Re: [R] Error with predict and newdata
On Aug 7, 2015, at 2:41 PM, kira taylor wrote:
> Hi!
>
> I am trying to use predict to apply my model to data from one time period to
> see what might be the values for another time period. I did this
> successfully for one dataset, and then tried on another with identical code
> and got the following error:
>
> Error in eval(predvars, data, env) :
> numeric 'envir' arg not of length one
>
> The only difference between the two datasets was that my predictor model for
> the first dataset had two predictor variables and my model for the second
> dataset had only one. Why would this make a difference?
>
> My dougfir.csv contains just two columns with thirty numbers in each,
> labeled height and dryshoot.
>
> my lm is: fitdougfir <- lm(dryshoot~height,data=dougfir)
>
> It gets a little complicated (and messy, sorry! I am new to R) because I
> then made a second .csv - the one I used to make my model contained values
> from just June. My new .csv (called alldatadougfir.csv) includes values
> from October as well, and also contains a "date" column that labels the
> values either "june" or "october."
>
> I did the following to separate the height data by date:
>
> alldatadougfir[alldatadougfir$date=="june",c("height")]->junedatadougfir
> alldatadougfir[alldatadougfir$date=="october",c("height")]->
> octoberdatadougfir
Those are no longer lists or dataframe, which are the proper classes of object
to pass to predict.
--
David.
>
> I then want to use my June model to predict my October dryshoots using
> height as my variable and I did the following:
>
> predict(fitdougfir, newdata=junedatadougfir)
> predict(fitdougfir, newdata=octoberdatadougfir)
>
> Again, I did this with an identical dataset successfully - the only
> difference was that my model in the successful dataset had two predictor
> variables instead of the one variable (height) I have in this dataset.
>
> Sorry again for my messy code!
>
> Thank you very much,
>
> Kira
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 Winsemius
Alameda, CA, USA
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Piecewise (segmented) linear regression with center section slope constraint
On Aug 7, 2015, at 12:05 PM, Drew Morrison wrote: > Thanks, Jean. I've actually looked at that source before. The issue is that I > can't constrain the slope of the /center/ section to be zero - in fact, I've > applied similar code to a three-segment regression and I can get a zero > slope either of the two sides, but not in the middle. If you replaced the values during the interval in question with their mean values during that interval, you should then get a zero slope. -- David. > > Here's a list of the main resources I've consulted so far: > > https://climateecology.wordpress.com/2012/08/19/r-for-ecologists-putting-together-a-piecewise-regression/ > > http://www.stackoverflow.dluat.com/questions/30060278/creating-piecewise-linear-regression-with-flat-slope-in-r > > https://rpubs.com/MarkusLoew/12164 > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/Piecewise-segmented-linear-regression-with-center-section-slope-constraint-tp4710839p4710875.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Cant upgrade R in ubuntu 14.04
I am trying to install R programming language and able to install rbase using this code without adding repository in *source.list* sudo apt-get install r-base After that i tried to upgrade it using this code sudo add-apt-repository ‘deb http://star-www.st-andrews.ac.uk/cran/bin/linux/ubuntu/trusty/’ sudo apt-get update sudo apt-get upgrade But when i tried the first code sudo add-apt-repository ‘deb http://star-www.st-andrews.ac.uk/cran/bin/linux/ubuntu/trusty/’ its giving this error Error: need a single repository as argument -- View this message in context: http://r.789695.n4.nabble.com/Cant-upgrade-R-in-ubuntu-14-04-tp4710885.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] creating a funct
I think the readers of this mailing list would have to be psychic to know what went wrong given that description. This kind of situation usually requires in-person help, so I recommend looking for an educational environment that offers such assistance... a seminar, university class, tutor, or users group, for example. --- 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. On August 7, 2015 6:23:23 PM EDT, "Jose Betancourt B." wrote: >Dear > >i am develeping a function, first I attach r command and later r >executer >script, the conection fails and I do not realize why > >best regards > > > > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >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 -- To UNSUBSCRIBE and more, see 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] creating a funct
Dear i am develeping a function, first I attach r command and later r executer script, the conection fails and I do not realize why best regards 100 38 1 80 19 5 90 31 2 70 21 6 85 30 3 75 22 5 99 37 1 100 38 1 80 19 5 90 31 2 70 21 6 85 30 3 75 22 5 99 37 1__ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Error with predict and newdata
Hi!
I am trying to use predict to apply my model to data from one time period to
see what might be the values for another time period. I did this
successfully for one dataset, and then tried on another with identical code
and got the following error:
Error in eval(predvars, data, env) :
numeric 'envir' arg not of length one
The only difference between the two datasets was that my predictor model for
the first dataset had two predictor variables and my model for the second
dataset had only one. Why would this make a difference?
My dougfir.csv contains just two columns with thirty numbers in each,
labeled height and dryshoot.
my lm is: fitdougfir <- lm(dryshoot~height,data=dougfir)
It gets a little complicated (and messy, sorry! I am new to R) because I
then made a second .csv - the one I used to make my model contained values
from just June. My new .csv (called alldatadougfir.csv) includes values
from October as well, and also contains a "date" column that labels the
values either "june" or "october."
I did the following to separate the height data by date:
alldatadougfir[alldatadougfir$date=="june",c("height")]->junedatadougfir
alldatadougfir[alldatadougfir$date=="october",c("height")]->
octoberdatadougfir
I then want to use my June model to predict my October dryshoots using
height as my variable and I did the following:
predict(fitdougfir, newdata=junedatadougfir)
predict(fitdougfir, newdata=octoberdatadougfir)
Again, I did this with an identical dataset successfully - the only
difference was that my model in the successful dataset had two predictor
variables instead of the one variable (height) I have in this dataset.
Sorry again for my messy code!
Thank you very much,
Kira
[[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.
[R] TVP-ECM modelling in R
Hello, I want to estimate a TVP-ECM model in R. Is there a specific package in R that can handle TVP-ECM models? Thank you -- View this message in context: http://r.789695.n4.nabble.com/TVP-ECM-modelling-in-R-tp4710874.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Piecewise (segmented) linear regression with center section slope constraint
Thanks, Jean. I've actually looked at that source before. The issue is that I can't constrain the slope of the /center/ section to be zero - in fact, I've applied similar code to a three-segment regression and I can get a zero slope either of the two sides, but not in the middle. Here's a list of the main resources I've consulted so far: https://climateecology.wordpress.com/2012/08/19/r-for-ecologists-putting-together-a-piecewise-regression/ http://www.stackoverflow.dluat.com/questions/30060278/creating-piecewise-linear-regression-with-flat-slope-in-r https://rpubs.com/MarkusLoew/12164 -- View this message in context: http://r.789695.n4.nabble.com/Piecewise-segmented-linear-regression-with-center-section-slope-constraint-tp4710839p4710875.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Why does R start in wrong working directory despite R_USER setting?
Hi Mauricio,
You can also run a directory selection file by including something like this:
source("SelectAnalysis.R")
in the .First function (see "An Introduction to R", section 10.8
Customizing the environment). Mine currently looks like this:
cat("(A)custudy\n(I)nterval analysis\n(O)mbo
mapping\nR\n(C)ourse\nStressaly(Z)er\n")
answer<-toupper(readline("Choose the project - "))
if(answer=="A") setwd("/home/jim/research/im/acustudy")
if(answer=="I") setwd("/home/jim/research/interval_analysis")
if(answer=="O") setwd("/home/jim/research/ombo/mapping")
if(answer=="R") setwd("/home/jim/R")
if(answer=="C") setwd("/home/jim/bitwrit/R_programming_course")
if(answer=="Z") setwd("/home/jim/research/stressalyser/naomi")
print(list.files(pattern="[.]R"))
options(browser="konqueror",editor="kwrite",show.signif.stars=FALSE)
This should work on any system, regardless of your privileges.
Jim
On Sat, Aug 8, 2015 at 4:02 AM, Jeff Newmiller wrote:
> Not really a question about R, but you can make a Windows shortcut that sets
> the directory where you want it.
>
> My preference is to start in different working directories depending on which
> project I am working on. R_USER is not a project directory. One way to do
> that is to double-click on an RData file located where you want to start.
> Another way is to create a new shortcut in each directory. Another way is to
> add a line to your script that sets the directory appropriately, though that
> makes sharing the scripts harder. Another way is to use RStudio projects.
> ---
> 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.
>
> On August 7, 2015 12:31:16 PM EDT, Mauricio Cornejo via R-help
> wrote:
>>Hi
>>After launching newly-installed R 3.2.1 (on Windows 7), I run the
>>following two commands:
>>> getwd()[1] "C:/ProgramData/Microsoft/Windows/Start Menu/Programs/R"
>>> Sys.getenv('R_USER')[1] "C:\\UsersDocuments"
>>I would like the startup working directory to be that pointed to by
>>R_USER.
>>I don't have administrative access to the machine.
>>Many thanks for any insight anyone can provide.
>>Mauricio
>> [[alternative HTML version deleted]]
>>
>>__
>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>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 -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] compare grupos dichotomus dependent variable
Hi Aurora, Perhaps what you are seeking is a test of proportions. prop.test(c(sum(men),sum(women)),c(length(men),length(women))) 2-sample test for equality of proportions with continuity correction data: c(sum(men), sum(women)) out of c(length(men), length(women)) X-squared = 1.0378e-30, df = 1, p-value = 1 alternative hypothesis: two.sided 95 percent confidence interval: -0.02903701 0.01046116 sample estimates: prop 1 prop 2 0.0 0.009287926 Warning message: In prop.test(c(sum(men), sum(women)), c(length(men), length(women))) : Chi-squared approximation may be incorrect If the question was "Have you had a baby in the past year?" the answer is not too far off, but your sample is a bit small. Jim On Sat, Aug 8, 2015 at 3:09 AM, AURORA GONZALEZ VIDAL wrote: > Hello everybody. I have a statistics question: > > let's say that I want to compaire answers between men and women to a yes/no > question but I have so much more women than men, then, it looks like I > cannot use chi squared test. Would it be correct to use U test (or ranked > Wilcoxon test)?? What do you think?? The code is below, than you so much!! > > men<-rep( 0,12 ) > women <- c( 0,1,0,0,0,1,0,0,0,rep( 0,114 ),1,rep( 0,199 ) ) > wilcox.test( men, women ) > chisq.test( men, women ) > > > -- > Aurora González Vidal > > Sección Apoyo Estadístico. > Servicio de Apoyo a la Investigación (SAI). > Vicerrectorado de Investigación. > Universidad de Murcia > Edif. SACE . Campus de Espinardo. > 30100 Murcia > > @. aurora.gonzal...@um.es > T. 868 88 7315 > F. 868 88 7302 > www.um.es/sai > www.um.es/ae > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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] compare grupos dichotomus dependent variable
What does this have to do with R programming? Bert On Friday, August 7, 2015, AURORA GONZALEZ VIDAL wrote: > Hello everybody. I have a statistics question: > > let's say that I want to compaire answers between men and women to a yes/no > question but I have so much more women than men, then, it looks like I > cannot use chi squared test. Would it be correct to use U test (or ranked > Wilcoxon test)?? What do you think?? The code is below, than you so much!! > > men<-rep( 0,12 ) > women <- c( 0,1,0,0,0,1,0,0,0,rep( 0,114 ),1,rep( 0,199 ) ) > wilcox.test( men, women ) > chisq.test( men, women ) > > > -- > Aurora González Vidal > > Sección Apoyo Estadístico. > Servicio de Apoyo a la Investigación (SAI). > Vicerrectorado de Investigación. > Universidad de Murcia > Edif. SACE . Campus de Espinardo. > 30100 Murcia > > @. aurora.gonzal...@um.es > T. 868 88 7315 > F. 868 88 7302 > www.um.es/sai > www.um.es/ae > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and > more, see > 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 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] testing whether two character vectors contain (the same) items in the same order
On Aug 7, 2015, at 12:22 AM, Federico Calboli wrote:
>
>> On 7 Aug 2015, at 01:59, Bert Gunter wrote:
>>
>> Boris:
>>
>> You may be right, but it seems like esp to me based on the op's
>> non-description of likelihood of coming from the same noisy process. My
>> response would be: seek local statistical help, as your replies indicate a
>> good deal of statistical confusion.
>>
>> Cheers,
>> Bert
>
> Bert,
>
> as this is R-help and not cross-validated I am looking for a precanned
> function that would test whether the order of characters in two character
> vectors comes from the same (noisy) process. I would thus expect you to say
> something on the lines of:
>
> function X uses method Y to do something like that
> function W uses method Z to do something like that
> …
>
> look into those, figure out exactly what you are testing and use the most
> appropiate function.
>
> The whys and wherefores are for me to deal with, I just want to know whether
> someone has built a function that does, or seems to do, what I asked for. As
> I said, this is R-help, and I seek help for R use.
> findFn("levenshtein")
found 57 matches; retrieving 3 pages
2 3
Downloaded 44 links in 17 packages.
stringdist::stringdist( paste0(x, collapse=""), paste0(letters[y],
collapse="") )
[1] 30
--
HTH;
David.
>
> I do concede that my original question might have left many wondering, but I
> guess my reply to Boris would have cleared any doubts. I am therefore
> puzzled by the great deal of confusion on your part in understanding the
> purpose of my question and, in general, of this list.
>
> Best wishes
>
> F
>
>
>>
>>
>>
>> On Thursday, August 6, 2015, Boris Steipe wrote:
>> You are looking for what is known as the "Cayley distance" between vectors -
>> an edit distance that allows only transpositions. RSeek mentions PerMallows
>> (https://cran.r-project.org/web/packages/PerMallows/PerMallows.pdf) and
>> Rankluster
>> (https://cran.r-project.org/web/packages/Rankcluster/Rankcluster.pdf) as
>> packages that support work with Cayley distances. It seems to me that
>> distCayley() in Rankcluster does what you want. From the examples:
>>
>> x=1:5
>> y=c(2,3,1,4,5)
>> distCayley(x,y)
>> 8
>>
>>
>> Cheers,
>> Boris
>>
>>
>>
>>
>>
>> On Aug 6, 2015, at 9:51 AM, Federico Calboli
>> wrote:
>>
On 6 Aug 2015, at 15:40, Bert Gunter wrote:
Define "goodness of match" . For exact matches, see ?"==" , all.equal,
etc.
>>>
>>> Fair point. I would define it as a number that tells me how likely it is
>>> that the same (noisy) process produced both lists.
>>>
>>> BW
>>>
>>> F
>>>
>>>
>>>
>>>
Bert
On Thursday, August 6, 2015, Federico Calboli
wrote:
Hi All,
let’s assume I have a vector of letters drawn only once from the alphabet:
x = sample(letters, 15, replace = F)
x
[1] "z" "t" "g" "l" "u" "d" "w" "x" "a" "q" "k" "j" "f" "n" “v"
y = x[c(1:7,9:8, 10:12, 14, 15, 13)]
I would now like to test how good a match y is for x. Obviously I can
transform the letters in numbers and use a rank test, but I was left
wondering whether this is the only solution and whether there are more
appropriate solutions that are already implemented in R (I am not going to
reinvent the wheel if I can avoid it).
BW
F
--
Federico Calboli
Ecological Genetics Research Unit
Department of Biosciences
PO Box 65 (Biocenter 3, Viikinkaari 1)
FIN-00014 University of Helsinki
Finland
federico.calb...@helsinki.fi
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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
"Data is not information. Information is not knowledge. And knowledge is
certainly not wisdom."
-- Clifford Stoll
>>>
>>>
>>> --
>>> Federico Calboli
>>> Ecological Genetics Research Unit
>>> Department of Biosciences
>>> PO Box 65 (Biocenter 3, Viikinkaari 1)
>>> FIN-00014 University of Helsinki
>>> Finland
>>>
>>> federico.calb...@helsinki.fi
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> 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 -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/post
Re: [R] help plotting glmm values
Luis Fernando García gmail.com> writes:
>
> Dear Fellows,
>
> I´m sorry if my question is very basic, but I'm still new in the field of R
> and the GLMM.
In future, you might consider posting to r-sig-mixed-mod...@r-project.org
instead ...
> I have made a following glmm, and I need to plot the predicted mean values
> from the model and the CI, with this barplot +/- the CI, using the prey as
> explanatory factor.
>
> Although I have been looking for it, I have not found
> a website which show
> the way to do this, so I'm unsure about the right procedure.
> If any of you
> could help me with the correct procedure I would really apprreciate it!
See:
http://glmm.wikidot.com/faq#predconf
http://ms.mcmaster.ca/~bolker/R/misc/foxchapter/
Some modified analysis:
library(lme4)
glmm1 <- glmer(Acc ~ Prey + (1 | Sp), data=Lac, family=binomial)
summary(glmm1)
deviance(glmm1)/df.residual(glmm1)
glmm2 <- update(glmm1,nAGQ=10)
## aggregate
library(plyr)
Lac_agg <- ddply(Lac,c("Prey","Sp"),
summarise,
N=length(Acc),
p=mean(Acc))
Lac_agg <- aggregate(Acc~Prey*Sp,FUN=function(x) c(k=sum(x),N=length(x)),
data=Lac)
glmm3 <- glmer(p ~ Prey + (1 | Sp), weights=N,
data=Lac_agg, family=binomial)
deviance(glmm3)/df.residual(glmm3)
## model with ind-level obs blows up: leave it alone ...
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] Why does R start in wrong working directory despite R_USER setting?
Not really a question about R, but you can make a Windows shortcut that sets
the directory where you want it.
My preference is to start in different working directories depending on which
project I am working on. R_USER is not a project directory. One way to do that
is to double-click on an RData file located where you want to start. Another
way is to create a new shortcut in each directory. Another way is to add a line
to your script that sets the directory appropriately, though that makes sharing
the scripts harder. Another way is to use RStudio projects.
---
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.
On August 7, 2015 12:31:16 PM EDT, Mauricio Cornejo via R-help
wrote:
>Hi
>After launching newly-installed R 3.2.1 (on Windows 7), I run the
>following two commands:
>> getwd()[1] "C:/ProgramData/Microsoft/Windows/Start Menu/Programs/R"
>> Sys.getenv('R_USER')[1] "C:\\UsersDocuments"
>I would like the startup working directory to be that pointed to by
>R_USER.
>I don't have administrative access to the machine.
>Many thanks for any insight anyone can provide.
>Mauricio
> [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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.
[R] Treemap error - missing value where TRUE/FALSE needed
Dear R users,
I am trying to generate a treemap using the package Treemap on R and I'm
encountering the subsequent error:
*Error in if (rec[3] < rec[4]) { : missing value where TRUE/FALSE needed*
I did traceback() and I got:
*5: pivotSize(numeric(0), c(NA_real_, NA_real_, NA_real_, NA_real_*
* ))*
*4: do.call(algorithm, list(value, rec))*
*3: subTM(datlist[datlist$l == 1])*
*2: tmGenerateRect(datlist, vps, indexList, algorithm)*
*1: treemap(stuff, index = c("representative", "description"), vSize =
"value", *
* type = "categorical", vColor = "representative", title = "REVIGO
Gene Ontology treemap", *
* inflate.labels = FALSE, lowerbound.cex.labels = 0, bg.labels =
"#CCAA", *
* position.legend = "none")*
My script is attached.
I have no idea about how to fix it. Can anyone please help me?
Thanks in advance,
Alicia
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why does R start in wrong working directory despite R_USER setting?
Assuming you are using the GUI you can use the Properties of the
shortcut to tell R where to start.
On 07/08/2015 17:31, Mauricio Cornejo via R-help wrote:
Hi
After launching newly-installed R 3.2.1 (on Windows 7), I run the following two
commands:
getwd()[1] "C:/ProgramData/Microsoft/Windows/Start Menu/Programs/R"
Sys.getenv('R_USER')[1] "C:\\UsersDocuments"
I would like the startup working directory to be that pointed to by R_USER.
I don't have administrative access to the machine.
Many thanks for any insight anyone can provide.
Mauricio
[[alternative HTML version deleted]]
__
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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.
--
Michael
http://www.dewey.myzen.co.uk/home.html
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and provide commented, minimal, self-contained, reproducible code.
[R] compare grupos dichotomus dependent variable
Hello everybody. I have a statistics question: let's say that I want to compaire answers between men and women to a yes/no question but I have so much more women than men, then, it looks like I cannot use chi squared test. Would it be correct to use U test (or ranked Wilcoxon test)?? What do you think?? The code is below, than you so much!! men<-rep( 0,12 ) women <- c( 0,1,0,0,0,1,0,0,0,rep( 0,114 ),1,rep( 0,199 ) ) wilcox.test( men, women ) chisq.test( men, women ) -- Aurora González Vidal Sección Apoyo Estadístico. Servicio de Apoyo a la Investigación (SAI). Vicerrectorado de Investigación. Universidad de Murcia Edif. SACE . Campus de Espinardo. 30100 Murcia @. aurora.gonzal...@um.es T. 868 88 7315 F. 868 88 7302 www.um.es/sai www.um.es/ae [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Why does R start in wrong working directory despite R_USER setting?
Hi
After launching newly-installed R 3.2.1 (on Windows 7), I run the following two
commands:
> getwd()[1] "C:/ProgramData/Microsoft/Windows/Start Menu/Programs/R"
> Sys.getenv('R_USER')[1] "C:\\UsersDocuments"
I would like the startup working directory to be that pointed to by R_USER.
I don't have administrative access to the machine.
Many thanks for any insight anyone can provide.
Mauricio
[[alternative HTML version deleted]]
__
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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.
Re: [R] fpc package - computing silhouette value returns error
help(distcritmulti) says that its 2nd argument is "clustering: vector of integers indicating the clustering" and you supplied the output of hclust, which is not a vector of group identifiers. You can make a group identifier vector from hc with cutree(hc, k=4), where k is the number of groups. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Aug 7, 2015 at 7:40 AM, Ziqi Zhang wrote: > Hi > I am using R to do clustering and compute a number of cluster statistics. > Below are my code. I do not understand why I get the error: > > "Error in summary(silhouette(clustering[ss[[i]]], dx)) : error in > evaluating the argument 'object' in selecting a method for function > 'summary': Error in round(x) : non-numeric argument to mathematical > function" > > Any suggestsion highly appreciated! > Code: > -- > library(fpc) > require(graphics) > distance <- dist(USArrests, "euclidean") > hc <-hclust(distance, "average") > distcritmulti(USArrests, hc, criterion="asw", fun="dist", > metric="euclidean") > - > > > > -- > Ziqi Zhang > Research Associate > Department of Computer Science > University of Sheffield > > > --- > This email has been checked for viruses by Avast antivirus software. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Potencial bug in R.adjust ("holm" method)
On 07 Aug 2015, at 16:20 , Iker Vaquero Alba wrote:
>
>
>Hello, Peter, and thank you for your clarifying reply. Actually, that was
> another doubt I had. As I take my data from different files (every "bunch of
> 5" values is taken from a different file), I assumed that, if I wanted to
> adjust for the error due to repeated measures, it should be enough to do it
> inside each file, right? I mean, the possible error due to repeated measures
> shouldn't go beyond each file. Once you close one file, open and attach a new
> one, the count, let's say, starts from scratch.
> Am I right? And if I'm not, what is the reason why should I pool all the
> p-values in a massive column and adjust them in bulk?
>
There's no clear answer to that kind of question. It depends on which kind of
error rate you want to control, but in principle multiple response variables
are not different than multiple comparisons. If you test 20 response variables
at level 5%, on average 1 will come out significant even if there are no actual
effects (if the variables are highly correlated, this may mean that all 20 come
out significant with 5% probability, though).
>Thank you very much for your help.
>Iker
>
> __
>
>Dr. Iker Vaquero-Alba
>Visiting Postdoctoral Research Associate
>Laboratory of Evolutionary Ecology of Adaptations,
>School of Life Sciences, University of Lincoln,
>Riseholme Park Campus, Lincoln
>LN2 2LG,
>UK.
>
>https://eric.exeter.ac.uk/repository/handle/10036/3381
>
>
> De: peter dalgaard
> Para: Iker Vaquero Alba
> CC: "r-help@r-project.org"
> Enviado: Viernes 7 de agosto de 2015 14:40
> Asunto: Re: [R] Potencial bug in R.adjust ("holm" method)
>
>
> On 06 Aug 2015, at 19:20 , Iker Vaquero Alba wrote:
>
> >Hello all,
> >I am doing some Bonferroni correction analyses with R.adjust function. I
> > have a spreadsheet with 24 columns, each with 5 values. When I use the
> > "holm" method, it gives me adjusted figures for all the original values
> > except from the ones in the 4th row of each column. I mean, the value on
> > the 4th row for every column is exactly the same either in the original
> > data or in the corrected one. I've tried using another algorithm just to
> > see what happens ("bonferroni", for example) and everything is fine, I get
> > corrected figures for all the values, even the ones on the 4th row.
> >
> >Does anyone know whether this is any kind of known bug of the "holm"
> > algorithm of P.adjust function. If so, should I worry about it? If so, can
> > anybody suggest any possible solution?
> >Thank you very much.
> >Iker
>
> p.adjust(), I presume?
>
> The Holm procedure is essentially to sort p-values in decreasing order and
> mutiplying by 1:n plus a little fiddling to keep the order and prevent p > 1.
> The logic is that if you reject the hypothesis corresponding to the smallest
> p after Bonferroni-correction by N, you only have N-1 simultaneous tests to
> consider, etc. The smallest multiplier will be 1, so it's not strange that
> one value appears uncorrected. It's curious that it is always in the 4th row,
> but it might be that the p-values in the 4 other rows are all considerably
> smaller.
>
> You do realize that if you run p.adjust for each column, you are not actually
> adjusting for the total of 120 tests, only for 5 of them, effectively
> ignoring the 23 other columns every time?
>
> -pd
>
>
>
>
> >
> >
> > __
> >
> >Dr. Iker Vaquero-Alba
> >Visiting Postdoctoral Research Associate
> >Laboratory of Evolutionary Ecology of Adaptations,
> >School of Life Sciences, University of Lincoln,Riseholme Park
> > Campus, Lincoln
> >LN2 2LG,
> >UK.
> >
> >https://eric.exeter.ac.uk/repository/handle/10036/3381
>
> >
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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
> Office: A 4.23
> 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
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
[R] fpc package - computing silhouette value returns error
Hi I am using R to do clustering and compute a number of cluster statistics. Below are my code. I do not understand why I get the error: "Error in summary(silhouette(clustering[ss[[i]]], dx)) : error in evaluating the argument 'object' in selecting a method for function 'summary': Error in round(x) : non-numeric argument to mathematical function" Any suggestsion highly appreciated! Code: -- library(fpc) require(graphics) distance <- dist(USArrests, "euclidean") hc <-hclust(distance, "average") distcritmulti(USArrests, hc, criterion="asw", fun="dist", metric="euclidean") - -- Ziqi Zhang Research Associate Department of Computer Science University of Sheffield --- This email has been checked for viruses by Avast antivirus software. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Potencial bug in R.adjust ("holm" method)
Hello, Peter, and thank you for your clarifying reply. Actually, that was
another doubt I had. As I take my data from different files (every "bunch of 5"
values is taken from a different file), I assumed that, if I wanted to adjust
for the error due to repeated measures, it should be enough to do it inside
each file, right? I mean, the possible error due to repeated measures shouldn't
go beyond each file. Once you close one file, open and attach a new one, the
count, let's say, starts from scratch.
Am I right? And if I'm not, what is the reason why should I pool all the
p-values in a massive column and adjust them in bulk?
Thank you very much for your help. Iker
__
Dr. Iker Vaquero-Alba
Visiting Postdoctoral Research Associate
Laboratory of Evolutionary Ecology of Adaptations,
School of Life Sciences, University of Lincoln, Riseholme Park Campus,
Lincoln
LN2 2LG,
UK.
https://eric.exeter.ac.uk/repository/handle/10036/3381
De: peter dalgaard
CC: "r-help@r-project.org"
Enviado: Viernes 7 de agosto de 2015 14:40
Asunto: Re: [R] Potencial bug in R.adjust ("holm" method)
> Hello all,
> I am doing some Bonferroni correction analyses with R.adjust function. I
>have a spreadsheet with 24 columns, each with 5 values. When I use the "holm"
>method, it gives me adjusted figures for all the original values except from
>the ones in the 4th row of each column. I mean, the value on the 4th row for
>every column is exactly the same either in the original data or in the
>corrected one. I've tried using another algorithm just to see what happens
>("bonferroni", for example) and everything is fine, I get corrected figures
>for all the values, even the ones on the 4th row.
>
> Does anyone know whether this is any kind of known bug of the "holm"
>algorithm of P.adjust function. If so, should I worry about it? If so, can
>anybody suggest any possible solution?
> Thank you very much.
> Iker
p.adjust(), I presume?
The Holm procedure is essentially to sort p-values in decreasing order and
mutiplying by 1:n plus a little fiddling to keep the order and prevent p > 1.
The logic is that if you reject the hypothesis corresponding to the smallest p
after Bonferroni-correction by N, you only have N-1 simultaneous tests to
consider, etc. The smallest multiplier will be 1, so it's not strange that one
value appears uncorrected. It's curious that it is always in the 4th row, but
it might be that the p-values in the 4 other rows are all considerably smaller.
You do realize that if you run p.adjust for each column, you are not actually
adjusting for the total of 120 tests, only for 5 of them, effectively ignoring
the 23 other columns every time?
-pd
>
>
> __
>
> Dr. Iker Vaquero-Alba
> Visiting Postdoctoral Research Associate
> Laboratory of Evolutionary Ecology of Adaptations,
> School of Life Sciences, University of Lincoln, Riseholme Park Campus,
>Lincoln
> LN2 2LG,
> UK.
>
> https://eric.exeter.ac.uk/repository/handle/10036/3381
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] Potencial bug in R.adjust ("holm" method)
On 06 Aug 2015, at 19:20 , Iker Vaquero Alba wrote:
>Hello all,
>I am doing some Bonferroni correction analyses with R.adjust function. I
> have a spreadsheet with 24 columns, each with 5 values. When I use the "holm"
> method, it gives me adjusted figures for all the original values except from
> the ones in the 4th row of each column. I mean, the value on the 4th row for
> every column is exactly the same either in the original data or in the
> corrected one. I've tried using another algorithm just to see what happens
> ("bonferroni", for example) and everything is fine, I get corrected figures
> for all the values, even the ones on the 4th row.
>
>Does anyone know whether this is any kind of known bug of the "holm"
> algorithm of P.adjust function. If so, should I worry about it? If so, can
> anybody suggest any possible solution?
>Thank you very much.
>Iker
p.adjust(), I presume?
The Holm procedure is essentially to sort p-values in decreasing order and
mutiplying by 1:n plus a little fiddling to keep the order and prevent p > 1.
The logic is that if you reject the hypothesis corresponding to the smallest p
after Bonferroni-correction by N, you only have N-1 simultaneous tests to
consider, etc. The smallest multiplier will be 1, so it's not strange that one
value appears uncorrected. It's curious that it is always in the 4th row, but
it might be that the p-values in the 4 other rows are all considerably smaller.
You do realize that if you run p.adjust for each column, you are not actually
adjusting for the total of 120 tests, only for 5 of them, effectively ignoring
the 23 other columns every time?
-pd
>
>
> __
>
>Dr. Iker Vaquero-Alba
>Visiting Postdoctoral Research Associate
>Laboratory of Evolutionary Ecology of Adaptations,
>School of Life Sciences, University of Lincoln,Riseholme Park Campus,
> Lincoln
>LN2 2LG,
>UK.
>
>https://eric.exeter.ac.uk/repository/handle/10036/3381
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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] Piecewise (segmented) linear regression with center section slope constraint
This posting on StackOverflow might be useful to you. http://stackoverflow.com/questions/13810607/in-r-package-segmented-how-could-i-set-the-slope-of-one-of-lines-in-the-model Jean On Thu, Aug 6, 2015 at 3:01 PM, Drew Morrison wrote: > Hi, > > I'm working on a way to predict the electricity consumption of electrically > heated buildings as a function of outdoor air temperature. I've identified > a > three-segment linear model as a candidate for a good fit, with the slope of > the center section constrained to zero. I'm working with the segmented > package. I've searched some of the other posts on this forum and they've > been very helpful, but they don't address my big sticking point: how do I > constrain the slope of the center section of the model to 0, rather than > the > left or right section? > > Below is a script with simulated data and my first attempt at fitting the > model. You should be able to copy, paste, and run it. Thanks in advance. > Drew > > # three-piece segmented regression > # center section constrained to slope of 0. > > > # simulate and plot data > T<- 1:100 > energy<- 100+75*pmax(55-T,0)+25*pmax(T-70,0)+150*rnorm(50) > plot(T, energy) > > # create a linear model > model <- lm(energy~T) > #print(summary(model)) > > # start segmented regression > library(segmented) > seg_model <- segmented(model, seg.Z = ~ T, psi = list(T = c(52, 71))) > print(summary(seg_model)) > print(seg_model$psi) > print(slope(seg_model)) > > # plot regression lines > fitted_energy <- fitted(seg_model) > regression_model <- data.frame(Temperature = T, kWh = fitted_energy) > lines(x = T, y = fitted_energy, col = 1) > > # try constrained regression > TT<- -T # change signs of independent variable > model <- lm(energy~1) # constrain slope > seg_model <- segmented(model, seg.Z = ~ TT, psi = list(TT = c(-71, -52))) > print(summary(seg_model)) > print(seg_model$psi) > print(slope(seg_model)) > > # plot constrained regression > fitted_energy <- fitted(seg_model) > regression_model <- data.frame(Temperature = T, kWh = fitted_energy) > lines(x = T, y = fitted_energy, col = 2) > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/Piecewise-segmented-linear-regression-with-center-section-slope-constraint-tp4710839.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Potencial bug in R.adjust ("holm" method)
Please send a reproducible example.
Best,
Uwe Ligges
On 06.08.2015 19:20, Iker Vaquero Alba wrote:
Hello all,
I am doing some Bonferroni correction analyses with R.adjust function. I have a spreadsheet
with 24 columns, each with 5 values. When I use the "holm" method, it gives me adjusted
figures for all the original values except from the ones in the 4th row of each column. I mean, the
value on the 4th row for every column is exactly the same either in the original data or in the
corrected one. I've tried using another algorithm just to see what happens
("bonferroni", for example) and everything is fine, I get corrected figures for all the
values, even the ones on the 4th row.
Does anyone know whether this is any kind of known bug of the "holm"
algorithm of P.adjust function. If so, should I worry about it? If so, can anybody
suggest any possible solution?
Thank you very much.
Iker
__
Dr. Iker Vaquero-Alba
Visiting Postdoctoral Research Associate
Laboratory of Evolutionary Ecology of Adaptations,
School of Life Sciences, University of Lincoln,Riseholme Park Campus,
Lincoln
LN2 2LG,
UK.
https://eric.exeter.ac.uk/repository/handle/10036/3381
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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 -- To UNSUBSCRIBE and more, see
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] testing whether two character vectors contain (the same) items in the same order
> On 7 Aug 2015, at 01:59, Bert Gunter wrote: > > Boris: > > You may be right, but it seems like esp to me based on the op's > non-description of likelihood of coming from the same noisy process. My > response would be: seek local statistical help, as your replies indicate a > good deal of statistical confusion. > > Cheers, > Bert Bert, as this is R-help and not cross-validated I am looking for a precanned function that would test whether the order of characters in two character vectors comes from the same (noisy) process. I would thus expect you to say something on the lines of: function X uses method Y to do something like that function W uses method Z to do something like that … look into those, figure out exactly what you are testing and use the most appropiate function. The whys and wherefores are for me to deal with, I just want to know whether someone has built a function that does, or seems to do, what I asked for. As I said, this is R-help, and I seek help for R use. I do concede that my original question might have left many wondering, but I guess my reply to Boris would have cleared any doubts. I am therefore puzzled by the great deal of confusion on your part in understanding the purpose of my question and, in general, of this list. Best wishes F > > > > On Thursday, August 6, 2015, Boris Steipe wrote: > You are looking for what is known as the "Cayley distance" between vectors - > an edit distance that allows only transpositions. RSeek mentions PerMallows > (https://cran.r-project.org/web/packages/PerMallows/PerMallows.pdf) and > Rankluster > (https://cran.r-project.org/web/packages/Rankcluster/Rankcluster.pdf) as > packages that support work with Cayley distances. It seems to me that > distCayley() in Rankcluster does what you want. From the examples: > > x=1:5 > y=c(2,3,1,4,5) > distCayley(x,y) > 8 > > > Cheers, > Boris > > > > > > On Aug 6, 2015, at 9:51 AM, Federico Calboli > wrote: > > >> > >> On 6 Aug 2015, at 15:40, Bert Gunter wrote: > >> > >> Define "goodness of match" . For exact matches, see ?"==" , all.equal, > >> etc. > > > > Fair point. I would define it as a number that tells me how likely it is > > that the same (noisy) process produced both lists. > > > > BW > > > > F > > > > > > > > > >> > >> Bert > >> > >> On Thursday, August 6, 2015, Federico Calboli > >> wrote: > >> Hi All, > >> > >> let’s assume I have a vector of letters drawn only once from the alphabet: > >> > >> x = sample(letters, 15, replace = F) > >> x > >> [1] "z" "t" "g" "l" "u" "d" "w" "x" "a" "q" "k" "j" "f" "n" “v" > >> > >> y = x[c(1:7,9:8, 10:12, 14, 15, 13)] > >> > >> I would now like to test how good a match y is for x. Obviously I can > >> transform the letters in numbers and use a rank test, but I was left > >> wondering whether this is the only solution and whether there are more > >> appropriate solutions that are already implemented in R (I am not going to > >> reinvent the wheel if I can avoid it). > >> > >> BW > >> > >> F > >> > >> > >> -- > >> Federico Calboli > >> Ecological Genetics Research Unit > >> Department of Biosciences > >> PO Box 65 (Biocenter 3, Viikinkaari 1) > >> FIN-00014 University of Helsinki > >> Finland > >> > >> federico.calb...@helsinki.fi > >> > >> __ > >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > >> 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 > >> > >> "Data is not information. Information is not knowledge. And knowledge is > >> certainly not wisdom." > >> -- Clifford Stoll > >> > > > > > > -- > > Federico Calboli > > Ecological Genetics Research Unit > > Department of Biosciences > > PO Box 65 (Biocenter 3, Viikinkaari 1) > > FIN-00014 University of Helsinki > > Finland > > > > federico.calb...@helsinki.fi > > > > __ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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 -- To UNSUBSCRIBE and more, see > 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 > > "Data is not information. Information is not knowledge. And knowledge is > certainly not wisdom." >-- Clifford Stoll > -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland
