date:20160405

Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread PIKAL Petr

Hi

Or some rounding when comparing results with threshold exactly.

> round(abs(0.95 - 1),2) > 0.05
[1] FALSE
> round(abs(0.95 - 1),2) < 0.05
[1] FALSE
>
Cheers
Petr

> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Rainer
> Johannes
> Sent: Tuesday, April 5, 2016 4:33 PM
> To: Thierry Onkelinx 
> Cc: r-help@r-project.org; Adrian Dușa 
> Subject: Re: [R] Problem with <= (less than or equal): not giving the expected
> result
>
> Thanks!
>
> On 05 Apr 2016, at 16:07, Thierry Onkelinx
> > wrote:
>
> You could use something like this
>
> x <- abs(0.95 - 1)
> treshold <- 0.05
> x < treshold | abs(x - treshold) < 1e-6
>
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality
> Assurance Kliniekstraat 25
> 1070 Anderlecht
> Belgium
>
> To call in the statistician after the experiment is done may be no more than
> asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of
> anecdote is not data. ~ Roger Brinner The combination of some data and an
> aching desire for an answer does not ensure that a reasonable answer can be
> extracted from a given body of data. ~ John Tukey
>
> 2016-04-05 14:46 GMT+02:00 Rainer Johannes
> >:
> Thanks Adrian and Thierry (from the previous answer).
>
> I was aware of the all.equal function, but there is nothing similar for <= 
> (e.g.
> all.smallerEqual)?
>
> cheers, jo
>
> On 05 Apr 2016, at 14:31, Adrian Dușa
>  n...@unibuc.ro>> wrote:
>
> Yes, that does have to do with floating point representation.
> I use this function for these types of comparisons (works with values as well
> as with vectors):
>
> check.equal <- function(x, y) {
> check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
> check.vector[is.na(check.vector)] <- FALSE
> return(check.vector)
> }
>
> See:
> ?all.equal
>
> Hth,
> Adrian
>
> On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes
>  johannes.rai...@eurac.edu>> wrote:
> Dear All,
>
> I have the following problem:
>
> I have a function in which I check if the difference between values is smaller
> or equal to a certain threshold. I however realized that I might get there
> some unexpected results:
>
> > abs(1 - 0.95) >= 0.05
> [1] TRUE
> ## So that’s fine, but:
> > abs(1 - 0.95) <= 0.05
> [1] FALSE
>
> Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite
> disturbing.
>
> Along these lines:
> > abs(0.95 - 1) > 0.05
> [1] TRUE
> > abs(0.95 - 1) < 0.05
> [1] FALSE
>
> I guess that has to do with the floating point representation of the data?
>
> Is there something I miss or is there any solution to this?
> Thanks for any help!
>
> cheers, jo
>
>
>
> I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The R-
> version I used for the code above is:
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> __
> R-help@r-project.org 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 project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To
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> and provide commented, minimal, self-contained, reproducible code.
>
>
>
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>
>

Re: [R] Fwd: as.Date gives NAs when transforming from factor

2016-04-05 Thread PIKAL Petr

Hi

I did not have problems transforming factors to dates, only when trying to 
transform nonexistent date.

> as.Date(factor(c("31.3.2015", "29.2.2015")), format="%d.%m.%Y")
[1] "2015-03-31" NA
>
Cheers
Petr

> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Jeff
> Newmiller
> Sent: Wednesday, April 6, 2016 2:05 AM
> To: Omar André Gonzáles Díaz ; r-help@R-
> project.org
> Subject: Re: [R] Fwd: as.Date gives NAs when transforming from factor
>
> Don't give a factor to as.Date. Convert it to character first, or avoid 
> letting it
> become a factor in the first place by using the stringsAsFactors =FALSE option
> to the read.table function or its related functions.
> --
> Sent from my phone. Please excuse my brevity.
>
> On April 5, 2016 4:53:56 PM PDT, "Omar André Gonzáles Díaz"
>  wrote:
> >Hi,
> >
> >I would appreciate your help.
> >
> >I’m having problems when transforming  a column from “factor” to
> >“date”.
> >
> >
> >
> >It does not convert just: 31/03/2016 correctly, it out puts: NA.
> >
> >
> >
> >04/04/2016  turns out as: 2016-04-04
> >
> >
> >
> >02/04/2016 turns out as: 2016-02-04
> >
> >
> >
> >31/03/2016 turns out as: NA
> >
> >03/04/2016 turns out as: 2016-03-04.
> >
> >
> >
> >
> >
> >
> >
> >Code:
> >
> >a <- read.csv("dates.csv", stringsAsFactors = F)
> >
> >
> >
> >a$Date <- as.Date(a$Date, format = "%m/%d/%Y")
> >
> >
> >
> >
> >Posible Solutions:
> >
> >
> >
> >I’ve read here that it has to do with the Sys Locale, and the solution
> >was
> >using: “LC_TIME”, “C”. But I didn’t have success.
> >
> >http://stackoverflow.com/questions/15566875/as-date-returning-na-in-r
> >
> >
> >
> >
> >
> >
> ># Sys.getlocale("LC_TIME")
> >
> >#
> >
> ># Sys.setlocale("LC_TIME", "C")
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >Slds,
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >---
> >-
> >> Disclaimer The information in this email and any attachments may
> >contain
> >proprietary and privileged information that is intended for the
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> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>
>   [[alternative HTML version deleted]]
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> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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Re: [R] R-dvel [robustness Simulation study of 2 sample test on several combination of factors ]

2016-04-05 Thread Jim Lemon

You have quite a few mistakes in your example. The code below works
for me - you can wrap it in a function if you like. I think you will
need a lot more practice before you can write something like this in R
as you are missing close braces and haven't really worked out the
difference between the number of calculations you are doing for each
replication and the number of replications. It takes 5-10 minutes to
run.

 ## Put the samples sizes into matrix then use a loop for sample sizes
sample_sizes<-
 matrix(c(10,10,10,25,25,25,25,50,25,100,50,25,50,100,100,25,100,100),
 nrow=2)

#create vector to combine all std deviations
sds<-c(4,6,8,10,12,14)
# this number is needed below
nsds<-length(sds)
set.seed(8)

#number of simulations
nSims<-1
#set significance level,alpha for the whole simulatio
alpha<-0.05

#set empty vector of length no.of _calculations_ to store p-values
# Note: you have 54 calculations, not 1
ncalcs<-dim(sample_sizes)[2]*nsds
t_equal <-c(rep(0,length=ncalcs))
t_unequal <-c(rep(0,length=ncalcs))
mann <-c(rep(0,length=ncalcs))

#set up matrix for storing data from the vectors
# but you do want 1 replications of each calculation
matrix_Equal<-matrix(rep(NA,ncalcs*nSims),nrow=nSims)
matrix_Unequal<-matrix(rep(NA,ncalcs*nSims),nrow=nSims)
matrix_mann<-matrix(rep(NA,ncalcs*nSims),nrow=nSims)

Simulations

for (sim in 1:nSims){
 # this loop steps through the sample sizes
 for(ss in 1:dim(sample_sizes)[2]) {
  m<-sample_sizes[1,ss]
  n<-sample_sizes[2,ss]
  # initialize the index for results
  i<-1
  for (sd in sds) {  #first group's standard deviation
   #generate random samples from 2 normal distribution
   x_norm1<-rnorm(m,5,sds)
   y_norm2<-rnorm(n,5,4)
   #extract p-value out and store it in vectors
   t_equal[(ss-1)*nsds+i]<-t.test(x_norm1,y_norm2,var.equal=TRUE)$p.value
   t_unequal[(ss-1)*nsds+i]<-t.test(x_norm1,y_norm2,var.equal=FALSE)$p.value
   mann[(ss-1)*nsds+i] <-wilcox.test(x_norm1,y_norm2)$p.value
   i<-i+1
  }
 }
 #store the current result into matrices by rows
 matrix_Equal[sim,]<-t_equal
 matrix_Unequal[sim,]<-t_unequal
 matrix_mann[sim,]<-mann
}
##print results
matrix_Equal
matrix_Unequal
matrix_mann

Jim

On Wed, Apr 6, 2016 at 12:43 AM, tan sj  wrote:
> Hi, Jim, i read through your example,
> I tried to write a code modified yours example and my ideas ...
> In last email, you replied that 
> "results[[(ss-1)*nssds+ssd_index]]<-" ,can i know further about 
> this ? Because i am not very understand about this .
> I am sorry that i am really a new bird in this field...
> but the code turn out it have some error ...
> Below shown my attempt...
>
>  ## Put the samples sizes into matrix then use a loop for sample sizes
> sample_sizes<-
>  matrix(c(10,10,10,25,25,25,25,50,25,100,50,25,50,100,100,25,100,100),
>  nrow=2)
>
> #create vector to combine all std deviations
> sds<-c(4,6,8,10,12,14)
>
> set.seed(8)
>
> #number of simulations
> nSims<-1
> #set significance level,alpha for the whole simulatio
> alpha<-0.05
>
> #set empty vector of length no.of simulation(1) to store p-value
> t_equal <-c(length=nSims)
> t_unequal <-c(length=nSims)
> mann <-c(length=nSims)
>
> #set up matrix for storing data from the vectors
> matrix_Equal<-matrix(t_equal,nrow=nSims)
> matrix_Unequal<-matrix(t_unequal,nrow=nSims)
> matrix_mann<-matrix(mann,nrow=nSims)
>
> Simulations
>
> #BULID A FUNCTION for a collection of statement
> f<-function(m,n,sd)
> {
> for (i in 1:nSims){
>
> # this loop steps through the sample sizes
> for(ss in 1:dim(sample_sizes)[2])
> {
> m<-sample_sizes[1,ss]
> n<-sample_sizes[2,ss]
> {
> for (sd in sds)   #first group's standard deviation
> {
> #generate random samples from 2 normal distribution
> x_norm1<-rnorm(m,5,sds)
> y_norm2<-rnorm(n,5,4)
>
> #extract p-value out and store it in vectors
> t_equal[i]<-t.test(x_norm1,y_norm2,var.equal=TRUE)$p.value
> t_unequal[i]<-t.test(x_norm1,y_norm2,var.equal=FALSE)$p.value
> mann[i] <-wilcox.test(x_norm1,y_norm2)$p.value
>
> ##store the result into matrix defined before
> matrix_Equal<-t_equal
> matrix_Unequal<-t_unequal
> matrix_mann<-mann
>
> ##print results
> matrix_Equal
> matrix_Unequal
> matrix_mann
>
> }
>  }
>   }
> }
> }
> 
> From: Jim Lemon 
> Sent: Tuesday, April 5, 2016 2:38 AM
> To: tan sj
> Cc: r-help@r-project.org
> Subject: Re: [R] R-dvel [robustness Simulation study of 2 sample test on 
> several combination of factors ]
>
> Hi sst,
> You could set up your sample sizes as a matrix if you don't want all
> of the combinations:
>
> sample_sizes<-matrix(c(10,10,10,25,25,25,...),nrow=2)
>
> and then use one loop for the sample sizes:
>
> for(ss in 1:dim(sample_sizes)[2]) {
>  ss1<-sample_sizes[1,ss]
>  ss2<-sample_sizes[2,ss]
>
> then step through your SDs:
>
> for(ssd in  c(4,4.4,5,6,8)) {
>
> Jim
>
> On Tue, Apr 5, 2016 at 11:15 AM, tan sj  wrote:
>> hi, i am new in

Re: [R] Good pointers for understanding the R language implementation

2016-04-05 Thread David Winsemius

> On Apr 5, 2016, at 8:26 AM, Francisco Banha  
> wrote:
> 
> Dear All,
> 
> I'm currently working on a project with the purpose of remotely executing R 
> code, which requires me to have to work with the code of R itself. I've 
> searched the Internet for good information that will help me understand how R 
> is implemented but what I've got so far isn't detailed enough.

This is too vague for commentary. If you claim that you have digested  all of 
"The R Language Definition", "R Internals", and "R Installation and 
Administration", (all of which are shipped with the standard R distro) then I 
suggest you are either the wisest man on Earth, or you should be evaluated by a 
psychiatrist who is also a skilled R programmer. (Are there any such?) 

> I've looked specifically at CRAN's manuals on the official website but they 
> only address this issue briefly. I've also looked at other contents online 
> but so far nothing has turned up that has the level of detail that I need to 
> properly understand the inner workings of R.
> For example, I need to understand how exactly an expression is parsed and 
> evaluated, because I will need to intervene in the process to decide whether 
> to execute it remotely or not.
> Does anyone know of good pointers that would help me understand this?

If you run candidate text through the `parse`-function you can determine 
whether it is syntactically evaluable. But then what? Are you trying to filter 
expressions on the basis of some sort of "safety index"?

> Thanks for any help!
> 
> Best regards,
> Francisco
> 
>   [[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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges

2016-04-05 Thread David Winsemius


> On Apr 5, 2016, at 10:27 AM, 何尧  wrote:
> 
> I do have a bunch of genes ( nearly ~5)  from the whole genome, which 
> read in genomic ranges
> 
> A range(gene) can be seem as an observation has three columns chromosome, 
> start and end, like that
> 
>   seqnames start end width strand
> 
> gene1 chr1 1   5 5  +
> 
> gene2 chr110  15 6  +
> 
> gene3 chr112  17 6  +
> 
> gene4 chr120  25 6  +
> 
> gene5 chr130  4011  +
> 
> I just wondering is there an efficient way to find overlapped, upstream and 
> downstream genes for each gene in the granges

The data.table package (in CRAN) and the iRanges package (in bioC) have 
formalized efficient approaches to those problems.


> 
> For example, assuming all_genes_gr is a ~5 genes genomic range, the 
> result I want like belows:
> 
> gene_nameupstream_genedownstream_geneoverlapped_gene
> gene1NAgene2NA
> gene2gene1gene4gene3
> gene3gene1gene4gene2
> gene4gene3gene5NA
> 
> Currently ,  the strategy I use is like that,  
> library(GenomicRanges)
> find_overlapped_gene <- function(idx, all_genes_gr) {
>  #cat(idx, "\n")
>  curr_gene <- all_genes_gr[idx]
>  other_genes <- all_genes_gr[-idx]
>  n <- countOverlaps(curr_gene, other_genes)
>  gene <- subsetByOverlaps(curr_gene, other_genes)
>  return(list(n, gene))
> }
> 
> system.time(lapply(1:100, function(idx)  find_overlapped_gene(idx, 
> all_genes_gr)))
> However, for 100 genes, it use nearly ~8s by system.time().That means if I 
> had 5 genes, nearly one hour for just find overlapped gene. 
> 
> I am just wondering any algorithm or strategy to do that efficiently, perhaps 
> 5 genes in ~10min or even less
> 
I suspect this would happen on a much faster basis for such a small dataset.

-- 
David.



>   [[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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] File 1 is not in sorted order Error

2016-04-05 Thread Duncan Murdoch


On 02/04/2016 10:40 PM, Michael Morrison wrote:

Hi, I'm trying to build R on windows and i'm getting the following error
when i run the "make all recommended" command:

C:/Rtools/mingw_64/bin/windres -F pe-x86-64   -i dllversion.rc -o
dllversion.o
comm: file 1 is not in sorted order
make[4]: *** [Rgraphapp.def] Error 1
make[3]: *** [rlibs] Error 1
make[2]: *** [../../bin/x64/R.dll] Error 2
make[1]: *** [rbuild] Error 2
make: *** [all] Error 2


Can someone please help me figure out this error. I've tried researching on
my own but i'm out of options. Thanks in advance.



Set the environment variable LC_COLLATE equal to C.  Some parts of the R 
build system do this, and some parts use your locale's collation 
sequence.  You need to make sure they're all consistent.


Duncan Murdoch

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Re: [R] Heatmap Colnames

2016-04-05 Thread Jim Lemon

Hi Nils,
I don't have the GMD library, but this looks like some axis labels are
being ignored to avoid overlapping. If heatmap.3 uses base graphics
you can probably get your labels by passing empty strings to heatmap.3
and then displaying the axis with staxlab (plotrix).

Jim

On Wed, Apr 6, 2016 at 9:58 AM, Nils Korte <20406...@student.gla.ac.uk> wrote:
> Hello,
> please see below my code for a heatmap. Unfortunately my column names do not 
> completely appear. Can you please send me the appropriate code to visualise 
> them?
> Many Thanks!
> Nils
>
>
> library(GMD)
>
> dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), 
> EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))
>
> rownames(dat)=c("hsa-miR-200c","hsa-miR-520b","hsa-miR-199a-3p","mmu-miR-124a","hsa-miR-302a","hsa-miR-454","mmu-miR-137")
>
> colnames(dat)=c("24", "72")
>
> heatmap.3(dat, srtCol=70)
>
> ndat<-as.matrix(dat)
>
> heatmap.3(ndat, Rowv=FALSE, Colv=FALSE)
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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[R] Heatmap Colnames

2016-04-05 Thread Nils Korte

Hello,
please see below my code for a heatmap. Unfortunately my column names do not 
completely appear. Can you please send me the appropriate code to visualise 
them?
Many Thanks!
Nils


library(GMD)

dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), 
EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))

rownames(dat)=c("hsa-miR-200c","hsa-miR-520b","hsa-miR-199a-3p","mmu-miR-124a","hsa-miR-302a","hsa-miR-454","mmu-miR-137")
 

colnames(dat)=c("24", "72")

heatmap.3(dat, srtCol=70)

ndat<-as.matrix(dat)

heatmap.3(ndat, Rowv=FALSE, Colv=FALSE)

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Re: [R] Fwd: as.Date gives NAs when transforming from factor

2016-04-05 Thread Duncan Murdoch


On 05/04/2016 7:53 PM, Omar André Gonzáles Díaz wrote:

Hi,

I would appreciate your help.

I’m having problems when transforming  a column from “factor” to “date”.



It does not convert just: 31/03/2016 correctly, it out puts: NA.



04/04/2016  turns out as: 2016-04-04



02/04/2016 turns out as: 2016-02-04



31/03/2016 turns out as: NA

03/04/2016 turns out as: 2016-03-04.







Code:

a <- read.csv("dates.csv", stringsAsFactors = F)



a$Date <- as.Date(a$Date, format = "%m/%d/%Y")



You are specifying month/day/year format. There's no month 31.
You probably want

a$Date <- as.Date(a$Date, format = "%d/%m/%Y")


Duncan Murdoch






Posible Solutions:



I’ve read here that it has to do with the Sys Locale, and the solution was
using: “LC_TIME”, “C”. But I didn’t have success.

http://stackoverflow.com/questions/15566875/as-date-returning-na-in-r






# Sys.getlocale("LC_TIME")

#

# Sys.setlocale("LC_TIME", "C")












Slds,













Disclaimer The information in this email and any attachments may contain

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Re: [R] Fwd: as.Date gives NAs when transforming from factor

2016-04-05 Thread Jeff Newmiller

Don't give a factor to as.Date. Convert it to character first, or avoid letting 
it become a factor in the first place by using the stringsAsFactors =FALSE 
option to the read.table function or its related functions. 
-- 
Sent from my phone. Please excuse my brevity.

On April 5, 2016 4:53:56 PM PDT, "Omar André Gonzáles Díaz" 
 wrote:
>Hi,
>
>I would appreciate your help.
>
>I’m having problems when transforming  a column from “factor” to
>“date”.
>
>
>
>It does not convert just: 31/03/2016 correctly, it out puts: NA.
>
>
>
>04/04/2016  turns out as: 2016-04-04
>
>
>
>02/04/2016 turns out as: 2016-02-04
>
>
>
>31/03/2016 turns out as: NA
>
>03/04/2016 turns out as: 2016-03-04.
>
>
>
>
>
>
>
>Code:
>
>a <- read.csv("dates.csv", stringsAsFactors = F)
>
>
>
>a$Date <- as.Date(a$Date, format = "%m/%d/%Y")
>
>
>
>
>Posible Solutions:
>
>
>
>I’ve read here that it has to do with the Sys Locale, and the solution
>was
>using: “LC_TIME”, “C”. But I didn’t have success.
>
>http://stackoverflow.com/questions/15566875/as-date-returning-na-in-r
>
>
>
>
>
>
># Sys.getlocale("LC_TIME")
>
>#
>
># Sys.setlocale("LC_TIME", "C")
>
>
>
>
>
>
>
>
>
>
>
>
>Slds,
>
>
>
>
>
>
>
>
>
>
>
>
>> Disclaimer The information in this email and any attachments may
>contain
>proprietary and privileged information that is intended for the
>addressee(s) only. If you are not the intended recipient, you are
>hereby
>notified that any disclosure, copying, distribution, retention or use
>of
>the contents of this information is prohibited. When addressed to our
>clients or vendors, any information contained in this e-mail or any
>attachments is subject to the terms and conditions in any governing
>contract. If you have received this e-mail in error, please immediately
>contact the sender and delete the e-mail..
>__
>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]]

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[R] Fwd: as.Date gives NAs when transforming from factor

2016-04-05 Thread Omar André Gonzáles Díaz

Hi,

I would appreciate your help.

I’m having problems when transforming  a column from “factor” to “date”.



It does not convert just: 31/03/2016 correctly, it out puts: NA.



04/04/2016  turns out as: 2016-04-04



02/04/2016 turns out as: 2016-02-04



31/03/2016 turns out as: NA

03/04/2016 turns out as: 2016-03-04.







Code:

a <- read.csv("dates.csv", stringsAsFactors = F)



a$Date <- as.Date(a$Date, format = "%m/%d/%Y")




Posible Solutions:



I’ve read here that it has to do with the Sys Locale, and the solution was
using: “LC_TIME”, “C”. But I didn’t have success.

http://stackoverflow.com/questions/15566875/as-date-returning-na-in-r






# Sys.getlocale("LC_TIME")

#

# Sys.setlocale("LC_TIME", "C")












Slds,












> Disclaimer The information in this email and any attachments may contain
proprietary and privileged information that is intended for the
addressee(s) only. If you are not the intended recipient, you are hereby
notified that any disclosure, copying, distribution, retention or use of
the contents of this information is prohibited. When addressed to our
clients or vendors, any information contained in this e-mail or any
attachments is subject to the terms and conditions in any governing
contract. If you have received this e-mail in error, please immediately
contact the sender and delete the e-mail..
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[R] Is that an efficient way to find the overlapped , upstream and downstream rangess for a bunch of rangess

2016-04-05 Thread Yao He

I do have a bunch of genes ( nearly ~5)  from the whole genome, which
read in genomic ranges

A range(gene) can be seem as an observation has three columns chromosome,
start and end, like that

   seqnames start end width strand

gene1 chr1 1   5 5  +

gene2 chr110  15 6  +

gene3 chr112  17 6  +

gene4 chr120  25 6  +

gene5 chr130  4011  +

I just wondering is there an efficient way to find *overlapped, upstream
and downstream genes for each gene in the granges*

For example, assuming all_genes_gr is a ~5 genes genomic range, the
result I want like belows:
gene_name upstream_gene downstream_gene overlapped_gene
gene1 NA gene2 NA
gene2 gene1 gene4 gene3
gene3 gene1 gene4 gene2
gene4 gene3 gene5 NA

Currently ,  the strategy I use is like that,

library(GenomicRanges)

find_overlapped_gene <- function(idx, all_genes_gr) {
  #cat(idx, "\n")
  curr_gene <- all_genes_gr[idx]
  other_genes <- all_genes_gr[-idx]
  n <- countOverlaps(curr_gene, other_genes)
  gene <- subsetByOverlaps(curr_gene, other_genes)
  return(list(n, gene))
}

system.time(lapply(1:100, function(idx)  find_overlapped_gene(idx,
all_genes_gr)))

However, for 100 genes, it use nearly ~8s by system.time().That means if I
had 5 genes, nearly one hour for just find overlapped gene.

I am just wondering any algorithm or strategy to do that efficiently,
perhaps 5 genes in ~10min or even less

Yao He

[[alternative HTML version deleted]]

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[R] Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges

2016-04-05 Thread 何尧

I do have a bunch of genes ( nearly ~5)  from the whole genome, which read 
in genomic ranges

A range(gene) can be seem as an observation has three columns chromosome, start 
and end, like that

   seqnames start end width strand

gene1 chr1 1   5 5  +

gene2 chr110  15 6  +

gene3 chr112  17 6  +

gene4 chr120  25 6  +

gene5 chr130  4011  +

I just wondering is there an efficient way to find overlapped, upstream and 
downstream genes for each gene in the granges

For example, assuming all_genes_gr is a ~5 genes genomic range, the result 
I want like belows:

gene_nameupstream_genedownstream_geneoverlapped_gene
gene1NAgene2NA
gene2gene1gene4gene3
gene3gene1gene4gene2
gene4gene3gene5NA

Currently ,  the strategy I use is like that,  
library(GenomicRanges)
find_overlapped_gene <- function(idx, all_genes_gr) {
  #cat(idx, "\n")
  curr_gene <- all_genes_gr[idx]
  other_genes <- all_genes_gr[-idx]
  n <- countOverlaps(curr_gene, other_genes)
  gene <- subsetByOverlaps(curr_gene, other_genes)
  return(list(n, gene))
}

system.time(lapply(1:100, function(idx)  find_overlapped_gene(idx, 
all_genes_gr)))
However, for 100 genes, it use nearly ~8s by system.time().That means if I had 
5 genes, nearly one hour for just find overlapped gene. 

I am just wondering any algorithm or strategy to do that efficiently, perhaps 
5 genes in ~10min or even less

 



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[R] Good pointers for understanding the R language implementation

2016-04-05 Thread Francisco Banha

Dear All,

I'm currently working on a project with 
the purpose of remotely executing R code, which requires me to have to 
work with the code of R itself. I've searched the Internet for good 
information that will help me understand how R is implemented but what 
I've got so far isn't detailed enough.
I've looked specifically at 
CRAN's manuals on the official website but they only address this issue 
briefly. I've also looked at other contents online but so far nothing 
has turned up that has the level of detail that I need to properly 
understand the inner workings of R.
For example, I need to understand
 how exactly an expression is parsed and evaluated, because I will need 
to intervene in the process to decide whether to execute it remotely or 
not.
Does anyone know of good pointers that would help me understand this?
Thanks for any help!

Best regards,
Francisco 
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Re: [R] Specifying path to a windows server

2016-04-05 Thread Jeff Newmiller

Each \ has to be escaped. Two becomes four, not three. 
-- 
Sent from my phone. Please excuse my brevity.

On April 5, 2016 10:23:11 AM PDT, John Sorkin  
wrote:
>Windows 7 (local computer)
>Windows server (server I am trying to reach)
> 
>I need to read a file whose windows path is of the form
> 
>\\Theserver\mydirectory\data.csv
> 
>You will note that as per windows standards the server name is preceded
>by two backslashes.
> 
>I am not sure how to specify this in R.  One usually needs to specify
>an escape characters in a path new which would suggest my path should
>be
> 
> 
>\\\Theserver\\mydirectory\\data.csv
> 
>This does not work; the file is not found.
> 
>What is the correct way to specify a path to a server
> 
>Thanks,
>John
>
> 
>John David Sorkin M.D., Ph.D.
>Professor of Medicine
>Chief, Biostatistics and Informatics
>University of Maryland School of Medicine Division of Gerontology and
>Geriatric Medicine
>Baltimore VA Medical Center
>10 North Greene Street
>GRECC (BT/18/GR)
>Baltimore, MD 21201-1524
>(Phone) 410-605-7119
>(Fax) 410-605-7913 (Please call phone number above prior to faxing) 
>
>Confidentiality Statement:
>This email message, including any attachments, is for t...{{dropped:15}}

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Re: [R] Specifying path to a windows server

2016-04-05 Thread Bert Gunter

almost ...

Theserver\\mydirectory\\data.csv

## should do it


-- Bert




On Tue, Apr 5, 2016 at 10:23 AM, John Sorkin
 wrote:
> Windows 7 (local computer)
> Windows server (server I am trying to reach)
>
> I need to read a file whose windows path is of the form
>
> \\Theserver\mydirectory\data.csv
>
> You will note that as per windows standards the server name is preceded by 
> two backslashes.
>
> I am not sure how to specify this in R.  One usually needs to specify an 
> escape characters in a path new which would suggest my path should be
>
>
> \\\Theserver\\mydirectory\\data.csv
>
> This does not work; the file is not found.
>
> What is the correct way to specify a path to a server
>
> Thanks,
> John
>
>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and 
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
> Confidentiality Statement:
> This email message, including any attachments, is for ...{{dropped:12}}

__
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[R] Specifying path to a windows server

2016-04-05 Thread John Sorkin

Windows 7 (local computer)
Windows server (server I am trying to reach)
 
I need to read a file whose windows path is of the form
 
\\Theserver\mydirectory\data.csv
 
You will note that as per windows standards the server name is preceded by two 
backslashes.
 
I am not sure how to specify this in R.  One usually needs to specify an escape 
characters in a path new which would suggest my path should be
 
 
\\\Theserver\\mydirectory\\data.csv
 
This does not work; the file is not found.
 
What is the correct way to specify a path to a server
 
Thanks,
John

 
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 

Confidentiality Statement:
This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain confidential and privileged information. 
Any unauthorized use, disclosure or distribution is prohibited. If you are not 
the intended recipient, please contact the sender by reply email and destroy 
all copies of the original message. 
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Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread David Winsemius


> On Apr 5, 2016, at 5:46 AM, Rainer Johannes  wrote:
> 
> Thanks Adrian and Thierry (from the previous answer).
> 
> I was aware of the all.equal function, but there is nothing similar for <= 
> (e.g. all.smallerEqual)?

Perhaps you will gain understanding by looking at this:

> abs(1 - 0.95) - 0.05
[1] 4.163336e-17

Perhaps you want to make your own `all.<=`

> '%all.<=%'   <- function (e1,e2){ e1 < e2 | abs(e1-e2) < 
> .Machine$double.eps^0.5 }
> abs(1 - 0.95) %all.<=% 0.05
[1] TRUE


-- 
David.
> 
> cheers, jo
> 
> On 05 Apr 2016, at 14:31, Adrian Dușa 
> > wrote:
> 
> Yes, that does have to do with floating point representation.
> I use this function for these types of comparisons (works with values as well 
> as with vectors):
> 
> check.equal <- function(x, y) {
>check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
>check.vector[is.na(check.vector)] <- FALSE
>return(check.vector)
> }
> 
> See:
> ?all.equal
> 
> Hth,
> Adrian
> 
> On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes 
> > wrote:
> Dear All,
> 
> I have the following problem:
> 
> I have a function in which I check if the difference between values is 
> smaller or equal to a certain threshold. I however realized that I might get 
> there some unexpected results:
> 
>> abs(1 - 0.95) >= 0.05
> [1] TRUE
> ## So that’s fine, but:
>> abs(1 - 0.95) <= 0.05
> [1] FALSE
> 
> Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite 
> disturbing.
> 
> Along these lines:
>> abs(0.95 - 1) > 0.05
> [1] TRUE
>> abs(0.95 - 1) < 0.05
> [1] FALSE
> 
> I guess that has to do with the floating point representation of the data?
> 
> Is there something I miss or is there any solution to this?
> Thanks for any help!
> 
> cheers, jo
> 
> 
> 
> I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The 
> R-version I used for the code above is:
> 
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> __
> 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.
> 
> 
> 
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

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Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Rainer Johannes

Thanks!

On 05 Apr 2016, at 16:07, Thierry Onkelinx 
> wrote:

You could use something like this

x <- abs(0.95 - 1)
treshold <- 0.05
x < treshold | abs(x - treshold) < 1e-6

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and 
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more than 
asking him to perform a post-mortem examination: he may be able to say what the 
experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure 
that a reasonable answer can be extracted from a given body of data. ~ John 
Tukey

2016-04-05 14:46 GMT+02:00 Rainer Johannes 
>:
Thanks Adrian and Thierry (from the previous answer).

I was aware of the all.equal function, but there is nothing similar for <= 
(e.g. all.smallerEqual)?

cheers, jo

On 05 Apr 2016, at 14:31, Adrian Dușa 
>>
 wrote:

Yes, that does have to do with floating point representation.
I use this function for these types of comparisons (works with values as well 
as with vectors):

check.equal <- function(x, y) {
check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
check.vector[is.na(check.vector)] <- FALSE
return(check.vector)
}

See:
?all.equal

Hth,
Adrian

On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes 
>>
 wrote:
Dear All,

I have the following problem:

I have a function in which I check if the difference between values is smaller 
or equal to a certain threshold. I however realized that I might get there some 
unexpected results:

> abs(1 - 0.95) >= 0.05
[1] TRUE
## So that’s fine, but:
> abs(1 - 0.95) <= 0.05
[1] FALSE

Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite 
disturbing.

Along these lines:
> abs(0.95 - 1) > 0.05
[1] TRUE
> abs(0.95 - 1) < 0.05
[1] FALSE

I guess that has to do with the floating point representation of the data?

Is there something I miss or is there any solution to this?
Thanks for any help!

cheers, jo

I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The 
R-version I used for the code above is:

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
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--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr.90
050663 Bucharest sector 5
Romania

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Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Thierry Onkelinx

You could use something like this

x <- abs(0.95 - 1)
treshold <- 0.05
x < treshold | abs(x - treshold) < 1e-6


ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2016-04-05 14:46 GMT+02:00 Rainer Johannes :

> Thanks Adrian and Thierry (from the previous answer).
>
> I was aware of the all.equal function, but there is nothing similar for <=
> (e.g. all.smallerEqual)?
>
> cheers, jo
>
> On 05 Apr 2016, at 14:31, Adrian Dușa > wrote:
>
> Yes, that does have to do with floating point representation.
> I use this function for these types of comparisons (works with values as
> well as with vectors):
>
> check.equal <- function(x, y) {
> check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
> check.vector[is.na(check.vector)] <- FALSE
> return(check.vector)
> }
>
> See:
> ?all.equal
>
> Hth,
> Adrian
>
> On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes  > wrote:
> Dear All,
>
> I have the following problem:
>
> I have a function in which I check if the difference between values is
> smaller or equal to a certain threshold. I however realized that I might
> get there some unexpected results:
>
> > abs(1 - 0.95) >= 0.05
> [1] TRUE
> ## So that’s fine, but:
> > abs(1 - 0.95) <= 0.05
> [1] FALSE
>
> Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite
> disturbing.
>
> Along these lines:
> > abs(0.95 - 1) > 0.05
> [1] TRUE
> > abs(0.95 - 1) < 0.05
> [1] FALSE
>
> I guess that has to do with the floating point representation of the data?
>
> Is there something I miss or is there any solution to this?
> Thanks for any help!
>
> cheers, jo
>
>
>
> I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The
> R-version I used for the code above is:
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> __
> 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<
> http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
>
>
> [[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.

[[alternative HTML version deleted]]

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[R-es] familia gamma / cero inflated

2016-04-05 Thread Eliana Eberle

Estimado,

Tengo dos consultas,

-Tengo datos que contienen ceros en datos con distribución Poisson, y quisiera 
utilizar una familia gamma para la realización de GLM. 
Como puedo modificar los ceros para poder aplicar la familia?


- Tengo 98 datos y 20 son ceros, debería considerar zero inflated?

Saludos

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Re: [R] RWeka Error

2016-04-05 Thread Jeff Newmiller

Read the Posting Guide mentioned at the bottom of this email. Highlights you 
should be sure to address:

* HTML formatted email gets messed up on the R mailing lists, so post in plain 
text. Yes,  you can and need to do this. 

* Make sure the problem occurs in R by trying it without RStudio. Sometimes 
RStudio interferes with R, and you have to ask elsewhere about such problems. 

* Give us details about your setup and the exact commands you used. The 
sessionInfo function is helpful here, as is a sample of what you entered into a 
clean R session to get that error (for completeness). Make sure you are clear 
in your post about what operating system you are using, and what Java runtime 
(version and 32/64 bitness) is installed. 
-- 
Sent from my phone. Please excuse my brevity.

On April 5, 2016 5:14:55 AM PDT, "‪Rini John‬ ‪ via R-help" 
 wrote:
>
>When I use any function of RWeka Package in Rstudio I get an error,
>"Error in .jnew (name): java.lang.ClassFormatError." can anyone guide
>me in this?
>
>   [[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.

[[alternative HTML version deleted]]

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Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Rainer Johannes

Thanks Adrian and Thierry (from the previous answer).

I was aware of the all.equal function, but there is nothing similar for <= 
(e.g. all.smallerEqual)?

cheers, jo

On 05 Apr 2016, at 14:31, Adrian Dușa 
> wrote:

Yes, that does have to do with floating point representation.
I use this function for these types of comparisons (works with values as well 
as with vectors):

check.equal <- function(x, y) {
check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
check.vector[is.na(check.vector)] <- FALSE
return(check.vector)
}

See:
?all.equal

Hth,
Adrian

On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes 
> wrote:
Dear All,

I have the following problem:

I have a function in which I check if the difference between values is smaller 
or equal to a certain threshold. I however realized that I might get there some 
unexpected results:

> abs(1 - 0.95) >= 0.05
[1] TRUE
## So that’s fine, but:
> abs(1 - 0.95) <= 0.05
[1] FALSE

Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite 
disturbing.

Along these lines:
> abs(0.95 - 1) > 0.05
[1] TRUE
> abs(0.95 - 1) < 0.05
[1] FALSE

I guess that has to do with the floating point representation of the data?

Is there something I miss or is there any solution to this?
Thanks for any help!

cheers, jo

I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The 
R-version I used for the code above is:

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base
__
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.

--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr.90
050663 Bucharest sector 5
Romania

[[alternative HTML version deleted]]

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Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Adrian Dușa

Yes, that does have to do with floating point representation.
I use this function for these types of comparisons (works with values as
well as with vectors):

check.equal <- function(x, y) {
check.vector <- as.logical(unlist(lapply(x, all.equal, y)))
check.vector[is.na(check.vector)] <- FALSE
return(check.vector)
}

See:
?all.equal

Hth,
Adrian

On Tue, Apr 5, 2016 at 2:34 PM, Rainer Johannes 
wrote:

> Dear All,
>
> I have the following problem:
>
> I have a function in which I check if the difference between values is
> smaller or equal to a certain threshold. I however realized that I might
> get there some unexpected results:
>
> > abs(1 - 0.95) >= 0.05
> [1] TRUE
> ## So that’s fine, but:
> > abs(1 - 0.95) <= 0.05
> [1] FALSE
>
> Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite
> disturbing.
>
> Along these lines:
> > abs(0.95 - 1) > 0.05
> [1] TRUE
> > abs(0.95 - 1) < 0.05
> [1] FALSE
>
> I guess that has to do with the floating point representation of the data?
>
> Is there something I miss or is there any solution to this?
> Thanks for any help!
>
> cheers, jo
>
>
>
> I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The
> R-version I used for the code above is:
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> __
> 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.




-- 
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr.90
050663 Bucharest sector 5
Romania

[[alternative HTML version deleted]]

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

Re: [R] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Thierry Onkelinx

FAQ 7.31

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2016-04-05 13:34 GMT+02:00 Rainer Johannes :

> Dear All,
>
> I have the following problem:
>
> I have a function in which I check if the difference between values is
> smaller or equal to a certain threshold. I however realized that I might
> get there some unexpected results:
>
> > abs(1 - 0.95) >= 0.05
> [1] TRUE
> ## So that’s fine, but:
> > abs(1 - 0.95) <= 0.05
> [1] FALSE
>
> Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite
> disturbing.
>
> Along these lines:
> > abs(0.95 - 1) > 0.05
> [1] TRUE
> > abs(0.95 - 1) < 0.05
> [1] FALSE
>
> I guess that has to do with the floating point representation of the data?
>
> Is there something I miss or is there any solution to this?
> Thanks for any help!
>
> cheers, jo
>
>
>
> I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The
> R-version I used for the code above is:
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> __
> 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]]

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

[R] RWeka Error

2016-04-05 Thread ‪Rini John‬ ‪ via R-help


When I use any function of RWeka Package in Rstudio I get an error, "Error in 
.jnew (name): java.lang.ClassFormatError." can anyone guide me in this?

[[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] Problem with <= (less than or equal): not giving the expected result

2016-04-05 Thread Rainer Johannes

Dear All,

I have the following problem:

I have a function in which I check if the difference between values is smaller 
or equal to a certain threshold. I however realized that I might get there some 
unexpected results:

> abs(1 - 0.95) >= 0.05
[1] TRUE
## So that’s fine, but:
> abs(1 - 0.95) <= 0.05
[1] FALSE

Apparently, abs(1 - 0.95) is not equal to 0.05, which I find however quite 
disturbing.

Along these lines:
> abs(0.95 - 1) > 0.05
[1] TRUE
> abs(0.95 - 1) < 0.05
[1] FALSE

I guess that has to do with the floating point representation of the data?

Is there something I miss or is there any solution to this?
Thanks for any help!

cheers, jo



I tried this on different R-version (including 3.2.3 and 3.3.0 alpha); The 
R-version I used for the code above is:

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base   
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R-dvel [robustness Simulation study of 2 sample test on several combination of factors ]

2016-04-05 Thread Jim Lemon

Okay, here is a more complete example:

sample_sizes<-
 matrix(c(10,10,10,25,25,25,25,50,25,100,50,25,50,100,100,25,100,100),
 nrow=2)
# see what it looks like
sample_sizes
ssds<-c(4,4.4,5,6,8)
nssds<-length(ssds)
results<-list()
# first loop steps through the sample
for(ss in 1:dim(sample_sizes)[2]) {
 # get the two sample sizes
 ss1<-sample_sizes[1,ss]
 ss2<-sample_sizes[2,ss]
 then step through your SDs:
 ssd_index<-1
 for(ssd in  ssds) {
  # generate the two samples with the SDs
  sample1<-rnorm(ss1,ssd)
  sample2<-rnorm(ss2,ssd)
  # here run your tests, recording the results that you want
  results[[(ss-1)*nssds+ssd_index]]<-
  ssd_index<-ssd_index+1
 }
}

The list "results" should now contain the results of whatever test you
run. Be careful to get the order right.

Jim

On Tue, Apr 5, 2016 at 8:07 PM, tan sj  wrote:
> hi, Jim,
> i am not very clear about yours idea.
> How can i able to test them under the combination of factors?
> I am now trying to do three for loopsbut i am stucking 
> Please, I need help 
> 

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] use one way ANOVA to select genes

2016-04-05 Thread PIKAL Petr

Hi

Others can have better insight in your question so i tis preferable to post 
your mails to the Rhelp list too.

I hope your datafile is all numeric. If not after t(datafile) can be character.

AFAIK your pvalue is not propagated to aov function.

Based on artificial data your construction arrives to result, which in this 
case tells you that there is almost no difference in those 5 groups..

m <- data.frame(groups, data = rnorm(length(groups)))

>   anova(aov(data ~ groups, m))
Analysis of Variance Table

Response: data
   Df Sum Sq Mean Sq F value  Pr(>F)
groups  4   9.20  2.2999  2.2117 0.06751 .
Residuals 326 338.99  1.0399
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>

So I still wonder what is the problem. If you want to know whether 
anova(aov(…)) is appropriate for your case you shall consult local statistician 
or post your question e.g. on stackexchange or hope that somebody with deeper 
statistical knowledge from R help subscribers can help you.

But you probably need to post some more info.

Cheers
Petr

From: hehsham alpukhity [mailto:hesham...@yahoo.com]
Sent: Tuesday, April 5, 2016 12:04 PM
To: PIKAL Petr 
Subject: Re: [R] use one way ANOVA to select genes

thanks Petr
 Actually , i have wrote code for One way ANOVA ,but still i am sure is it true 
or not  for analysis data  , because I have 5 groups i want to  select the 
significant gene from this groups , .
 this code
###
datafile <- read.csv("brcaResultsclust.csv",header = T,row.names = 1)

datafile <- t(datafile)

groups <- factor(rep(c("c1","c2","c3","c4","c5"),c(116,83,28,80,24))) # here 
one factor with 5 groups

# define ANOVA function

aoftest <- function(data  ,pvalue=0.05) {

  m<-data.frame(groups, data);
  anova(aov(data ~ groups, m))
}

anovaresultstest <- apply(datafile, 1, aoftest)

#
is the design factor and the function for ANOVA test is true ?

thank
hesham

On Monday, April 4, 2016 3:29 PM, PIKAL Petr 
> wrote:

Hi

Your message is scrambled by using HTML post and if I deciphered it correctly 
you just want to use anova for some data.

What is preventing you from doing it?

Cheers
Petr

-Original Message-
From: R-help 
[mailto:r-help-boun...@r-project.org] On 
Behalf Of hehsham alpukhity via R-help
Sent: Sunday, April 3, 2016 4:45 PM
To: R-help Mailing List >
Subject: [R] use one way ANOVA to select genes

i want to select the significant genes form  5 clusters (groups) by one way 
ANOVA  in 
r###
# i want use One way ANOVA to select the siginificant from the clusters above 
selectgene <- function(GropuData,pvalue=0.05, na.rm=TRUE, file=1:5){# if each 
gruop in one  txt filefdata <- list.files(data,full.names = 
TRUE)for(i in file) {anova()
}  }##

Hisham AL-bukhaiti Ph.D Student (Information system ) China, changsha,Hunan 
university. Mobile: 0068-15 111 4246 91.
[[alternative HTML version deleted]]

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Re: [R] R cases on predictive maintenance

2016-04-05 Thread Giorgio Garziano

Generically:

http://rseek.org/?q=predictive+maintenance

and among those:

https://rpubs.com/Simionsv/97830

http://blog.revolutionanalytics.com/2016/03/predictive-maintenance.html


--

Best,

GG

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