Re: [R] Potencial bug in R.adjust (holm method)
On 06 Aug 2015, at 19:20 , Iker Vaquero Alba karrasp...@yahoo.es 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] compare grupos dichotomus dependent variable
What does this have to do with R programming? Bert On Friday, August 7, 2015, AURORA GONZALEZ VIDAL aurora.gonzal...@um.es 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 javascript:; 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 javascript:; 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] 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 jdnew...@dcn.davis.ca.us 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:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. 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
r-help@r-project.org 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:\\Users\\my username\\Documents
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
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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 aurora.gonzal...@um.es 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] function ndq()
Use an internet search engine. The one I used told me that the book Statistics and Data with R: An Applied Approach Through Examples by Yosef Cohen, Jeremiah Y. Cohen contains a function definition of nqd in section 1.11.4. Best, Uwe Ligges On 06.08.2015 23:31, kle...@sxmail.de wrote: Hello everyone!I had to notice that it is better to be curious about packages and functions contained therein, as I (yet new to R) recognised that there is a number of 'convenient' R packages simplifying and possibilitating a lot. At the moment, I have 'retrofitted' (install packages not delivered with R's basic version) my R version (3.0.2); that number of packages already turned out to be more than helpful.Though, I have one problem lingering: It concerns a function that according to literature (Cohen Cohen, ISBN-13 978-0-470-75805-2, 2008) is called nqd() and, as that reference put it, would enable the R user to print data (when working with matrices) without quotes and dimension names on the R console.I have but had difficulties getting to know to which package function nqd() belongs and would like to ask the R help community which package that was.Thanks a lot in advance yet!Best regards,Markus [[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] 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.
[R] help plotting glmm values
Dear Fellows,
I´m sorry if my question is very basic, but I'm still new in the field of R
and the GLMM.
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!
Sorry for attaching the dataset, but it is too long.
##GLMM
Lac=read.table(loxoacc10.txt,header=T)
library(lme4)
glmm1 - glmer(Acc ~ Prey + (1 | Sp), family=binomial)
summary(glmm1)
overdisp_fun - function(model) {
## number of variance parameters in
## an n-by-n variance-covariance matrix
vpars - function(m) {
nrow(m)*(nrow(m)+1)/2
}
overdisp_fun(glmm1)#Check for overdispersal
Sp Acc Prey
1 1 hormiga
1 1 termita
1 1 larva
1 0 cochinilla
2 0 hormiga
2 1 termita
2 0 larva
2 0 cochinilla
3 0 hormiga
3 1 termita
3 1 larva
3 1 cochinilla
4 1 hormiga
4 0 termita
4 0 larva
4 1 cochinilla
5 1 hormiga
5 0 termita
5 1 larva
5 0 cochinilla
6 1 hormiga
6 1 termita
6 1 larva
6 0 cochinilla
7 1 hormiga
7 1 termita
7 1 larva
7 1 cochinilla
8 1 hormiga
8 1 termita
8 1 larva
8 1 cochinilla
9 1 hormiga
9 1 termita
9 1 larva
9 0 cochinilla
10 1 hormiga
10 1 termita
10 0 larva
10 1 cochinilla
11 1 hormiga
11 1 termita
11 1 larva
11 0 cochinilla
12 1 hormiga
12 1 termita
12 1 larva
12 1 cochinilla
13 1 hormiga
13 1 termita
13 1 larva
13 1 cochinilla
14 1 hormiga
14 1 termita
14 1 larva
14 0 cochinilla
15 1 hormiga
15 1 termita
15 1 larva
15 0 cochinilla
16 1 hormiga
16 1 termita
16 1 larva
16 0 cochinilla
17 1 hormiga
17 0 termita
17 1 larva
17 0 cochinilla
18 1 hormiga
18 1 termita
18 1 larva
18 1 cochinilla
19 0 hormiga
19 1 termita
19 1 larva
19 0 cochinilla
20 0 hormiga
20 1 termita
20 1 larva
20 1 cochinilla
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Re: [R] testing whether two character vectors contain (the same) items in the same order
On 7 Aug 2015, at 01:59, Bert Gunter bgunter.4...@gmail.com 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 boris.ste...@utoronto.ca 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 federico.calb...@helsinki.fi wrote: On 6 Aug 2015, at 15:40, Bert Gunter bgunter.4...@gmail.com 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 federico.calb...@helsinki.fi 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 federico.calb...@helsinki.fi __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help
Re: [R] Potencial bug in R.adjust (holm method)
On 07 Aug 2015, at 16:20 , Iker Vaquero Alba karrasp...@yahoo.es 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 pda...@gmail.com Para: Iker Vaquero Alba karrasp...@yahoo.es CC: r-help@r-project.org 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 karrasp...@yahoo.es 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 the posting guide http://www.R-project.org/posting-guide.html and
[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.
[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:\\Users\\my username\\Documents
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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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 ziqi.zh...@sheffield.ac.uk 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)
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 pda...@gmail.com CC: r-help@r-project.org 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.
[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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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:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. 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
r-help@r-project.org 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:\\Users\\my username\\Documents
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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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] help plotting glmm values
Luis Fernando García luysgarcia at 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.
[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.
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:\\Users\\my username\\Documents
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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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 bgunter.4...@gmail.com 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 boris.ste...@utoronto.ca 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 federico.calb...@helsinki.fi wrote: On 6 Aug 2015, at 15:40, Bert Gunter bgunter.4...@gmail.com 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 federico.calb...@helsinki.fi 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,
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 dmorri...@seventhwave.org 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.
[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.
[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]] __ 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.
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:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. 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. betans...@gmail.com 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] 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.
