Re: [R] shorten str() output for long list
DW == David Winsemius dwinsem...@comcast.net
on Fri, 4 Dec 2009 01:18:56 -0500 writes:
DW On Dec 3, 2009, at 10:11 PM, Peng Yu wrote:
x=split(1:1000,1:1000)
str(x)
Although str() can suppress long output for vectors, but it can not
suppress long output for list. I'm wondering how to suppress the
output for long lists.
DW Very simple ... You examine the code (for str.default it's not short,
DW I will admit) and modify it to your specifications:
DW str.default contains a section which is clearly for lists. These minor
DW modifications to the list portion of the function will achieve what
DW you request:
DW Argument ... ,max.list=200 ) defined in the invocation segment:
DW + for (i in seq_len(min(max.list,le) ) ){
DW
DW + cat(indent.str, comp.str, nam.ob[i], :, sep = )
DW + envir - if (typeof(object[[i]]) == promise) {
DW + structure(object, nam = as.name(nam.ob[i]))
DW + }
DW ...and ... since it is a recursive data structure...
DW + str(object[[i]], nest.lev = nest.lev + 1,
DW indent.str = paste(indent.str,
DW + ..), nchar.max = nchar.max, max.level =
DW max.level,
DW + vec.len = vec.len, digits.d = digits.d,
DW give.attr = give.attr,
DW + give.head = give.head, give.length = give.length,
DW + width = width, envir = envir, max.list)
DW
(defensive programming requires to use 'max.list=max.list' in the line above.)
David, I know you as a smart R user.
If you provide patches against the *sources* , i.e.
https://svn.r-project.org/R/trunk/src/library/utils/R/str.R
*and* the help file man/str.Rd
I'll incorporate these into str() ,
not anymore for R 2.10.1 though.
With regards,
Martin Maechler, ETH Zurich
x=split(1:10,1:10)
str(x)
DW List of 10
DW $ 1 : int 1
DW $ 2 : int 2
DW $ 3 : int 3
DW $ 4 : int 4
DW $ 5 : int 5
DW $ 6 : int 6
DW $ 7 : int 7
DW $ 8 : int 8
DW $ 9 : int 9
DW $ 10: int 10
x=split(1:10,1:10)
str(x, max.list=5)
DW List of 10
DW $ 1 : int 1
DW $ 2 : int 2
DW $ 3 : int 3
DW $ 4 : int 4
DW $ 5 : int 5
DW --
DW David Winsemius, MD
DW Heritage Laboratories
DW West Hartford, CT
DW __
DW R-help@r-project.org mailing list
DW https://stat.ethz.ch/mailman/listinfo/r-help
DW PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
DW and provide commented, minimal, self-contained, reproducible code.
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Re: [R] R igraph clusters component
Hi,
On Fri, Dec 4, 2009 at 3:12 AM, Gaurav Kumar gau...@gauravkumar.org wrote:
Hi R-users,
I'm using igraph for an undirected graph.
i used clusters() igraph function to know the component size(subgraphs) as
shown bellow:
c -clusters(g)
# component sizes
size - sort(c$csize, decreasing=TRUE)
cat(Top 20 cluster of the graph,\n)
for (i in 1:20)
{
cat(i, size:,size[i] ,\n)
}
Can anyone help how to extract the subgraph components based on the size as
edgelist-format.
V(g)$name - seq_len(vcount(g))-1
lapply(head(order(c$csize, decreasing=TRUE), 20), g, c$membership,
FUN=function(w, g, m) {
get.edgelist(subgraph(g, which(m==w-1)-1))
})
This gives you the largest 20 components. Best,
Gabor
ps. there is also an igraph-help mailing list, see
http://igraph.sf.net. Just in case you get no answer on R-help.
Thanks in advance
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--
Gabor Csardi gabor.csa...@unil.ch UNIL DGM
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Re: [R] Formatting of numbers on y axis
On 12/04/2009 03:16 AM, Wells Oliver wrote: Hello all. I have the following: plot(salaries$yearID, salaries$salary, type='n', xaxt='n', xlab='', yaxt='n', ylab='') axis(1, at=unique(salaries$yearID), labels=unique(salaries$yearID), lwd=.25, tck=-0.05) axis(2, axTicks(2), format(axTicks(2), scientific = F)) Which nicely creates the Y axis with the raw numbers, which are in the range of .5 - 7 million. However, it displays them as 100, and so on- I'd like it to show just whole numbers 1, 2, 3, through 7, so I can label the Y axis in millions. Any tips? Hi Oliver, Have a look at axis.mult in the plotrix package. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Manipulation Question
On Thu, Dec 3, 2009 at 9:52 PM, John Filben johnfil...@yahoo.com wrote: Can R support data manipulation programming that is available in the SAS datastep? Specifically, can R support the following: - Read multiple dataset one record at a time and compare values from each; then base on if-then logic write to multiple output files - Load a lookup table and then process a different file; based on if-then logic, access and lookup values in the table - Support modular “gosub”programming - Sort files - Date math and conversions - Would it be able to support the following type of logic: o Start § Read Record from File 1 § Read Record from File 2 § Match · If Key 1 Key 2 and Key 1 Key 2, Write to output file A · If Key 1 = Key 2, Write to output file B · If Key 1 Key 2 and Key 1 Key 2, Write to output file C§ Goto Start until File 1 Done John Filben I'll expand on Hadley Wickham's Yes, to say Yes, and it wouldn't be much of a 'system for statistical computation and graphics' if it couldn't do that. Remember R uses the 'S' and C programming languages and is Open Source. If it _cant_ do something you want it to do, you can write code that does it. Like the date math and conversions. Originally, maybe wy back in R version 0.something, it didn't have that. But someone wrote it, and wisely contributed it, and the community saw that it was good. And now we have date math and conversions. And nobody has to write any date math or conversion codes ever again. Now tell me how to get something into the SAS core code. Barry P.S. I see a very obvious optimisation you can do on this line: If Key 1 Key 2 and Key 1 Key 2, Write to output file A but maybe that's some kind of weird SASism __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to draw a big heatmap?
Hi everyone. How can I draw a big heatmaps? png(foo.png,1,1) heatmap(x) dev.off() where x is a big matrix, say 200*200. The code above generates a small heatmap in the middle of the png file and leaves big margins. I expect it to take up more space so that the labels are not overlapping. Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Solve linear program without objective function
Dear R-users, i try to solve to following linear programm in R 0 * x_1 + 2/3 * x_2 + 1/3 * x_3 + 1/3 * x_4 = 0.3 x_1 + x_2 + x_3 + x_4 = 1 x_1, x_2, x_3, x_4 0, x_1, x_2, x_3, x_4 1 as you can see i have no objective function here besides that i use the following code. library(lpSolve) f.obj-c(1,1,1,1) f.con-matrix(c(0,2/3,1/3,1/3, 1,1,1,1, 1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1),nrow=6,byrow=TRUE) f.dir - c(=, =, , , , ) f.rhs - c(0.3, 1, 0, 0, 0, 0) lp (max, f.obj, f.con, f.dir, f.rhs)$solution the problem is, the condition x_1, x_2, x_3, x_4 0 is not fulfilled. Any advice would be very helpful. best regards Andreas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Combinations and joint probabilities
 Dear R helpers  Suppose I have two sets of ranges (interest rates) as  Range 1 : (7 â 7.50, 7.50 â 8.50, 8.50 â 10.00) with respective probabilities 0.42, 0.22 and 0.36.   Range II : (11-12, 12-14, 14-21) with respective probabilities 0.14, 0.56 and 0.30 respectively.   My problem is to form the combinations of these ranges in a decreasing order of joint probabilities. It is assumed that these ranges are independent.  Suppose A represents (7-7.50), B represents (7.50-8.50) and C represents (8.50 â 10.00). Also let X be (11-12), Y is (12-14) and Z is (14-21).                        These two groups are independent i.e. Prob(A and Y) = P(A) * P(Y)  So there are 9 combinations possible as (AX, AY, AZ, BX, BY, BZ, CX, CY and CZ) respectively with the joint probabilities (0.059, 0.235, 0.126, 0.031, 0.123, 0.066, 0.05, 0.202, 0.108) respectively.  My problem is (i)                              How to obtain these 9 combinations of probabilities in the sense how do I obtain the various combinations of these two ranges along-with their respective probabilities; (ii)                            How to arrange these 9 probabilities in descending order against the respective group combination i.e. for the combination AY, the joint probability is maximum at 0.235, followed by CY at 0.202 and so on.  I sincerely apologize as perhaps I might not have raised the query properly. I have become member of this group today only and its been hardly a week since I have started learning R language. I have easily done this in Excel. My output should be something like this â  Combination  Probability AY                  0.235 CY                  0.202 AZ                 0.126 BY                  0.123 CZ                 0.108 BZ                 0.066 AX                 0.059 CX                 0.050 BX                 0.031   I request you to guide me.  Thanking in advance  Amelia    [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Logarithm interpolation
Dear all, i want to know if in R exist a method that give a logarithm interpolation of a two columns of dates. I try to do the lm of logarithm of the dates: a-lm(log(vettore)~log(as.numeric(pippo2[3,]))) but this is a linear correlation and not that i want. thanks giuseppe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Confidence Intervals for proportion according to Blyth, Still Casella
Are the confidence Intervals for proportion according to Blyth,Still Casella implemented in R? Thank you in advance! Cheers, Patrik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dividing a pixel image into factors - (cut.im(), cut.default())
Hi, I have a numeric pixel image which I would like to divide into factors for analysis in Spatstat. I have found that I can use cut.im() function to divide the range of pixel values into a series of equal length intervals (e.g. if my pixels values range from 0 to 60, cut.im(X.im,breaks=2) will produce two factors one containing pixel values 0-30 and one containing pixel values of 30 - 60, or thereabouts). However, I would like to specify the pixel value at which the factors are created - e.g. create one factor containing pixel values of 0-5 and another factor containing all other pixel values. I have been struggling to work out how to do this using either cut.im() or cut.default(). Can anyone help? Many thanks, Lauren This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] pseudoreplication - LME
Need some help please I am trying to use this model because I have temporal replication in my data results-read.table(file=file.choose(),header=T) attach(results) names(results) results-na.omit(results) library(nlme) library(lattice) results-groupedData(weight~date|group,outer=~diet,results) plot(results) plot(results,outer=T) model-lme(weight~diet,random=~date|group,results) everything worked till here although when I compute the model this error appears Error in lme.formula(weight ~ diet, random = ~date | group, results) : nlminb problem, convergence error code = 1 message = iteration limit reached without convergence (9) summary(model) http://n4.nabble.com/file/n948321/rawoctobercalciumexperiment2.xlsx rawoctobercalciumexperiment2.xlsx kind regards thank you in advance Ana -- View this message in context: http://n4.nabble.com/pseudoreplication-LME-tp948321p948321.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] matrix^(-1/2)
re [R] matrix^(-1/2) re the discussion in November on this thread. I don't know about expm but the problem must be equivalent to solve(B^(1/2)) and a solution will exist iff B is invertible and has a square root A with A%*%A = B. For 2x2 matrices necessary and sufficient conditions for B to have a square root are that either B = diag(0,2) or B%*%B != diag(0,2). This follows from the fact that B%*%B - t(B)*B + det(B) = 0 and A%*%A - t(A)*A + det(A) = 0. Many non-symmetric B satisfy B%*%B != diag(0,2) and many of them are invertible. e.g. all the rotations. If expm has a function, perhaps Exp, which exponentiates matrices using matrix multiplication, then if B = Exp(C), B^(-1/2) = Exp(-C/2) would be a solution. There is an open neighbourhood of the identity matrix in which B = Exp(C) must hold. Since t(B) = Exp(t(C)), such B will not in general be symmetric. If N satisfies N%*%N=0, then B = I+N where I is the identity matrix will have B^(-1/2) = 1-N/2. Such B are not symmetric as N cannot be symmetric (for non-zero N). So, for B^(-1/2) to exist, B must be invertible but need not be symmetric. hope that helps Greg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice : Help with changing the labels of x-axis in respective panels
On Fri, Dec 4, 2009 at 11:53 AM, Sunny Srivastava
research.b...@gmail.com wrote:
Dear R-Helpers,
I am not very experienced in using lattice and I am still in the learning
stage
I have a data set which looks like this: (I have deleted a few lines in
order to save space)
Chromosome marker Marker.Name Distance
1 1 1 PeMm261 0.
2 1 2 Xtxp8 10.1013
..
20 1 20 EbMi148 210.3099
21 1 21 Xtxp25 232.0118
22 2 1 EcMm152 0.
23 2 2 EeMp342 5.1474
...
36 2 15 EaMp217 124.5115
37 2 16 EaMp131 136.9033
40 3 1 TEak2908 0.
41 3 2 Xtxp303 4.7094
42 3 3 EhMm195 10.1694
(I have 11 chromosome in total .. so conditioning on chromosome gives me 11
panels)
This is a data.frame which contains Chromosome Number, Marker Number for
that chromosome and the corresponding Marker.Name and Distance.
I want to plot the genetic distance conditioned on chromosome and the marker
name listed below the distance where the marker is situated on chromosome
(something like this picture)
Panel 1 : Chromosome 1
|---|- (so and so forth)
PeMm261 Xtxp8
10.1013 - (the distance b/w these markers is same as the
corresponding value in marker$Distance - see 1 and 2 row in the sample
output)
and similarly for other chromosomes.
Here's one attempt; hopefully it will give you useful ideas:
df -
structure(list(Chromosome = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
3L, 3L, 3L), marker = c(1L, 2L, 20L, 21L, 1L, 2L, 15L, 16L, 1L,
2L, 3L), Marker.Name = structure(c(7L, 11L, 3L, 9L, 4L, 5L, 2L,
1L, 8L, 10L, 6L), .Label = c(EaMp131, EaMp217, EbMi148,
EcMm152, EeMp342, EhMm195, PeMm261, TEak2908, Xtxp25,
Xtxp303, Xtxp8), class = factor), Distance = c(0, 10.1013,
210.3099, 232.0118, 0, 5.1474, 124.5115, 136.9033, 0, 4.7094,
10.1694)), .Names = c(Chromosome, marker, Marker.Name,
Distance), class = data.frame, row.names = c(1, 2, 20,
21, 22, 23, 36, 37, 40, 41, 42))
library(lattice)
## single panel
dotplot(Chromosome ~ Distance, df, mnames = df$Marker.Name,
panel = function(x, y, ..., mnames, subscripts) {
panel.dotplot(x, y, ...)
panel.text(x, y, labels = mnames[subscripts],
srt = 90, adj = -0.1)
})
## multiple panels
dotplot( ~ Distance | factor(Chromosome), df, mnames = df$Marker.Name,
layout = c(1, 3), strip = FALSE, strip.left = TRUE,
panel = function(x, y, ..., mnames, subscripts) {
panel.dotplot(x, y, ...)
panel.text(x, y, labels = mnames[subscripts],
srt = 90, adj = -0.1)
})
-Deepayan
I tried:
plt1 = dotplot( ~ Distance | Chromosome, data=marker,par.strip.text =
list(cex = 0.75), layout = c(1,11),
lattice.options=list(legend=right), xlab=Distance in cM,
ylab=,
scales= list(cex=0.5),
panel = function(x, y) {
panel.grid(h=1,v= 345)
panel.xyplot(x, y,pch=20,type=o,lwd=2,cex=1.5)
},
)
update(plt1, main=Genetic Map,
strip = strip.custom(factor.levels = c(1,
2,3,4,5,6,7,8,9,10,11), strip.levels = TRUE))
This gives me the location of markers on the respective chromosomes
corresponding to the distances in the above data.frame. The markers are just
shown as points.
MY QUESTIONS - 1) If I want to label these dots with the corresponding
marker names - How do I do that?
2) Is there a way in lattice - to know which
panel I am in.
I tried inserting panel.text in the panel function - but it doesn't like
that. (I also played around with scales - but without any success)
Any help will be greatly appreciated.
Thx,
S.
---
sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.17-25 qtl_1.14-2
loaded via a namespace (and not attached):
[1] grid_2.9.1 tools_2.9.1
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Re: [R] R will not load
Hi
It sometimes occur if I work on different computers. When I save work on
one and try to start with another it has to have installed all packages
used in a saved session. So I need to add a package(s) yet uninstalled and
than the session is started.
Petr Pikal
petr.pi...@precheza.cz
724008364, 581 252 256,
581 252 140, 581 252 257
r-help-boun...@r-project.org napsal dne 02.12.2009 23:29:35:
David, Erik, Uwe, Peter
Thanks to everyone. I found .Rdata (it was hidden) deleted it and all is
well.
P.S. The suggestion to launch R from the command line with the --vanilla
option allowed the program to start, but it did not solve the problem of
launching from startall programsR
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
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)
Uwe
Ligges lig...@statistik.tu-dortmund.de 12/2/2009 5:12 PM
John Sorkin wrote:
I delete my R directory, and searched for and file of the form .RData,
I
don't have any. I re-installed R. my problem persists. Any suggestions?
You do have it. Otherwise R would not give that error message.
Please take a look in the directory that is used as the working
directory of R. Note that files beginning with a dot are not visible in
the Windows Explorer by default and may not be found with Windows search
in default settings.
Best wishes,
Uwe Ligges
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
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)
David
Winsemius dwinsem...@comcast.net 12/2/2009 4:40 PM
Corrupted datasets have been a fairly commonly observed cause of such
problems. Correction is through deletion (or removal to a different
directory if you want to check without committing to that solution) of
the offending .Rdata file.
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[R] writing 'output.csv' file
Dear R helpers Suppose M - c(1:10) # length(M) = 10 N - c(25:50) # length(N) = 26 I wish to have an outut file giving M and N. So I have tried write.csv(data.frame(M, N), 'output.csv', row.names = FALSE) but I get the following error message Error in data.frame(M, N) : arguments imply differing number of rows: 10, 26 How do I modify my write.csv command to get my output in a single (csv) file irrespective of lengths. Plese Guide Thanks in advance Maithili The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing 'output.csv' file
On 12/4/2009 5:12 AM, Maithili Shiva wrote: Dear R helpers Suppose M - c(1:10) # length(M) = 10 N - c(25:50) # length(N) = 26 I wish to have an outut file giving M and N. So I have tried write.csv(data.frame(M, N), 'output.csv', row.names = FALSE) but I get the following error message Error in data.frame(M, N) : arguments imply differing number of rows: 10, 26 How do I modify my write.csv command to get my output in a single (csv) file irrespective of lengths. The first argument to write.csv() is preferably a matrix or data frame. If it is something else, write.csv() will try to make it a data frame. You may want to create the data frame like this: data.frame(M = c(M, rep(NA,length(N) - length(M))), N=N) M N 1 1 25 2 2 26 3 3 27 4 4 28 5 5 29 6 6 30 7 7 31 8 8 32 9 9 33 10 10 34 11 NA 35 12 NA 36 13 NA 37 14 NA 38 15 NA 39 16 NA 40 17 NA 41 18 NA 42 19 NA 43 20 NA 44 21 NA 45 22 NA 46 23 NA 47 24 NA 48 25 NA 49 26 NA 50 Plese Guide Thanks in advance Maithili The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GLM Question
Peter Flom schrieb: What do you mean by better? Dear Peter Thank you for your kind respons as well. You are right, we are in constant debate whether it makes sense to remove variables (no matter whether significant or not) from a total dataset which in itself has a certain meaning and may not stand for other studies with differing variables. However, in biology it is common practice to remove non significant factors (and sometimes also variables)from data sets (so called: forward and backward elimination process), usually when they are permanently non significant on all the paticular positions in the factor list. Some authors suggest only to remove data which may have similar meanings, and therefore may be understod as pseudorepliaions. Best regards Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get back to the console with ssh access
On Fri, Dec 04, 2009 at 02:23:18AM +0100, Timothée Poisot wrote: I am currently learning how to work with a new shared computer (a Mac pro) in our lab, that is dedicated to execute R code for large simulations (over a few days). We have a VNC option to remote control the computer, with a shared used session, but this is not really needed in most of the cases. I would like to do some ssh access. This is pretty straigthforward, and I am able to launch commands using R -e 'source(myfile.R)' However, it could be useful to check the advancement of the computation from time to time, again via ssh. Is there any way to do this? On Linux you can type in the terminal (I guess the command will work in Mac too): tail -f myfile.Rout Then you hit Ctrl+C to stop tail from following myfile.Rout. Another option would be the use of screen (again, this is a *nix solution that may be available to Mac too). With screen you can run R interactively detach the session, logout, come back and reattach the session. But it seems that tail -f is what you really needs since the R script is finished and you just need to run it. -- Jakson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Saving predict
Hi all,,I´m using function arima()
I.e
series is my data
model-arima(series,c(1,0,0))
forecast-predict(model,80)
I want to create a variable:
b1-forecast$pred - 1.96*forecast$se
and save in a txt file
but using this:
save(b1, file= b1.txt)
creates afile butwith this inside:
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êÂÞó{·â6ƽ l?øÃÃOõÆMw_Ãìûâ¯â¢5ãëK÷ÃéÃZ+òÃÃ
ô=éâëæ ÃÃ(â¢YV·â÷BçXùÃ(²E2 â uaÂÃz J
Yj±+PâtSU[PtÂgÃÂïoÃ...@¶,Å Ãx�...@Ã)k¤$â¢Tìà $/¼ÃAË
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mhdiÃ...@ã§â¹ÂiÃ¥Â�...@êÃÂÃ/@£2ú èÂÃM³¡ ôV#
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ûÃEÃTÅéÃìcÂõêâ¢Â©X§(Ãø,
Ã/ë2óM¬š°â°JIÊð¬ºjÃÃÂîâ¢~ÃÅ â]êDÃ|¹°¿{9£tnà *ââÿäÃýõ\lrâoö*6aâæ±1:e¨{¢ÃËû 'öî°Ãâ¡{ZÃl^Bb6ÃÃÃWbGŽ¤¯aÃ¥ÃeKÿÆâ°5Ãâ°Ã®ü7â¢TaÂcM*ŸÃZ1â¦Ã-£WË?ëŸ'ô%ÃÃ
âÅ0ÿžðBKeò7âÃ¥'
Can anyone help me to do it?
Do you know also a document wich expalin how works and calculates
modelpredictions?
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Re: [R] writing 'output.csv' file
Dear Mr Signer and Mr Cleland, Thanks a lot for you great help. However, the output which I am getting is as given below - x 1;25 2;26 3;27 4;28 5;29 6;30 7;31 8;32 9;33 10;34 ;35 ;36 ;37 ;38 ;39 ;40 ;41 ;42 ;43 ;44 ;45 ;46 ;47 ;48 ;49 ;50 However, my requirement is I should get the csv file as M N 1 25 2 26 3 27 10 34 35 36 37 .. .. 50 So that I can acrry out further calcualtions on this output file. Please guide. Regards Maithili --- On Fri, 4/12/09, Johannes Signer j.m.sig...@gmail.com wrote: From: Johannes Signer j.m.sig...@gmail.com Subject: Re: [R] writing 'output.csv' file To: Maithili Shiva maithili_sh...@yahoo.com Date: Friday, 4 December, 2009, 10:29 AM Hello, maybe that helps: write.csv(paste((c(m,rep( ,length(N)-length(M,n, sep=;), output.csv, row.names=F) Johannes On Fri, Dec 4, 2009 at 11:12 AM, Maithili Shiva maithili_sh...@yahoo.com wrote: Dear R helpers Suppose M - c(1:10) # length(M) = 10 N - c(25:50) # length(N) = 26 I wish to have an outut file giving M and N. So I have tried write.csv(data.frame(M, N), 'output.csv', row.names = FALSE) but I get the following error message Error in data.frame(M, N) : arguments imply differing number of rows: 10, 26 How do I modify my write.csv command to get my output in a single (csv) file irrespective of lengths. Plese Guide Thanks in advance Maithili The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[elided Yahoo spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Substitute Object not found with NA
Hi everybody, I'm trying to create a script that picks a txt file with 2 columns of coordinates (depth and variable1) and automatically tries to fit several polynomial with the function nls(). After that, it creates a list of observed, predict, residuals and other, and then it calculates AIC, RMSD, MAD and R^2. At the end of the script I create a series of vectors with MAD for all polynomials, RMSD for all polynomial and so on, and from a matrix a .csv file. This script is completely automatic, but there is a problem if one or more models don't fit, because if one or more data is missing I cannot create the vectors and the matrix, as well. So, my question is: is it possible to create a vector with a missing object, substituting that object with NA in the vector? For example: I want to create this vector Vec1-c(MAD1,MAD2,MAD3,MAD4) but MAD4 is missing and as a consequence R return an error like this: object 'MAD4' not found Is it possible to say to R that if it does not find an object it must substitute that object with NA in the vector? Many Thanks, Fabio Mr. Fabio Veronesi Ph.D. student Cranfield University, Bld.37 School of Applied Sciences MK43 0AL Cranfield, Bedfordshire Tel. +44 (0)7984049316 e-mail: f.veron...@cranfield.ac.uk [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Solve linear program without objective function
Andreas Wittmann andreas_wittmann at gmx.de writes: Dear R-users, i try to solve to following linear programm in R 0 * x_1 + 2/3 * x_2 + 1/3 * x_3 + 1/3 * x_4 = 0.3 x_1 + x_2 + x_3 + x_4 = 1 x_1, x_2, x_3, x_4 0, x_1, x_2, x_3, x_4 1 as you can see i have no objective function here besides that i use the following code. library(lpSolve) f.obj-c(1,1,1,1) f.con-matrix(c(0,2/3,1/3,1/3, 1,1,1,1, 1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1),nrow=6,byrow=TRUE) f.dir - c(=, =, , , , ) f.rhs - c(0.3, 1, 0, 0, 0, 0) lp (max, f.obj, f.con, f.dir, f.rhs)$solution the problem is, the condition x_1, x_2, x_3, x_4 0 is not fulfilled. With strict inequalities x_i 0 your problem will not have a solution. That is why in linear programming strict inequalities are replaced with non-strict inequalities, or as the lp_solve manual says: The inequalities can be =, = or = Because all numbers are real values, = is the same as and = is the same as . Try x_i = eps 0 with some eps appropriate for your problem. Hans Werner Any advice would be very helpful. best regards Andreas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Confidence Intervals for proportion according to Blyth, Still Casella
Are the confidence Intervals for proportion according to Blyth,Still Casella implemented in R? Thank you in advance! Cheers, Patrik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems while plotting with ROCR
Hello all, I have two problems with the ROCR package. First Problem: the add=TRUE option does not work for plotting performance objects The following code is taken from the reference manual (example for ROCR.hiv, page2) data(ROCR.hiv) attach(ROCR.hiv) pred.svm - prediction(hiv.svm$predictions, hiv.svm$labels) perf.svm - performance(pred.svm, 'tpr', 'fpr') pred.nn - prediction(hiv.nn$predictions, hiv.svm$labels) perf.nn - performance(pred.nn, 'tpr', 'fpr') plot(perf.svm, lty=3, col=red,main=SVMs and NNs for prediction of HIV-1 coreceptor usage) now I see some dotted red ROC curves. Now after the next command: plot(perf.nn, lty=3, col=blue,add=TRUE) there happens exactly the same as if i would call: plot(perf.nn, lty=3, col=blue) I now see only some dotted blue ROC curves, the red ones and the main caption of the plot are gone. Second problem: the averaging of multiple performance curves does not work correctly (using the same example code, skipping some comands) data(ROCR.hiv) attach(ROCR.hiv) pred.svm - prediction(hiv.svm$predictions, hiv.svm$labels) perf.svm - performance(pred.svm, 'tpr', 'fpr') pred.nn - prediction(hiv.nn$predictions, hiv.svm$labels) perf.nn - performance(pred.nn, 'tpr', 'fpr') plot(perf.svm, avg=vertical, lwd=3, col=red, spread.estimate=stderror,plotCI.lwd=2) this does not give me an average curve, but multiple ones: see screenshot: http://www-stud.uni-due.de/~sfhestra/Bildschirmfoto.png I already tried reinstalling R and ROCR thanks for your help Heiko __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Substitute Object not found with NA
Veronesi, Fabio wrote:
Hi everybody,
I'm trying to create a script that picks a txt file with 2 columns of
coordinates (depth and variable1) and automatically tries to fit several
polynomial with the function nls().
After that, it creates a list of observed, predict, residuals and other, and
then it calculates AIC, RMSD, MAD and R^2.
At the end of the script I create a series of vectors with MAD for all
polynomials, RMSD for all polynomial and so on, and from a matrix a .csv file.
This script is completely automatic, but there is a problem if one or more
models don't fit, because if one or more data is missing I cannot create the
vectors and the matrix, as well.
So, my question is: is it possible to create a vector with a missing object,
substituting that object with NA in the vector?
For example:
I want to create this vector
Vec1-c(MAD1,MAD2,MAD3,MAD4)
but MAD4 is missing and as a consequence R return an error like this:
object 'MAD4' not found
Is it possible to say to R that if it does not find an object it must
substitute that object with NA in the vector?
Not automatically, but you can write an expression to do that:
if (exists(MAD4)) MAD4 else NA
or
tryCatch(MAD4, error=function(e) NA)
You could write a function to do this. I wouldn't recommend trying the
first version; it will be messy. But the second is:
defaultNA - function(x) {
tryCatch(x, error=function(e) NA)
}
then defaultNA(MAD4) will do what you want.
Duncan Murdoch
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[R] Odp: Substitute Object not found with NA
Hi
r-help-boun...@r-project.org napsal dne 04.12.2009 12:09:08:
Hi everybody,
I'm trying to create a script that picks a txt file with 2 columns of
coordinates (depth and variable1) and automatically tries to fit several
polynomial with the function nls().
After that, it creates a list of observed, predict, residuals and
other, and
then it calculates AIC, RMSD, MAD and R^2.
At the end of the script I create a series of vectors with MAD for all
polynomials, RMSD for all polynomial and so on, and from a matrix a .csv
file.
This script is completely automatic, but there is a problem if one or
more
models don't fit, because if one or more data is missing I cannot create
the
vectors and the matrix, as well.
So, my question is: is it possible to create a vector with a missing
object,
substituting that object with NA in the vector?
For example:
I want to create this vector
Vec1-c(MAD1,MAD2,MAD3,MAD4)
but MAD4 is missing and as a consequence R return an error like this:
object 'MAD4' not found
Look at ?try function.
I did something similar
#this is just a selection if inputed start values shall be used
fit-try(nls(formula[[i]], data, ...))
} else {
fit-try(nls(formula[[i]], data, start, ...)) }
}
#here is a test whether fit had some result, if yes values are extracted
from fit if not, NA is put into list
if( class(fit)==try-error) result1[i] - NA else result1[i] -
sum(resid(fit)^2, na.rm=T)
if( class(fit)==try-error) result2[[i]] - NA else result2[[i]] -
coef(fit)
}
Regards
Petr
Is it possible to say to R that if it does not find an object it must
substitute that object with NA in the vector?
Many Thanks, Fabio
Mr. Fabio Veronesi
Ph.D. student
Cranfield University, Bld.37
School of Applied Sciences
MK43 0AL
Cranfield, Bedfordshire
Tel. +44 (0)7984049316
e-mail: f.veron...@cranfield.ac.uk
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[R] Odp: How build hist combining data
Hi r-help-boun...@r-project.org napsal dne 03.12.2009 10:45:44: I would like to ask if there is some simple way for building a hist from the following data. mm -c(2,3,0,4,5,0,2,9,0) mmm - matrix(mm,ncol=3, nrow=3) x - c(0,1.45,2.9) in mmm there are frequencies (each column is separate histogram and each row corresponds to value of x). So that for the first histogram we have 2 times interval [0,1.45] and 3 times [1.45,2.90]. If I understand correctly basically you want barplot barplot(mmm[,1], names.arg=x) Regards Petr Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multidimensional point.in.polygon??
Hi,
I seek to identify those points in/outside a multidimensional convex hull
(geometry::convhulln). Any suggestions?
Background just in case I'm going down a really wrong road:
Given an observed data set with one dependent/observed variable (Y) and
multiple (3 to 10) independent/design variables (X1, X2, ...) I want to
increase the number of points by interpolating. I'm using expand.grid(X) to
generate the X points and locfit::predict.locfit to interpolate the Y
values. No problem so far.
BUT my observed X data set is very far from rectangular, so the set of
points produced by expand.grid includes many extrapolations which I'd
want to remove. I'm aware of the problems of defining extrapolation in
multiple dimensions and am minded to define it as outside the convex hull,
hence my question.
In searching r-project.org I came across a thread in which baptiste auguie
said one general way to do this would be to compute the convex hull
(?chull) of the augmented set of points and test if the point belongs to
it; an approach I'd considered generalising to multiple points thus (pseudo
R code)...
baseHull - convhulln(baseSet)
augHull - convhulln(augSet)
while (augHull != baseHull)
{ augSet - augSet [-(augHull !%in% baseHull)]
augHull - convhulln(augSet)
}
... but this has that horrible loop including a convhulln!
In the (real, typical) test data set I'm using for development baseSet is 5
columns by 2637 rows while baseHull has only 42 distinct points. If augHull
has a similarly simple hull, then each time round the loop will remove only
a few dozen points; I need to remove many thousands.
And (in my naivete) I think there must be a better way of testing for a
point inside a polygon, I'd have thought convhulln must need to do that
often!
Thanks in advance for any pointers,
Keith Jewell
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[R] length of a density curve (or any curve)
Hello R users, When I type d - density(MyData$x) I obtain a density object I can plot, But I wonder if there is a way to easily compute the length of the density curve ? ( I imagine I could compute the distances between the 512 equally spaced points using their x and y, but does it exist a smarter way ?) Regards, SW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Solve linear program without objective function
Andreas, I don't know what it is exactly that you want to do, but perhaps you can try using limSolve, which solves for the equations Ex=F, Gx=H. In the code below, lsei calculates the least squares solution (min sum(x^2)), xranges estimates the range of your variables, and xsample takes a random sample of solutions. f.con-matrix(c(0,2/3,1/3,1/3, 1,1,1,1, 1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1),nrow=6,byrow=TRUE) f.rhs - c(0.3, 1, 0, 0, 0, 0) E- f.con[1:2,] G- f.con[-(1:2),] F- f.rhs[1:2] H-f.rhs[-(1:2)] require(limSolve) lsei(E=E,F=F,G=G,H=H) xranges(E=E,F=F,G=G,H=H) xs - xsample(E=E,F=F,G=G,H=H) pairs(xs$X) Hope this helps, Karline [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] length of a density curve (or any curve)
hi Sylvain, did you try ?density regards milton On Fri, Dec 4, 2009 at 7:19 AM, sylvain willart sylvain.will...@gmail.comwrote: Hello R users, When I type d - density(MyData$x) I obtain a density object I can plot, But I wonder if there is a way to easily compute the length of the density curve ? ( I imagine I could compute the distances between the 512 equally spaced points using their x and y, but does it exist a smarter way ?) Regards, SW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combinations and joint probabilities
Dear Amelia, On 12/4/09, Amelia Livington amelia_living...@yahoo.com wrote: Dear R helpers Suppose I have two sets of ranges (interest rates) as Range 1 : (7 – 7.50, 7.50 – 8.50, 8.50 – 10.00) with respective probabilities 0.42, 0.22 and 0.36. Range II : (11-12, 12-14, 14-21) with respective probabilities 0.14, 0.56 and 0.30 respectively. My problem is to form the combinations of these ranges in a decreasing order of joint probabilities. It is assumed that these ranges are independent. Suppose A represents (7-7.50), B represents (7.50-8.50) and C represents (8.50 – 10.00). Also let X be (11-12), Y is (12-14) and Z is (14-21). These two groups are independent i.e. Prob(A and Y) = P(A) * P(Y) So there are 9 combinations possible as (AX, AY, AZ, BX, BY, BZ, CX, CY and CZ) respectively with the joint probabilities (0.059, 0.235, 0.126, 0.031, 0.123, 0.066, 0.05, 0.202, 0.108) respectively. My problem is (i) How to obtain these 9 combinations of probabilities in the sense how do I obtain the various combinations of these two ranges along-with their respective probabilities; (ii) How to arrange these 9 probabilities in descending order against the respective group combination i.e. for the combination AY, the joint probability is maximum at 0.235, followed by CY at 0.202 and so on. I sincerely apologize as perhaps I might not have raised the query properly. I have become member of this group today only and its been hardly a week since I have started learning R language. I have easily done this in Excel. My output should be something like this – Combination Probability AY 0.235 CY 0.202 AZ 0.126 BY 0.123 CZ 0.108 BZ 0.066 AX 0.059 CX 0.050 BX 0.031 I request you to guide me. Thanking in advance Amelia This sounds like a homework problem, which is a strict no-no for this list; be sure to read the Posting Guide. I will give you the benefit of the doubt for now, but be warned for the future. Are you looking for something like the following? Probspace - expand.grid(LETTERS[1:3], LETTERS[24:26]) marginals - list() marginals[[1]] - c(0.42, 0.22, 0.36) marginals[[2]] - c(0.14, 0.56, 0.30) pdf - expand.grid(marginals) Probspace$probs - apply(pdf, 1, prod) # the joint pmf xtabs(probs ~ Var1 + Var2, data = Probspace) # sorted by probability Probspace[order(Probspace$probs), ] See the prob package for other utilities in this vein. You can make the labels better with c(7 – 7.50, 7.50 – 8.50, 8.50 – 10.00), etc, in the first line instead of LETTERS. Welcome to R. Jay P.S. Please don't send HTML. Again, in the Posting Guide. [[alternative HTML version deleted]] *** G. Jay Kerns, Ph.D. Associate Professor Department of Mathematics Statistics Youngstown State University Youngstown, OH 44555-0002 USA Office: 1035 Cushwa Hall Phone: (330) 941-3310 Office (voice mail) -3302 Department -3170 FAX VoIP: gjke...@ekiga.net E-mail: gke...@ysu.edu http://people.ysu.edu/~gkerns/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing 'output.csv' file
The csv file is exactly as you describe it. ;35 represents two columns of data. If you read it is, you will probably get NA as the value in the first column. So what problem are you having in reading in the data? x - read.csv(textConnection(8;32 + 9;33 + 10;34 + ;35 + ;36 + ;37 + ;38), header=FALSE, sep=';') closeAllConnections() x V1 V2 1 8 32 2 9 33 3 10 34 4 NA 35 5 NA 36 6 NA 37 7 NA 38 On Fri, Dec 4, 2009 at 5:49 AM, Maithili Shiva maithili_sh...@yahoo.comwrote: Dear Mr Signer and Mr Cleland, Thanks a lot for you great help. However, the output which I am getting is as given below - x 1;25 2;26 3;27 4;28 5;29 6;30 7;31 8;32 9;33 10;34 ;35 ;36 ;37 ;38 ;39 ;40 ;41 ;42 ;43 ;44 ;45 ;46 ;47 ;48 ;49 ;50 However, my requirement is I should get the csv file as M N 1 25 2 26 3 27 10 34 35 36 37 .. .. 50 So that I can acrry out further calcualtions on this output file. Please guide. Regards Maithili --- On Fri, 4/12/09, Johannes Signer j.m.sig...@gmail.com wrote: From: Johannes Signer j.m.sig...@gmail.com Subject: Re: [R] writing 'output.csv' file To: Maithili Shiva maithili_sh...@yahoo.com Date: Friday, 4 December, 2009, 10:29 AM Hello, maybe that helps: write.csv(paste((c(m,rep( ,length(N)-length(M,n, sep=;), output.csv, row.names=F) Johannes On Fri, Dec 4, 2009 at 11:12 AM, Maithili Shiva maithili_sh...@yahoo.com wrote: Dear R helpers Suppose M - c(1:10) # length(M) = 10 N - c(25:50) # length(N) = 26 I wish to have an outut file giving M and N. So I have tried write.csv(data.frame(M, N), 'output.csv', row.names = FALSE) but I get the following error message Error in data.frame(M, N) : arguments imply differing number of rows: 10, 26 How do I modify my write.csv command to get my output in a single (csv) file irrespective of lengths. Plese Guide Thanks in advance Maithili The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[elided Yahoo spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] length of a density curve (or any curve)
Yes, sure (and I just did it again) but I can't see an answer... did I miss sthg ? regards, SW 2009/12/4 milton ruser milton.ru...@gmail.com: hi Sylvain, did you try ?density regards milton On Fri, Dec 4, 2009 at 7:19 AM, sylvain willart sylvain.will...@gmail.com wrote: Hello R users, When I type d - density(MyData$x) I obtain a density object I can plot, But I wonder if there is a way to easily compute the length of the density curve ? ( I imagine I could compute the distances between the 512 equally spaced points using their x and y, but does it exist a smarter way ?) Regards, SW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] length of a density curve (or any curve)
True enough -- ?density does not address the issue of computing the length pf the curve! One simple way of implementing the idea you first thought of would be on the following lines: d - density(MyData$x) sum(sqrt(diff(d$x)^2 + diff(d$y)^2)) which simply sums the lengths of the line-segments. You would get a better approximation to the ideal length by increasing the value of 'n' in the call to density() (perhaps as a separate calculation, since a relatively small value of 'n' is likely to be adeqaute for plotting, but possibly inadequate for the accurate computation of the length). Hpoing this helps, Ted. On 04-Dec-09 12:41:22, sylvain willart wrote: Yes, sure (and I just did it again) but I can't see an answer... did I miss sthg ? regards, SW 2009/12/4 milton ruser milton.ru...@gmail.com: hi Sylvain, did you try ?density regards milton On Fri, Dec 4, 2009 at 7:19 AM, sylvain willart sylvain.will...@gmail.com wrote: Hello R users, When I type d - density(MyData$x) I obtain a density object I can plot, But I wonder if there is a way to easily compute the length of the density curve ? ( I imagine I could compute the distances between the 512 equally spaced points using their x and y, but does it exist a smarter way ?) Regards, SW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 04-Dec-09 Time: 13:02:27 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] selective subsetting of a correlation matrix
Dear All, I have a correlation matrix say 'M' (4000x4000) for 4000 genes and I want to subset it to 'N' (190x190) for 190 genes. The list of those 190 genes are in variable 't'. So the idea is to read the names of genes from variable 't' and subset the matrix M accordingly. Any thoughts are welcome! Best Lee [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selective subsetting of a correlation matrix
On 12/04/2009 02:18 PM, Lee William wrote: Dear All, I have a correlation matrix say 'M' (4000x4000) for 4000 genes and I want to subset it to 'N' (190x190) for 190 genes. The list of those 190 genes are in variable 't'. So the idea is to read the names of genes from variable 't' and subset the matrix M accordingly. Any thoughts are welcome! Best Lee Hi, Assuming the correlation matrix has dimnames, you can do : x[ rownames(x) %in% t, colnames(x) %in% t ] Here is a reproducible example, please make sure you provide one next time. x - expand.grid( x1 = 1:2, x2 = 1:2, x3 = 1:2, x4 = 1:2 ) y - cor( x ) t - c(x1, x2) y[ rownames(y) %in% t, colnames(y) %in% t ] Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/Gq7i : ohloh |- http://tr.im/FtUu : new package : highlight `- http://tr.im/EAD5 : LondonR slides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selective subsetting of a correlation matrix
Will something like this work for you:
x - matrix(1:100,10)
dimnames(x) - list(letters[1:10], LETTERS[1:10])
x
A B C D E F G H I J
a 1 11 21 31 41 51 61 71 81 91
b 2 12 22 32 42 52 62 72 82 92
c 3 13 23 33 43 53 63 73 83 93
d 4 14 24 34 44 54 64 74 84 94
e 5 15 25 35 45 55 65 75 85 95
f 6 16 26 36 46 56 66 76 86 96
g 7 17 27 37 47 57 67 77 87 97
h 8 18 28 38 48 58 68 78 88 98
i 9 19 29 39 49 59 69 79 89 99
j 10 20 30 40 50 60 70 80 90 100
x[c('c','g','j'), c(B,E,I)]
B E I
c 13 43 83
g 17 47 87
j 20 50 90
On Fri, Dec 4, 2009 at 8:18 AM, Lee William leeon...@gmail.com wrote:
Dear All,
I have a correlation matrix say 'M' (4000x4000) for 4000 genes and I want
to
subset it to 'N' (190x190) for 190 genes.
The list of those 190 genes are in variable 't'. So the idea is to read the
names of genes from variable 't' and subset the matrix M accordingly.
Any thoughts are welcome!
Best
Lee
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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[R] z to r transformation within print.rma.uni and forest from the package metafor
Dear R community, I'm using the ,metafor'-package by Wolfgang Viechtbauer (Version: 0.5-5) to calculate random-effects meta-analyses using Correlations and Sample Sizes as the raw data. (By the way: Really a nice piece of work, Wolfgang! Thanks heaps.) I specified the rma.uni' function so that it looks like this: MAergebnis-rma.uni(ri=PosOutc, ni=N, mods=NULL, data=dm, intercept=TRUE, slab=c(dm$Article, dm$StudyNo), subset=NULL, measure=ZCOR, add=1/2, to=only0, vtype=LS, method=DL, weighted=TRUE, level=95, digits=4, btt=NULL, tau2=NULL, knha=FALSE, control=list()) With PosOutc being the column containing the raw correlations and N being the column with the sample sizes. I assume that this will imply that a) although the 'tau2' value is set to NULL, still a random-effects analysis is calculated b) the raw correlation coefficients are transformed to fisher-z-values c) the according variances of the fisher-z-values are calculated from the sample sizes d) these calculated z-values and sample sizes are then used to calculate summary effect and confidence interval limits e) the resulting object contains z-values and not raw correlations Now, the problem is: How do I get the calculated results back into the form of raw correlation coefficients? (In order to report them in an article.) I see two cases, where this might be relevant: A) When reporting numeric results: I tried the following: print.rma.uni(MAergebnis, transf=transf.ztor) but then noticed that the following will bring up the same result: print.rma.uni(MAergebnis) (When using the z2r and r2z functions out of the psychometric-package on the separate numbers, the values change, so it can't simply be a matter of rounding.) B) When drawing a forest plot: forest(MAergebnis, ., transf=transf.ztor, .) should to the trick, right? Does anyone have any experience or greater insight knowledge regarding this little problem? Best regards Sebastian [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Manipulation Question
This is probably far more discussion than the question warranted, but... On Thu, Dec 3, 2009 at 11:14 PM, David Winsemius dwinsem...@comcast.net wrote: On Dec 3, 2009, at 10:52 PM, Gray Calhoun wrote: The data import/export manual can elaborate on a lot of these; this is all straightforward, although many people would prefer to use a relational database for some of the things you mentioned. See Wickham's pithy response to this. Sure. My (indirect) point is that representing query results as separate files is usually not the right approach, regardless of statistical language/package one uses. I'm not aware of a goto command in R, though (although I could be wrong). In fairness to the OP, he did not ask if there were a go-to construct, but rather whether there were a gosub construct that supported modular programming. My response would have been that calling modular functions (i.e., subroutines with defined arguments) is fundamental to R and the key to understanding how to use it with grace and efficiency. I would say that the concept of functional programming is to a much greater extent supported by R than by SAS, whose datastep mechanisms (as I remember them from earlier incarnation) in no way supported modular programming. I suspect that S and R arose precisely because of the mental straightjackets imposed by SAS. From the original: Goto Start until File 1 Done. But, yes, probably unfair and certainly less informative than your response. -- David. --Gray On Thu, Dec 3, 2009 at 1:52 PM, John Filben johnfil...@yahoo.com wrote: Can R support data manipulation programming that is available in the SAS datastep? Specifically, can R support the following: - Read multiple dataset one record at a time and compare values from each; then base on if-then logic write to multiple output files - Load a lookup table and then process a different file; based on if-then logic, access and lookup values in the table - Support modular “gosub”programming - Sort files - Date math and conversions - Would it be able to support the following type of logic: o Start § Read Record from File 1 § Read Record from File 2 § Match · If Key 1 Key 2 and Key 1 Key 2, Write to output file A · If Key 1 = Key 2, Write to output file B · If Key 1 Key 2 and Key 1 Key 2, Write to output file C§ Goto Start until File 1 Done John Filben Cell Phone - 773.401.2822 Email - johnfil...@yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selective subsetting of a correlation matrix
On 12/04/2009 02:24 PM, Romain Francois wrote: On 12/04/2009 02:18 PM, Lee William wrote: Dear All, I have a correlation matrix say 'M' (4000x4000) for 4000 genes and I want to subset it to 'N' (190x190) for 190 genes. The list of those 190 genes are in variable 't'. So the idea is to read the names of genes from variable 't' and subset the matrix M accordingly. Any thoughts are welcome! Best Lee Hi, Assuming the correlation matrix has dimnames, you can do : x[ rownames(x) %in% t, colnames(x) %in% t ] Here is a reproducible example, please make sure you provide one next time. x - expand.grid( x1 = 1:2, x2 = 1:2, x3 = 1:2, x4 = 1:2 ) y - cor( x ) t - c(x1, x2) y[ rownames(y) %in% t, colnames(y) %in% t ] Or even : y[t,t] -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/Gq7i : ohloh |- http://tr.im/FtUu : new package : highlight `- http://tr.im/EAD5 : LondonR slides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] set working directory in Windows XP
Hello everybody,
I'm new in the R world and I'm struggling to set the working directory.
Up to now, I just set it up every time I start R ( 'setwd()' ) but I'd
like it to be set automatically. I've read the FAQ as well as the help
on Startup ('?Startup') about the environment variables and profiles but
I could not understand what to do: which command line, which variable,
which file etc.
I hope you'll be able to help me.
Thanks a lot in advance,
Ivan
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Re: [R] multidimensional point.in.polygon??
Hi,
Yet another one of my very naive ideas on the subject: maybe you can
first evaluate the circumscribed and inscribed spheres of the base set
of points (maximum and minimum of their distances to the center of
gravity). Any points within a distance smaller than the infimum is
good, any point further than the supremum is not good. This should be
faster than the calculation of a convex hull for each point. Of course
the usefulness of this first test really depends on how aspherical is
your base convex hull.
I do hope to read a real answer from someone who knows this stuff!
HTH,
baptiste
2009/12/4 Keith Jewell k.jew...@campden.co.uk:
Hi,
I seek to identify those points in/outside a multidimensional convex hull
(geometry::convhulln). Any suggestions?
Background just in case I'm going down a really wrong road:
Given an observed data set with one dependent/observed variable (Y) and
multiple (3 to 10) independent/design variables (X1, X2, ...) I want to
increase the number of points by interpolating. I'm using expand.grid(X) to
generate the X points and locfit::predict.locfit to interpolate the Y
values. No problem so far.
BUT my observed X data set is very far from rectangular, so the set of
points produced by expand.grid includes many extrapolations which I'd
want to remove. I'm aware of the problems of defining extrapolation in
multiple dimensions and am minded to define it as outside the convex hull,
hence my question.
In searching r-project.org I came across a thread in which baptiste auguie
said one general way to do this would be to compute the convex hull
(?chull) of the augmented set of points and test if the point belongs to
it; an approach I'd considered generalising to multiple points thus (pseudo
R code)...
baseHull - convhulln(baseSet)
augHull - convhulln(augSet)
while (augHull != baseHull)
{ augSet - augSet [-(augHull !%in% baseHull)]
augHull - convhulln(augSet)
}
... but this has that horrible loop including a convhulln!
In the (real, typical) test data set I'm using for development baseSet is 5
columns by 2637 rows while baseHull has only 42 distinct points. If augHull
has a similarly simple hull, then each time round the loop will remove only
a few dozen points; I need to remove many thousands.
And (in my naivete) I think there must be a better way of testing for a
point inside a polygon, I'd have thought convhulln must need to do that
often!
Thanks in advance for any pointers,
Keith Jewell
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[R] cycling k times a realization of a random walk.....problems..
hello R-masters.
i have an R-issue here that i don't know if you'd wish to help me about it:
briefly i'd like to generate many (say hundred) realizations of a random walk,
execute a few operations on each of them (mean time of return), and graph each
realization on the same plot.
IN OTHER WORDS I'D LIKE TO IMPOSE A LOOPING CYCLE TO THE COMMAND NOT THE
ARGUMENT OF THE COMMAND.
for some of these questions i have already a partial answer: my main problem
here is automatizing the process for 100 times.
my random walk generating function is:
rwalk - function(n,p, x0=0)
{
x - rbinom(n,1,p)
x[which(x==0)] - -1
y-c(x0,x)
y - cumsum(y)
}
THIS IS THE CODE THAT I'D LIKE TO REITERATE
a- rwalk(n,p,x0=0) #whish to generate 100 of those
#and for each calculate the following
o-which(a==0)
N-length(o) # number of times the walk returns to 0
Nn-(o[-1]-N) # number of steps to get to 0
V-mean(Nn) # mean time of return to 0
par(mfrow=c(1,1))
plot(0:n, a, type= l, main=..., xlab=tempo, ylab=stato,
ylim=c(...), lwd=3, col=red, lty=1)
par(new=T)
plot(0:n, b, type= l, main=, xlab=, ylab=,
ylim=c(), lwd=3, col=green, lty=2)
#technically i've tryed to fuse all those parts in a function reiterating k=100
times with a for cycle, but with no succes, and i dare there must be something
really disturbing in the code below
function(k){
for (i in 1:k){
a[i]-rwalk(1e+04,0.5,0)
o[i]-which(a[i]==0)
N[i]-length(o[i])
Nn[i]-(o[i][-1]-N[i])
V[i]-mean(Nn[i])
w-c(V[1]:V[k])
M-mean(w) #mean over all the realizations
par(mfrow=c(1,1))
plot(0:n, a[1], type= l, main=..., xlab=tempo, ylab=stato,
ylim=c(...), lwd=3, col=red, lty=1)
par(new=T)
plot(0:n, a[i], type= l, main=, xlab=, ylab=,
ylim=c(...), lwd=3, col=c(1:i), lty=2)
}
} #NOTE: I'VE ALSO TRIED TO REITERATE THE WALK WITH THE rep()
# t-rep(rwalk(1e+04,0.5,0),100)
# then of course i have the problem of splicing this ridicolously #one
milion long vector in 100 bits of tenthousand, and still goig through all the
calculations and plotting i meant before
i wonder what..
THANK YOU FOR YOUR PRECIUOS ATTENTION!!!
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[R] question about invers gamma trancted
Hi I want to generate from invers gamma distribution truncated but when I use the rinvegamma() function, the system can not find this function. Is ther someone to help me please? thanks soleiman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error when running Conditional Logit Model
Dear R-helpers, I am very new to R and trying to run the conditional logit model using clogit command. I have more than 4000 observations in my dataset and try to predict the dependent variable from 14 independent variables. My command is as follows clmtest1 - clogit(Pin~Income+Bus+Pop+Urbpro+Health+Student+Grad+NE+NW+NCC+SCC+CH+SE+MRD+strata(IDD),data=clmdata) However, it produces the following errors: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning messages: 1: In Surv(rep(1, 4096L), Pinmig) : Invalid status value, converted to NA 2: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge I search the error message from R forums but it does not say anything for Conditional Logit Model. Please check for me what it says and what should I do to solve it. Thanks a lot for your help Hien Nguyen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Logistic geographical weighted regression
Dear all, is it possible to perform logstic type of geographical weighted regression in R software? thanks in advance. robert. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] latex.table for table with character and numeric columns
Hallo, I have a dataset with one or two columns with character data and the rest with numeric data. Using latex.table from the quantreg package produced a table, but I cannot set the decimals. For instance: --- x-data.frame(Name=c(Jan,Piet,Jan), V=c(1,2.991,3)) latex.table(as.matrix(x),file=x,caption=x) latex.table(as.matrix(x),file=x,caption=x,dec=2) Error in round(x, dec) : Non-numeric argument to mathematical function --- Am I not using the right command, or is there a way around? Thanks, Gerrit. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] curve fitting to data
Hi to all This is the first time I am quoting a question and I hope, my question is not too basic... For the following data, I wish to draw a fitted curve. x - c(123,129,141,144,144,145,149,150,158,159,163,174,183,187,242,248) y - c(14.42,26.96,31.3,19.95,36.36,15.4,24.76,35.39,28.07,40.97,26.23,42.83,46.53,14.79,49.18,48.08) If I plot the data, it looks somehow that a logistic function would render good results. My questions are: How do I use nls and/or SSlogis (or other) to fit the curve? How can I see the summary statistics of the fit? How do I finally draw the line to my x,y (untransformed data) plot? Any help would be highly appreciated. Thank you and cheers Pascale -- ..___ Dr. Pascale Weber Swiss Federal Research Institute WSL Zuercherstrasse 111 CH-8903 Birmensdorf Switzerland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] length of a density curve (or any curve)
Thanks for your answer, @Dennis Murphy: no, I don't know the functionnal form, this is purely empirical data @ Ted Harding: Thank you for your lines of code, they are actually a pretty smart way... SW 2009/12/4 Ted Harding ted.hard...@manchester.ac.uk: True enough -- ?density does not address the issue of computing the length pf the curve! One simple way of implementing the idea you first thought of would be on the following lines: d - density(MyData$x) sum(sqrt(diff(d$x)^2 + diff(d$y)^2)) which simply sums the lengths of the line-segments. You would get a better approximation to the ideal length by increasing the value of 'n' in the call to density() (perhaps as a separate calculation, since a relatively small value of 'n' is likely to be adeqaute for plotting, but possibly inadequate for the accurate computation of the length). Hpoing this helps, Ted. On 04-Dec-09 12:41:22, sylvain willart wrote: Yes, sure (and I just did it again) but I can't see an answer... did I miss sthg ? regards, SW 2009/12/4 milton ruser milton.ru...@gmail.com: hi Sylvain, did you try ?density regards milton On Fri, Dec 4, 2009 at 7:19 AM, sylvain willart sylvain.will...@gmail.com wrote: Hello R users, When I type d - density(MyData$x) I obtain a density object I can plot, But I wonder if there is a way to easily compute the length of the density curve ? ( I imagine I could compute the distances between the 512 equally spaced points using their x and y, but does it exist a smarter way ?) Regards, SW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 04-Dec-09 Time: 13:02:27 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] flexmix and mclust help
Hello, I'm trying out flexmix and mclust for the first time on some univariate data which is typically best described as lognormal, but can sometimes be gamma distributed as well. I first tried using EM on mclust assuming the data was lognormally distributed and could only get it to work in E mode, i.e. the equal variance mode. I could never get it to work on V mode [ the warning message was Warning message: In meV(data, z = z, prior = prior, control = control, Vinv = parameters$Vinv, : sigma-squared falls below threshold ] so I gave up even after trying the two suggestions I encountered on the web (eliminating zeros in the data and changing the version of R and mclust). Does anyone understand what's going on here? My EM script in MATLAB has no problem with this data, but is slow, which is why I want to use R. I then tried to understand and use flexmix assuming the data are actually better described as a gamma mixture. From what I could understand of the function call I wrote flextest - flexmix( Data ~ unmap(priors_from_kmeans_call$cluster), data=Data, k = number_clusters, model = FLXMRglm(family = Gamma ) ) and found Error in model.frame.default(mo...@fullformula, data = data, na.action = NULL) : invalid type (list) for variable 'chr18_test_binned' I think it wants a list (like NPreg in the examples, a struct in MATLAB), but I'm so new at R that I don't really know what I'm doing. Can anyone give me a simple example of how take a vector of data and ask it to perform a gamma mixture EM on it using flexmix, or even more ideally, how to use do either lognormal or gamma mixtures? Also, are there any lists of examples that people can use to test agglomerative hclust methods on this same data (instead of using kmeans) as initialization for these EM methods? Thanks a lot for your help. -- View this message in context: http://n4.nabble.com/flexmix-and-mclust-help-tp948545p948545.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] stepAIC function
Hi All, I am trying to run the following script but have problem, coxm- coxph(Surv(sdat$time, sdat$cens)~hd+nawtg+nwwg+ntpg+cy+nseas,data=sdat) coxm-stepAIC(coxm,~.^2) The error message is Error: could not find function stepAIC I tried to install the package but I could not find it. Where can i get it? The other question is that I want to get the Kaplan-Meier Estimate for each covariate in the model, Like covaraite n Events Mean, S.E.(mean) ,Median, 95% LCL, 95% UCL 0 14 10 2.87 .03 2.2 1.938 infi 1 11 9 1.06 .67 1.1 0.29 2.48 I used sdat.fit0 - survfit(Surv(sdat$time, sdat$cens)~sdat$ntpg, data = sdat, type = kaplan-meier, conf.type=plain) sdat.fit0 Instead I got the following, Call: survfit(formula = Surv(sdat$time, sdat$cens) ~ sdat$ntpg, data = sdat, type = kaplan-meier, conf.type = plain) records n.max n.start events median 0.95LCL 0.95UCL sdat$ntpg=03576 35763576311 NA NA NA sdat$ntpg=14851 48514851466 NA NA NA I would appreciate if some one can help me. thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cycling k times a realization of a random walk.....problems..
On Fri, 2009-12-04 at 05:54 -0800, Federico Bonofiglio wrote:
hello R-masters.
i have an R-issue here that i don't know if you'd wish to help me
about it:
briefly i'd like to generate many (say hundred) realizations of a
random walk, execute a few operations on each of them (mean time of
return), and graph each realization on the same plot.
IN OTHER WORDS I'D LIKE TO IMPOSE A LOOPING CYCLE TO THE COMMAND NOT
THE ARGUMENT OF THE COMMAND.
for some of these questions i have already a partial answer: my main
problem here is automatizing the process for 100 times.
my random walk generating function is:
rwalk - function(n,p, x0=0)
{
x - rbinom(n,1,p)
x[which(x==0)] - -1
y-c(x0,x)
y - cumsum(y)
}
snip /
#NOTE: I'VE ALSO TRIED TO REITERATE THE WALK WITH THE rep()
# t-rep(rwalk(1e+04,0.5,0),100)
# then of course i have the problem of splicing this
ridicolously #one milion long vector in 100 bits of tenthousand, and
still goig through all the calculations and plotting i meant
before
One way of doing away with the loop, is to just get all the rbinoms you
want and format it appropriately, before cumsum: Try this:
rwalk - function(n, p, x0 = 0, sim = 1)
{
x - rbinom(n * sim, 1, p)
x[!x] - -1
x - matrix(x, nrow = sim, byrow = TRUE)
x - cbind(rep(x0, sim), x)
y - t(apply(x, 1, cumsum))
return(y)
}
sim is the extra argument, indicating the number of walks you want. Set
it to 100 to get what you need. Each row in the returned matrix is a
random walk of the form you describe.
You can then use the apply() function to compute your statistics on each
row (walk) and aggregate the results, e.g.
set.seed(123)
system.time(walks - rwalk(1, p = 0.5, x0 = 0, sim = 100))
user system elapsed
0.747 0.010 0.759
tmp[1:10, 1:10] # first 10 walks, first 10 data in each
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]01010 -10 -1 -2-3
[2,]0 -1 -2 -3 -4 -3 -4 -5 -6-7
[3,]01210 -10 -1 -2-3
[4,]010 -10 -10 -10-1
[5,]010 -10 -1 -2 -3 -4-3
[6,]0 -1 -2 -3 -4 -5 -4 -5 -4-3
[7,]0 -1010 -1 -2 -10-1
[8,]010 -1 -2 -3 -2 -3 -2-1
[9,]0 -1 -2 -3 -4 -3 -4 -5 -4-3
[10,]0 -1 -2 -3 -2 -3 -4 -5 -4-3
apply(tmp[1:10, ], 1, function(x) which(x == 0))
[[1]]
[1] 1 3 5 7
[[2]]
[1] 1
[[3]]
[1] 1 5 7
[[4]]
[1] 1 3 5 7 9
[[5]]
[1] 1 3 5
[[6]]
[1] 1
[[7]]
[1] 1 3 5 9 11 17 23 27 29
[[8]]
[1] 1 3
[[9]]
[1] 1
[[10]]
[1] 1
That might make it easier to work with as you only need to generate the
walks once and then develop each summary function independently. If you
start with a small example, say n = 10 and sim = 10, you should be able
to follow the computations and check they are correct.
HTH
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] curve fitting to data
A simple y vs log(x) fit seems to work pretty well here: fit - lm(y ~ log(x)) summary(fit) plot(y ~ log(x)) abline(fit) On Fri, Dec 4, 2009 at 9:06 AM, Pascale Weber pascale.we...@wsl.ch wrote: Hi to all This is the first time I am quoting a question and I hope, my question is not too basic... For the following data, I wish to draw a fitted curve. x - c(123,129,141,144,144,145,149,150,158,159,163,174,183,187,242,248) y - c(14.42,26.96,31.3,19.95,36.36,15.4,24.76,35.39,28.07,40.97,26.23,42.83,46.53,14.79,49.18,48.08) If I plot the data, it looks somehow that a logistic function would render good results. My questions are: How do I use nls and/or SSlogis (or other) to fit the curve? How can I see the summary statistics of the fit? How do I finally draw the line to my x,y (untransformed data) plot? Any help would be highly appreciated. Thank you and cheers Pascale -- ..___ Dr. Pascale Weber Swiss Federal Research Institute WSL Zuercherstrasse 111 CH-8903 Birmensdorf Switzerland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tobit model fluid milk consumption
First, note that all attachments are removed from messages sent to R-help, please use plain text only. I took the time to bring up the attachment in a web browser (there is a link to it), but you are unlikely to get a lot of readers when the question is captured as a pdf. 1. Tobit regression on the raw data: The scale is the residual standard deviation, or estimate of sigma in the usual linear models terminology. For linear regression with uncensored data, the estimate of scale is independent of the estimate of the other coefficients, and can be computed at the end. For censored data this is not so, the scale and the coefficients must be estimated together. During the maximization step the routine uses log(scale), it forces positive coefficients and also works better numerically; as a consequence the full variance/covariance matrix includes both beta and log(scale). 2. Tobit regression on the rescaled data. You must have rescaled both x and y, since the estimated residual variance changed. I see multiple disadvantages, and no advantages, to regression on rescaled data. I know it is common in some fields, but why? With respect to your questions on how to interpret rescaled coefficients, I don't know how to interpret them either. 3. The residual for a censored observation is not a well defined quantity. Hence both the computation and meaning of R^2 are unclear to me. Terry Therneau Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Arules - Association Rules
Alexandre, You are mining for association rules with an absolute support count of 1001*0.01 = 10.1. From your 40 minutes processing time I guess that your survey data set is very dense and that results in an enormous number of frequent itemsets (potentially up to 2^k - k - 1 which is in your case for k=71 about 10^21) which causes you to run out of memory. You have the following options: * increase minimum support (e.g., start with 0.1) and see how low you can go without using up all your memory (I don't know how to watch memory usage on Windows). * restrict the maximal length of frequent itemsets by using parameter=list(maxlen = 3, support = ...) If that does not help I will need your dataset and some code to reproduce and study the problem. -Michael Hi I'm a windows XP user. My notebook have 1gb ram, 160gb hd, processor amd turion64 1,6gh. For processing, it takes about 40 minutes. This is the code i used: dados=read.csv(C:/Documents and Settings/Administrador/Meus documentos/My Dropbox/Estat?stica/Association Rules/Top2009 alterado.csv, header=T, sep=;) library(arules) bin=as(dados, transactions) rules - apriori(bin, parameter = list(support = 0.01, confidence = 0.6)) Below is a sample of the file. I export data as CSV from excel. I have 71 columns (variabels) an 1001 lines (responses) 1. Churrascaria 2. Supermercado 3. Restaurante Self Service 4. Restaurante Chin?s 5. Buffet 6. Sorvete Galp?o Nelore Super Muffato N?o Sabe Jin Jin Planalto S?vio Vento Sul Super Muffato N?o Sabe N?o Sabe N?o Sabe Doce Ver?o Ga?cha Super Muffato N?o Sabe N?o Sabe N?o Sabe Kibon Tradi??o Ga?cha Super Muffato N?o Sabe N?o Sabe N?o Sabe Nestl? N?o Sabe Super Muffato N?o Sabe N?o Sabe Estilo S?vio Rancho Grill Viscardi Akira Akira N? o Sabe N?o Sabe Thank you very for your helping!!! On 3 dez, 01:46, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, On Wed, Dec 2, 2009 at 6:57 PM, Alexandre - UEL shima...@gmail.com wrote: Hello everybody! I'm trying some datamining, but i'm having some problems with arule package, in the end of processing R had to be closed. I already tryied to reinstall the 2.10 version, change the computer and realocated more virtual memory. Does anyone had this problem to? I had a hiphoteses that i have to prepare the data, somehow i don't know. Thanks for helping!!! Can you provide more info here? 1. I'm assuming since you're talking about reallocating virtual memory, or whatever, you're on windows? 2. What's the exact error you're getting (what's it saying before R 'had to be closed'? 3. What's the size of your data? What type of data is it? 4. How much RAM do you have? 5. Are you on a 32 or 64 bit system? 6 What happens if you cut your data in half? 6. Can you provide a (very small) reproducible example of your data + code? ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:http://cbio.mskcc.org/~lianos/contact __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Hahsler email: mich...@hahsler.net web: http://michael.hahsler.net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] csimtest function in multcomp package
Hello all, Quick question: I want to do posthoc contrasts for a linear mixed effects model. However, when trying to use the csimtest function in multcomp package I receive an error message saying it cannot find the function, even after installing and loading package multcomp. Any pointers would be greatly appreciated Daniel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Converting a Matrix in a colum vector
Hi all, Imagine I have a matrix G with N rows and M columns So L=NxM is the number of different cells in my matrix. I want to create a column vector F whose size will be F(L,1) So the fisrt row in F is G(1,1) Second row in F is G(1,2) When we arrive to a point M the element M+1 will be G(2, 1) Element M+2 will be G(2,2) and so on. I´m trying but allways error Easy Example: G= 2 3 4 8 8 9 N=2 M=3 L=6 F= 2 3 4 8 8 9 Can anyone guide me? Thanks in advance [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] stepAIC function
On Dec 4, 2009, at 9:29 AM, Ashta wrote: Hi All, I am trying to run the following script but have problem, coxm- coxph(Surv(sdat$time, sdat$cens)~hd+nawtg+nwwg+ntpg+cy +nseas,data=sdat) coxm-stepAIC(coxm,~.^2) The error message is Error: could not find function stepAIC Perhaps you have not loaded the package that contains that function? I tried to install the package but I could not find it. Where can i get it? The other question is that I want to get the Kaplan-Meier Estimate for each covariate in the model, Not exactly sure what that means. Kaplan-Meier estimate of ... what? Like covaraite n Events Mean, S.E.(mean) ,Median, 95% LCL, 95% UCL 0 14 10 2.87 .03 2.2 1.938 infi 1 11 9 1.06 .67 1.1 0.29 2.48 I used sdat.fit0 - survfit(Surv(sdat$time, sdat$cens)~sdat$ntpg, data = sdat, type = kaplan-meier, conf.type=plain) sdat.fit0 Instead I got the following, Call: survfit(formula = Surv(sdat$time, sdat$cens) ~ sdat$ntpg, data = sdat, type = kaplan-meier, conf.type = plain) records n.max n.start events median 0.95LCL 0.95UCL sdat$ntpg=03576 35763576311 NA NA NA sdat$ntpg=14851 48514851466 NA NA NA If you have a dataset with 300-400 events out of 3000-4000 subject, then why are you expressing surprise that you do not get a non- parametric estimate of the median survival? The median is the time at which half of the subjects would have experienced an event and you only have 1/10 of them with events. -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Source code for some grid package documentation
Dear R-users, I was wondering if anybody would have the source code used to create the last figure in the frame.pdf documentation distributed with the grid package. Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] csimtest function in multcomp package
On Fri, 4 Dec 2009, d.m.perk...@qmul.ac.uk wrote: Hello all, Quick question: I want to do posthoc contrasts for a linear mixed effects model. However, when trying to use the csimtest function in multcomp package I receive an error message saying it cannot find the function, even after installing and loading package multcomp. Any pointers would be greatly appreciated The function is not part of the package interface anymore. The interface was generalized and streamlined compared to earlier versions. The the package vignettes for the current version. hth, Z Daniel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] csimtest function in multcomp package
Daniel, quick guess: There has been a major change in the package some time ago, with quite a few functions vanishing and others added. So I guess your recycled code was based on an older version of multcomp. My current version (1.1-0) does not have csimtest anymore either. I guess you want to look into ?glht in the same package, and check the archives to find out more about the changes (and yes, you will have to modify your code to some extent, at least so had I, it's not just replacing the function name). HTH, Michael -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of d.m.perk...@qmul.ac.uk Sent: Freitag, 4. Dezember 2009 16:47 To: r-help@r-project.org Subject: [R] csimtest function in multcomp package Hello all, Quick question: I want to do posthoc contrasts for a linear mixed effects model. However, when trying to use the csimtest function in multcomp package I receive an error message saying it cannot find the function, even after installing and loading package multcomp. Any pointers would be greatly appreciated Daniel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with date x-axis
Hello, I have a friday problem. I'm trying to plot the number of measures by day with this command between the 2008-07-31 and the 2009-11-13 (it works) : plot(unique(as.Date(strptime(data$date, format=%Y-%m-%d %H:%M:%S))), measuresbyday) then I would like to plot vertical lines for each month. But it doesn't work because par()$usr gives 14071.16 14579.84 -7.16 213.16 and as.numeric(as.POSIXct(unique(as.Date(strptime(data$date, format=%Y-%m-%d %H:%M:%S)))[1])) corresponding to 2008-08-01 gives 1217376000 I think the last value is ok but I don't understand why the par()$usr values are so low. Any idea ? Thanks in advance and have a nice week-end, Ptit Bleu. -- View this message in context: http://n4.nabble.com/Problem-with-date-x-axis-tp948642p948642.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting a Matrix in a colum vector
matrix(t(G), nc=1) b On Dec 4, 2009, at 1:19 PM, Jose Narillos de Santos wrote: Hi all, Imagine I have a matrix G with N rows and M columns So L=NxM is the number of different cells in my matrix. I want to create a column vector F whose size will be F(L,1) So the fisrt row in F is G(1,1) Second row in F is G(1,2) When we arrive to a point M the element M+1 will be G(2, 1) Element M+2 will be G(2,2) and so on. I´m trying but allways error Easy Example: G= 2 3 4 8 8 9 N=2 M=3 L=6 F= 2 3 4 8 8 9 Can anyone guide me? Thanks in advance [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for some grid package documentation
On 12/04/2009 04:28 PM, Sebastien Bihorel wrote: Dear R-users, I was wondering if anybody would have the source code used to create the last figure in the frame.pdf documentation distributed with the grid package. file.show( vignette( frame, package = grid )$file ) Thanks in advance. -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/Gq7i : ohloh |- http://tr.im/FtUu : new package : highlight `- http://tr.im/EAD5 : LondonR slides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] set working directory in Windows XP
You set this on the properties of the shortcut you use to start R,
just like any other Windows application.
R's working directory is always initially the directory it is started
from.
This *is* in the FAQ:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-run-it_003f
even though we do not pretend to give a Windows tutorial.
On Fri, 4 Dec 2009, Ivan Calandra wrote:
Hello everybody,
I'm new in the R world and I'm struggling to set the working directory.
Up to now, I just set it up every time I start R ( 'setwd()' ) but I'd like
it to be set automatically. I've read the FAQ as well as the help on Startup
('?Startup') about the environment variables and profiles but I could not
understand what to do: which command line, which variable, which file etc.
I hope you'll be able to help me.
Thanks a lot in advance,
Ivan
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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Re: [R] z to r transformation within print.rma.uni and forest from the package metafor
Dear Sebastian, Glad to hear you find the package useful. Before I get to your questions, just as an aside - you can leave default arguments out of the call. So: MAergebnis-rma.uni(ri=PosOutc, ni=N, data=dm, slab=c(dm$Article, dm$StudyNo), measure=ZCOR, method=DL) would do exactly the same as your call. As for your questions: a) Correct. The tau2 argument is only there if you want to fix tau2 to a particular value (e.g., for sensitivity analyses). If tau2=NULL (the default), then tau2 is estimated from the data. Hmmm, I see how tau2=NULL could be misleading. Maybe I should change the default to something else. b) Correct. c) Correct (i.e., 1/(ni-3)). d) And again correct. e) Correct. Since the meta-analysis is conducted on the transformed values, they are also stored in the model object. The results shown (e.g., the model intercept) is the estimated value of mu in the transformed units. Now, if you want the estimated value of mu in correlation units, use: predict(MAergebnis, transf=transf.ztor) When you draw a forest plot and you want to show the study results in correlation units (and not the transformed units), you have two options: forest(MAergebnis, transf=transf.ztor) will backtransform the transformed values (and the corresponding CI bounds). Since this is not a linear transformation, the CIs will not be symmetric. Alternatively, you can use: forest(MAergebnis, atransf=transf.ztor) which will transform the x-axis appropriately so that you do get symmetric CIs (but a non-linear x-axis). So, try out: forest(MAergebnis) forest(MAergebnis, transf=transf.ztor) forest(MAergebnis, atransf=transf.ztor) and see how the plot changes to better understand this. I hope this helps! Best, -- Wolfgang Viechtbauerhttp://www.wvbauer.com/ Department of Methodology and StatisticsTel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) Original Message From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sebastian Stegmann Sent: Friday, December 04, 2009 14:28 To: r-help@r-project.org Subject: [R] z to r transformation within print.rma.uni and forest from the package metafor Dear R community, I'm using the ,metafor'-package by Wolfgang Viechtbauer (Version: 0.5-5) to calculate random-effects meta-analyses using Correlations and Sample Sizes as the raw data. (By the way: Really a nice piece of work, Wolfgang! Thanks heaps.) I specified the rma.uni' function so that it looks like this: MAergebnis-rma.uni(ri=PosOutc, ni=N, mods=NULL, data=dm, intercept=TRUE, slab=c(dm$Article, dm$StudyNo), subset=NULL, measure=ZCOR, add=1/2, to=only0, vtype=LS, method=DL, weighted=TRUE, level=95, digits=4, btt=NULL, tau2=NULL, knha=FALSE, control=list()) With PosOutc being the column containing the raw correlations and N being the column with the sample sizes. I assume that this will imply that a) although the 'tau2' value is set to NULL, still a random-effects analysis is calculated b) the raw correlation coefficients are transformed to fisher-z-values c) the according variances of the fisher-z-values are calculated from the sample sizes d) these calculated z-values and sample sizes are then used to calculate summary effect and confidence interval limits e) the resulting object contains z-values and not raw correlations Now, the problem is: How do I get the calculated results back into the form of raw correlation coefficients? (In order to report them in an article.) I see two cases, where this might be relevant: A) When reporting numeric results: I tried the following: print.rma.uni(MAergebnis, transf=transf.ztor) but then noticed that the following will bring up the same result: print.rma.uni(MAergebnis) (When using the z2r and r2z functions out of the psychometric-package on the separate numbers, the values change, so it can't simply be a matter of rounding.) B) When drawing a forest plot: forest(MAergebnis, ., transf=transf.ztor, .) should to the trick, right? Does anyone have any experience or greater insight knowledge regarding this little problem? Best regards Sebastian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Logistic geographical weighted regression
Pazur, Robert wrote: Dear all, is it possible to perform logstic type of geographical weighted regression in R software? thanks in advance. robert. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Can't answer your question, but reposting at the r-sig-geo mailing list might get you more responses. cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error when running Conditional Logit Model
On Dec 4, 2009, at 9:22 AM, Hien Nguyen wrote: Dear R-helpers, I am very new to R and trying to run the conditional logit model using clogit command. I have more than 4000 observations in my dataset and try to predict the dependent variable from 14 independent variables. My command is as follows clmtest1 - clogit(Pin~Income+Bus+Pop+Urbpro+Health+Student+Grad+NE+NW+NCC+SCC+CH +SE+MRD+strata(IDD),data=clmdata) However, it produces the following errors: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning messages: 1: In Surv(rep(1, 4096L), Pinmig) : Invalid status value, converted to NA 2: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge I search the error message from R forums but it does not say anything for Conditional Logit Model. With that many predictors in a small dataset, you may have created matrix singularities. Perhaps you created a stratum where all of the subjects experience the event and others where none did so. The coefficients might be driven to infinities. Try simplifying the model. Please check for me what it says and what should I do to solve it. -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for some grid package documentation
Thank you Romain, I appreciate the help. Romain Francois wrote: On 12/04/2009 04:28 PM, Sebastien Bihorel wrote: Dear R-users, I was wondering if anybody would have the source code used to create the last figure in the frame.pdf documentation distributed with the grid package. file.show( vignette( frame, package = grid )$file ) Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving predict
?arima
?write.table
groet,
Paul
Jose Narillos de Santos wrote:
Hi all,,I´m using function arima()
I.e
series is my data
model-arima(series,c(1,0,0))
forecast-predict(model,80)
I want to create a variable:
b1-forecast$pred - 1.96*forecast$se
and save in a txt file
but using this:
save(b1, file= b1.txt)
creates afile butwith this inside:
‹ ]Ã’{H“Q ðï~Ÿß|¦›ùÊÊLJI³ÔiÃ�W*¥þ‘Ã�-l)Ëœ%¤ )Å
mæ#)±,›
É�¹RIñ¸ åœÈÊiSÂfµd›bÒ�ôGuážß¹çr9p9œø´»4;‚
H‚´Å‘©‰¦Â¥žLâ€�#ÃŽR€ez´
ãÊÃ�¹1ìy‡÷3pN8Ä®°{,IÚ6¡¢˜ÊW²–Þà ôâ!ã“6 éúžù=ÂÃ
ê��žó{·â6ƒ½ l?øß×OõƒMw_�Â�¬û—¯•5ãëK÷Ö�©ÀZ+òÛ×
ô=é„ëæ ÉÊ(•YV·‘÷BçXùÔ(²E2 †ua��z J
Yj±+P‘tSU[PtÂgÃÂ�ïoÆ...@¶,ŠËx�...@Þ)k¤$â„¢TìÜ $/¼ÈAËœ
dôz®‡p ÈÀù¢iþ
½Êwâ„¢�...@²räÖoÂ�dÅ“bë¤r@c¾Â�Ã¥n€~ô™óW§ }û\M*g -¹wÂ�â€
ûšÛŸìj
hfEs�! 4�¡»Q‘h’Ë6%G ÒöJ
mhdiÃ...@㧋Â�iÃ¥Â�...@êÃÂ�Ç/@£2Ôº èÂ�ÃœM³¡ ôV#
x=†Ã�Â¥ l8 h¤jgɨkrÂ¥Â...@õŽ|u=ö¿Ùæ ¡Ånº2
ûÔEÙTŒ�©ËÔ¬c�õꙩX§(Õø,
Ã�/ë2óM¬š°â°JIÄŠÛ°¬ºjÂÞÂî•~ÄÅ
—]êDØ|¹°¿{9£tnË *‘âÿäÈýõ\lr—oö*6a’Ǧ±1:e¨{¢Îˆû 'öî°Ü‡{ZÎl^Bb6ØËÌWbGŽ¤¯aåÆeKÿƒ‰5ß—°Ú®ü7™Ta�cM*ŸØZ1…Â-£Wˆ?ëŸ'ô%�Å‚œ0ÿžðBKeÓ²7–å'
Can anyone help me to do it?
Do you know also a document wich expalin how works and calculates
modelpredictions?
[[alternative HTML version deleted]]
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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul
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Re: [R] question about invers gamma trancted
On Dec 4, 2009, at 9:02 AM, khaz...@ceremade.dauphine.fr wrote: Hi I want to generate from invers gamma distribution truncated but when I use the rinvegamma() function, the system can not find this function. Is ther someone to help me please? Check your spledding. thanks soleiman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dividing a pixel image into factors - (cut.im(), cut.default())
Lauren, I think (?) you mean to say that you wish to create a factor and control the range of values assigned to each level. The breaks argument can specify either the number of intervals you desire OR the values you wish to use to define levels of your factor. See '?cut' and the following example: #A numeric vector x - 1:10 #Assign equal number of values #2 each of 2 automatically #determined intervals levels1 - cut(x,breaks=2) #User-specified intervals levels2 - cut(x,breaks=c(0,3,Inf)) data.frame(x,levels1,levels2) x levels1 levels2 1 1 (0.991,5.5] (0,3] 2 2 (0.991,5.5] (0,3] 3 3 (0.991,5.5] (0,3] 4 4 (0.991,5.5] (3,Inf] 5 5 (0.991,5.5] (3,Inf] 6 6(5.5,10] (3,Inf] 7 7(5.5,10] (3,Inf] 8 8(5.5,10] (3,Inf] 9 9(5.5,10] (3,Inf] 10 10(5.5,10] (3,Inf] 'Inf' is an easy way to create an interval that contains all values larger than some cutoff. Good luck with your analysis, Glen Gough Lauren wrote: I have a numeric pixel image which I would like to divide into factors for analysis in Spatstat. I have found that I can use cut.im() function to divide the range of pixel values into a series of equal length intervals (e.g. if my pixels values range from 0 to 60, cut.im(X.im,breaks=2) will produce two factors one containing pixel values 0-30 and one containing pixel values of 30 - 60, or thereabouts). However, I would like to specify the pixel value at which the factors are created - e.g. create one factor containing pixel values of 0-5 and another factor containing all other pixel values. I have been struggling to work out how to do this using either cut.im() or cut.default(). Can anyone help? - Glen Sargeant Research Wildlife Biologist -- View this message in context: http://n4.nabble.com/Dividing-a-pixel-image-into-factors-cut-im-cut-default-tp948346p948676.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Apparent different in symbol scaling between xyplot and grid.points
Dear R-users,
For the past few days, I have been trying to find the reason why some of
my plots were showing symbols of different sizes, while I thought I was
using the same .cex arguments everywhere. The problem is exemplified by
the following example code where the xyplot and grid.points functions
are used. The scaling factor is set to 0.84 in both the functions
settings, but one can see that, in the pdf file, the blue symbols
plotted by xyplot are smaller than the single black symbol created by
grid.points. Playing with the trellis settings did not seem to solve the
problem. I am missing a hidden scaling factor somewhere, but don't know
where to look anymore
I would greatly appreciate the feedback of the list on this issue.
library(lattice)
library(grid)
pdf(file=test.pdf)
df - data.frame(a=1:12,b=1:12,c=rep(1:4,each=3))
#trellis.par.set(superpose.symbol=list(cex=1))
xyplot(b~a|c,
data=df,
panel = function(x,y){
panel.xyplot(x,y,pch=3,cex=0.84)}
)
str(trellis.par.get())
str(get.gpar())
grid.points(x=100,y=85,pch=3,gp=gpar(cex=0.84))
dev.off()
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Re: [R] Logistic geographical weighted regression
On Dec 4, 2009, at 6:55 AM, Pazur, Robert wrote: Dear all, is it possible to perform logstic type of geographical weighted regression in R software? We even have a fortune for such questions: library(fortunes) fortune(Yoda) Evelyn Hall: I would like to know how (if) I can extract some of the information from the summary of my nlme. Simon Blomberg: This is R. There is no if. Only how. -- Evelyn Hall and Simon 'Yoda' Blomberg R-help (April 2005) Try the geospatial Task View as a start: http://finzi.psych.upenn.edu/views/Spatial.html And perhaps: RSiteSearch(spatial logistic) David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and eclipse
Sorry, but i was out for two days! I just want to call R scripts from java code. So i think i need to review the jri and the REngine API. I will tell you whatever i find. Thank you so much, because i was really lost! 2009/12/4 Romain Francois romain.franc...@dbmail.com On 12/03/2009 08:43 PM, Gene Leynes wrote: I thought of your email when I ran across this link: http://romainfrancois.blog.free.fr/index.php?post/2009/09/02/R-capable-version-of-ant I don't understand why you post this link with regards to this question. The link is about the ant package that lets you have R code inside an ant build script. If you want to call R from java, look at jri (part of rJava) and the REngine API. If you want to call java from R, use rJava. I think that you would have word your question more carefully for a longer response. yes please. Also, I use StatEt almost everyday. It works great with R. I have not used Eclipse for any other language. On Wed, Dec 2, 2009 at 12:20 PM, catuxa-2catuxa...@gmail.com wrote: I found the eclipse plugin for R StatEt, hass anyone already worked with it? It's posible to put inside of java code a R script with it? Thank you -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/Gq7i : ohloh |- http://tr.im/FtUu : new package : highlight `- http://tr.im/EAD5 : LondonR slides [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Machine Learning and Sample Size
In developing a machine learner to classify sentences in plain text sources of scientific documents I have been using the caret package and following the procedures described in the vignettes. What I miss in the package -- but quite possibly I am overlooking it! -- is functions that allow me to estimate whether a model has too much variance or too much bias. In particular, I am looking for something that helps me compare the training and test errors as functions of training set size. Clearly, I can program something in R, but if there is already a function in some package to do that, I would prefer to use it, of course. Regards, Richard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Renaming columns of a data.frame
A question that has come up a few times on r-help is how to rename columns
of a data.frame. There are several ways to do this by hand (see the list
archives). There is also a 'rename' function in the reshape package.
I often use the 'transform' function shortly after reading in a data file
and wanted to have a renaming function that has a syntax consistent with the
'transform' function (unlike 'rename', whose arguments have a reverse syntax
compared to 'transform').
Here is my attempt at a rename function similar to 'transform'.
Improvements are welcome.
ren - function(`_data`, ...){
# Influenced by transform.data.frame
e - unlist(list(...))
inx - match(e, names(`_data`))
if(any(is.na(inx)))
stop(Couldn't find these columns in the data: ,
paste(as.vector(e)[is.na(inx)], collapse= ) )
names(`_data`)[inx] - names(e)
return(`_data`)
}
d0 - data.frame(Year = c(2009, 2009, 2009),
Mst = c(27.9, 28.9, 31.0),
Yield = c(110, 180.1, 25))
ren(d0, yield='Yield')
ren(d0, 'yield'='Yield')
ren(d0, yield='Yield', year='Year')
ren(d0, yield='Yield', mst='Mst')
ren(d0, yield='YIELD', mst='MST') # Error caught.
# ren(d0, yield=Yield, year=Year) # Fails. Not caught. Might be nice to
allow this syntax.
--
Kevin Wright
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Three-dimensional (3D) movement using 'R'
On Dec 4, 2009, at 7:07 AM, StRose, Suzanne wrote: Hi again, Apologies for the last email I forwarded. Apparently, my data was not legible. So, I have a question regarding the construction of 3D graphs in ‘R’, BUT these graphs also need to illustrate movement (with time) of the prostate gland (using radiological techniques). I am not sure how to do this in ‘R’ although I’m sure there is some way of doing it. Below, I have copied and pasted some of the data on which I’m working. The data are for axial images of the prostate for one patient at 10 time points. On the axial images, A=anterior and positive; L=left and positive, so that A negative=posterior and L negative =right (see Figure 1 below). The signs (positive and negative) indicate movement away from or toward the baseline, respectively. So, any deviation away from the baseline is ‘+’ and any excursion toward baseline is negative (with the baseline indicated by Time=0). [Vector means the largest average directional change relative to the nominated direction of assessment; numbers are in mm]. It may be clear to radiographers in the audience, but what those 4 x n numbers represent is not clear to me. Are they the lateral and AP boundaries of the prostate? What you write suggests these might be called relative vectors, i.e. any point would be the vector sum? And why would we be plotting locations in 3d when this is an axial slice? I would like to plot 3D graphs illustrating movement of the prostate with time for each of the four patients but do not know how. Apologies again for the first email. I’ve attached an Excel file (hope this is okay) with the same data as in Table 1. Hopefully this is a bit clearer. Thanks. Best wishes, Suzanne Table 1 Patient_Axial Time Vector L Vector R Vector A Vector P 316868HO_DGE_cine1_ax_px SNIPPED DATA that arrived as an xls file to my mail client ... since I suspect it did not reach most of the list: This is an R form of the data from what appears to be one patient as all rows are labeled: 316868HO_DGE_cine1_ax_px. Note to Suzanne... do not use spaces in R variable names. dput(pat1) structure(list(Time = 0:10, VectorL = c(0, 1.6, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.3, 0, 0.2), VectorR = c(0, 1.5, 0.3, 0.3, 0.3, 1.6, 1.6, 1.8, 2.5, 2.3, -0.3), VectorA = c(0, 0, -0.3, -0.3, -0.3, -0.3, -0.3, -0.3, -0.4, -0.3, -0.2), VectorP = c(0, 1.9, -0.1, -0.1, -0.1, 0.1, 0.1, -0.1, 0.1, 0.4, 0.2)), .Names = c(Time, VectorL, VectorR, VectorA, VectorP), class = data.frame, row.names = c(NA, -11L)) Figure 1. image001.gif Suzanne St.Rose (DVM, MSc, PhD) Data_Three dimensional_01.xls David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question about R Functions
Stephanie Cooke wrote: Is there a place to find the code for R functions like lsoda? Thanks Yes, all code is in the source version of the package that contains that function. Best, Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Apparent different in symbol scaling between xyplot and grid.points
Hi,
I think the size mismatch occurs because of a different default for
the fontsize (and grid.points has a size of 1 character by default).
Compare the following two examples,
# default
grid.newpage()
pushViewport(viewport(x=unit(0.5, npc), y=unit(0.5, npc)))
lplot.xy(data.frame(x=0.55,y=0.5),type=p, pch=3)
grid.points(x=0.45,y=0.5, pch=3, gp=gpar(col=red))
trellis.par.set(fontsize, list(points=12))
grid.newpage()
pushViewport(viewport(x=unit(0.5, npc), y=unit(0.5, npc)))
lplot.xy(data.frame(x=0.55,y=0.5),type=p, pch=3)
grid.points(x=0.45,y=0.5, pch=3, gp=gpar(col=red))
HTH,
baptiste
2009/12/4 Sebastien Bihorel sebastien.biho...@cognigencorp.com:
Dear R-users,
For the past few days, I have been trying to find the reason why some of my
plots were showing symbols of different sizes, while I thought I was using
the same .cex arguments everywhere. The problem is exemplified by the
following example code where the xyplot and grid.points functions are used.
The scaling factor is set to 0.84 in both the functions settings, but one
can see that, in the pdf file, the blue symbols plotted by xyplot are
smaller than the single black symbol created by grid.points. Playing with
the trellis settings did not seem to solve the problem. I am missing a
hidden scaling factor somewhere, but don't know where to look anymore
I would greatly appreciate the feedback of the list on this issue.
library(lattice)
library(grid)
pdf(file=test.pdf)
df - data.frame(a=1:12,b=1:12,c=rep(1:4,each=3))
#trellis.par.set(superpose.symbol=list(cex=1))
xyplot(b~a|c,
data=df,
panel = function(x,y){
panel.xyplot(x,y,pch=3,cex=0.84)}
)
str(trellis.par.get()) str(get.gpar())
grid.points(x=100,y=85,pch=3,gp=gpar(cex=0.84))
dev.off()
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[R] Class attributes
Dear R forum,
I want to replace all the elements in a data frame (dd) which match the
character x with 0.
What's the most elegant way of doing this (there must be an easy way which
I've missed)? I settled on the following loop:
for(i in 5:12){# These are the column of dd I am interested
in
dd[which(dd[,i]==x),i]-0
}
The problem with this is that the columns which used to contain x are
still considered factors and I am unable to coerce them into numeric:
mean.species.biomass-colMeans(as.numeric(dd.p[,5:12]))
Error in inherits(x, data.frame) :
(list) object cannot be coerced to type 'double'
I'm tried unclassing reclassing, other functions etc. but nothing seems to
work. What is wrong?
Thanks in advance,
Allen
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Re: [R] How to compute contrast where there are interaction terms in the linear model?
On Tue, Dec 1, 2009 at 4:04 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Tue, 1 Dec 2009, Peng Yu wrote: Could somebody recommend some textbook how to compute contrast when there are interactions terms? Applied Linear Regression Models (book) mentioned contrast, but I cannot extend it to the case where there are interaction terms. Textbook? Schmextbook! You have the power of R at your fingertips! Use it to explore concepts you are trying to wrap your brain around! df - expand.grid(x1=1:20,x2=factor(letters[1:2])) vanilla - model.matrix(~0+poly(x1,degree=3), df ) matplot(row( vanilla) , vanilla, type='b') inter - model.matrix(~0+poly(x1,degree=3):x2, df ) matplot(row( inter ) , inter, type='b') I don't understand. Where the contrast is? BTW, what does 'schmextbook' mean? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Class attributes
Here a way of doing it:
for (i in 5:12){
# convert to character so you can substitute 'x'
a - as.character(dd[,i])
a[a == 'x'] - '0' replace with zero
dd[,i] - as.numeric(a)
}
On Fri, Dec 4, 2009 at 11:55 AM, Allen L allen.laroc...@gmail.com wrote:
Dear R forum,
I want to replace all the elements in a data frame (dd) which match the
character x with 0.
What's the most elegant way of doing this (there must be an easy way which
I've missed)? I settled on the following loop:
for(i in 5:12){# These are the column of dd I am
interested
in
dd[which(dd[,i]==x),i]-0
}
The problem with this is that the columns which used to contain x are
still considered factors and I am unable to coerce them into numeric:
mean.species.biomass-colMeans(as.numeric(dd.p[,5:12]))
Error in inherits(x, data.frame) :
(list) object cannot be coerced to type 'double'
I'm tried unclassing reclassing, other functions etc. but nothing seems
to
work. What is wrong?
Thanks in advance,
Allen
--
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http://n4.nabble.com/Class-attributes-tp948693p948693.html
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http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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Re: [R] Class attributes
On Dec 4, 2009, at 11:55 AM, Allen L wrote:
Dear R forum,
I want to replace all the elements in a data frame (dd) which match
the
character x with 0.
What's the most elegant way of doing this (there must be an easy way
which
I've missed)? I settled on the following loop:
for(i in 5:12){# These are the column of dd I am
interested
in
dd[which(dd[,i]==x),i]-0
}
The problem with this is that the columns which used to contain x
are
still considered factors and I am unable to coerce them into numeric:
Converting the labels of fac.obj (a factor object) to numeric values
is a FAQ (I forget the number, 7.something)
as.numeric(as.character( fac.obj ))
Factors are internally sets of numbers, but those numbers are not
generally what people assign meaning to, and certainly not in your
case where you assigned the character 0 to those rows where the
labels were previously x.
mean.species.biomass-colMeans(as.numeric(dd.p[,5:12]))
Error in inherits(x, data.frame) :
(list) object cannot be coerced to type 'double'
I'm tried unclassing reclassing, other functions etc. but nothing
seems to
work. What is wrong?
Thanks in advance,
Allen
--
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] grep() exclude certain patterns?
The external grep program has an option -v to select non-matching lines. I'm wondering if how to exclude certain patterns in grep() in R? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grep() exclude certain patterns?
On 04/12/2009 12:52 PM, Peng Yu wrote: The external grep program has an option -v to select non-matching lines. I'm wondering if how to exclude certain patterns in grep() in R? ?grep Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Standard deviation for each element in a set of matrices
Hello R-users, I would like to know how to find the standard deviation for each element in a set of matrices. Given the following files, File1File2File3 1 1 1 4 4 4 7 7 7 2 2 2 5 5 5 8 8 8 3 3 3 6 6 6 9 9 9 I want to calculate the standard deviation for every cell in the file (I'm using gridded data). The desired output is Output 3 3 3 3 3 3 3 3 3 Thanks. Muhammad -- Muhammad Rahiz | Doctoral Student in Regional Climate Modeling Climate Research Laboratory, School of Geography the Environment Oxford University Centre for the Environment South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194 Mobile: +44 (0)7854-625974 Email: muhammad.ra...@ouce.ox.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] User's function
Hello, All,
I want to write a function to do some works based on the arguments. For
example, bind some variables (arguments) as this:
myfunction - function(arg1, arg2, arg3, …)
{
x - cbind(arg1, arg2, arg3, …)
}
myfunction(arg1, arg2, arg3, …)
The function can automatically determine the number of arguments and bind
them, which means if I assign 2 arguments, the function can bind those two
arguments, or if I assign 3 arguments, the function can bind those three
arguments, and so on. Here assume the arguments are all continuous variables
and have the same length. Is it possible?
I would appreciate if some one can help me. Thanks!
Lisa
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Re: [R] Can we get rid of bar charts with error bars?
This reminds me of a quote I saw once (I think it may have been in one of those Murphy's Laws calendars), my parahpase: If you make someone think that they are thinking, They will love you for it. If you make them actually think, They will hate you for it. This explains why people love pie charts and hate more effective graphs. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jim Lemon Sent: Thursday, December 03, 2009 7:58 PM To: Frank E Harrell Jr Cc: r-help@r-project.org Subject: Re: [R] Can we get rid of bar charts with error bars? On 12/04/2009 12:56 AM, Frank E Harrell Jr wrote: Bar charts with error bars are far inferior to dot charts and other types of displays. One of many problems is demonstrated if you draw a bar chart displaying temperature in F then re-draw it on the degrees C scale. See http://biostat.mc.vanderbilt.edu/DynamitePlots for much more information. The error bars lull us into an assumption that symmetric confidence intervals are OK, among other things. Frank I could promote the dispersion function as capable of displaying asymmetric confidence intervals on whatever location indicators you prefer (have a look at the second example for hierobarp for example), but the problem is deeper than that. The point of graphic displays is to convey information to someone else, not to tell ourselves what we already know. Do people cheat with pie charts, bar charts, etc? Sure, and we could cheat with dot charts, too. Graphic displays are typically shown to an audience that knows less about the topic than the presenter in the hope that an obscure relationship will be clarified. If I am presenting to colleagues in my field, I will use much more informative and difficult to understand graphics than if I am summarizing the same results to the general public. If both groups leave the respective presentations enlightened, I have done well. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] User's function
Hi,
try ?do.call
do.call(cbind, replicate(3, 1:10, simplify=FALSE))
HTH,
baptiste
2009/12/4 Lisa lisa...@gmail.com:
Hello, All,
I want to write a function to do some works based on the arguments. For
example, bind some variables (arguments) as this:
myfunction - function(arg1, arg2, arg3, …)
{
x - cbind(arg1, arg2, arg3, …)
}
myfunction(arg1, arg2, arg3, …)
The function can automatically determine the number of arguments and bind
them, which means if I assign 2 arguments, the function can bind those two
arguments, or if I assign 3 arguments, the function can bind those three
arguments, and so on. Here assume the arguments are all continuous variables
and have the same length. Is it possible?
I would appreciate if some one can help me. Thanks!
Lisa
--
View this message in context:
http://n4.nabble.com/User-s-function-tp948737p948737.html
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Re: [R] shorten str() output for long list
An alternative to str is the TkListView function in the TeachingDemos package. You still get the long listing, but it is in a separate window that you can control the scrolling on by hand. For more complicated lists/objects it provides a tree structure so that you can look at only the detailed parts that you are interested in. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Peng Yu Sent: Thursday, December 03, 2009 8:11 PM To: r-h...@stat.math.ethz.ch Subject: [R] shorten str() output for long list x=split(1:1000,1:1000) str(x) Although str() can suppress long output for vectors, but it can not suppress long output for list. I'm wondering how to suppress the output for long lists. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to compute contrast where there are interaction terms in the linear model?
On Fri, 4 Dec 2009, Peng Yu wrote: On Tue, Dec 1, 2009 at 4:04 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Tue, 1 Dec 2009, Peng Yu wrote: Could somebody recommend some textbook how to compute contrast when there are interactions terms? Applied Linear Regression Models (book) mentioned contrast, but I cannot extend it to the case where there are interaction terms. Textbook? Schmextbook! You have the power of R at your fingertips! Use it to explore concepts you are trying to wrap your brain around! df - expand.grid(x1=1:20,x2=factor(letters[1:2])) vanilla - model.matrix(~0+poly(x1,degree=3), df ) matplot(row( vanilla) , vanilla, type='b') inter - model.matrix(~0+poly(x1,degree=3):x2, df ) matplot(row( inter ) , inter, type='b') I don't understand. Where the contrast is? The numbered curves are the terms of polynomial contrasts. See ?poly ?contr.poly and note all( contr.poly(5) == poly(1:5,degree=4) ) BTW, what does 'schmextbook' mean? Well, repeating a word and prepending 'schm' (in place of the initial consonant sound, if any) is a slang idiom for asserting low regard for the idea expressed by the word. As in 'Birthday-Schmirthday' when moaning about getting older: http://www.berkeleydailyplanet.com/issue/2009-01-29/article/32134?headline=First-Person-Birthday-Schmirthday-Whinings-on-Mortality or 'Middle-schmiddle' which expresses low regard for the 'middle' policy, see http://aussiethule.blogspot.com/2006/03/olmerts-middle-schmiddle.html Or 'Nilsson-Schmilsson', a self-deprecating title for an album by Harry Nilsson: http://en.wikipedia.org/wiki/Nilsson_Schmilsson Or 'textbook-schmextbook', in which I express the idea that a textbook really isn't needed. Chuck __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Standard deviation for each element in a set of matrices
Muhammad -
Here's one way:
files = c('File1','File2','File3')
themats = lapply(files,read.table)
ans = matrix(0,3,3)
for(i in 1:3)for(j in 1:3)ans[i,j] = sd(sapply(themats,function(x)x[i,j]))
Here's another
files = c('File1','File2','File3')
themats = lapply(files,read.table)
ans =
outer(1:3,1:3,Vectorize(function(i,j)sd(sapply(themats,function(x)x[i,j]
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Fri, 4 Dec 2009, Muhammad Rahiz wrote:
Hello R-users,
I would like to know how to find the standard deviation for each element in a
set of matrices.
Given the following files,
File1File2File3
1 1 1 4 4 4 7 7 7
2 2 2 5 5 5 8 8 8
3 3 3 6 6 6 9 9 9
I want to calculate the standard deviation for every cell in the file (I'm
using gridded data). The desired output is
Output
3 3 3
3 3 3
3 3 3
Thanks.
Muhammad
--
Muhammad Rahiz | Doctoral Student in Regional Climate Modeling
Climate Research Laboratory, School of Geography the Environment
Oxford University Centre for the Environment
South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194
Mobile: +44 (0)7854-625974
Email: muhammad.ra...@ouce.ox.ac.uk
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[R] Network Graph Add Labels
Hi Everyone, I am new to R and just trying my hand at plotting a network from my dataset. I am trying to teach myself network analysis, so this is probably an easy question. Using the package network, I have successfully plotted my network. I simply want to add labels to my vertices, with the label corresponding to the data I fed into the edgelist. For simplicity sake, my edgelist looks like 1 4 3 4 I want to plot the labels, 1, 3, 4, and so on. Here is my code. library(network) path - path myedges - read.table(path) net - network(myedges) plot(net) Any help will be greatly appreciated. I am not looking to do advanced analysis, just plotting it to get going is all I really need. Many thanks in advance for help and/or suggestions, Brock __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] curve fitting to data
Pascale, If you do want an nls fit with the associated error structure assumptions, check ?SSlogis. fm - nls(y ~ SSlogis(x, Asy, xmid, scal)) summary(fm) xx - seq(123, 248, length = 101) yy - predict(fm, list(x = xx)) plot(x, y) lines(xx, yy) -Peter Ehlers Gabor Grothendieck wrote: A simple y vs log(x) fit seems to work pretty well here: fit - lm(y ~ log(x)) summary(fit) plot(y ~ log(x)) abline(fit) On Fri, Dec 4, 2009 at 9:06 AM, Pascale Weber pascale.we...@wsl.ch wrote: Hi to all This is the first time I am quoting a question and I hope, my question is not too basic... For the following data, I wish to draw a fitted curve. x - c(123,129,141,144,144,145,149,150,158,159,163,174,183,187,242,248) y - c(14.42,26.96,31.3,19.95,36.36,15.4,24.76,35.39,28.07,40.97,26.23,42.83,46.53,14.79,49.18,48.08) If I plot the data, it looks somehow that a logistic function would render good results. My questions are: How do I use nls and/or SSlogis (or other) to fit the curve? How can I see the summary statistics of the fit? How do I finally draw the line to my x,y (untransformed data) plot? Any help would be highly appreciated. Thank you and cheers Pascale -- ..___ Dr. Pascale Weber Swiss Federal Research Institute WSL Zuercherstrasse 111 CH-8903 Birmensdorf Switzerland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Standard deviation for each element in a set of matrices
Hi Muhammad, Load the data from all of the files into an array (probably using a for loop), then call apply on the resulting array: ie ## replace the first line with code to load your data rr - array(c(rep(1:3,3), rep(4:6,3), rep(7:9,3)), c(3,3,3)) apply(rr, c(1,2), sd) [,1] [,2] [,3] [1,]333 [2,]333 [3,]333 --Gray On Fri, Dec 4, 2009 at 11:56 AM, Muhammad Rahiz muhammad.ra...@ouce.ox.ac.uk wrote: Hello R-users, I would like to know how to find the standard deviation for each element in a set of matrices. Given the following files, File1 File2 File3 1 1 1 4 4 4 7 7 7 2 2 2 5 5 5 8 8 8 3 3 3 6 6 6 9 9 9 I want to calculate the standard deviation for every cell in the file (I'm using gridded data). The desired output is Output 3 3 3 3 3 3 3 3 3 Thanks. Muhammad -- Muhammad Rahiz | Doctoral Student in Regional Climate Modeling Climate Research Laboratory, School of Geography the Environment Oxford University Centre for the Environment South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194 Mobile: +44 (0)7854-625974 Email: muhammad.ra...@ouce.ox.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gray Calhoun Assistant Professor of Economics Iowa State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Standard deviation for each element in a set of matrices
On Dec 4, 2009, at 1:27 PM, Gray Calhoun wrote: Hi Muhammad, Load the data from all of the files into an array (probably using a for loop), then call apply on the resulting array: ie I like that idea a lot and it does not need an explicit loop: apply( array(c(File1, File2, File3), dim=c(3,3,3) ) , 1:2, sd) I had come up with this rather messy solution before seeing your much more elegant one: matrix( apply(sapply(list(File1, File2, File3), [), 1,sd), nrow(File1), ncol(File1) ) -- David ## replace the first line with code to load your data rr - array(c(rep(1:3,3), rep(4:6,3), rep(7:9,3)), c(3,3,3)) apply(rr, c(1,2), sd) [,1] [,2] [,3] [1,]333 [2,]333 [3,]333 --Gray On Fri, Dec 4, 2009 at 11:56 AM, Muhammad Rahiz muhammad.ra...@ouce.ox.ac.uk wrote: Hello R-users, I would like to know how to find the standard deviation for each element in a set of matrices. Given the following files, File1File2File3 1 1 1 4 4 4 7 7 7 2 2 2 5 5 5 8 8 8 3 3 3 6 6 6 9 9 9 I want to calculate the standard deviation for every cell in the file (I'm using gridded data). The desired output is Output 3 3 3 3 3 3 3 3 3 Thanks. Muhammad -- Muhammad Rahiz | Doctoral Student in Regional Climate Modeling Climate Research Laboratory, School of Geography the Environment Oxford University Centre for the Environment South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194 Mobile: +44 (0)7854-625974 Email: muhammad.ra...@ouce.ox.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gray Calhoun Assistant Professor of Economics Iowa State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] User's function
Thank you for your reply. But this is not what I want.
For example, I have several variables, like
arg1 - c(1, 2, 3, 5, 6, 6)
arg2 - c(3, 1, 5, 5, 7, 8)
arg3 - c(8, 10, 4, 0, 9, 1)
arg4 - c(11, 22, 30, 5, 61, 22)
…
I just want to bind some of these variables based on the arguments assigned
in myfunction()
myfunction - function(arg1, arg2, arg3, …)
{
x - cbind(arg1, arg2, arg3, …)
}
myfunction(arg1, arg2, arg3, …)
If I assign 2 arguments, the function can bind those two arguments, or if I
assign 3 arguments, the function can bind those three arguments, and so on.
Lisa
baptiste auguie-5 wrote:
Hi,
try ?do.call
do.call(cbind, replicate(3, 1:10, simplify=FALSE))
HTH,
baptiste
2009/12/4 Lisa lisa...@gmail.com:
Hello, All,
I want to write a function to do some works based on the arguments. For
example, bind some variables (arguments) as this:
myfunction - function(arg1, arg2, arg3, …)
{
x - cbind(arg1, arg2, arg3, …)
}
myfunction(arg1, arg2, arg3, …)
The function can automatically determine the number of arguments and bind
them, which means if I assign 2 arguments, the function can bind those
two
arguments, or if I assign 3 arguments, the function can bind those three
arguments, and so on. Here assume the arguments are all continuous
variables
and have the same length. Is it possible?
I would appreciate if some one can help me. Thanks!
Lisa
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[R] options(width=100) ignored on start-up
Dear all Is it normal that R ignores options(width=100) at start-up? Although li...@debian-liv:~$ cat /usr/lib/R/etc/Rprofile.site | grep width options(width = 100) , R will start with [Previously saved workspace restored] options()$width [1] 80 Am I doing something wrong? Liviu sessionInfo() R version 2.10.0 (2009-10-26) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] datasets grid splines graphics stats utils grDevices [8] tcltk methods base other attached packages: [1] fortunes_1.3-6 RcmdrPlugin.HH_1.1-25HH_2.1-32 [4] leaps_2.9multcomp_1.1-2 mvtnorm_0.9-8 [7] lattice_0.17-26 RcmdrPlugin.sos_0.1-0RcmdrPlugin.Export_0.3-0 [10] Hmisc_3.7-0 survival_2.35-7 xtable_1.5-6 [13] Rcmdr_1.5-4 car_1.2-16 relimp_1.0-1 [16] sos_1.1-7brew_1.0-3 hints_1.0.1-1 loaded via a namespace (and not attached): [1] cluster_1.12.1 -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
