value.
> 
> Nelder-Mead will very happily "bounce off" high walls of this
> kind, and if the minimum of the function is at the wall will
> happily converge as close to it as you please.

  In addition to these options, there is also a derivative-free
box-constrained optimizer (bobyqa) in the 'minqa' package (and in
an optim-like wrapper via the optimx package), and
a box-constrained Nelder-Mead optimizer in the development
(r-forge) version of lme4, which is based on the NLopt optimization
library (also accessible via the nloptr package).

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Re: [R] How to Export an R outcome to an Excel Spreadshee​t

[R. Michael Weylandt]

? write.csv

Michael

On May 1, 2012, at 4:52 PM, PaulJr  wrote:

> Hello R community,
> 
> 
> 
> I basically created a normal distribution with mean 2500 and standard
> deviation = 450 with a sample of size 50 and assigned that to a variable
> named genvar2 with the following command:
> 
> 
> 
> genvar2<-rnorm(mean=2500, sd=450, n=50)
> 
> 
> 
> Now, the output of genvar2 generates de following:
> 
> 
> 
> [1] 2478.126 2671.259 2163.879 2440.796 2702.234 1871.514 2525.127 2830.688
> [9] 2704.148 3464.478 2609.795 3368.288 2661.613 2731.901 2535.846 2165.461
> [17] 1870.069 3513.533 2053.342 2447.887 2605.913 2188.192 2514.004 2965.374
> [25] 3550.454 1783.323 2568.323 2324.673 2528.994 2433.895 2751.111 2727.282
> [33] 1837.081 1896.721 3445.993 1357.462 2348.177 2368.423 2029.738 2500.372
> [41] 2000.008 3088.112 3003.325 2763.740 2475.636 1860.988 2292.909 2134.172
> [49] 2291.116 2851.066
> 
> 
> I want to export all of these numbers into a column in an excel file (in an
> xlsx and .csv format).
> 
> 
> 
> How can I do this?
> 
> 
> 
> Any help will be greatly appreciated,
> 
> 
> 
> Best regards,
> 
> 
> 
> Paul
> 
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/How-to-Export-an-R-outcome-to-an-Excel-Spreadshee-t-tp4601703.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.

__
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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] Forecast Package for 2.15.0

[Nordlund, Dan (DSHS/RDA)]

> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of slipkid90515
> Sent: Tuesday, May 01, 2012 2:41 PM
> To: r-help@r-project.org
> Subject: Re: [R] Forecast Package for 2.15.0
> 
> After poking around a little bit, I was able to install the package
> using the
> "Install packages from local zip(s) files" command from the Packages
> menu.
> I had to go grab the zip file from
> "http://cran.stat.sfu.ca/bin/windows/contrib/2.15/"; because it looked
> like R
> was going to a nonexistent URL when I just used the install.packages
> command
> in the console.
> 
> I had to do the same thing for the tseries package, so could that
> suggest
> that it's a problem with R?  Is it pointing to the wrong places?
> 
> In any case, problem solved :)
> 
> Thanks,
> Jess
> 

Jess,

We need a reproducible example, i.e. you need to tell us exactly what you typed 
or what you selected from the menu and also what didn't work (error messages, 
etc) before we can help.  Did you use install.packages() from the console or 
terminal window, or did you use "Install package(s)..." from the packages menu? 
 Are you behind a proxy server?  If so, you may need to see ?setInternet2 help 
page.

Hope this is helpful,

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204


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Re: [R] Where to find the p-value of a correlation test

[Aaditya Nanduri]

Im sorry. I meant cor.test()

On Tue, May 1, 2012 at 6:16 PM, Aaditya Nanduri
wrote:

> Awesome! cor.text() is what I was looking for! Thank you Duncan!
>
>
> On Wed, Apr 25, 2012 at 9:43 AM, Duncan Murdoch 
> wrote:
>
>> On 12-04-25 9:30 AM, Aaditya Nanduri wrote:
>>
>>> Hey everyone,
>>>
>>>
>>> I hope this finds you in good cheer.
>>>
>>> I just have a quick question: What is the function that outputs the
>>> p-value
>>> for correlation?
>>>
>>> cor(x,y) only provides the R value. I would like the p-value associated
>>> with it.
>>>
>>
>> cor(x,y) calculates the correlation, it doesn't perform a test, so there
>> is no p-value.
>>
>> cor.test() performs a test.
>>
>> Duncan Murdoch
>>
>
>
>
> --
>
> *Aaditya Nanduri | Statistical Analyst***
>
> Business Analytics
>
> Aflac Worldwide Headquarters
>
> 1932 Wynnton Road, Columbus, Georgia 31999
>
> Tel: 706.596.2986 | Cell: 908.380.4560
>
>
>
>


-- 

*Aaditya Nanduri | Statistical Analyst***

Business Analytics

Aflac Worldwide Headquarters

1932 Wynnton Road, Columbus, Georgia 31999

Tel: 706.596.2986 | Cell: 908.380.4560

[[alternative HTML version deleted]]

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Re: [R] Where to find the p-value of a correlation test

[Aaditya Nanduri]

Awesome! cor.text() is what I was looking for! Thank you Duncan!

On Wed, Apr 25, 2012 at 9:43 AM, Duncan Murdoch wrote:

> On 12-04-25 9:30 AM, Aaditya Nanduri wrote:
>
>> Hey everyone,
>>
>>
>> I hope this finds you in good cheer.
>>
>> I just have a quick question: What is the function that outputs the
>> p-value
>> for correlation?
>>
>> cor(x,y) only provides the R value. I would like the p-value associated
>> with it.
>>
>
> cor(x,y) calculates the correlation, it doesn't perform a test, so there
> is no p-value.
>
> cor.test() performs a test.
>
> Duncan Murdoch
>



-- 

*Aaditya Nanduri | Statistical Analyst***

Business Analytics

Aflac Worldwide Headquarters

1932 Wynnton Road, Columbus, Georgia 31999

Tel: 706.596.2986 | Cell: 908.380.4560

[[alternative HTML version deleted]]

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

Re: [R] Forecast Package for 2.15.0

[slipkid90515]

After poking around a little bit, I was able to install the package using the
"Install packages from local zip(s) files" command from the Packages menu. 
I had to go grab the zip file from
"http://cran.stat.sfu.ca/bin/windows/contrib/2.15/"; because it looked like R
was going to a nonexistent URL when I just used the install.packages command
in the console.

I had to do the same thing for the tseries package, so could that suggest
that it's a problem with R?  Is it pointing to the wrong places?

In any case, problem solved :)

Thanks,
Jess 

--
View this message in context: 
http://r.789695.n4.nabble.com/Forecast-Package-for-2-15-0-tp4601328p4601792.html
Sent from the R help mailing list archive at Nabble.com.

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

[R] How to Export an R outcome to an Excel Spreadshee​t

[PaulJr]

Hello R community,

 

I basically created a normal distribution with mean 2500 and standard
deviation = 450 with a sample of size 50 and assigned that to a variable
named genvar2 with the following command:

 

genvar2<-rnorm(mean=2500, sd=450, n=50)

 

Now, the output of genvar2 generates de following:

 

[1] 2478.126 2671.259 2163.879 2440.796 2702.234 1871.514 2525.127 2830.688
 [9] 2704.148 3464.478 2609.795 3368.288 2661.613 2731.901 2535.846 2165.461
[17] 1870.069 3513.533 2053.342 2447.887 2605.913 2188.192 2514.004 2965.374
[25] 3550.454 1783.323 2568.323 2324.673 2528.994 2433.895 2751.111 2727.282
[33] 1837.081 1896.721 3445.993 1357.462 2348.177 2368.423 2029.738 2500.372
[41] 2000.008 3088.112 3003.325 2763.740 2475.636 1860.988 2292.909 2134.172
[49] 2291.116 2851.066


I want to export all of these numbers into a column in an excel file (in an
xlsx and .csv format).

 

How can I do this?

 

Any help will be greatly appreciated,

 

Best regards,

 

Paul

--
View this message in context: 
http://r.789695.n4.nabble.com/How-to-Export-an-R-outcome-to-an-Excel-Spreadshee-t-tp4601703.html
Sent from the R help mailing list archive at Nabble.com.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

[Ted Harding]

On 01-May-2012 19:58:41 Arnaud Mosnier wrote:
> Dear UseRs,
> 
> Is there a way to define the lower-upper bounds for parameters
> fitted by optim using the Nelder-Mead method ?
> 
> Thanks,
> Arnaud

The Nelder-Mead method does not provide built-in capability
to set bounds on the range of paramaters. However, you can
achieve it "by hand" by re-defining the function being
minimised, so that it tests whether an out-of-range parameter
parameter value is being used.

If not out-of-range, then return the standard value of the function.
If out-of range, then return a very large value.

Nelder-Mead will very happily "bounce off" high walls of this
kind, and if the minimum of the function is at the wall will
happily converge as close to it as you please.

Hoping this helps,
Ted.

-
E-Mail: (Ted Harding) 
Date: 01-May-2012  Time: 22:39:15
This message was sent by XFMail

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[David Winsemius]

On May 1, 2012, at 1:33 PM, Bert Gunter wrote:


AdvisoRs:

Is the following a bug, feature, hinky error message, or dumb Bert?


mtest <- matrix(1:12,nr=4)
dftest <- data.frame(mtest)
ix <- cbind(1:2,2:3)
mtest[ix] <- NA
mtest

   [,1] [,2] [,3]
[1,]1   NA9
[2,]26   NA
[3,]37   11
[4,]48   12

## But ...

dftest[ix] <- NA

Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
only logical matrix subscripts are allowed in replacement


I'm not sure _I_ would have expected '[<-.data.frame' to recognize  
that a matrix was being offered because the "[.]" formalism  without a  
comma (called "i-indexing" on the help page) would generally be  
referencing only columns (i.e. list elements). I had not realized the  
possibilitiy of offering a logical matrix to df but it does succeed as  
predicted by


?"[.data.frame"

" For replacement, a logical matrix (only) can be used to select the  
elements to be replaced in the same way as for a matrix."


So how you want to characterize documented behavior is your call. I  
would never choose the label you offered.



> mtest <- matrix(FALSE, 4,4)
> ix <- cbind(1:2,2:3)
> dftest <- data.frame(mtest)
> mtest[ix] <- TRUE
> dftest[mtest] <- "a"
> dftest
X1X2X3X4
1 FALSE a FALSE FALSE
2 FALSE FALSE a FALSE
3 FALSE FALSE FALSE FALSE
4 FALSE FALSE FALSE FALSE

The nonassignment operation still succeeds:

> dftest[ix]
[1] "a" "a"



Obviously, I was expecting matrix indexing for replacement to work
similarly in both cases; however, I can see why it would be
problematic for data frames (mixed types), but was a bit nonplussed by
the error message, which seems hinky to me.

Cheers,
Bert

--

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Forecast Package for 2.15.0

[R. Michael Weylandt]

No What have you tried?

OS? R build? Install method? Error messages?

Note this has some C++ dependencies so it might be a little tricky to compile 
if you are missing necessary tools. 

Michael

On May 1, 2012, at 2:05 PM, slipkid90515  wrote:

> Anyone else having problems installing this package?  Any ideas for fixing?
> 
> Thanks,
> Jess
> 
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/Forecast-Package-for-2-15-0-tp4601328.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] How to Export an R outcome to an Excel Spreadsheet

[Roy Mendelssohn]

?write.table

Googling it would find the same thing

-Roy

On May 1, 2012, at 1:41 PM, Paul Bernal wrote:

> Hello R community,
> 
> I basically created a normal distribution with mean 2500 and standard
> deviation = 450 with a sample of size 50 and assigned that to a variable
> named genvar2 with the following command:
> 
> genvar2<-rnorm(mean=2500, sd=450, n=50)
> 
> Now, the output of genvar2 generates de following:
> 
> [1] 2478.126 2671.259 2163.879 2440.796 2702.234 1871.514 2525.127 2830.688
> [9] 2704.148 3464.478 2609.795 3368.288 2661.613 2731.901 2535.846 2165.461
> [17] 1870.069 3513.533 2053.342 2447.887 2605.913 2188.192 2514.004 2965.374
> [25] 3550.454 1783.323 2568.323 2324.673 2528.994 2433.895 2751.111 2727.282
> [33] 1837.081 1896.721 3445.993 1357.462 2348.177 2368.423 2029.738 2500.372
> [41] 2000.008 3088.112 3003.325 2763.740 2475.636 1860.988 2292.909 2134.172
> [49] 2291.116 2851.066
> I want to export all of these numbers into a column in an excel file (in an
> xlsx and .csv format).
> 
> How can I do this?
> 
> Any help will be greatly appreciated,
> 
> Best regards,
> 
> Paul
> 
>   [[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.

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: roy.mendelss...@noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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[R] How to Export an R outcome to an Excel Spreadsheet

[Paul Bernal]

Hello R community,

I basically created a normal distribution with mean 2500 and standard
deviation = 450 with a sample of size 50 and assigned that to a variable
named genvar2 with the following command:

genvar2<-rnorm(mean=2500, sd=450, n=50)

Now, the output of genvar2 generates de following:

[1] 2478.126 2671.259 2163.879 2440.796 2702.234 1871.514 2525.127 2830.688
 [9] 2704.148 3464.478 2609.795 3368.288 2661.613 2731.901 2535.846 2165.461
[17] 1870.069 3513.533 2053.342 2447.887 2605.913 2188.192 2514.004 2965.374
[25] 3550.454 1783.323 2568.323 2324.673 2528.994 2433.895 2751.111 2727.282
[33] 1837.081 1896.721 3445.993 1357.462 2348.177 2368.423 2029.738 2500.372
[41] 2000.008 3088.112 3003.325 2763.740 2475.636 1860.988 2292.909 2134.172
[49] 2291.116 2851.066
I want to export all of these numbers into a column in an excel file (in an
xlsx and .csv format).

How can I do this?

Any help will be greatly appreciated,

Best regards,

Paul

[[alternative HTML version deleted]]

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Rui Barradas]

Hello,


Bert Gunter wrote
> 
> Duncan:
> 
> Maybe there **is** a bug, then.
> 
>  > zmat <- matrix(1:12,nr=4)
>> zdf <- data.frame(zmat)
>> ix <- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
>> zmat[ix]
> [1]  2  3  4  6  7  8 10 11 12
>> zdf[ix]
> [1]  2  3  4  6  7  8 10 11 12
>> zmat[ix] <- NA
>> zmat
>  [,1] [,2] [,3]
> [1,]159
> [2,]   NA   NA   NA
> [3,]   NA   NA   NA
> [4,]   NA   NA   NA
> 
> ## ??
> 
>> zdf[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>   only logical matrix subscripts are allowed in replacement
> 
> That matrix replacement should not work with (in general mixed type)
> data frames seems reasonable, actually. Trying to "fix things" may not
> be. But I leave this to you and your fellow expeRts,
> 
> Cheers,
> Bert
> 
> 
> On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
>  wrote:
>> On 01/05/2012 2:12 PM, Bert Gunter wrote:
>>>
>>> Many thanks, Ista:
>>>
>>> I only looked in "].default" so the answer is: Alternative 4: dumb
>>> Bert. Rap knuckles with ruler.
>>>
>>> Actually, indexing by a logical matrix doesn't make much  sense to me
>>> in either case, as it does not have the effect of selecting individual
>>> elements, which is what numeric matrix indices do. But that's a matter
>>> of usage, neither bug nor feature.
>>>
>>> If I had gotten something like the error message: "Matrix indices not
>>> allowed for replacement in data frames," I would not have been
>>> surprised. But as you said, the behavior **IS** documented.
>>
>>
>> Your version is not correct:  matrix indices *are* allowed for
>> replacement,
>> but only logical matrix indices, not two column numerical ones.   The
>> message might be clearer if instead of saying "only logical matrix
>> subscripts are allowed in replacement"
>> it said "matrix subscripts must be logical matrices in replacement", but
>> I
>> think the basic problem is the limitation.  I'll fix that.
>>
>> Duncan Murdoch
>>
>>>
>>> Best,
>>> Bert
>>>
>>>
>>>
>>> On Tue, May 1, 2012 at 10:49 AM, Ista Zahn  wrote:
>>> >  Hi Bert,
>>> >
>>> >  The failure itself is the documented behavior: ?'[.data.frame' says
>>> >
>>> >  "Matrix indexing ('x[i]' with a logical or a 2-column integer
>>> >       matrix 'i') using '[' is not recommended, and barely supported.
>>> >       For extraction, 'x' is first coerced to a matrix.  For
>>> >       replacement, a logical matrix (only) can be used to select the
>>> >       elements to be replaced in the same way as for a matrix."
>>> >
>>> >  The error message may be a bit hinky, as obviously data.frames can be
>>> >  indexed by things other than logical matricies. Or is there another
>>> >  reason this strikes you as odd?
>>> >
>>> >  Best,
>>> >  Ista
>>> >
>>> >  On Tue, May 1, 2012 at 1:33 PM, Bert Gunter
>>> >  wrote:
>>> >>  AdvisoRs:
>>> >>
>>> >>  Is the following a bug, feature, hinky error message, or dumb Bert?
>>> >>
>>> >>>  mtest<- matrix(1:12,nr=4)
>>> >>>  dftest<- data.frame(mtest)
>>> >>>  ix<- cbind(1:2,2:3)
>>> >>>  mtest[ix]<- NA
>>> >>>  mtest
>>> >>       [,1] [,2] [,3]
>>> >>  [1,]    1   NA    9
>>> >>  [2,]    2    6   NA
>>> >>  [3,]    3    7   11
>>> >>  [4,]    4    8   12
>>> >>
>>> >>  ## But ...
>>> >>>  dftest[ix]<- NA
>>> >>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>>> >>    only logical matrix subscripts are allowed in replacement
>>> >>
>>> >>  Obviously, I was expecting matrix indexing for replacement to work
>>> >>  similarly in both cases; however, I can see why it would be
>>> >>  problematic for data frames (mixed types), but was a bit nonplussed
>>> by
>>> >>  the error message, which seems hinky to me.
>>> >>
>>> >>  Cheers,
>>> >>  Bert
>>> >>
>>> >>  --
>>> >>
>>> >>  Bert Gunter
>>> >>  Genentech Nonclinical Biostatistics
>>> >>
>>> >>  Internal Contact Info:
>>> >>  Phone: 467-7374
>>> >>  Website:
>>> >>
>>> >>
>>>  http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>>> >>
>>> >>  __
>>> >>  R-help@ mailing list
>>> >>  https://stat.ethz.ch/mailman/listinfo/r-help
>>> >>  PLEASE do read the posting guide
>>> >> http://www.R-project.org/posting-guide.html
>>> >>  and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>>
>>
> 
> 
> 
> -- 
> 
> Bert Gunter
> Genentech Nonclinical Biostatistics
> 
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
> 
> __
> R-help@ mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

Actually, it works, as long as the logical index matrix has the same
dimensions as the data frame.


zmat <- matrix(1:12,nr=4)
zdf <- data.frame(zmat)

# Nu

[R] Fitting a first order compartment model in nlme

[Ranae]

Hello,

I am using SSfol in nlme to fit some data for the change of N concentration
(N) in plant tissue over time (gdd).  The model works nicely for 2 out of 3
treatments, so I would really like to use it, but it consistently has a bad
fit for my third treatment.  I am pasting the figure for the third treatment
only.  I feel that I have my fixed and random effects properly identified,
but have also tried many combinations to see if I can improve the fit.  

Are there any other ideas of what I can do to capture the highest point of N
with the model?

http://r.789695.n4.nabble.com/file/n4601419/Predicted_N_2.png 

Here is my code for the figure followed by a link to the dataset.

library(nlme)
cna<-read.table("aboveground C and N, dates removed, zeros added.txt",
header=TRUE)

###Aboveground 2011, treatment PF only
n11a<-subset(cna, cna$year == "2011" & cna$ground == "Above" & cna$trt ==
"PF")
n11a$plotF <- as.factor(n11a$plot)
n11aG<-groupedData(N ~ gdd | plotF, data=n11a)

fit.dose<- nlsList(N ~ SSfol(dose, gdd, lke, lka, lCl), data = n11aG)
plot(intervals(fit.dose), layout=c(3,1))

fit.nlme.11a<- nlme(fit.dose, random=pdDiag(lCl ~ 1))

fit.nlme2.11a<-update(fit.nlme.11a, random = list(lCl + lka ~ 1))
png("thermaltimefigs/Predicted N 1.png")
plot(augPred(fit.nlme.11a), level = 0:1)
dev.off()

png("thermaltimefigs/Predicted N 2.png")
plot(augPred(fit.nlme2.11a), level = 0:1)
dev.off()

data at:
http://dl.dropbox.com/u/21080842/aboveground%20C%20and%20N%2C%20dates%20removed%2C%20zeros%20added.txt

Thanks,

Ranae








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[R] Hypothesis Testing using Wald Criterion for two regression models with dummy variables

[meredith]

I have two models, controlled by dummy variables to see if the models can be
combined into one model with similar intercepts and slopes. Has anyone tried
to conduct this type of test in R. I am utilizing the econometric idea of
hypothesis testing through the hypothesis of coincidence. I have tried to
run an anova with test of Chisq, but I am not sure what the results are
telling. In addition, I used the rms package with a lrm model in an anova
test, again I am not sure what the results are telling me:

Try 1
anova(H,Ha,test="Chi")
Analysis of Variance Table

Model 1: logload ~ logflow
Model 2: logload ~ dummy + logflow
  Res.DfRSS Df Sum of Sq  Pr(>Chi)
1 17 4.6742   
2 16 2.6314  12.0428 0.0004245 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

Try 2:
fit<-lrm(logload~logflow+dummy)
> anova(fit)
Wald Statistics  Response: logload 

 Factor Chi-Square d.f. P 
 logflow17.56  1<.0001
 dummy   5.22  10.0224
 TOTAL  18.03  20.0001

Can anyone help me with this?
Thanks!

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[R] Problems accessing environment() in function

[Heiko Neuhaus]

Hi all,

I am trying to create a list of all variable/value combinations in 
environment().


When a function with unset arguments is called, the method I have been 
using fails with a "missing argument" error. However it should be 
possible to simply skip these missing objects in the generation of the list?


Could anyone recommend me a better way (that does not use a slow 
for/eval-combination) to achieve the desired effect?


You can easily reproduce my problem using this code:

--

test1 <- function(a, b, c)
{
  x <- as.list(environment())
  print ("hi from test1!")
  test2(a = a, b = b, c = c)
}

test2 <- function(a, b, c)
{
  # PROBLEM: Why can't I get a list as in test1() here?
  x <- as.list(environment())
  print ("hi from test2!")
}

test1()

--

I want my list "x" in test2() to work behave just like "x" in test1(). 
(In this example the correct list in test2() would be empty).


Thanks a lot for your time.

Best wishes,
Heiko Neuhaus

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[R] Plotting shapefiles on existing maps

[Brandon Boyd]

Very helpful. One (possible) correction inline below...

On Thu, 30 Mar 2006, Ray Brownrigg wrote:
> > From: nhy303 at abdn.ac.uk
> >
> > I have plotted a map of the Barents Sea and surrounding coastline using:
> >
> > map('worldHires',ylim=c(50,85),xlim=c(5,65),fill=T,resolution=0)
> > map.axes()
> > map.scale(x=30,metric=T)
> >
> > Next, I imported a shapefile with depth contours for the sea:
> >
> > contours<-read.shape("D://My Documents/BarentsSea.shp",dbf.data=T)
> >
> > (This is in mercator projection).
> >
> > Despite extensive searches of the help files and R site, I cannot find a
> > way to plot the contours onto the map.  Does anyone have any
suggestions?
> >
> It is not clear to me exactly what you are having difficulty with, but
> if you are able to produce a contour plot from that data, then note that
> both contour() and map() have an "add" argument, so as long as the axis
> limits are conformant (i.e. both longitude/latitude) you can add one
> plot to the other.
You cannot add projected data to a map() plot - as Ray suggests, the
input shapefile has to be in geographical, not projected coordinates.
If you know the projection of the shapefile (or if there is a *.prj file
accompanying the *.shp), try using the transform() method in the rgdal
package to do this.

If there is a *.prj file, this should work:
library(rgdal)
my_lines <- readOGR(, )
my_lines1 <- transform(my_lines, CRS("+proj=longlat +ellps=WGS84"))

*I believe the above line should be: my_lines1 <- spTransform(my_lines,
CRS("+proj=longlat +ellps=WGS84"))

plot(my_lines1, add=TRUE)

If not, you'll need to work out exactly what the projection is, and set it
in PROJ.4 notation by:
proj4string(my_lines) <- CRS("")
before transform(). Please in both cases do bbox(my_lines1) to see if you
are in the right ballpark.
>
> Perhaps the trick is in converting your contours data into
> longitude/latitude form for the x and y components.
>
> Hope this helps,
> Ray Brownrigg
>
> __
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
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>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no

Brandon

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Rui Barradas]

P.S.

The way the logical matrix is constructed is NOT general purpose.
Quoting myself quoting Bert,
>
> Actually, it works, as long as the logical index matrix has the same
> dimensions as the data frame.
> 
> zmat <- matrix(1:12,nr=4)
> zdf <- data.frame(zmat)
> 
> # Numeric index matrix.
> ix <- cbind(1:2,2:3)
> # Logical index matrix.
> ix2 <- row(zdf) == ix[, 1] & col(zdf) == ix[, 2]
> 

Here the number of rows in zdf is a multiple of the vectors ix[, 1] and ix[
, 2] lengths.
The recycling rules makes it work. But if the numeric index matrix has, say,
3 rows,
another way of constructing the logical one would be needed.

jx <- cbind(1:3, c(2:3, 3))
row(zdf) == jx[, 1] & col(zdf) == jx[, 2]
  [,1]  [,2]  [,3]
[1,] FALSE FALSE FALSE
[2,] FALSE FALSE FALSE
[3,] FALSE FALSE FALSE
[4,] FALSE FALSE FALSE

(Anyway, I don't believe that was the point.)

R.B.



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[R] Forecast Package for 2.15.0

[slipkid90515]

Anyone else having problems installing this package?  Any ideas for fixing?

Thanks,
Jess

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[R] Arules and different item columns with same item labelsŠ.

[Levent TERLEMEZ]

Dear Users,

I have data that have different data columns (hair color, eye color, etc. ) 
with same item labels and I do not want to recode them like haircolor=brown, 
etc. Is it possible to do it automatically?

Thanks right now for your tips and given directions.
--
Levent TERLEMEZ


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Re: [R] [fields:image.plot] subtitle under title (not image)?

[Doug Nychka]

Tom, 
The sub argument will always put text at the bottom -- this is all plotting in 
R not just image.plot
If you want two lines in the title just build in a new line:

z<- outer( 1:15, 1:10,"+")
 image.plot( z, main="the title \n the subtitle")

Best, 
Doug

 
- 
Doug Nychka,

Institute for Mathematics Applied to Geosciences
National Center for Atmospheric Research 
Boulder, CO 
Email: nychka "AT" ucar "DOT" edu  Web: www.image.ucar.edu/~nychka
Voice: 303-497-1711 FAX: 303-497-1298   Business Cell: 303-725-3199


On May 1, 2012, at 10:25 AM, Tom Roche wrote:

> 
> summary: how to make image.plot print a subtitle between the title and
> the image, rather than under the image?
> 
> details:
> 
> I've got a project
> 
> https://github.com/TomRoche/ioapi-hack-R
> 
> that illustrates the use of (et al) the R packages {ncdf4, fields, M3}
> for processing and visualizing IOAPI data. The data being visualized
> consists of a series of layers (mostly representing emissions from a
> particular tuple of agricultural {cultivar, cultivation technique})
> over a surface (in the upper midwest US). I'm currently plotting
> 
> https://github.com/downloads/TomRoche/ioapi-hack-R/compare.DN2.layers.pdf
> 
> each layer, and including some information about the layer in a title
> and subtitle. The title is where I want it--above the image--but the
> subtitle is printing below the image; I'd prefer it between the title
> and the image. Can this be done? FWIW, the code that plots (in
> 
> https://github.com/TomRoche/ioapi-hack-R/blob/master/plotLayersForTimestep.r
> 
> ) is like
> 
>  if (data to plot is not all NA) {
># determine quantiles, then
>image.plot(plot.list, xlab="", ylab="", axes=F, col=colors(100),
>  axis.args=list(at=quantiles, labels=quantiles.formatted),
>  main=title, sub=subtitle)
>lines(map)
>  } else {
>plot(0, type="n", axes=F, xlab="", ylab="",
>  xlim=range(x.centers), ylim=range(y.centers),
>  main=title, sub=subtitle)
>lines(map)
>  } # end testing data
> 
> TIA, Tom Roche 


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Re: [R] 95% confidence interval of the coefficients from a bootstrap analysis

[baconbeach]

Hi Rui,

You are awesome!!! It worked perfectly!!

Thanks 

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Duncan Murdoch]

On 12-05-01 3:57 PM, Nordlund, Dan (DSHS/RDA) wrote:

Bert,

I think this is what is needed for the data frame

ix<- cbind(1:2,2:3)
ixm<- matrix(FALSE,4,3)
ixm[ix]<- TRUE
zdf[ixm]<- NA

Hope this is helpful,


That's essentially what I did in adding the numeric indexing.  The only 
complication was handling the case where ix contains out of bound 
values; users don't want to hear that ixm[ix] <- TRUE failed.


Duncan Murdoch



Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204



-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Bert Gunter
Sent: Tuesday, May 01, 2012 11:46 AM
To: Duncan Murdoch
Cc: r-help@r-project.org
Subject: Re: [R] Data frame vs matrix quirk: Hinky error message?

Duncan:

Maybe there **is** a bug, then.

  >  zmat<- matrix(1:12,nr=4)

zdf<- data.frame(zmat)
ix<- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
zmat[ix]

[1]  2  3  4  6  7  8 10 11 12

zdf[ix]

[1]  2  3  4  6  7  8 10 11 12

zmat[ix]<- NA
zmat

  [,1] [,2] [,3]
[1,]159
[2,]   NA   NA   NA
[3,]   NA   NA   NA
[4,]   NA   NA   NA

## ??


zdf[ix]<- NA

Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
   only logical matrix subscripts are allowed in replacement

That matrix replacement should not work with (in general mixed type)
data frames seems reasonable, actually. Trying to "fix things" may not
be. But I leave this to you and your fellow expeRts,

Cheers,
Bert


On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
  wrote:

On 01/05/2012 2:12 PM, Bert Gunter wrote:


Many thanks, Ista:

I only looked in "].default" so the answer is: Alternative 4: dumb
Bert. Rap knuckles with ruler.

Actually, indexing by a logical matrix doesn't make much  sense to

me

in either case, as it does not have the effect of selecting

individual

elements, which is what numeric matrix indices do. But that's a

matter

of usage, neither bug nor feature.

If I had gotten something like the error message: "Matrix indices

not

allowed for replacement in data frames," I would not have been
surprised. But as you said, the behavior **IS** documented.



Your version is not correct:  matrix indices *are* allowed for

replacement,

but only logical matrix indices, not two column numerical ones.   The
message might be clearer if instead of saying "only logical matrix
subscripts are allowed in replacement"
it said "matrix subscripts must be logical matrices in replacement",

but I

think the basic problem is the limitation.  I'll fix that.

Duncan Murdoch



Best,
Bert



On Tue, May 1, 2012 at 10:49 AM, Ista Zahn

  wrote:

  Hi Bert,

  The failure itself is the documented behavior: ?'[.data.frame'

says


  "Matrix indexing ('x[i]' with a logical or a 2-column integer
   matrix 'i') using '[' is not recommended, and barely

supported.

   For extraction, 'x' is first coerced to a matrix.  For
   replacement, a logical matrix (only) can be used to select

the

   elements to be replaced in the same way as for a matrix."

  The error message may be a bit hinky, as obviously data.frames

can be

  indexed by things other than logical matricies. Or is there

another

  reason this strikes you as odd?

  Best,
  Ista

  On Tue, May 1, 2012 at 1:33 PM, Bert

Gunter

  wrote:

  AdvisoRs:

  Is the following a bug, feature, hinky error message, or dumb

Bert?



  mtest<- matrix(1:12,nr=4)
  dftest<- data.frame(mtest)
  ix<- cbind(1:2,2:3)
  mtest[ix]<- NA
  mtest

   [,1] [,2] [,3]
  [1,]1   NA9
  [2,]26   NA
  [3,]37   11
  [4,]48   12

  ## But ...

  dftest[ix]<- NA

  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
only logical matrix subscripts are allowed in replacement

  Obviously, I was expecting matrix indexing for replacement to

work

  similarly in both cases; however, I can see why it would be
  problematic for data frames (mixed types), but was a bit

nonplussed by

  the error message, which seems hinky to me.

  Cheers,
  Bert

  --

  Bert Gunter
  Genentech Nonclinical Biostatistics

  Internal Contact Info:
  Phone: 467-7374
  Website:

  http://pharmadevelopment.roche.com/index/pdb/pdb-functional-

groups/pdb-biostatistics/pdb-ncb-home.htm


  __
  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.










--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-
biostatistics/pdb-ncb-home.htm

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PLEASE do read the pos

Re: [R] Data frame vs matrix quirk: Hinky error message?

[Bert Gunter]

Many thanks to all. I appreciate your kindness and patience.

The point is, of course, that matrix subscripting by logicals requires
different semantics than by numeric indices, as it must. I'd still say
this is a case of option 4, dumb Bert: I should have figured this out.

Duncan's proposed changes to both behavior and documentation would
certainly address all my points of confusion. However, I agree that
numeric replacement indices for data frames may be a can of worms:
presumably silent type conversion would be required when replacing
values in mixed type columns. Keeping the warnings in -- and maybe
issuing some more when the type conversion occurs -- is certainly a
good idea.

Best,
Bert

On Tue, May 1, 2012 at 12:57 PM, Nordlund, Dan (DSHS/RDA)
 wrote:
> Bert,
>
> I think this is what is needed for the data frame
>
> ix <- cbind(1:2,2:3)
> ixm <- matrix(FALSE,4,3)
> ixm[ix] <- TRUE
> zdf[ixm] <- NA
>
> Hope this is helpful,
>
> Dan
>
> Daniel J. Nordlund
> Washington State Department of Social and Health Services
> Planning, Performance, and Accountability
> Research and Data Analysis Division
> Olympia, WA 98504-5204
>
>
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
>> project.org] On Behalf Of Bert Gunter
>> Sent: Tuesday, May 01, 2012 11:46 AM
>> To: Duncan Murdoch
>> Cc: r-help@r-project.org
>> Subject: Re: [R] Data frame vs matrix quirk: Hinky error message?
>>
>> Duncan:
>>
>> Maybe there **is** a bug, then.
>>
>>  > zmat <- matrix(1:12,nr=4)
>> > zdf <- data.frame(zmat)
>> > ix <- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
>> > zmat[ix]
>> [1] 2 3 4 6 7 8 10 11 12
>> > zdf[ix]
>> [1] 2 3 4 6 7 8 10 11 12
>> > zmat[ix] <- NA
>> > zmat
>>      [,1] [,2] [,3]
>> [1,]    1    5    9
>> [2,]   NA   NA   NA
>> [3,]   NA   NA   NA
>> [4,]   NA   NA   NA
>>
>> ## ??
>>
>> > zdf[ix] <- NA
>> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>>   only logical matrix subscripts are allowed in replacement
>>
>> That matrix replacement should not work with (in general mixed type)
>> data frames seems reasonable, actually. Trying to "fix things" may not
>> be. But I leave this to you and your fellow expeRts,
>>
>> Cheers,
>> Bert
>>
>>
>> On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
>>  wrote:
>> > On 01/05/2012 2:12 PM, Bert Gunter wrote:
>> >>
>> >> Many thanks, Ista:
>> >>
>> >> I only looked in "].default" so the answer is: Alternative 4: dumb
>> >> Bert. Rap knuckles with ruler.
>> >>
>> >> Actually, indexing by a logical matrix doesn't make much  sense to
>> me
>> >> in either case, as it does not have the effect of selecting
>> individual
>> >> elements, which is what numeric matrix indices do. But that's a
>> matter
>> >> of usage, neither bug nor feature.
>> >>
>> >> If I had gotten something like the error message: "Matrix indices
>> not
>> >> allowed for replacement in data frames," I would not have been
>> >> surprised. But as you said, the behavior **IS** documented.
>> >
>> >
>> > Your version is not correct:  matrix indices *are* allowed for
>> replacement,
>> > but only logical matrix indices, not two column numerical ones.   The
>> > message might be clearer if instead of saying "only logical matrix
>> > subscripts are allowed in replacement"
>> > it said "matrix subscripts must be logical matrices in replacement",
>> but I
>> > think the basic problem is the limitation.  I'll fix that.
>> >
>> > Duncan Murdoch
>> >
>> >>
>> >> Best,
>> >> Bert
>> >>
>> >>
>> >>
>> >> On Tue, May 1, 2012 at 10:49 AM, Ista Zahn
>>  wrote:
>> >> >  Hi Bert,
>> >> >
>> >> >  The failure itself is the documented behavior: ?'[.data.frame'
>> says
>> >> >
>> >> >  "Matrix indexing ('x[i]' with a logical or a 2-column integer
>> >> >       matrix 'i') using '[' is not recommended, and barely
>> supported.
>> >> >       For extraction, 'x' is first coerced to a matrix.  For
>> >> >       replacement, a logical matrix (only) can be used to select
>> the
>> >> >       elements to be replaced in the same way as for a matrix."
>> >> >
>> >> >  The error message may be a bit hinky, as obviously data.frames
>> can be
>> >> >  indexed by things other than logical matricies. Or is there
>> another
>> >> >  reason this strikes you as odd?
>> >> >
>> >> >  Best,
>> >> >  Ista
>> >> >
>> >> >  On Tue, May 1, 2012 at 1:33 PM, Bert
>> Gunter
>> >> >  wrote:
>> >> >>  AdvisoRs:
>> >> >>
>> >> >>  Is the following a bug, feature, hinky error message, or dumb
>> Bert?
>> >> >>
>> >> >>>  mtest<- matrix(1:12,nr=4)
>> >> >>>  dftest<- data.frame(mtest)
>> >> >>>  ix<- cbind(1:2,2:3)
>> >> >>>  mtest[ix]<- NA
>> >> >>>  mtest
>> >> >>       [,1] [,2] [,3]
>> >> >>  [1,]    1   NA    9
>> >> >>  [2,]    2    6   NA
>> >> >>  [3,]    3    7   11
>> >> >>  [4,]    4    8   12
>> >> >>
>> >> >>  ## But ...
>> >> >>>  dftest[ix]<- NA
>> >> >>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>> >> >>    only logical matrix subscripts are allowed in replacement
>> >> >>
>> >> >>  Obviously,

Re: [R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

[Thomas Lumley]

On Wed, May 2, 2012 at 7:58 AM, Arnaud Mosnier  wrote:
> Dear UseRs,
>
> Is there a way to define the lower-upper bounds for parameters fitted by
> optim using the Nelder-Mead method ?
>

It depends a bit on whether it's plausible that the solution is on the
boundary.  If not, simply returning Inf for values outside the range
will work.

-thomas

-- 
Thomas Lumley
Professor of Biostatistics
University of Auckland

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[R] Define lower-upper bound for parameters in Optim using Nelder-Mead method

[Arnaud Mosnier]

Dear UseRs,

Is there a way to define the lower-upper bounds for parameters fitted by
optim using the Nelder-Mead method ?

Thanks,

Arnaud

[[alternative HTML version deleted]]

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Nordlund, Dan (DSHS/RDA)]

Bert,

I think this is what is needed for the data frame

ix <- cbind(1:2,2:3)
ixm <- matrix(FALSE,4,3)
ixm[ix] <- TRUE
zdf[ixm] <- NA

Hope this is helpful,

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204


> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of Bert Gunter
> Sent: Tuesday, May 01, 2012 11:46 AM
> To: Duncan Murdoch
> Cc: r-help@r-project.org
> Subject: Re: [R] Data frame vs matrix quirk: Hinky error message?
> 
> Duncan:
> 
> Maybe there **is** a bug, then.
> 
>  > zmat <- matrix(1:12,nr=4)
> > zdf <- data.frame(zmat)
> > ix <- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
> > zmat[ix]
> [1]  2  3  4  6  7  8 10 11 12
> > zdf[ix]
> [1]  2  3  4  6  7  8 10 11 12
> > zmat[ix] <- NA
> > zmat
>  [,1] [,2] [,3]
> [1,]159
> [2,]   NA   NA   NA
> [3,]   NA   NA   NA
> [4,]   NA   NA   NA
> 
> ## ??
> 
> > zdf[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>   only logical matrix subscripts are allowed in replacement
> 
> That matrix replacement should not work with (in general mixed type)
> data frames seems reasonable, actually. Trying to "fix things" may not
> be. But I leave this to you and your fellow expeRts,
> 
> Cheers,
> Bert
> 
> 
> On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
>  wrote:
> > On 01/05/2012 2:12 PM, Bert Gunter wrote:
> >>
> >> Many thanks, Ista:
> >>
> >> I only looked in "].default" so the answer is: Alternative 4: dumb
> >> Bert. Rap knuckles with ruler.
> >>
> >> Actually, indexing by a logical matrix doesn't make much  sense to
> me
> >> in either case, as it does not have the effect of selecting
> individual
> >> elements, which is what numeric matrix indices do. But that's a
> matter
> >> of usage, neither bug nor feature.
> >>
> >> If I had gotten something like the error message: "Matrix indices
> not
> >> allowed for replacement in data frames," I would not have been
> >> surprised. But as you said, the behavior **IS** documented.
> >
> >
> > Your version is not correct:  matrix indices *are* allowed for
> replacement,
> > but only logical matrix indices, not two column numerical ones.   The
> > message might be clearer if instead of saying "only logical matrix
> > subscripts are allowed in replacement"
> > it said "matrix subscripts must be logical matrices in replacement",
> but I
> > think the basic problem is the limitation.  I'll fix that.
> >
> > Duncan Murdoch
> >
> >>
> >> Best,
> >> Bert
> >>
> >>
> >>
> >> On Tue, May 1, 2012 at 10:49 AM, Ista Zahn
>  wrote:
> >> >  Hi Bert,
> >> >
> >> >  The failure itself is the documented behavior: ?'[.data.frame'
> says
> >> >
> >> >  "Matrix indexing ('x[i]' with a logical or a 2-column integer
> >> >       matrix 'i') using '[' is not recommended, and barely
> supported.
> >> >       For extraction, 'x' is first coerced to a matrix.  For
> >> >       replacement, a logical matrix (only) can be used to select
> the
> >> >       elements to be replaced in the same way as for a matrix."
> >> >
> >> >  The error message may be a bit hinky, as obviously data.frames
> can be
> >> >  indexed by things other than logical matricies. Or is there
> another
> >> >  reason this strikes you as odd?
> >> >
> >> >  Best,
> >> >  Ista
> >> >
> >> >  On Tue, May 1, 2012 at 1:33 PM, Bert
> Gunter
> >> >  wrote:
> >> >>  AdvisoRs:
> >> >>
> >> >>  Is the following a bug, feature, hinky error message, or dumb
> Bert?
> >> >>
> >> >>>  mtest<- matrix(1:12,nr=4)
> >> >>>  dftest<- data.frame(mtest)
> >> >>>  ix<- cbind(1:2,2:3)
> >> >>>  mtest[ix]<- NA
> >> >>>  mtest
> >> >>       [,1] [,2] [,3]
> >> >>  [1,]    1   NA    9
> >> >>  [2,]    2    6   NA
> >> >>  [3,]    3    7   11
> >> >>  [4,]    4    8   12
> >> >>
> >> >>  ## But ...
> >> >>>  dftest[ix]<- NA
> >> >>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
> >> >>    only logical matrix subscripts are allowed in replacement
> >> >>
> >> >>  Obviously, I was expecting matrix indexing for replacement to
> work
> >> >>  similarly in both cases; however, I can see why it would be
> >> >>  problematic for data frames (mixed types), but was a bit
> nonplussed by
> >> >>  the error message, which seems hinky to me.
> >> >>
> >> >>  Cheers,
> >> >>  Bert
> >> >>
> >> >>  --
> >> >>
> >> >>  Bert Gunter
> >> >>  Genentech Nonclinical Biostatistics
> >> >>
> >> >>  Internal Contact Info:
> >> >>  Phone: 467-7374
> >> >>  Website:
> >> >>
> >> >>  http://pharmadevelopment.roche.com/index/pdb/pdb-functional-
> groups/pdb-biostatistics/pdb-ncb-home.htm
> >> >>
> >> >>  __
> >> >>  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,

Re: [R] error bars for a barchart

[Walmes Zeviani]

I have a repoducibe example here

http://ridiculas.wordpress.com/2011/11/23/media-e-desvio-padrao-de-muitas-variaveis-separado-por-grupos/

Sorry for it be in Portuguese.

Walmes.

==
Walmes Marques Zeviani
LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
Departamento de Estatística - Universidade Federal do Paraná
fone: (+55) 41 3361 3573
VoIP: (3361 3600) 1053 1173
e-mail: wal...@ufpr.br
twitter: @walmeszeviani
homepage: http://www.leg.ufpr.br/~walmes
linux user number: 531218
==

[[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] VarCorr procedure from lme4

[Walmes Zeviani]

It could be a bad coexistence between packages in the same R session. Are
you using nlme and/or doBy packages too?

Bests.
Walmes.

==
Walmes Marques Zeviani
LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
Departamento de Estatística - Universidade Federal do Paraná
fone: (+55) 41 3361 3573
VoIP: (3361 3600) 1053 1173
e-mail: wal...@ufpr.br
twitter: @walmeszeviani
homepage: http://www.leg.ufpr.br/~walmes
linux user number: 531218
==

[[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] Data frame vs matrix quirk: Hinky error message?

[Duncan Murdoch]

On 01/05/2012 2:45 PM, Bert Gunter wrote:

Duncan:

Maybe there **is** a bug, then.

  >  zmat<- matrix(1:12,nr=4)
>  zdf<- data.frame(zmat)
>  ix<- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
>  zmat[ix]
[1]  2  3  4  6  7  8 10 11 12
>  zdf[ix]
[1]  2  3  4  6  7  8 10 11 12
>  zmat[ix]<- NA
>  zmat
  [,1] [,2] [,3]
[1,]159
[2,]   NA   NA   NA
[3,]   NA   NA   NA
[4,]   NA   NA   NA

## ??

>  zdf[ix]<- NA
Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
   only logical matrix subscripts are allowed in replacement

That matrix replacement should not work with (in general mixed type)
data frames seems reasonable, actually. Trying to "fix things" may not
be. But I leave this to you and your fellow expeRts,


My intention is to allow two column numeric indices, not to change the 
behaviour for logical matrix indices.  I'm planning to leave the "not 
recommended" note in the help page, because there will still be 
surprises as above, but the error message will just say


illegal matrix index in replacement

The rule will remain that a logical matrix needs to be of the same 
dimension as the original dataframe.  I'm not sure if this is documented 
currently, but it will be.


Duncan Murdoch



Cheers,
Bert


On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
  wrote:
>  On 01/05/2012 2:12 PM, Bert Gunter wrote:
>>
>>  Many thanks, Ista:
>>
>>  I only looked in "].default" so the answer is: Alternative 4: dumb
>>  Bert. Rap knuckles with ruler.
>>
>>  Actually, indexing by a logical matrix doesn't make much  sense to me
>>  in either case, as it does not have the effect of selecting individual
>>  elements, which is what numeric matrix indices do. But that's a matter
>>  of usage, neither bug nor feature.
>>
>>  If I had gotten something like the error message: "Matrix indices not
>>  allowed for replacement in data frames," I would not have been
>>  surprised. But as you said, the behavior **IS** documented.
>
>
>  Your version is not correct:  matrix indices *are* allowed for replacement,
>  but only logical matrix indices, not two column numerical ones.   The
>  message might be clearer if instead of saying "only logical matrix
>  subscripts are allowed in replacement"
>  it said "matrix subscripts must be logical matrices in replacement", but I
>  think the basic problem is the limitation.  I'll fix that.
>
>  Duncan Murdoch
>
>>
>>  Best,
>>  Bert
>>
>>
>>
>>  On Tue, May 1, 2012 at 10:49 AM, Ista Zahnwrote:
>>  >Hi Bert,
>>  >
>>  >The failure itself is the documented behavior: ?'[.data.frame' says
>>  >
>>  >"Matrix indexing ('x[i]' with a logical or a 2-column integer
>>  > matrix 'i') using '[' is not recommended, and barely supported.
>>  > For extraction, 'x' is first coerced to a matrix.  For
>>  > replacement, a logical matrix (only) can be used to select the
>>  > elements to be replaced in the same way as for a matrix."
>>  >
>>  >The error message may be a bit hinky, as obviously data.frames can be
>>  >indexed by things other than logical matricies. Or is there another
>>  >reason this strikes you as odd?
>>  >
>>  >Best,
>>  >Ista
>>  >
>>  >On Tue, May 1, 2012 at 1:33 PM, Bert Gunter
>>  >wrote:
>>  >>AdvisoRs:
>>  >>
>>  >>Is the following a bug, feature, hinky error message, or dumb Bert?
>>  >>
>>  >>>mtest<- matrix(1:12,nr=4)
>>  >>>dftest<- data.frame(mtest)
>>  >>>ix<- cbind(1:2,2:3)
>>  >>>mtest[ix]<- NA
>>  >>>mtest
>>  >> [,1] [,2] [,3]
>>  >>[1,]1   NA9
>>  >>[2,]26   NA
>>  >>[3,]37   11
>>  >>[4,]48   12
>>  >>
>>  >>## But ...
>>  >>>dftest[ix]<- NA
>>  >>Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>>  >>  only logical matrix subscripts are allowed in replacement
>>  >>
>>  >>Obviously, I was expecting matrix indexing for replacement to work
>>  >>similarly in both cases; however, I can see why it would be
>>  >>problematic for data frames (mixed types), but was a bit nonplussed by
>>  >>the error message, which seems hinky to me.
>>  >>
>>  >>Cheers,
>>  >>Bert
>>  >>
>>  >>--
>>  >>
>>  >>Bert Gunter
>>  >>Genentech Nonclinical Biostatistics
>>  >>
>>  >>Internal Contact Info:
>>  >>Phone: 467-7374
>>  >>Website:
>>  >>
>>  >>
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>>  >>
>>  >>__
>>  >>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.
>>
>>
>>
>





__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://ww

Re: [R] Data frame vs matrix quirk: Hinky error message?

[David L Carlson]

The difference is in recycling. If the logical matrix has the same
dimensions, it seems to work:

> jx <- cbind(c(FALSE, TRUE, FALSE, TRUE), c(TRUE, FALSE, TRUE, FALSE),
c(FALSE, TRUE, FALSE, TRUE))
> zmat[jx] <- NA
> zmat
 [,1] [,2] [,3]
[1,]1   NA9
[2,]   NA6   NA
[3,]3   NA   11
[4,]   NA8   NA
> zdf[jx] <- NA
> zdf
  X1 X2 X3
1  1 NA  9
2 NA  6 NA
3  3 NA 11
4 NA  8 NA

--
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352



> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of Bert Gunter
> Sent: Tuesday, May 01, 2012 1:46 PM
> To: Duncan Murdoch
> Cc: r-help@r-project.org
> Subject: Re: [R] Data frame vs matrix quirk: Hinky error message?
> 
> Duncan:
> 
> Maybe there **is** a bug, then.
> 
>  > zmat <- matrix(1:12,nr=4)
> > zdf <- data.frame(zmat)
> > ix <- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
> > zmat[ix]
> [1]  2  3  4  6  7  8 10 11 12
> > zdf[ix]
> [1]  2  3  4  6  7  8 10 11 12
> > zmat[ix] <- NA
> > zmat
>  [,1] [,2] [,3]
> [1,]159
> [2,]   NA   NA   NA
> [3,]   NA   NA   NA
> [4,]   NA   NA   NA
> 
> ## ??
> 
> > zdf[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>   only logical matrix subscripts are allowed in replacement
> 
> That matrix replacement should not work with (in general mixed type)
> data frames seems reasonable, actually. Trying to "fix things" may not
> be. But I leave this to you and your fellow expeRts,
> 
> Cheers,
> Bert
> 
> 
> On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
>  wrote:
> > On 01/05/2012 2:12 PM, Bert Gunter wrote:
> >>
> >> Many thanks, Ista:
> >>
> >> I only looked in "].default" so the answer is: Alternative 4: dumb
> >> Bert. Rap knuckles with ruler.
> >>
> >> Actually, indexing by a logical matrix doesn't make much  sense to
> me
> >> in either case, as it does not have the effect of selecting
> individual
> >> elements, which is what numeric matrix indices do. But that's a
> matter
> >> of usage, neither bug nor feature.
> >>
> >> If I had gotten something like the error message: "Matrix indices
> not
> >> allowed for replacement in data frames," I would not have been
> >> surprised. But as you said, the behavior **IS** documented.
> >
> >
> > Your version is not correct:  matrix indices *are* allowed for
> replacement,
> > but only logical matrix indices, not two column numerical ones.   The
> > message might be clearer if instead of saying "only logical matrix
> > subscripts are allowed in replacement"
> > it said "matrix subscripts must be logical matrices in replacement",
> but I
> > think the basic problem is the limitation.  I'll fix that.
> >
> > Duncan Murdoch
> >
> >>
> >> Best,
> >> Bert
> >>
> >>
> >>
> >> On Tue, May 1, 2012 at 10:49 AM, Ista Zahn
>  wrote:
> >> >  Hi Bert,
> >> >
> >> >  The failure itself is the documented behavior: ?'[.data.frame'
> says
> >> >
> >> >  "Matrix indexing ('x[i]' with a logical or a 2-column integer
> >> >       matrix 'i') using '[' is not recommended, and barely
> supported.
> >> >       For extraction, 'x' is first coerced to a matrix.  For
> >> >       replacement, a logical matrix (only) can be used to select
> the
> >> >       elements to be replaced in the same way as for a matrix."
> >> >
> >> >  The error message may be a bit hinky, as obviously data.frames
> can be
> >> >  indexed by things other than logical matricies. Or is there
> another
> >> >  reason this strikes you as odd?
> >> >
> >> >  Best,
> >> >  Ista
> >> >
> >> >  On Tue, May 1, 2012 at 1:33 PM, Bert
> Gunter
> >> >  wrote:
> >> >>  AdvisoRs:
> >> >>
> >> >>  Is the following a bug, feature, hinky error message, or dumb
> Bert?
> >> >>
> >> >>>  mtest<- matrix(1:12,nr=4)
> >> >>>  dftest<- data.frame(mtest)
> >> >>>  ix<- cbind(1:2,2:3)
> >> >>>  mtest[ix]<- NA
> >> >>>  mtest
> >> >>       [,1] [,2] [,3]
> >> >>  [1,]    1   NA    9
> >> >>  [2,]    2    6   NA
> >> >>  [3,]    3    7   11
> >> >>  [4,]    4    8   12
> >> >>
> >> >>  ## But ...
> >> >>>  dftest[ix]<- NA
> >> >>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
> >> >>    only logical matrix subscripts are allowed in replacement
> >> >>
> >> >>  Obviously, I was expecting matrix indexing for replacement to
> work
> >> >>  similarly in both cases; however, I can see why it would be
> >> >>  problematic for data frames (mixed types), but was a bit
> nonplussed by
> >> >>  the error message, which seems hinky to me.
> >> >>
> >> >>  Cheers,
> >> >>  Bert
> >> >>
> >> >>  --
> >> >>
> >> >>  Bert Gunter
> >> >>  Genentech Nonclinical Biostatistics
> >> >>
> >> >>  Internal Contact Info:
> >> >>  Phone: 467-7374
> >> >>  Website:
> >> >>
> >> >>  http://pharmadevelopment.roche.com/index/pdb/pdb-functional-
> groups/pdb-biostatistics/pdb-ncb-home.htm
> >> >>
> >> >>  __
> >> >>  R-help@r-project.org mailing

Re: [R] VarCorr procedure from lme4

[Doran, Harold]

Can you give sessionInfo()? It is working fine for me. 

> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of David Stevens
> Sent: Tuesday, May 01, 2012 2:38 PM
> To: r-help@r-project.org
> Subject: [R] VarCorr procedure from lme4
> 
> Folks
> 
> In trying to use lmer for a hierarchical model, I encountered the
> following message:
> 
> 
> Error in UseMethod("VarCorr") :
>no applicable method for 'VarCorr' applied to an object of class "mer"
> 
> foo.mer <- lmer(y ~ TP + (TP|M),data=joe.q)
> 
>  > head(joe.q[,1:5])
>TP   M AB Trty
> 1  1 Jan  A  NN 19.20002
> 2  1 Jan  A  NN 19.06378
> 3  1 Jan  A  NN 21.36292
> 4  1 Jan  A  NN 16.85191
> 5  1 Jan  A   N 17.89363
> 6  1 Jan  A   N 15.53853
> I tried this through the display(foo.mer) from arm and by VarCorr(foo.mer)
> My understanding is the VarCorr was essentially designed to work with
> 'mer' objects. Am I wrong about this?  The lmer procedure seemed to work
> fine
> 
> --
> David K Stevens, P.E., Ph.D., Professor
> Civil and Environmental Engineering
> Utah Water Research Laboratory
> 8200 Old Main Hill
> Logan, UT  84322-8200
> 435 797 3229 - voice
> 435 797 1363 - fax
> david.stev...@usu.edu
> 
> 
> 
> 
>   [[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.

__
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] Data frame vs matrix quirk: Hinky error message?

[Bert Gunter]

Duncan:

Maybe there **is** a bug, then.

 > zmat <- matrix(1:12,nr=4)
> zdf <- data.frame(zmat)
> ix <- cbind(c(FALSE,TRUE),c(TRUE,TRUE))
> zmat[ix]
[1]  2  3  4  6  7  8 10 11 12
> zdf[ix]
[1]  2  3  4  6  7  8 10 11 12
> zmat[ix] <- NA
> zmat
 [,1] [,2] [,3]
[1,]159
[2,]   NA   NA   NA
[3,]   NA   NA   NA
[4,]   NA   NA   NA

## ??

> zdf[ix] <- NA
Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
  only logical matrix subscripts are allowed in replacement

That matrix replacement should not work with (in general mixed type)
data frames seems reasonable, actually. Trying to "fix things" may not
be. But I leave this to you and your fellow expeRts,

Cheers,
Bert


On Tue, May 1, 2012 at 11:30 AM, Duncan Murdoch
 wrote:
> On 01/05/2012 2:12 PM, Bert Gunter wrote:
>>
>> Many thanks, Ista:
>>
>> I only looked in "].default" so the answer is: Alternative 4: dumb
>> Bert. Rap knuckles with ruler.
>>
>> Actually, indexing by a logical matrix doesn't make much  sense to me
>> in either case, as it does not have the effect of selecting individual
>> elements, which is what numeric matrix indices do. But that's a matter
>> of usage, neither bug nor feature.
>>
>> If I had gotten something like the error message: "Matrix indices not
>> allowed for replacement in data frames," I would not have been
>> surprised. But as you said, the behavior **IS** documented.
>
>
> Your version is not correct:  matrix indices *are* allowed for replacement,
> but only logical matrix indices, not two column numerical ones.   The
> message might be clearer if instead of saying "only logical matrix
> subscripts are allowed in replacement"
> it said "matrix subscripts must be logical matrices in replacement", but I
> think the basic problem is the limitation.  I'll fix that.
>
> Duncan Murdoch
>
>>
>> Best,
>> Bert
>>
>>
>>
>> On Tue, May 1, 2012 at 10:49 AM, Ista Zahn  wrote:
>> >  Hi Bert,
>> >
>> >  The failure itself is the documented behavior: ?'[.data.frame' says
>> >
>> >  "Matrix indexing ('x[i]' with a logical or a 2-column integer
>> >       matrix 'i') using '[' is not recommended, and barely supported.
>> >       For extraction, 'x' is first coerced to a matrix.  For
>> >       replacement, a logical matrix (only) can be used to select the
>> >       elements to be replaced in the same way as for a matrix."
>> >
>> >  The error message may be a bit hinky, as obviously data.frames can be
>> >  indexed by things other than logical matricies. Or is there another
>> >  reason this strikes you as odd?
>> >
>> >  Best,
>> >  Ista
>> >
>> >  On Tue, May 1, 2012 at 1:33 PM, Bert Gunter
>> >  wrote:
>> >>  AdvisoRs:
>> >>
>> >>  Is the following a bug, feature, hinky error message, or dumb Bert?
>> >>
>> >>>  mtest<- matrix(1:12,nr=4)
>> >>>  dftest<- data.frame(mtest)
>> >>>  ix<- cbind(1:2,2:3)
>> >>>  mtest[ix]<- NA
>> >>>  mtest
>> >>       [,1] [,2] [,3]
>> >>  [1,]    1   NA    9
>> >>  [2,]    2    6   NA
>> >>  [3,]    3    7   11
>> >>  [4,]    4    8   12
>> >>
>> >>  ## But ...
>> >>>  dftest[ix]<- NA
>> >>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>> >>    only logical matrix subscripts are allowed in replacement
>> >>
>> >>  Obviously, I was expecting matrix indexing for replacement to work
>> >>  similarly in both cases; however, I can see why it would be
>> >>  problematic for data frames (mixed types), but was a bit nonplussed by
>> >>  the error message, which seems hinky to me.
>> >>
>> >>  Cheers,
>> >>  Bert
>> >>
>> >>  --
>> >>
>> >>  Bert Gunter
>> >>  Genentech Nonclinical Biostatistics
>> >>
>> >>  Internal Contact Info:
>> >>  Phone: 467-7374
>> >>  Website:
>> >>
>> >>  http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>> >>
>> >>  __
>> >>  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.
>>
>>
>>
>



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

__
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] VarCorr procedure from lme4

[David Stevens]

Folks

In trying to use lmer for a hierarchical model, I encountered the 
following message:


Error in UseMethod("VarCorr") :
   no applicable method for 'VarCorr' applied to an object of class "mer"

foo.mer <- lmer(y ~ TP + (TP|M),data=joe.q)

 > head(joe.q[,1:5])
   TP   M AB Trty
1  1 Jan  A  NN 19.20002
2  1 Jan  A  NN 19.06378
3  1 Jan  A  NN 21.36292
4  1 Jan  A  NN 16.85191
5  1 Jan  A   N 17.89363
6  1 Jan  A   N 15.53853
I tried this through the display(foo.mer) from arm and by VarCorr(foo.mer)
My understanding is the VarCorr was essentially designed to work with 
'mer' objects. Am I wrong about this?  The lmer procedure seemed to work 
fine

-- 
David K Stevens, P.E., Ph.D., Professor
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT  84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stev...@usu.edu




[[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] rbind-ing numeric matrices

[Sarah Goslee]

On Tue, May 1, 2012 at 2:12 PM, Nick Switanek  wrote:
> Thank you, Sarah!
>
> Yes, unlist() looks like it will do just what I need. Thank you.
>
> I took a different tack. I'd changed the function returning A to coerce the
> row from the data.frame using as.numeric(). Any reason to prefer your way or
> mine?

Possibly, but we would need to know what you did to produce A to be certain.

Sarah


> thanks again,
> Nick
>
>
> On Tue, May 1, 2012 at 2:08 PM, Sarah Goslee  wrote:
>>
>> Hi Nick,
>>
>> On Tue, May 1, 2012 at 1:56 PM, Nick Switanek  wrote:
>> > Thank you, Steve and Sarah, for your swift replies.
>> >
>> > I didn't know about dput(). class() returns "matrix" for A, B, and C,
>> > but
>> > here:
>> >
>> >> class(A)
>> > [1] "matrix"
>> >> class(B)
>> > [1] "matrix"
>> >> dput(A)
>> > structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
>> >    17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
>> >    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>> >    "k")))
>>
>> I'm not sure how you created A, but it's a list - see the structure
>> given by dput(), and also:
>>
>> > is.list(A)
>> [1] TRUE
>> > is.list(B)
>> [1] FALSE
>>
>>
>> >> dput(B)
>> > structure(c(1239197400, 1239199200, 1239202800, 1239199199, 1239202799,
>> > 1239206399, 14342, 14342, 14342, 3, 3, 3, 0, 0, 0, 0, 0, 0, 9,
>> > 10, 11, 35999, 39599, 43199, 7199, 10799, 14399, 1799, 5399,
>> > 8999, 1799, 5399, 8999), .Dim = c(3L, 11L), .Dimnames = list(
>> >    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>> >    "k")))
>>
>> Note that the structure for B doesn't say anything about it being a list.
>>
>> In this particular case, you can fix that with:
>> > rbind(unlist(A), B)
>>              a          b     c d e f  g     h     i     j      k
>> [1,] 1239814462 1239814601 14349 3 4 0 12 46601 17801 12401 106001
>> [2,] 1239197400 1239199199 14342 3 0 0  9 35999  7199  1799   1799
>> [3,] 1239199200 1239202799 14342 3 0 0 10 39599 10799  5399   5399
>> [4,] 1239202800 1239206399 14342 3 0 0 11 43199 14399  8999   8999
>>
>> But now I'm curious where A came from.
>>
>> Sarah
>>
>> >> C <- rbind(A,B)
>> >> dput(C)
>> > structure(list(1239814462, 1239197400, NULL, NULL, 1239814601,
>> >    1239199200, NULL, NULL, 14349, 1239202800, NULL, NULL, 3,
>> >    1239199199, NULL, NULL, 4, 1239202799, NULL, NULL, 0, 1239206399,
>> >    NULL, NULL, 12, 14342, NULL, NULL, 46601, 14342, NULL, NULL,
>> >    17801, 14342, NULL, NULL, 12401, 3, NULL, NULL, 106001, 3,
>> >    NULL, NULL), .Dim = c(4L, 11L), .Dimnames = list(NULL, c("a",
>> > "b", "c", "d", "e", "f", "g", "h", "i", "j", "k")))
>> >
>> > But how do I convert A to the appropriate form for rbinding? Not simply
>> > with as.matrix(). Witness:
>> >> dput(as.matrix(A))
>> > structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
>> >    17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
>> >    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>> >    "k")))
>> >
>> > I think we're closer but I still need your help!
>> >
>> > Nick
>> >
>> >
>> > On Tue, May 1, 2012 at 12:02 PM, Steve Lianoglou <
>> > mailinglist.honey...@gmail.com> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Tue, May 1, 2012 at 11:52 AM, Nick Switanek 
>> >> wrote:
>> >> > Good morning,
>> >> >
>> >> > I'm running into trouble rbind-ing numeric matrices with differing
>> >> numbers
>> >> > of rows. In particular, there seem to be issues whenever a one-row
>> >> numeric
>> >> > matrix is involved.
>> >> >
>> >> > Assume A is a numeric matrix with 1 row and Y columns and B is a
>> >> > numeric
>> >> > matrix with X rows and Y columns. Let C be the result of rbinding A
>> >> > and
>> >> B.
>> >> > Then C is a numeric matrix with X + 1 rows and Y columns, only
>> >> > instead of
>> >> > the rows of B being "stacked" beneath the row of A as expected, the
>> >> first Y
>> >> > elements of the 1st column of B are placed in the 2nd row of C, the
>> >> > remaining values of B are discarded, and NULL values fill out the
>> >> > rest of
>> >> > the matrix C.
>> >> >
>> >> > The number of columns of A and B match. The colnames of A and B
>> >> > match.
>> >> Both
>> >> > are numeric matrices. I've pored over the rbind/cbind documentation
>> >> > but
>> >> > can't identify why I'm getting this behavior from rbind. I'd be
>> >> > extremely
>> >> > grateful for your suggestions or thoughts.
>> >>
>> >> If everything you say is true (and I'm understanding what you're
>> >> saying), there must be something else going on with your data.
>> >> Consider:
>> >>
>> >> R> m1 <- matrix(-(1:5), nrow=1)
>> >> R> m2 <- matrix(1:20, ncol=5)
>> >> R> rbind(m1, m2)
>> >>      [,1] [,2] [,3] [,4] [,5]
>> >> [1,]   -1   -2   -3   -4   -5
>> >> [2,]    1    5    9   13   17
>> >> [3,]    2    6   10   14   18
>> >> [4,]    3    7   11   15   19
>> >> [5,]    4    8   12   16   20
>> >>
>> >> Can you provide a small example of your data that reproduces the
>> >> problem you're seeing?
>> >>
>> >> Co

Re: [R] Data frame vs matrix quirk: Hinky error message?

[Duncan Murdoch]

On 01/05/2012 2:12 PM, Bert Gunter wrote:

Many thanks, Ista:

I only looked in "].default" so the answer is: Alternative 4: dumb
Bert. Rap knuckles with ruler.

Actually, indexing by a logical matrix doesn't make much  sense to me
in either case, as it does not have the effect of selecting individual
elements, which is what numeric matrix indices do. But that's a matter
of usage, neither bug nor feature.

If I had gotten something like the error message: "Matrix indices not
allowed for replacement in data frames," I would not have been
surprised. But as you said, the behavior **IS** documented.


Your version is not correct:  matrix indices *are* allowed for 
replacement, but only logical matrix indices, not two column numerical 
ones.   The message might be clearer if instead of saying "only logical 
matrix subscripts are allowed in replacement"
it said "matrix subscripts must be logical matrices in replacement", but 
I think the basic problem is the limitation.  I'll fix that.


Duncan Murdoch



Best,
Bert



On Tue, May 1, 2012 at 10:49 AM, Ista Zahn  wrote:
>  Hi Bert,
>
>  The failure itself is the documented behavior: ?'[.data.frame' says
>
>  "Matrix indexing ('x[i]' with a logical or a 2-column integer
>   matrix 'i') using '[' is not recommended, and barely supported.
>   For extraction, 'x' is first coerced to a matrix.  For
>   replacement, a logical matrix (only) can be used to select the
>   elements to be replaced in the same way as for a matrix."
>
>  The error message may be a bit hinky, as obviously data.frames can be
>  indexed by things other than logical matricies. Or is there another
>  reason this strikes you as odd?
>
>  Best,
>  Ista
>
>  On Tue, May 1, 2012 at 1:33 PM, Bert Gunter  wrote:
>>  AdvisoRs:
>>
>>  Is the following a bug, feature, hinky error message, or dumb Bert?
>>
>>>  mtest<- matrix(1:12,nr=4)
>>>  dftest<- data.frame(mtest)
>>>  ix<- cbind(1:2,2:3)
>>>  mtest[ix]<- NA
>>>  mtest
>>   [,1] [,2] [,3]
>>  [1,]1   NA9
>>  [2,]26   NA
>>  [3,]37   11
>>  [4,]48   12
>>
>>  ## But ...
>>>  dftest[ix]<- NA
>>  Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>>only logical matrix subscripts are allowed in replacement
>>
>>  Obviously, I was expecting matrix indexing for replacement to work
>>  similarly in both cases; however, I can see why it would be
>>  problematic for data frames (mixed types), but was a bit nonplussed by
>>  the error message, which seems hinky to me.
>>
>>  Cheers,
>>  Bert
>>
>>  --
>>
>>  Bert Gunter
>>  Genentech Nonclinical Biostatistics
>>
>>  Internal Contact Info:
>>  Phone: 467-7374
>>  Website:
>>  
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>>
>>  __
>>  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] rbind-ing numeric matrices

[Nick Switanek]

Thank you, Sarah!

Yes, unlist() looks like it will do just what I need. Thank you.

I took a different tack. I'd changed the function returning A to coerce the
row from the data.frame using as.numeric(). Any reason to prefer your way
or mine?

thanks again,
Nick


On Tue, May 1, 2012 at 2:08 PM, Sarah Goslee  wrote:

> Hi Nick,
>
> On Tue, May 1, 2012 at 1:56 PM, Nick Switanek  wrote:
> > Thank you, Steve and Sarah, for your swift replies.
> >
> > I didn't know about dput(). class() returns "matrix" for A, B, and C, but
> > here:
> >
> >> class(A)
> > [1] "matrix"
> >> class(B)
> > [1] "matrix"
> >> dput(A)
> > structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
> >17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
> >NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
> >"k")))
>
> I'm not sure how you created A, but it's a list - see the structure
> given by dput(), and also:
>
> > is.list(A)
> [1] TRUE
> > is.list(B)
> [1] FALSE
>
>
> >> dput(B)
> > structure(c(1239197400, 1239199200, 1239202800, 1239199199, 1239202799,
> > 1239206399, 14342, 14342, 14342, 3, 3, 3, 0, 0, 0, 0, 0, 0, 9,
> > 10, 11, 35999, 39599, 43199, 7199, 10799, 14399, 1799, 5399,
> > 8999, 1799, 5399, 8999), .Dim = c(3L, 11L), .Dimnames = list(
> >NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
> >"k")))
>
> Note that the structure for B doesn't say anything about it being a list.
>
> In this particular case, you can fix that with:
> > rbind(unlist(A), B)
>  a  b c d e f  g h i j  k
> [1,] 1239814462 1239814601 14349 3 4 0 12 46601 17801 12401 106001
> [2,] 1239197400 1239199199 14342 3 0 0  9 35999  7199  1799   1799
> [3,] 1239199200 1239202799 14342 3 0 0 10 39599 10799  5399   5399
> [4,] 1239202800 1239206399 14342 3 0 0 11 43199 14399  8999   8999
>
> But now I'm curious where A came from.
>
> Sarah
>
> >> C <- rbind(A,B)
> >> dput(C)
> > structure(list(1239814462, 1239197400, NULL, NULL, 1239814601,
> >1239199200, NULL, NULL, 14349, 1239202800, NULL, NULL, 3,
> >1239199199, NULL, NULL, 4, 1239202799, NULL, NULL, 0, 1239206399,
> >NULL, NULL, 12, 14342, NULL, NULL, 46601, 14342, NULL, NULL,
> >17801, 14342, NULL, NULL, 12401, 3, NULL, NULL, 106001, 3,
> >NULL, NULL), .Dim = c(4L, 11L), .Dimnames = list(NULL, c("a",
> > "b", "c", "d", "e", "f", "g", "h", "i", "j", "k")))
> >
> > But how do I convert A to the appropriate form for rbinding? Not simply
> > with as.matrix(). Witness:
> >> dput(as.matrix(A))
> > structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
> >17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
> >NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
> >"k")))
> >
> > I think we're closer but I still need your help!
> >
> > Nick
> >
> >
> > On Tue, May 1, 2012 at 12:02 PM, Steve Lianoglou <
> > mailinglist.honey...@gmail.com> wrote:
> >
> >> Hi,
> >>
> >> On Tue, May 1, 2012 at 11:52 AM, Nick Switanek 
> >> wrote:
> >> > Good morning,
> >> >
> >> > I'm running into trouble rbind-ing numeric matrices with differing
> >> numbers
> >> > of rows. In particular, there seem to be issues whenever a one-row
> >> numeric
> >> > matrix is involved.
> >> >
> >> > Assume A is a numeric matrix with 1 row and Y columns and B is a
> numeric
> >> > matrix with X rows and Y columns. Let C be the result of rbinding A
> and
> >> B.
> >> > Then C is a numeric matrix with X + 1 rows and Y columns, only
> instead of
> >> > the rows of B being "stacked" beneath the row of A as expected, the
> >> first Y
> >> > elements of the 1st column of B are placed in the 2nd row of C, the
> >> > remaining values of B are discarded, and NULL values fill out the
> rest of
> >> > the matrix C.
> >> >
> >> > The number of columns of A and B match. The colnames of A and B match.
> >> Both
> >> > are numeric matrices. I've pored over the rbind/cbind documentation
> but
> >> > can't identify why I'm getting this behavior from rbind. I'd be
> extremely
> >> > grateful for your suggestions or thoughts.
> >>
> >> If everything you say is true (and I'm understanding what you're
> >> saying), there must be something else going on with your data.
> >> Consider:
> >>
> >> R> m1 <- matrix(-(1:5), nrow=1)
> >> R> m2 <- matrix(1:20, ncol=5)
> >> R> rbind(m1, m2)
> >>  [,1] [,2] [,3] [,4] [,5]
> >> [1,]   -1   -2   -3   -4   -5
> >> [2,]159   13   17
> >> [3,]26   10   14   18
> >> [4,]37   11   15   19
> >> [5,]48   12   16   20
> >>
> >> Can you provide a small example of your data that reproduces the
> >> problem you're seeing?
> >>
> >> Construct these objects in your workspace and copy/paste the output of
> >> dput on your m1 and m2 matrices so we can easily work w/ them.
> >>
> >> Cheers,
> >> -steve
> >>
>
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>

[[alternative HTML version deleted]]

__
R-h

Re: [R] Data frame vs matrix quirk: Hinky error message?

[Bert Gunter]

Many thanks, Ista:

I only looked in "].default" so the answer is: Alternative 4: dumb
Bert. Rap knuckles with ruler.

Actually, indexing by a logical matrix doesn't make much  sense to me
in either case, as it does not have the effect of selecting individual
elements, which is what numeric matrix indices do. But that's a matter
of usage, neither bug nor feature.

If I had gotten something like the error message: "Matrix indices not
allowed for replacement in data frames," I would not have been
surprised. But as you said, the behavior **IS** documented.

Best,
Bert



On Tue, May 1, 2012 at 10:49 AM, Ista Zahn  wrote:
> Hi Bert,
>
> The failure itself is the documented behavior: ?'[.data.frame' says
>
> "Matrix indexing ('x[i]' with a logical or a 2-column integer
>     matrix 'i') using '[' is not recommended, and barely supported.
>     For extraction, 'x' is first coerced to a matrix.  For
>     replacement, a logical matrix (only) can be used to select the
>     elements to be replaced in the same way as for a matrix."
>
> The error message may be a bit hinky, as obviously data.frames can be
> indexed by things other than logical matricies. Or is there another
> reason this strikes you as odd?
>
> Best,
> Ista
>
> On Tue, May 1, 2012 at 1:33 PM, Bert Gunter  wrote:
>> AdvisoRs:
>>
>> Is the following a bug, feature, hinky error message, or dumb Bert?
>>
>>> mtest <- matrix(1:12,nr=4)
>>> dftest <- data.frame(mtest)
>>> ix <- cbind(1:2,2:3)
>>> mtest[ix] <- NA
>>> mtest
>>     [,1] [,2] [,3]
>> [1,]    1   NA    9
>> [2,]    2    6   NA
>> [3,]    3    7   11
>> [4,]    4    8   12
>>
>> ## But ...
>>> dftest[ix] <- NA
>> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>>  only logical matrix subscripts are allowed in replacement
>>
>> Obviously, I was expecting matrix indexing for replacement to work
>> similarly in both cases; however, I can see why it would be
>> problematic for data frames (mixed types), but was a bit nonplussed by
>> the error message, which seems hinky to me.
>>
>> Cheers,
>> Bert
>>
>> --
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>>
>> Internal Contact Info:
>> Phone: 467-7374
>> Website:
>> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>>
>> __
>> 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.



-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] rbind-ing numeric matrices

[Sarah Goslee]

Hi Nick,

On Tue, May 1, 2012 at 1:56 PM, Nick Switanek  wrote:
> Thank you, Steve and Sarah, for your swift replies.
>
> I didn't know about dput(). class() returns "matrix" for A, B, and C, but
> here:
>
>> class(A)
> [1] "matrix"
>> class(B)
> [1] "matrix"
>> dput(A)
> structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
>    17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
>    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>    "k")))

I'm not sure how you created A, but it's a list - see the structure
given by dput(), and also:

> is.list(A)
[1] TRUE
> is.list(B)
[1] FALSE


>> dput(B)
> structure(c(1239197400, 1239199200, 1239202800, 1239199199, 1239202799,
> 1239206399, 14342, 14342, 14342, 3, 3, 3, 0, 0, 0, 0, 0, 0, 9,
> 10, 11, 35999, 39599, 43199, 7199, 10799, 14399, 1799, 5399,
> 8999, 1799, 5399, 8999), .Dim = c(3L, 11L), .Dimnames = list(
>    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>    "k")))

Note that the structure for B doesn't say anything about it being a list.

In this particular case, you can fix that with:
> rbind(unlist(A), B)
  a  b c d e f  g h i j  k
[1,] 1239814462 1239814601 14349 3 4 0 12 46601 17801 12401 106001
[2,] 1239197400 1239199199 14342 3 0 0  9 35999  7199  1799   1799
[3,] 1239199200 1239202799 14342 3 0 0 10 39599 10799  5399   5399
[4,] 1239202800 1239206399 14342 3 0 0 11 43199 14399  8999   8999

But now I'm curious where A came from.

Sarah

>> C <- rbind(A,B)
>> dput(C)
> structure(list(1239814462, 1239197400, NULL, NULL, 1239814601,
>    1239199200, NULL, NULL, 14349, 1239202800, NULL, NULL, 3,
>    1239199199, NULL, NULL, 4, 1239202799, NULL, NULL, 0, 1239206399,
>    NULL, NULL, 12, 14342, NULL, NULL, 46601, 14342, NULL, NULL,
>    17801, 14342, NULL, NULL, 12401, 3, NULL, NULL, 106001, 3,
>    NULL, NULL), .Dim = c(4L, 11L), .Dimnames = list(NULL, c("a",
> "b", "c", "d", "e", "f", "g", "h", "i", "j", "k")))
>
> But how do I convert A to the appropriate form for rbinding? Not simply
> with as.matrix(). Witness:
>> dput(as.matrix(A))
> structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
>    17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
>    NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
>    "k")))
>
> I think we're closer but I still need your help!
>
> Nick
>
>
> On Tue, May 1, 2012 at 12:02 PM, Steve Lianoglou <
> mailinglist.honey...@gmail.com> wrote:
>
>> Hi,
>>
>> On Tue, May 1, 2012 at 11:52 AM, Nick Switanek 
>> wrote:
>> > Good morning,
>> >
>> > I'm running into trouble rbind-ing numeric matrices with differing
>> numbers
>> > of rows. In particular, there seem to be issues whenever a one-row
>> numeric
>> > matrix is involved.
>> >
>> > Assume A is a numeric matrix with 1 row and Y columns and B is a numeric
>> > matrix with X rows and Y columns. Let C be the result of rbinding A and
>> B.
>> > Then C is a numeric matrix with X + 1 rows and Y columns, only instead of
>> > the rows of B being "stacked" beneath the row of A as expected, the
>> first Y
>> > elements of the 1st column of B are placed in the 2nd row of C, the
>> > remaining values of B are discarded, and NULL values fill out the rest of
>> > the matrix C.
>> >
>> > The number of columns of A and B match. The colnames of A and B match.
>> Both
>> > are numeric matrices. I've pored over the rbind/cbind documentation but
>> > can't identify why I'm getting this behavior from rbind. I'd be extremely
>> > grateful for your suggestions or thoughts.
>>
>> If everything you say is true (and I'm understanding what you're
>> saying), there must be something else going on with your data.
>> Consider:
>>
>> R> m1 <- matrix(-(1:5), nrow=1)
>> R> m2 <- matrix(1:20, ncol=5)
>> R> rbind(m1, m2)
>>      [,1] [,2] [,3] [,4] [,5]
>> [1,]   -1   -2   -3   -4   -5
>> [2,]    1    5    9   13   17
>> [3,]    2    6   10   14   18
>> [4,]    3    7   11   15   19
>> [5,]    4    8   12   16   20
>>
>> Can you provide a small example of your data that reproduces the
>> problem you're seeing?
>>
>> Construct these objects in your workspace and copy/paste the output of
>> dput on your m1 and m2 matrices so we can easily work w/ them.
>>
>> Cheers,
>> -steve
>>


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

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Ted Harding]

On 01-May-2012 17:33:23 Bert Gunter wrote:
> AdvisoRs:
> 
> Is the following a bug, feature, hinky error message, or dumb Bert?
> 
>   mtest <- matrix(1:12,nr=4)
>   dftest <- data.frame(mtest)
>   ix <- cbind(1:2,2:3)
>   mtest[ix] <- NA
>   mtest
>  [,1] [,2] [,3]
> [1,]1   NA9
> [2,]26   NA
> [3,]37   11
> [4,]48   12
> 
>## But ...
>   dftest[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>   only logical matrix subscripts are allowed in replacement
> 
> Obviously, I was expecting matrix indexing for replacement to
> work similarly in both cases; however, I can see why it would
> be problematic for data frames (mixed types), but was a bit
> nonplussed by the error message, which seems hinky to me.
> 
> Cheers,
> Bert

Also interesting is that, prior to the substitution commands,

  mtest[ix]
  # [1]  5 10
  dftest[ix]
  # [1]  5 10

both as one would expect on Bert's "naive" gounds (which, I confess,
I also share[d]).

Ted.

-
E-Mail: (Ted Harding) 
Date: 01-May-2012  Time: 19:03:14
This message was sent by XFMail

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Re: [R] Data frame vs matrix quirk: Hinky error message?

[Ista Zahn]

Hi Bert,

The failure itself is the documented behavior: ?'[.data.frame' says

"Matrix indexing ('x[i]' with a logical or a 2-column integer
 matrix 'i') using '[' is not recommended, and barely supported.
 For extraction, 'x' is first coerced to a matrix.  For
 replacement, a logical matrix (only) can be used to select the
 elements to be replaced in the same way as for a matrix."

The error message may be a bit hinky, as obviously data.frames can be
indexed by things other than logical matricies. Or is there another
reason this strikes you as odd?

Best,
Ista

On Tue, May 1, 2012 at 1:33 PM, Bert Gunter  wrote:
> AdvisoRs:
>
> Is the following a bug, feature, hinky error message, or dumb Bert?
>
>> mtest <- matrix(1:12,nr=4)
>> dftest <- data.frame(mtest)
>> ix <- cbind(1:2,2:3)
>> mtest[ix] <- NA
>> mtest
>     [,1] [,2] [,3]
> [1,]    1   NA    9
> [2,]    2    6   NA
> [3,]    3    7   11
> [4,]    4    8   12
>
> ## But ...
>> dftest[ix] <- NA
> Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
>  only logical matrix subscripts are allowed in replacement
>
> Obviously, I was expecting matrix indexing for replacement to work
> similarly in both cases; however, I can see why it would be
> problematic for data frames (mixed types), but was a bit nonplussed by
> the error message, which seems hinky to me.
>
> Cheers,
> Bert
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
> __
> 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.

__
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Re: [R] rbind-ing numeric matrices

[Nick Switanek]

Thank you, Steve and Sarah, for your swift replies.

I didn't know about dput(). class() returns "matrix" for A, B, and C, but
here:

> class(A)
[1] "matrix"
> class(B)
[1] "matrix"
> dput(A)
structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
"k")))
> dput(B)
structure(c(1239197400, 1239199200, 1239202800, 1239199199, 1239202799,
1239206399, 14342, 14342, 14342, 3, 3, 3, 0, 0, 0, 0, 0, 0, 9,
10, 11, 35999, 39599, 43199, 7199, 10799, 14399, 1799, 5399,
8999, 1799, 5399, 8999), .Dim = c(3L, 11L), .Dimnames = list(
NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
"k")))
> C <- rbind(A,B)
> dput(C)
structure(list(1239814462, 1239197400, NULL, NULL, 1239814601,
1239199200, NULL, NULL, 14349, 1239202800, NULL, NULL, 3,
1239199199, NULL, NULL, 4, 1239202799, NULL, NULL, 0, 1239206399,
NULL, NULL, 12, 14342, NULL, NULL, 46601, 14342, NULL, NULL,
17801, 14342, NULL, NULL, 12401, 3, NULL, NULL, 106001, 3,
NULL, NULL), .Dim = c(4L, 11L), .Dimnames = list(NULL, c("a",
"b", "c", "d", "e", "f", "g", "h", "i", "j", "k")))

But how do I convert A to the appropriate form for rbinding? Not simply
with as.matrix(). Witness:
> dput(as.matrix(A))
structure(list(1239814462, 1239814601, 14349, 3, 4, 0, 12, 46601,
17801, 12401, 106001), .Dim = c(1L, 11L), .Dimnames = list(
NULL, c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
"k")))

I think we're closer but I still need your help!

Nick


On Tue, May 1, 2012 at 12:02 PM, Steve Lianoglou <
mailinglist.honey...@gmail.com> wrote:

> Hi,
>
> On Tue, May 1, 2012 at 11:52 AM, Nick Switanek 
> wrote:
> > Good morning,
> >
> > I'm running into trouble rbind-ing numeric matrices with differing
> numbers
> > of rows. In particular, there seem to be issues whenever a one-row
> numeric
> > matrix is involved.
> >
> > Assume A is a numeric matrix with 1 row and Y columns and B is a numeric
> > matrix with X rows and Y columns. Let C be the result of rbinding A and
> B.
> > Then C is a numeric matrix with X + 1 rows and Y columns, only instead of
> > the rows of B being "stacked" beneath the row of A as expected, the
> first Y
> > elements of the 1st column of B are placed in the 2nd row of C, the
> > remaining values of B are discarded, and NULL values fill out the rest of
> > the matrix C.
> >
> > The number of columns of A and B match. The colnames of A and B match.
> Both
> > are numeric matrices. I've pored over the rbind/cbind documentation but
> > can't identify why I'm getting this behavior from rbind. I'd be extremely
> > grateful for your suggestions or thoughts.
>
> If everything you say is true (and I'm understanding what you're
> saying), there must be something else going on with your data.
> Consider:
>
> R> m1 <- matrix(-(1:5), nrow=1)
> R> m2 <- matrix(1:20, ncol=5)
> R> rbind(m1, m2)
>  [,1] [,2] [,3] [,4] [,5]
> [1,]   -1   -2   -3   -4   -5
> [2,]159   13   17
> [3,]26   10   14   18
> [4,]37   11   15   19
> [5,]48   12   16   20
>
> Can you provide a small example of your data that reproduces the
> problem you're seeing?
>
> Construct these objects in your workspace and copy/paste the output of
> dput on your m1 and m2 matrices so we can easily work w/ them.
>
> Cheers,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

[[alternative HTML version deleted]]

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[R] Data frame vs matrix quirk: Hinky error message?

[Bert Gunter]

AdvisoRs:

Is the following a bug, feature, hinky error message, or dumb Bert?

> mtest <- matrix(1:12,nr=4)
> dftest <- data.frame(mtest)
> ix <- cbind(1:2,2:3)
> mtest[ix] <- NA
> mtest
 [,1] [,2] [,3]
[1,]1   NA9
[2,]26   NA
[3,]37   11
[4,]48   12

## But ...
> dftest[ix] <- NA
Error in `[<-.data.frame`(`*tmp*`, ix, value = NA) :
  only logical matrix subscripts are allowed in replacement

Obviously, I was expecting matrix indexing for replacement to work
similarly in both cases; however, I can see why it would be
problematic for data frames (mixed types), but was a bit nonplussed by
the error message, which seems hinky to me.

Cheers,
Bert

-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

__
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Re: [R] error bars for a barchart

[ilai]

Hi,
I think the issue is not "respecting the groups" but finding the
x-location of the center of bars in panel.barchart(groups,...). Don't
know about the memisc package, but doesn't look like it provides an
easy solution. This is how I do it:
http://www.mail-archive.com/r-help@r-project.org/msg162299.html

Might need to modify some for your data.

HTH

On Tue, May 1, 2012 at 8:01 AM, Beatriz De Francisco
 wrote:
> Hi
> I have the following barchart to which I want to add error bars.
>
>    library(lattice)
>    barchart(Change~fTreat,groups=Process,change,
>              auto.key=list(points=FALSE,rectangles=TRUE),
>              panel=function(x, y,...){
>                panel.barchart(x,y,origin = 0,...);
>                panel.abline(h=0,col="black",...);
>                }
>              )
>
> I have tried using the panel.errbars from the memisc package which works 
> great for xyplots, but when I add it to my code it does not respect the 
> groups.
>
>    library(memisc)
>    barchart(cbind(Change,lower,upper)~fTreat,groups=Process,change,
>         ylab="Pocertage change",
>         ylim=-115:50,
>         scales=list(alternating=FALSE,
>                     tick.number=7,
>                     tck=c(-1,0)),
>         panel=function(x, y,groups,...){
>           panel.barchart(x,y=change$Change,groups=change$Process,origin = 
> 0,...);
>           panel.abline(h=0,col="black",...);
>           panel.errbars(x,y,make.grid="none",ewidth=0.2,type="n",...)
>         }
>         )
>
> Any ideas of how to add error bars to my plot either using the panel.errbars 
> or any other function?
>
> The data:
>
>        structure(list(Treat = structure(c(3L, 4L, 1L, 2L, 3L, 4L, 1L,
>    2L), .Label = c("12-380", "12-750", "8-380", "8-750"), class = "factor"),
>        Process = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), .Label = 
> c("Resp",
>        "Cal"), class = c("ordered", "factor")), Change = c(-33.05,
>        -34.74, 20.94, 18.06, 6.85, -28.57, -8.1, -78.72), upper = 
> c(-13.22896628,
>        -28.61149669, 31.29930461, 27.30173776, 39.73271282, 9.458372948,
>        13.11035572, -47.03745704), lower = c(-52.86120694, -40.87446411,
>        10.57421563, 8.822042178, -26.03144161, -66.60447035, -29.30563327,
>        -110.3973761), fTreat = structure(c(1L, 2L, 3L, 4L, 1L, 2L,
>        3L, 4L), .Label = c("8-380", "8-750", "12-380", "12-750"), class = 
> c("ordered",
>        "factor"))), .Names = c("Treat", "Process", "Change", "upper",
>    "lower", "fTreat"), row.names = c(NA, -8L), class = "data.frame")
>
> Regards
>
> Beatriz de Francisco Mora
> PhD Student
> The Scottish Association for Marine Science
> Scottish Marine Institute
> Oban
> PA37 1QA
> Tel: 06131 559000 (switchboard)
> Fax: 01631559001
> E. beatriz.defranci...@sams.ac.uk
> http://www.smi.ac.uk/beatriz-de-franciso
>
> The Scottish Association for Marine Science (SAMS) is registered in Scotland 
> as a Company Limited by Guarantee (SC009292) and is a registered charity 
> (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS 
> Research Services Ltd a Limited Company (SC224404). All Companies in the 
> group are registered in Scotland and share a registered office at Scottish 
> Marine Institute, Oban Argyll PA37 1QA. The content of this message may 
> contain personal views which are not the views of SAMS unless specifically 
> stated. Please note that all email traffic is monitored for purposes of 
> security and spam filtering. As such individual emails may be examined in 
> more detail.
>
>        [[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.

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[R] [fields:image.plot] subtitle under title (not image)?

[Tom Roche]

summary: how to make image.plot print a subtitle between the title and
the image, rather than under the image?

details:

I've got a project

https://github.com/TomRoche/ioapi-hack-R

that illustrates the use of (et al) the R packages {ncdf4, fields, M3}
for processing and visualizing IOAPI data. The data being visualized
consists of a series of layers (mostly representing emissions from a
particular tuple of agricultural {cultivar, cultivation technique})
over a surface (in the upper midwest US). I'm currently plotting

https://github.com/downloads/TomRoche/ioapi-hack-R/compare.DN2.layers.pdf

each layer, and including some information about the layer in a title
and subtitle. The title is where I want it--above the image--but the
subtitle is printing below the image; I'd prefer it between the title
and the image. Can this be done? FWIW, the code that plots (in

https://github.com/TomRoche/ioapi-hack-R/blob/master/plotLayersForTimestep.r

) is like

  if (data to plot is not all NA) {
# determine quantiles, then
image.plot(plot.list, xlab="", ylab="", axes=F, col=colors(100),
  axis.args=list(at=quantiles, labels=quantiles.formatted),
  main=title, sub=subtitle)
lines(map)
  } else {
plot(0, type="n", axes=F, xlab="", ylab="",
  xlim=range(x.centers), ylim=range(y.centers),
  main=title, sub=subtitle)
lines(map)
  } # end testing data

TIA, Tom Roche 

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Re: [R] rbind-ing numeric matrices

[Steve Lianoglou]

Hi,

On Tue, May 1, 2012 at 11:52 AM, Nick Switanek  wrote:
> Good morning,
>
> I'm running into trouble rbind-ing numeric matrices with differing numbers
> of rows. In particular, there seem to be issues whenever a one-row numeric
> matrix is involved.
>
> Assume A is a numeric matrix with 1 row and Y columns and B is a numeric
> matrix with X rows and Y columns. Let C be the result of rbinding A and B.
> Then C is a numeric matrix with X + 1 rows and Y columns, only instead of
> the rows of B being "stacked" beneath the row of A as expected, the first Y
> elements of the 1st column of B are placed in the 2nd row of C, the
> remaining values of B are discarded, and NULL values fill out the rest of
> the matrix C.
>
> The number of columns of A and B match. The colnames of A and B match. Both
> are numeric matrices. I've pored over the rbind/cbind documentation but
> can't identify why I'm getting this behavior from rbind. I'd be extremely
> grateful for your suggestions or thoughts.

If everything you say is true (and I'm understanding what you're
saying), there must be something else going on with your data.
Consider:

R> m1 <- matrix(-(1:5), nrow=1)
R> m2 <- matrix(1:20, ncol=5)
R> rbind(m1, m2)
 [,1] [,2] [,3] [,4] [,5]
[1,]   -1   -2   -3   -4   -5
[2,]159   13   17
[3,]26   10   14   18
[4,]37   11   15   19
[5,]48   12   16   20

Can you provide a small example of your data that reproduces the
problem you're seeing?

Construct these objects in your workspace and copy/paste the output of
dput on your m1 and m2 matrices so we can easily work w/ them.

Cheers,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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Re: [R] rbind-ing numeric matrices

[Sarah Goslee]

Hi Nick,

We absolutely need a reproducible example, with code and data, to be
able to help you.

Because otherwise I can't replicate your problem:

> A <- matrix(1:5, nrow=1, ncol=5)
> B <- matrix(6:20, nrow=3, ncol=5)
> C <- rbind(A, B)
> A
 [,1] [,2] [,3] [,4] [,5]
[1,]12345
> B
 [,1] [,2] [,3] [,4] [,5]
[1,]69   12   15   18
[2,]7   10   13   16   19
[3,]8   11   14   17   20
> C
 [,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]69   12   15   18
[3,]7   10   13   16   19
[4,]8   11   14   17   20


Sarah

On Tue, May 1, 2012 at 11:52 AM, Nick Switanek  wrote:
> Good morning,
>
> I'm running into trouble rbind-ing numeric matrices with differing numbers
> of rows. In particular, there seem to be issues whenever a one-row numeric
> matrix is involved.
>
> Assume A is a numeric matrix with 1 row and Y columns and B is a numeric
> matrix with X rows and Y columns. Let C be the result of rbinding A and B.
> Then C is a numeric matrix with X + 1 rows and Y columns, only instead of
> the rows of B being "stacked" beneath the row of A as expected, the first Y
> elements of the 1st column of B are placed in the 2nd row of C, the
> remaining values of B are discarded, and NULL values fill out the rest of
> the matrix C.
>
> The number of columns of A and B match. The colnames of A and B match. Both
> are numeric matrices. I've pored over the rbind/cbind documentation but
> can't identify why I'm getting this behavior from rbind. I'd be extremely
> grateful for your suggestions or thoughts.
>
> Nick
>


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

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[R] rbind-ing numeric matrices

[Nick Switanek]

Good morning,

I'm running into trouble rbind-ing numeric matrices with differing numbers
of rows. In particular, there seem to be issues whenever a one-row numeric
matrix is involved.

Assume A is a numeric matrix with 1 row and Y columns and B is a numeric
matrix with X rows and Y columns. Let C be the result of rbinding A and B.
Then C is a numeric matrix with X + 1 rows and Y columns, only instead of
the rows of B being "stacked" beneath the row of A as expected, the first Y
elements of the 1st column of B are placed in the 2nd row of C, the
remaining values of B are discarded, and NULL values fill out the rest of
the matrix C.

The number of columns of A and B match. The colnames of A and B match. Both
are numeric matrices. I've pored over the rbind/cbind documentation but
can't identify why I'm getting this behavior from rbind. I'd be extremely
grateful for your suggestions or thoughts.

Nick

[[alternative HTML version deleted]]

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Re: [R] Regression

[Saint]

Thank u!

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[R] error bars for a barchart

[Beatriz De Francisco]

Hi
I have the following barchart to which I want to add error bars.

library(lattice)
barchart(Change~fTreat,groups=Process,change,
  auto.key=list(points=FALSE,rectangles=TRUE),
  panel=function(x, y,...){
panel.barchart(x,y,origin = 0,...);
panel.abline(h=0,col="black",...);
}
  )

I have tried using the panel.errbars from the memisc package which works great 
for xyplots, but when I add it to my code it does not respect the groups.

library(memisc)
barchart(cbind(Change,lower,upper)~fTreat,groups=Process,change,
 ylab="Pocertage change",
 ylim=-115:50,
 scales=list(alternating=FALSE,
 tick.number=7,
 tck=c(-1,0)),
 panel=function(x, y,groups,...){
   panel.barchart(x,y=change$Change,groups=change$Process,origin = 
0,...);
   panel.abline(h=0,col="black",...);
   panel.errbars(x,y,make.grid="none",ewidth=0.2,type="n",...)
 }
 )

Any ideas of how to add error bars to my plot either using the panel.errbars or 
any other function?

The data:

structure(list(Treat = structure(c(3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L), .Label = c("12-380", "12-750", "8-380", "8-750"), class = "factor"),
Process = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), .Label = 
c("Resp",
"Cal"), class = c("ordered", "factor")), Change = c(-33.05,
-34.74, 20.94, 18.06, 6.85, -28.57, -8.1, -78.72), upper = 
c(-13.22896628,
-28.61149669, 31.29930461, 27.30173776, 39.73271282, 9.458372948,
13.11035572, -47.03745704), lower = c(-52.86120694, -40.87446411,
10.57421563, 8.822042178, -26.03144161, -66.60447035, -29.30563327,
-110.3973761), fTreat = structure(c(1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L), .Label = c("8-380", "8-750", "12-380", "12-750"), class = 
c("ordered",
"factor"))), .Names = c("Treat", "Process", "Change", "upper",
"lower", "fTreat"), row.names = c(NA, -8L), class = "data.frame")

Regards

Beatriz de Francisco Mora
PhD Student
The Scottish Association for Marine Science
Scottish Marine Institute
Oban
PA37 1QA
Tel: 06131 559000 (switchboard)
Fax: 01631559001
E. beatriz.defranci...@sams.ac.uk
http://www.smi.ac.uk/beatriz-de-franciso

The Scottish Association for Marine Science (SAMS) is registered in Scotland as 
a Company Limited by Guarantee (SC009292) and is a registered charity (9206). 
SAMS has an actively trading wholly owned subsidiary company: SAMS Research 
Services Ltd a Limited Company (SC224404). All Companies in the group are 
registered in Scotland and share a registered office at Scottish Marine 
Institute, Oban Argyll PA37 1QA. The content of this message may contain 
personal views which are not the views of SAMS unless specifically stated. 
Please note that all email traffic is monitored for purposes of security and 
spam filtering. As such individual emails may be examined in more detail.

[[alternative HTML version deleted]]

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Re: [R] 95% confidence interval of the coefficients from a bootstrap analysis

[Rui Barradas]

Hello,


baconbeach wrote
> 
> Thanks again for your swift response!!
> 
> With your last line, I get 
> 
>> rowMeans(sapply(stor.confint, colMeans)) 
> 2.5 %97.5 % 
> 0.3256882 0.4604677 
> 
> I need the values (2.5% and 97.5%) for each variable of my model. I don't
> think this what I am getting.
> 
> This is what my script looks like now, after your help:
> 
> N = length (data_Pb[,1])
> B = 1
> stor.r2 = rep(0,B)
> stor.coeffs <- vector("list", B) 
> stor.confint <- vector("list", B) 
> 
> for (i in 1:B){
> idx = sample(1:N, replace=T)
> newdata = data_Pb[idx,]
> L_NPRI_25k <- log(newdata$NPRI_25k+1)
> data_Pb.boot = lm(newdata$Log_Level ~   
> newdata$Ind_5k + newdata$MineP_50k + 
>   newdata$NPRI_10k + L_NPRI_25k )
> 
> stor.r2[i] = summary(data_Pb.boot)$r.squared
> stor.coeffs [[i]] <- coef(data_Pb.boot) 
> stor.confint[[i]] <- confint(data_Pb.boot) 
> }
> 
> hist(stor.r2, xlab="R-squared",main="Distribution of R-squared - Lead
> (log)")
> summary(stor.r2)
> rowMeans(sapply(stor.confint, colMeans)) 
> rowMeans(sapply(stor.coeffs, colMeans))
> 
> 
> Thanks 
> 
> Steeve
> 

Ok, my mistake. Bootstrapped values for each coefficient, obviously.
Try, after the loop,

# Transform list into matrix, before applying 'colMeans'
stor.coeffs <- do.call(rbind, stor.coeffs)
colMeans(stor.coeffs)

# The same, but in two steps
Q2.5 <- lapply(stor.confint, function(x) x[ , 1])
Q2.5 <- do.call(rbind, Q2.5)
head(Q2.5)
Q97.5 <- lapply(stor.confint, function(x) x[ , 2])
Q97.5 <- do.call(rbind, Q97.5)
head(Q97.5)

colMeans(Q2.5)
colMeans(Q97.5)
# Maybe this is better
stor.ci <- data.frame(Q2.5=colMeans(Q2.5), Q97.5=colMeans(Q97.5))
rm(Q2.5, Q97.5) # Final clean-up

Maybe you could reuse the name 'stor.confint', it would save some memory.

Rui Barradas


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[R] error bars for a barchart

[Beatriz De Francisco]

Hi
I have the following barchart to which I want to add error bars.

library(lattice)
barchart(Change~fTreat,groups=Process,change,
  auto.key=list(points=FALSE,rectangles=TRUE),
  panel=function(x, y,...){
panel.barchart(x,y,origin = 0,...);
panel.abline(h=0,col="black",...);
}
  )

I have tried using the panel.errbars from the memisc package which works great 
for xyplots, but when I add it to my code it does not respect the groups.

library(memisc)
barchart(cbind(Change,lower,upper)~fTreat,groups=Process,change,
 ylab="Pocertage change",
 ylim=-115:50,
 scales=list(alternating=FALSE,
 tick.number=7,
 tck=c(-1,0)),
 panel=function(x, y,groups,...){
   panel.barchart(x,y=change$Change,groups=change$Process,origin = 
0,...);
   panel.abline(h=0,col="black",...);
   panel.errbars(x,y,make.grid="none",ewidth=0.2,type="n",...)
 }
 )

Any ideas of how to add error bars to my plot either using the panel.errbars or 
any other function?

The data:

structure(list(Treat = structure(c(3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L), .Label = c("12-380", "12-750", "8-380", "8-750"), class = "factor"),
Process = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), .Label = 
c("Resp",
"Cal"), class = c("ordered", "factor")), Change = c(-33.05,
-34.74, 20.94, 18.06, 6.85, -28.57, -8.1, -78.72), upper = 
c(-13.22896628,
-28.61149669, 31.29930461, 27.30173776, 39.73271282, 9.458372948,
13.11035572, -47.03745704), lower = c(-52.86120694, -40.87446411,
10.57421563, 8.822042178, -26.03144161, -66.60447035, -29.30563327,
-110.3973761), fTreat = structure(c(1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L), .Label = c("8-380", "8-750", "12-380", "12-750"), class = 
c("ordered",
"factor"))), .Names = c("Treat", "Process", "Change", "upper",
"lower", "fTreat"), row.names = c(NA, -8L), class = "data.frame")

Regards

Beatriz de Francisco Mora
PhD Student
The Scottish Association for Marine Science
Scottish Marine Institute
Oban
PA37 1QA
Tel: 06131 559000 (switchboard)
Fax: 01631559001
E. beatriz.defranci...@sams.ac.uk
http://www.smi.ac.uk/beatriz-de-franciso

The Scottish Association for Marine Science (SAMS) is registered in Scotland as 
a Company Limited by Guarantee (SC009292) and is a registered charity (9206). 
SAMS has an actively trading wholly owned subsidiary company: SAMS Research 
Services Ltd a Limited Company (SC224404). All Companies in the group are 
registered in Scotland and share a registered office at Scottish Marine 
Institute, Oban Argyll PA37 1QA. The content of this message may contain 
personal views which are not the views of SAMS unless specifically stated. 
Please note that all email traffic is monitored for purposes of security and 
spam filtering. As such individual emails may be examined in more detail.

[[alternative HTML version deleted]]

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Re: [R] Usage line in .pdf version of manual is truncated

[Yihui Xie]

There is actually another approach which can do the job automatically;
see the function reformat_code() in R2roxygen (remember to back up
your Rd files before you use it).

If you document your package with roxygen2, things can be even easier
-- just call the function rab() to roxygenize and reformat code. This
is what I do with all my packages.

Regards,
Yihui
--
Yihui Xie 
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Mon, Apr 30, 2012 at 10:37 PM, Joshua Wiley  wrote:
> Break the line :)
>
> On Mon, Apr 30, 2012 at 12:34 PM, Zeeberg, Barry (NIH/NCI) [E]
>  wrote:
>> I am creating a package, and a rather long usage line for one function 
>> becomes truncated in the generated .pdf manual. Is there a way that I can 
>> prevent that truncation?

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Re: [R] Question about expand.grid function in R

[peter dalgaard]

On May 1, 2012, at 15:36 , R. Michael Weylandt wrote:

> I don't think you can do it within expand.grid() but something like
> this might work:
> 
> rownames(x) <- apply(x, 1, paste, collapse = "")
> 

Also

rownames(x) <- do.call(paste, c(x, sep=""))

or, in recent versions,

rownames(x) <- do.call(paste0, x)

> Michael
> 
> On Tue, May 1, 2012 at 5:05 AM, Kelly Cool  wrote:
>> Hi,
>> 
>> I am extremely new to R, and was wondering if someone would be able to help 
>> me with a question regarding the expand.grid function. When I input
>> 
>> expand.grid.rep <- function(x, n=1) do.call(expand.grid, rep(list(x),n))
>> expand.grid.rep(c("a", "b", "c"), 3)
>> 
>> my output is as follows,
>> 
>> Var1 Var2 Var3
>> 1 aaa
>> 2 baa
>> 3 caa
>> 4 aba
>> 5 bba
>> 6 cba
>> 7 aca
>> 8 bca
>> 9 cca
>> 10aab
>> 11bab
>> 12cab
>> 13abb
>> 14bbb
>> 15cbb
>> 16acb
>> 17bcb
>> 18ccb
>> 19aac
>> 20bac
>> 21cac
>> 22abc
>> 23bbc
>> 24cbc
>> 25acc
>> 26bcc
>> 27ccc
>> 
>> I was wondering if there was anyway I can change the row numbers to labels 
>> that indicate what is in each row. Instead of a 1, I'd like to have a label 
>> saying "aaa", etc. I'm not sure if this is even possible within the 
>> expand.grid function but any help would be appreciated. Thanks.
>>[[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.
>> 
> 
> __
> 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.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] question on jitter in plot.Predict in rms

[Frank Harrell]

Mike,

Try plot(pref, ..., scat1d.opts=list(frac=0.025, lwd=0.3, nhistSpike=i))

where i = 1 to always use spike histograms (default is to use them if n >=
2000) or i=1e7 to never use them and to always jitter instead.  There are
many other scat1d options you can pass through scat1d.opts.

Frank



Mike Babyak wrote
> 
> Dear colleagues,
> 
> I have a question regarding controlling the jitter when plotting
> predictions in the rms package.  Below I've simulated some data that
> reflect what I'm working with.  The model predicts a continuous variable
> with an ordinal score, a two-level group, and a continuous covariate.  Of
> primary interest is a plot of the group by score interaction, where the
> score is the ordinal variable, and the group Ns are quite disparate.
> 
> When I produce the plot for the predicted values with the data=llist
> argument, as expected I get datadensity hatch marks.  However, in the
> group
> with the smaller N, I get jittered datadensity points, while in the group
> with the larger N, the jitter apparently defaults to single vertical
> lines,
> which I assume is because the jitter would look like a black blob.  Some
> of
> my co-authors are a bit worried about how that looks, so here I am.
> 
> Apart from abandoning data=llist altogether, is there a way to modify the
> jitter in the smaller group so it behaves like the larger one?
> 
> Of secondary importance, anything you can tell me about improving my
> clumsy
> little simulation code would be welcome--I have little to no idea what I'm
> doing there.  for example, would there be a way to produce the group
> variable with the disparate Ns more directly?
> 
> Thanks,
> 
> Mike Babyak
> Behavioral Medicine Research Center
> Duke University Medical Center
> 
> 
> 
> #question about jitter/llist in rms
> #R v 2.14.1 under windows 7
> 
> 
> #question about jitter/llist in rms
> require(rms)
> #simulate some data
> n = 5000
> age   = runif(n)
> score = runif(n) + 0.5*age
> group<- as.numeric(sample(c(FALSE,TRUE), 5000, replace=T, prob=c(.1, .9)))
> ordscore = as.numeric(factor(rep(1:5, length.out=n)))
> table(group,ordscore)
> e = rnorm(n, 0, 0.1)
> 
> #true model
> y = group + 0.6*ordscore + group*ordscore  + .2*age + e
> 
> #convert group to factor
> group.f<-as.factor(group)
> 
> #save data characterics
> dd1<-datadist(age,ordscore,group.f)
> options(datadist="dd1")
> 
> #estimate model
> reg1<-ols(y~group.f+ordscore+group.f*ordscore+age,x=T,y=T)
> 
> #plot results
> preg<-Predict(reg1,ordscore,group.f)
> 
> #produces interaction plot with datadensity hatch marks
> plot(preg,data=llist(ordscore,group.f))
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@ mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
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Re: [R] Optim (fct): Parameters=LowerBounds

[John C Nash]

There's no reason that the optimum cannot be at the bounds. Bounded problems 
really do
sometimes have solutions on those bounds.

Compute the unconstrained gradient of your objective function at the bounds and 
see if the
function is reduced when going across the bounds. The function here is assumed 
to be the
neg. LL that one is MINIMIZING.

There are many aspects of R, optimization in particular, where it would help if 
we
required an operator's license. It is not a magical spell that solves problems
automatically, but a tool much like a chainsaw that can as easily cut your arm 
off as saw
a log.

JN


On 05/01/2012 06:00 AM, r-help-requ...@r-project.org wrote:
> Message: 54 Date: Mon, 30 Apr 2012 08:30:24 -0700 (PDT) From: barb 
> 
> To: r-help@r-project.org Subject: [R] Optim (fct): Parameters=LowerBounds!? 
> Message-ID:
> <1335799824557-4598504.p...@n4.nabble.com> Content-Type: text/plain; 
> charset=UTF-8 Hey, i
> am trying to do the MLE for Garch and have a problem with the optim function. 
> Initally i
> tried optim with Method=BFGS. Reading trhough the forum i found out i would 
> neet bounds.
> So i went on with Method=L-BFGS-B. But now my parameters equal the lower 
> bounds.
>> > out <- optim(par=initial, fn=LogLik.GARCH,X=X, P=1, Q=1, method =
>> > "L-BFGS-B",lower =c(0.01,0.01,0.01), upper =c(0.99,0.99,0.99))
>> > out
> ---
> *$par
> [1] 0.01 0.01 0.01*
> [...]
> $convergence
> [1] 0
> 
> *$message
> [1] "CONVERGENCE: NORM OF PROJECTED GRADIENT <=
> PGTOL"*---
>

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Re: [R] Question about expand.grid function in R

[R. Michael Weylandt]

I don't think you can do it within expand.grid() but something like
this might work:

rownames(x) <- apply(x, 1, paste, collapse = "")

Michael

On Tue, May 1, 2012 at 5:05 AM, Kelly Cool  wrote:
> Hi,
>
> I am extremely new to R, and was wondering if someone would be able to help 
> me with a question regarding the expand.grid function. When I input
>
> expand.grid.rep <- function(x, n=1) do.call(expand.grid, rep(list(x),n))
> expand.grid.rep(c("a", "b", "c"), 3)
>
> my output is as follows,
>
> Var1 Var2 Var3
> 1     a    a    a
> 2     b    a    a
> 3     c    a    a
> 4     a    b    a
> 5     b    b    a
> 6     c    b    a
> 7     a    c    a
> 8     b    c    a
> 9     c    c    a
> 10    a    a    b
> 11    b    a    b
> 12    c    a    b
> 13    a    b    b
> 14    b    b    b
> 15    c    b    b
> 16    a    c    b
> 17    b    c    b
> 18    c    c    b
> 19    a    a    c
> 20    b    a    c
> 21    c    a    c
> 22    a    b    c
> 23    b    b    c
> 24    c    b    c
> 25    a    c    c
> 26    b    c    c
> 27    c    c    c
>
> I was wondering if there was anyway I can change the row numbers to labels 
> that indicate what is in each row. Instead of a 1, I'd like to have a label 
> saying "aaa", etc. I'm not sure if this is even possible within the 
> expand.grid function but any help would be appreciated. Thanks.
>        [[alternative HTML version deleted]]
>
>
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Re: [R] Area between 2 curves

[sappy]

Yes, i have install the Package Bolstad. And it works (sintegral).


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[R] Question about expand.grid function in R

[Kelly Cool]

Hi,

I am extremely new to R, and was wondering if someone would be able to help me 
with a question regarding the expand.grid function. When I input

expand.grid.rep <- function(x, n=1) do.call(expand.grid, rep(list(x),n))
expand.grid.rep(c("a", "b", "c"), 3)

my output is as follows,

Var1 Var2 Var3
1     a    a    a
2     b    a    a
3     c    a    a
4     a    b    a
5     b    b    a
6     c    b    a
7     a    c    a
8     b    c    a
9     c    c    a
10    a    a    b
11    b    a    b
12    c    a    b
13    a    b    b
14    b    b    b
15    c    b    b
16    a    c    b
17    b    c    b
18    c    c    b
19    a    a    c
20    b    a    c
21    c    a    c
22    a    b    c
23    b    b    c
24    c    b    c
25    a    c    c
26    b    c    c
27    c    c    c

I was wondering if there was anyway I can change the row numbers to labels that 
indicate what is in each row. Instead of a 1, I'd like to have a label saying 
"aaa", etc. I'm not sure if this is even possible within the expand.grid 
function but any help would be appreciated. Thanks. 
[[alternative HTML version deleted]]

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Re: [R] Why does the order of terms in a formula translate into different models/ model matrices?

[peter dalgaard]

I know this is three months old, but I had put it on a mental TODO list to see 
whether it was something that could be fixed, and I finally got a little spare 
time for that sort of thing. It turns out that it can NOT be fixed (without 
fundamental design changes), so I thought I'd better record the conclusion for 
the archives.

The reason is pretty simple: It is terms.formula that decides which terms 
require contrast coding and which need dummy coding. It does this based on the 
formula structure _only_; i.e., it has no information on whether variables are 
factors or numerical. E.g., you can do

> terms(~ a:x + a:b)
~a:x + a:b
attr(,"variables")
list(a, x, b)
attr(,"factors")
  a:x a:b
a   2   2
x   2   0
b   0   1
attr(,"term.labels")
[1] "a:x" "a:b"
attr(,"order")
[1] 2 2
attr(,"intercept")
[1] 1
attr(,"response")
[1] 0
attr(,".Environment")


in which there is no indication to terms() what kind of variable "x" is. So if 
you want different behavior if x is a factor than if it is continuous, you're 
out of luck...

Not quite sure the last three lines of my note below make sense, though.

-pd

On Jan 29, 2012, at 11:24 , peter dalgaard wrote:

> 
> On Jan 29, 2012, at 02:42 , Ben Bolker wrote:
>>> 
>> 
>> (quoting removed to make Gmane happy)
>> 
>> AFAICS, this is a bug.
>> 
>> 
>> I think so too, although I haven't got my head around it yet.
>> 
>> Chuck, are you willing to post a summary of this to r-devel
>> for discussion ... and/or post a bug report?
> 
> You have to be very specific about what the bug is, if any... I.e., which 
> precisely are the rules that are broken by the current behavior? 
> 
> Preferably also suggest a fix --- the corner cases of model.matrix and 
> friends is some of the more impenetrable code in the R sources.
> 
> Notice that order dependent parametrization of terms is not a bug per se, nor 
> is the automatic switch to dummy coding of factors. Consider these cases:
> 
> d <- cbind(expand.grid(a=c("a","b"),b=c("X","Y"),c=c("U","W")),x=1:8)
> model.matrix(~ a:b + a:c, d)
> model.matrix(~ a:c + a:b, d)
> model.matrix(~ a:b + a:x, d)
> model.matrix(~ a:x + a:b, d)
> 
> and notice that the logic applying to "x" is the same as that applying to 
> "c". 
> 
> The crux seems to be that the model ~a:c contains the model ~a whereas ~a:x 
> does not, and hence the rationale for _not_ expanding a subsequent a:b term 
> to dummies (namely that ~a is "already in" the model) fails. 
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] Different varable lengths

[John Kane]

> -Original Message-
> From: sarah.gos...@gmail.com
> Sent: Mon, 30 Apr 2012 17:06:19 -0400
> To: jrkrid...@inbox.com
> Subject: Re: [R] Different varable lengths
> 
> Because of the missing comma.

I knew I needed new glasses !

> 
> On Mon, Apr 30, 2012 at 4:56 PM, John Kane  wrote:
>>> length(Sweden.GDP.gap.adjust)
>> [1] 8
>>> Sweden.GDP.gap.adjust
>> [1]  0.673792123  1.196706756  1.196131539  0.646944002 -0.312886525
>> [6] -1.706584861 -0.369401194 -0.003280389
>> 
>> R is reading Sweden.GDP.gapp.adjust as having 8 elements.  Why I don't
>> know.
>> John Kane
>> Kingston ON Canada
>> 
>> 
>>> -Original Message-
>>> From: bahman.za...@comhem.se
>>> Sent: Mon, 30 Apr 2012 02:43:32 -0700 (PDT)
>>> To: r-help@r-project.org
>>> Subject: [R] Different varable lengths
>>> 
>>> Hi!
>>> 
>>> I'm trying to do a lm() test on three objects. My problem is that R
>>> protests
>>> and says that the variable lengths differ for one of the objects
>>> (Sweden.GDP.gap). But I have double checked that the number of
>>> observations
>>> are the same. All three objects should contain 9 observations but R
>>> only
>>> accepts 9 observations in two of the objects. The third must have 10!
>>> Very
>>> confusing because there is no 10th observation!
>>> 
>>>  # Adjusted Real rate - P
 Sweden.p.adjust <- c(4.70243, 1.3776655, 1.117755, 1.6695175, 1.59282,
 1.1017625, -0.04295, 2.2552875, 0.0552875)
 
 # Adjusted Inflation deviation
 Sweden.infl.dev.adjust  <- c(0.110382497, -0.261612509, 0.040847515,
 -0.195062497, -0.234362485, -0.023408728, 0.206421261, -0.079401261,
 0.071828752)
 
 # Adjusted GDP-gap
 Sweden.GDP.gap.adjust <- c(0.673792123, 1.196706756, 1.196131539,
 0.646944002, -0.312886525, -1.180620213 -0.525964648, -0.369401194,
 -0.003280389)
 
 # OLS regression using ADJUSTED data.#
 Sweden.Taylor.real.adjust <- lm(Sweden.p.adjust ~
 Sweden.infl.dev.adjust
 +
 Sweden.GDP.gap.adjust)
>>> Error in model.frame.default(formula = Sweden.p.adjust ~
>>> Sweden.infl.dev.adjust +  :
>>>   variable lengths differ (found for 'Sweden.GDP.gap.adjust')
>>> 
>>> Why is this happening?
>>> 
>>> / Saint
>>> 
>>> 
> 
> 
> --
> Sarah Goslee
> http://www.functionaldiversity.org


FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your 
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Re: [R] Clustering analysis with ordination plots

[Uwe Ligges]

On 30.04.2012 18:44, borinot wrote:

Hello to all,

I'm new to R so I have a lot of problems with it, but I'll only ask the main
one.

I have clustered an environmental matrix


We do not know what that is. Where is the example data? See the posting 
guide.





with 2 different methods,


Which? Where is the reproducible code? See the posting guide.



and I'd
like to plot them in a PCA


PCA is a method for reduction of dimensions. Frequently, if reduction 
works nicely, you can find clusters when plotting the first few PCs. But 
"plot them [clusters] in a PCA" is semantically invalid.



and a db-RDA.


What is a db-RDA?


I mean, I want see these clusters
in the plots like points of differents colours, together with the rest
information of the plot, but I don't know how to do this.


Tells us how you clustered the data and how you visualized it so far and 
we may be able to show you how to go ahead.




I've checked a lot of bibliography and forums, and I haven't found the
solution... it can't be so hard!

Well, thanks in advance! :)


But really, read the posting guide in advance of follow up questions: It 
helps to improve the way you ask questions and hence you will probably 
get more useful answers.


Uwe Ligges



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Re: [R] Subtract days to dates in POSIXct format

[Santiago Guallar]

Yes, sorting longitude and latitude correctly solves the problem! However, this 
only works near the Canaries. When selecting the January data (probable 
location: South African waters) sunrise time (but not sunset time) for the 
given coordinates is about 4 hours later than the local sunrise.

Sys.setenv( TZ="GMT" ) # set to the local timezone for column "time"
dta 
<-read.table("eg.txt",sep=',',col.names=c("ok","time","secs","lig"),stringsAsFactors=FALSE)
dta$dtm <- as.POSIXct(dta$time, format="%d/%m/%y %T" ) # depends on TZ
site <- SpatialPoints( matrix(c(-15.77, 27.82), 
nrow=1),proj4string=CRS("+proj=longlat +datum=WGS84")) # Canary Is
dta$rise <- sunriset(site, dta$dtm, direction="sunrise",POSIXct.out=TRUE)$time
dta$set <- sunriset( site, dta$dtm, direction="sunset", POSIXct.out=TRUE )$time
dta$isnight <- with( dta, !( rise < dtm & dtm < set ) )

A=cbind(dta,colsplit(dta$time, split = "\\s", names = c("date", "clock")))
B=cbind(A,colsplit(A$date, split = "/", names = c("d", "m", "y")))
C<-subset(B,B$m==1) # January data; the bird was in South Atlantic waters
write.table(C)

Thank you very much for your help,

Santi



>
> From: Jeff Newmiller 
>To: Santiago Guallar  
>Cc: "r-help@r-project.org"  
>Sent: Tuesday, May 1, 2012 1:14 AM
>Subject: Re: [R] Subtract days to dates in POSIXct format
> 
>The sunrise and sunset are calculated for each time value on the input vector, 
>but all times are treated in the TZ timezone. I can see that the Canary 
>Islands are in the GMT timezone, so the example TZ is right.
>
>I can see that you entered the latitude and longitude backward (longitude is 
>"x"), but I am not able to look at your data at the moment so I don't know 
>whether that fixes your problem. Maptools assumes one location Depending on 
>where the bird went in the South Atlantic, the assumed latitude could be 
>several hours wrong, though. Also, there is dependence of length of day on 
>latitude (made more noticeable by crossing the equator). 
>---
>Jeff Newmiller                        The     .       .  Go Live...
>DCN:        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.
>
>Santiago Guallar  wrote:
>
>>Thanks a lot, Jeff
>>
>>Yes, I applied colsplit in package reshape. Sorry, I forgot to state it
>>in the piece of code I attached.
>>Actually, these are archival data from a geolocator attached to a
>>seabird. The origin lies on Gran Canaria and data were gathered all
>>along its migratory journey for one full year, from the Canary Islands
>>all the way to the South Atlantic Ocean and back.
>>Variable lig, which stands for light, indicates daylight (aprox lig>2)
>>or its absence (lig<2), so I know when it is nighttime or daytime for
>>sure. However, I'd like to compare it with the output of the maptools
>>functions. 
>>If I understood well maptools functions use astronomical algorithms to
>>calculate sunrise and sunset based on one location and one POSIXct
>>time. If I changed your invented coordinates and time for the real ones
>>in my dataset would do the job correctly? When I put the aproximate
>>coordinates it yields an incorrect output:
>>site <- SpatialPoints( matrix(c(27.82, -15.77),
>>nrow=1),proj4string=CRS("+proj=longlat +datum=WGS84")) # didn't touch
>>the rest of your code
>>
>>But I'm probably doing something wrong.
>>
>>Santi 
>>
>>
>>
>>
>>>
>>> From: Jeff Newmiller 
>>>To: Santiago Guallar  
>>>Cc: "r-help@r-project.org"  
>>>Sent: Monday, April 30, 2012 5:51 PM
>>>Subject: Re: [R] Subtract days to dates in POSIXct format
>>> 
>>>On Mon, 30 Apr 2012, Santiago Guallar wrote:
>>>
 Hello,
 
 I'm having problems working with date values in POSIXct format.
>>>
>>>Indeed you are.
>>>
 Here is what I got (eg.lig attached):
 
 x <- read.table("eg.txt", sep = ',',
>>col.names=c("ok","time","secs","lig")) # it gives time as factor
 z <- cbind(x,colsplit(x$time, split="\\s", names=c("date",
>>"clock")))
>>>
>>>colsplit is not defined in base R, and it is redefined in a couple of
>>packages.  I am guessing you mean the one that is in the reshape
>>package.
>>>
 zh<-cbind(z,colsplit(z$clock,split=":",names=c("h","m","s")))
 zn <- subset(zh, zh$lig<= 5 & zh$h<8 | zh$h>=22) # nighttime
 zn$timepos<-as.POSIXct(zn$time,tz="GMT",format="%d/%m/%y %H:%M:%S")
>>>
 I want to assign timepos to its ?natural? night, that is, the night
>>that goes from sunset of day x to sunrise of day x+1 corresponds to day
>>x:
>>>
>>>You are working here with GMT, but there are many other possible
>>timezo

Re: [R] compiling an R script

[mlell08]

On 01.05.2012 00:12, strycker wrote:
> I'm interested in this question, too, not so I can hide code, but so I can
> run R code faster.  It's been my experience that compiled code always runs
> faster than interpreted code.  Can you explain further how to compile a
> front-end?
>
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/compiling-an-R-script-tp2195949p4599541.html
> Sent from the R help mailing list archive at Nabble.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.
Hello,

there is a thread on Stack Overflow concerning this:
http://stackoverflow.com/questions/1452235/does-an-r-compiler-exist

Regards!

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Re: [R] Questions

[peter dalgaard]

On May 1, 2012, at 06:47 , Jeff Newmiller wrote:

> This is not the RStudio support forum. I use it, I like it, but you need to 
> learn the difference between R and RStudio.
> 
> In this case, the fact that you are using RStudio is probably irrelevant. 
> What is more relevant is that you are not on windows, though I can't be sure 
> what OS you actually are using. Your error message refers to UNIX, you refer 
> to Excel, so you could be on MacOSX or on windows with a pipe into a UNIX 
> server. (If the latter, the RStudio support team may have a FAQ on this 
> problem.) Please read the Posting Guide mentioned at the end of every message 
> on this list.
> I Googled this problem and found 
> https://stat.ethz.ch/pipermail/r-help/2006-October/116363.html, which 
> probably applies, but only you can tell for sure.

A couple of red herrings here, I suspect. If it is a Mac issue, then R-sig-Mac 
could be relevant (although I'm beginning to have doubts that we should send 
_all_ entry-level Mac issues there, when corresponding Windows issues are not 
similarly diverted).

The Clipboard section in help(file) is informative. Indeed, on OSX, this works:

> write.table(airquality,pipe("pbcopy"))
> head(read.table(pipe("pbpaste")))
  Ozone Solar.R Wind Temp Month Day
141 190  7.4   67 5   1
236 118  8.0   72 5   2
312 149 12.6   74 5   3
418 313 11.5   62 5   4
5NA  NA 14.3   56 5   5
628  NA 14.9   66 5   6

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] Regression

[peter dalgaard]

On Apr 30, 2012, at 20:27 , Saint wrote:

> Trying to do a regression for four variables. I get information only for two.
> The rest is marked "NA". Why? And what does NA mean? 

Your design matrix is singular since p is constant and 
p+Sweden.infl.dev=Sweden.infl, so two coefficients are set to missing -- 
effectively, the corresponding predictors are removed from the model.

You may have to read up on the basics of multiple regression.

> 
> Thanks!
> 
> 
>> Sweden.infl.dev <- c(0.2, 0.6, -1, -0.2, -1, -1.5, -0.7, 0.7, -0.1, 0.3)
> 
>> Sweden.GDP.gap <- c(-0.024662769, -0.01519859, -0.027251109, -0.027129556,
>> -0.014561961, 0.007291667, 0.02695406, 0.01179481, 0.008348032,
>> 0.0683083)
> 
>> Sweden.nom.int.rate <- c(7.6, 8.91, 4.1, 4.35, 3.4, 3.25, 4, 3.75, 3.75,
>> 2.75)
> 
>> Sweden.infl <- c(2.2, 2.6, 1, 1.8, 1, 0.5, 1.3, 2.7, 1.9, 2.3)
> 
>> p <- c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2)
> 
>> Sweden.Taylor.nom.p.infl <-  lm(Sweden.nom.int.rate ~ Sweden.infl.dev +
>> Sweden.GDP.gap + p + Sweden.infl)
> 
> Call:
> lm(formula = Sweden.nom.int.rate ~ Sweden.infl.dev + Sweden.GDP.gap + 
>p + Sweden.infl)
> 
> Coefficients:
>(Intercept)  Sweden.infl.dev   Sweden.GDP.gapp  
>  4.6751.212  -43.695   NA  
>Sweden.infl  
> NA  
> 
> 
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/Regression-tp4598984.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> __
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-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] index moran

[peter dalgaard]

On May 1, 2012, at 09:06 , Ulfa Hasanah wrote:

> what is "nb2listw" in index moran? 


Did you try help(nb2listw) ?

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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[R] Re : index moran

[Pascal Oettli]

? nb2listw



- Mail original -
De : Ulfa Hasanah 
À : "r-h...@stat.math.ethz.ch" 
Cc : "r-h...@stat.math.ethz.ch" 
Envoyé le : Mardi 1 mai 2012 16h06
Objet : [R] index moran

what is "nb2listw" in index moran? 

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[R] index moran

[Ulfa Hasanah]

what is "nb2listw" in index moran? 

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[R] testing parallel slopes assumption for Ordinal Logistic Regression

[80past2]

Hi everyone, I'm a bit new here (and new to R), and I was trying to do an
OLR, and testing the parallel slope assumption seems be very important. I
browsed through past postings, and didn't find much to help me in this area.
I was wondering if anyone knew how I could go about doing this. Thank you.

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