Re: [R] Incorrect Dimension
Marcio
Looking at the script (not much explanation re your intention), I think
there is a couple of problems:
1. Not sure if the attached was supposed to be working code, but the
assignment operator is - not =
2. The functions should be defined OUTSIDE the loop, otherwise you are
redefining the function with every iteration
3. I think the reason you wanted to put it inside the loop is that you need
access to the local variables of the loop, i.e. i and j
The way to do that would be to pass i and j as parameters to your
function, for example
g2 - function(gen, j, i) sample (b1, 1, re = T)
4. Your function g1 returns a matrix and function g2 returns a number, these
should ideally both return objects of the same dimension and class. I think
this is what you wanted
g1 - function(gen, j, i) {
if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1]
else if (gen [j, i] == 2) al2 [i, 1] + al2 [i, 1]
else 999
}
5. To make people that respond's life easier, please also provide some code
to initialise variables
Here is working code, which I think does what you wanted:
###
# initialising some variables
loc=200
ind=1000
gen - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
al1 - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
al2 - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
b1 - c(1,2,3)
r2 = 0.7
g - matrix(nrow = ind,ncol = loc)
# defining the functions
g1 - function(gen, j, i) {
if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1]
else if (gen [j, i] == 2) al2 [i, 1] + al2 [i, 1]
else 999
}
g2 - function(gen, j, i) sample (b1, 1, re = T)
# now loop - this can be done more efficiently, but did not want to change
your code too much :-)
for (i in 1 : loc) {
for (j in 1 : ind) {
xx - if (runif(1) = (1 - r2)) g1 else g2
g[j, i] - xx(gen, j, i)
}
}
##
HTH
Schalk Heunis
On Fri, Sep 18, 2009 at 4:50 AM, Marcio Resende mresende...@yahoo.com.brwrote:
I am new in R and i am having trouble here. I´ve already searched in the
list
but hasn´t helped
When i run this script above i get the message Error in gen[j, i] :
incorrect number of dimensions. However gen is 1000x200 (ind x loc) and so
is g
could anybody help me
for (i in 1 : loc) { #loc=200
for (j in 1 : ind) { #ind=1000
g1 = function ( gen ) matrix ( if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1] else if (gen [j,
i] == 2) al2 [i, 1] + al2 [i, 1] else 999, ncol = loc, nrow = ind)
g2 = function ( gen ) sample (b1, 1, re = T) #b1 is 1x3 and came from a
vector 1000X1 (e.g b1 - c(x [1000,1]...)
xx = if (runif (1) = (1 - r2)) g1 else g2
g [j, i] = xx (gen [j, i])#g was already generated as an 0 matrix
(1000x200) and i would like to replace ##by those functios
}
}
Thank you very much
--
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Re: [R] Datetime conversion
On Sep 18, 2009, at 1:03 AM, premmad wrote: I'm relatively new to R .I tried converting the datetime column with values like 01apr1985:00:00:00.000 using strptime(datetime,%d%b%Y).Could anyone help me in this regard .Please reply ASAP i need . You will need to give us a more complete sample of your code, because I don't see a problem: strptime(01apr1985:00:00:00.000,%d%b%Y) [1] 1985-04-01 also works when hours, minutes and seconds format was used: strptime(01apr1985:00:00:00.000,%d%b%Y:%H:%M:%S) [1] 1985-04-01 strptime(01apr1985:00:00:00.000,%d%b%Y:%T) [1] 1985-04-01 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] Incorrect Dimension
On Fri, Sep 18, 2009 at 8:12 AM, Schalk Heunis
schalk.heu...@enerweb.co.zawrote:
Marcio
Looking at the script (not much explanation re your intention), I think
there is a couple of problems:
1. Not sure if the attached was supposed to be working code, but the
assignment operator is - not =
2. The functions should be defined OUTSIDE the loop, otherwise you are
redefining the function with every iteration
3. I think the reason you wanted to put it inside the loop is that you need
access to the local variables of the loop, i.e. i and j
The way to do that would be to pass i and j as parameters to your
function, for example
g2 - function(gen, j, i) sample (b1, 1, re = T)
4. Your function g1 returns a matrix and function g2 returns a number,
these should ideally both return objects of the same dimension and class. I
think this is what you wanted
g1 - function(gen, j, i) {
if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1]
else if (gen [j, i] == 2) al2 [i, 1] + al2 [i, 1]
else 999
}
5. To make people that respond's life easier, please also provide some code
to initialise variables
Here is working code, which I think does what you wanted:
###
# initialising some variables
loc=200
ind=1000
gen - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
al1 - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
al2 - matrix(rbinom(1000*200,1,0.3),nrow = ind,ncol = loc)
b1 - c(1,2,3)
r2 = 0.7
g - matrix(nrow = ind,ncol = loc)
# defining the functions
g1 - function(gen, j, i) {
if (gen[j, i] == 0) al1 [i, 1] + al1 [i, 1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1]
else if (gen [j, i] == 2) al2 [i, 1] + al2 [i, 1]
else 999
}
g2 - function(gen, j, i) sample (b1, 1, re = T)
# now loop - this can be done more efficiently, but did not want to
change your code too much :-)
for (i in 1 : loc) {
for (j in 1 : ind) {
xx - if (runif(1) = (1 - r2)) g1 else g2
g[j, i] - xx(gen, j, i)
}
}
##
HTH
Schalk Heunis
On Fri, Sep 18, 2009 at 4:50 AM, Marcio Resende
mresende...@yahoo.com.brwrote:
I am new in R and i am having trouble here. I´ve already searched in the
list
but hasn´t helped
When i run this script above i get the message Error in gen[j, i] :
incorrect number of dimensions. However gen is 1000x200 (ind x loc) and
so
is g
could anybody help me
for (i in 1 : loc) { #loc=200
for (j in 1 : ind) { #ind=1000
g1 = function ( gen ) matrix ( if (gen[j, i] == 0) al1 [i, 1] + al1 [i,
1]
else if (gen [j, i] == 1) al1 [i, 1] + al2 [i, 1] else if (gen [j,
i] == 2) al2 [i, 1] + al2 [i, 1] else 999, ncol = loc, nrow = ind)
g2 = function ( gen ) sample (b1, 1, re = T) #b1 is 1x3 and came from a
vector 1000X1 (e.g b1 - c(x [1000,1]...)
xx = if (runif (1) = (1 - r2)) g1 else g2
g [j, i] = xx (gen [j, i])#g was already generated as an 0 matrix
(1000x200) and i would like to replace ##by those functios
}
}
Thank you very much
--
View this message in context:
http://www.nabble.com/Incorrect-Dimension-tp25502336p25502336.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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[R] merging data frames with matrix objects when missing cases
Hi, I have faced a problem with the merge() function when trying to merge two data frames that have a common index but the second one does not have cases for all indexes in the first one. With usual variables R fills in the missing cases with NA if all=T is requested. But if the variable is a matrix R seems to insert NA only to the first column of the matrix and fill in the rest of the columns by recycling the values. Here is a toy example: df1-data.frame(a=1:3,X1=I(matrix(1:6,ncol=2))) df2-data.frame(a=1:2,X2=I(matrix(11:14,ncol=2))) merge(df1,df2) a X1.1 X1.2 X2.1 X2.2 1 114 11 13 2 225 12 14 # no all=T, missing cases are dropped merge(df1,df2,all=T) a X1.1 X1.2 X2.1 X2.2 1 114 11 13 2 225 12 14 3 336 NA 13 # X2.1 set to NA correctly but X2.2 set to 13 by recycling. Can I somehow get the behaviour that the third row of the second matrix X2 in the above example would be filled with NA for all columns? None of the merge() options does not seem to provide a solution. regards, Kari __ 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] RCurl and Google Scholar's EndNote references
Hi! Thanks for the code examples. I'll try to elaborate a bit here. If you paste this: http://scholar.google.fi/scholar?hl=fioe=ASCIIq=Frank+Harrell to your browser, you'll get the citations, and each citation lists a link (Import to EndNote) to export a citation in EndNote format. And, if you save this HTML-file, you'll get the links (they contain a string info:) pointing to these EndNote files. For example: a href=/scholar.enw?q=info:U6Gfb4QPVFMJ: scholar.google.com/amp;output=citationamp;hl=enamp;oe=ASCIIamp;oe=ASCIIamp;ct=citationamp;cd=0Import into EndNote/a Now, if you do this in R: curl = getCurlHandle() z = getForm(http://scholar.google.com/scholar;, q ='Frank Harrell', hl = 'en', btnG = 'Search', oe=ASCII, .opts = list(verbose = TRUE), curl = curl) object z does not contain any info:-containing links: grep(info:, z) integer(0) Fortunately there is a related:-link that gives us the same ID (U6Gfb4QPVFMJ) as the info:-link above: substr(z, gregexpr(related:, z)[[1]]+8, gregexpr(related:, z)[[1]]+19) [1] U6Gfb4QPVFMJ Now checking from the Google Scholar page, the correct format for the EndNote query would appear to be: http://scholar.google.fi/scholar.enw?q=info:U6Gfb4QPVFMJ:scholar.google.com/output=citationhl=enoe=ASCIIoe=ASCIIct=citationcd=0 You can copy and paste this link to your browser, and save the EndNote refence as a file. Yet, when this link is constracted in R: getURL(paste(http://scholar.google.fi/scholar.enw?q=info:;, substr(z, gregexpr(related:, z)[[1]]+8, gregexpr(related:, z)[[1]]+19), : scholar.google.com/output=citationhl=enoe=ASCIIoe=ASCIIct=citationcd=0, sep=), curl=curl) the result is an HTML-file containing 403 Forbidden error. But, this type of a functionality seems to be missing from the Google API (thank to Peter Konings for the link): http://code.google.com/p/google-ajax-apis/issues/detail?id=109 - Jarno 2009/9/18 Duncan Temple Lang dun...@wald.ucdavis.edu Hi Jarno You've only told us half the story. You didn't show how you i) performed the original query ii) retrieved the URL you used in subsequent queries But I can suggest two possible problems. a) specifying the cookiejar option tells libcurl where to write the cookies that the particular curl handle has collected during its life. These are written when the curl handle is destroyed. So that wouldn't change the getURL() operation, just change what happens when the curl handle is destroyed. b) You probably mean to use cookiefile rather than cookiejar so that the curl request would read existing cookies from a file. But in that case, how did that file get created with the correct cookies. c) libcurl will collect cookies in a curl handle as it receives them from a server as part of a response. And it will use these in subsequent requests to that server. But you must be using the same curl handle. Different curl handles are entirely independent (unless one is copied from another). So a possible solution may be that you need to do the initial query with the same curl handle So I would try something like curl = getCurlHandle() z = getForm(http://scholar.google.com/scholar;, q ='Frank Harrell', hl = 'en', btnG = 'Search', .opts = list(verbose = TRUE), curl = curl) dd = htmlParse(z) links = getNodeSet(dd, //a...@href]) # do something to identify the link you want tmp = getURL(linkIWant, curl = curl) Note that we are using the same curl object in both requests. This may not do what you want, but if you let us know the details about how you are doing the preceding steps, we should be able to sort things out. D. Jarno Tuimala wrote: Hi! I've performed a Google Scholar Search using a query, let's say Frank Harrell, and parsed the links to the EndNote references from the resulting HTML code. Now I'd like to download all the references automatically. For this, I have tried to use RCurl, but I can't seem to get it working: I always get error code 403 Forbidden from the web server. Initially I tried to do this without using cookies: library(RCurl) getURL( http://scholar.google.fi/scholar.enw?q=info:U6Gfb4QPVFMJ:scholar.google.com/output=citationhl=fioe=ASCIIct=citationcd=0 ) or getURLContent( http://scholar.google.fi/scholar.enw?q=info:U6Gfb4QPVFMJ:scholar.google.com/output=citationhl=fioe=ASCIIct=citationcd=0 ) Error: Forbidden and then with cookies: getURL( http://scholar.google.fi/scholar.enw?q=info:U6Gfb4QPVFMJ:scholar.google.com/output=citationhl=fioe=ASCIIct=citationcd=0 , .opts=list(cookiejar=cookiejar.txt)) But they both consistently fail the same way. What am I doing wrong? sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Finnish_Finland.1252;LC_CTYPE=Finnish_Finland.1252;LC_MONETARY=Finnish_Finland.1252;LC_NUMERIC=C;LC_TIME=Finnish_Finland.1252 attached base packages: [1] stats graphics grDevices
Re: [R] Suppressing script commands in R console when executing long program
Steve. Hi. I have a script composing of more than 1000 lines and would like suppress the R codes from the console when executing the script (to reduce the physical processing time) I have tried options(echo=T) but no luck.. *Q1. Are there any way of suppressing the commands in the R console?* Also, when importing spreadsheet consisting of numbers with 1,000 separator commas (i.e 1 as 10,000) into R and performing basic arithmetic, R does not seem to recognise these separators.. *Q2. Is R capable of reading numbers that are represented with 1,000 separator commas?* ** Many thanks for your expertise in resolving these problems. You can try putting this in your Rprofile options(keep.source=F) This will work in the R cmd but it will not work in the RGui Goodluck! :-) -- Regards, Ishwor Gurung __ 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] define a new family (and a new link function) for gam in gam package
Dear David, I am using gam in gam package (not in mgcv) it is possible to force gam in mgcv to behave like gam in gam package? On Thursday 17 September 2009 23:00:17 David Winsemius wrote: On Sep 17, 2009, at 1:39 PM, Topi, Corrado wrote: Dear R list, is it possible to define a new family (and a new link function) for gam in gam package? How? I read the help for gam, family, gam.model, make.link but I did not find a solution. Wood provides an example for negbin with alternate links in package mgcv; library(mgcv) ?negbin negbin # produces the code -- Corrado Topi Global Climate Change Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.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] problem regarding the data
Hi, This is Meghana Kulkarni. I have a problem regarding the data I am working with. I have a data frame as follows: x V1 V2 V3V10 414 A 416 A 417 A 417 B 418 A 421 A 421 B 421 C 422 A I want to conver this data frame in the following format. x V1 V2 V3V10 414 A 416 A 417 A 417 B 418 A 421 A 421 B 421 C 422 A i.e. I want to insert a blank row after new entry in the 1st column. So that it is easy for me to take readings in next columns when this data frame is printed. It would be great if you could tell me how this can be done. Thank you, Meghana. [[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] Datetime conversion
Thanks for your reply datetime 01OCT1987:00:00:00.000 12APR2004:00:00:00.000 01DEC1987:00:00:00.000 01OCT1975:00:00:00.000 01AUG1979:00:00:00.000 26JUN2003:00:00:00.000 01JAN1900:00:00:00.000 13MAY1998:00:00:00.000 30SEP1998:00:00:00.000 is in the file and i have imported it in to R and created dataframe test with variable datetime for extracting only the datepart from it. test$date-strptime(test$datetime,%d%b%Y) and i got the following error Error in `$-.data.frame`(`*tmp*`, rw, value = list(sec = c(0, 0, 0, : replacement has 9 rows, data has 14 Is there any other way to solve this, please do reply . David Winsemius wrote: On Sep 18, 2009, at 1:03 AM, premmad wrote: I'm relatively new to R .I tried converting the datetime column with values like 01apr1985:00:00:00.000 using strptime(datetime,%d%b%Y).Could anyone help me in this regard .Please reply ASAP i need . You will need to give us a more complete sample of your code, because I don't see a problem: strptime(01apr1985:00:00:00.000,%d%b%Y) [1] 1985-04-01 also works when hours, minutes and seconds format was used: strptime(01apr1985:00:00:00.000,%d%b%Y:%H:%M:%S) [1] 1985-04-01 strptime(01apr1985:00:00:00.000,%d%b%Y:%T) [1] 1985-04-01 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. -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25503907.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] generating unordered combinations
That's brilliant - thanks.
On 17 Sep 2009, at 23:36, William Dunlap wrote:
There is a 1-1 correspondance between your n-sets
consisting of m possible element types (0 through m-1
in your example) and the number of n-subsets of a (n+m-1)-set.
E.g., your example had m=3 and n=3 and subtracting
1:3 from each column of combn(3+3-1,3) gives your result:
t(combn(3+3-1, 3)-(1:3))
[,1] [,2] [,3]
[1,]000
[2,]001
[3,]002
[4,]011
[5,]012
[6,]022
[7,]111
[8,]112
[9,]122
[10,]222
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Dan Halligan
Sent: Thursday, September 17, 2009 1:31 PM
To: r-help@r-project.org
Subject: [R] generating unordered combinations
Hi,
I am trying to generate all unordered combinations of a set of
numbers / characters, and I can only find a (very) clumsy way of
doing
this using expand.grid. For example, all unordered combinations of
the numbers 0, 1, 2 are:
0, 0, 0
0, 0, 1
0, 0, 2
0, 1, 1
0, 1, 2
0, 2, 2
1, 1, 1
1, 1, 2
1, 2, 2
2, 2, 2
(I have not included, for example, 1, 0, 0, since it is equivalent to
0, 0, 1).
I have found a way to generate this data.frame using expand.grid as
follows:
g - expand.grid(c(0,1,2), c(0,1,2), c(0,1,2))
for(i in 1:nrow(g)) {
g[i,] - sort(as.character(g[i,]))
}
o - order(g$Var1, g$Var2, g$Var3)
unique(g[o,]).
This is obviously quite clumsy and hard to generalise to a greater
number of characters, so I'm keen to find any other solutions. Can
anyone suggest a better (more general, quicker) method?
Cheers
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and provide commented, minimal, self-contained, reproducible code.
[R] Help a newbie
Hello, To me as a beginner, every problem looks big. Below is what I was asked to do as part of a code that will solve my problem. I have used read.table to read my data into R and assigned the column names with colnames(dat)- ... . But to go from txt- to the last at the bottom of the table below is what I am unable to do. Could anybody please tell me how to type or arrive at txt- y m d count .. .. in R. Thank you for your attention Ogbos . Here is a more extensive example that shows also how to get date or counts associated to pits/peaks: txt - y m d count 93 02 07 3974.6 93 02 08 3976.7 93 02 09 3955.2 93 02 10 3955.0 93 02 11 3971.8 93 02 12 3972.8 93 02 13 3961.0 93 02 14 3972.8 93 02 15 4008.0 93 02 16 4004.2 93 02 17 3981.2 93 02 18 3996.8 93 02 19 4028.2 93 02 20 4029.5 93 02 21 3953.4 93 02 22 3857.3 93 02 23 3848.3 93 02 24 3869.8 93 02 25 3898.1 93 02 26 3920.5 93 02 27 3936.7 93 02 28 3931.9 con - textConnection(txt) dat - read.table(con, header = TRUE) close(con) dat$date - as.Date(paste(dat$y, dat$m, dat$d), format = %y %m %d) library(pastecs) tp - turnpoints(dat$count) [[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] A stat related question
Can I ask a small stat. related question here? Suppose I have two predictors for a time series processes and accuracy of predictor is measured from MSEs. My question is, if two predictors give same MSE then, necessarily they have to be identical? Can anyone provide me any counter example? Thanks. -- View this message in context: http://www.nabble.com/A-stat-related-question-tp25505618p25505618.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] Help a newbie
I don't understand your question. Where does your data come from in the first place? Is it stored in a file, or is it a result of a previous operation in R, or is it something you need to copy and paste in your script, or ...? the textConnection() construct is often used to make for self-contained examples on this list, but the real-world data are often stored in separate text files (which can be read in read.table() by specifying the filename). HTH, baptiste 2009/9/18 ogbos okike ogbos.ok...@gmail.com: Hello, To me as a beginner, every problem looks big. Below is what I was asked to do as part of a code that will solve my problem. I have used read.table to read my data into R and assigned the column names with colnames(dat)- ... . But to go from txt- to the last at the bottom of the table below is what I am unable to do. Could anybody please tell me how to type or arrive at txt- y m d count .. .. in R. Thank you for your attention Ogbos . Here is a more extensive example that shows also how to get date or counts associated to pits/peaks: txt - y m d count 93 02 07 3974.6 93 02 08 3976.7 93 02 09 3955.2 93 02 10 3955.0 93 02 11 3971.8 93 02 12 3972.8 93 02 13 3961.0 93 02 14 3972.8 93 02 15 4008.0 93 02 16 4004.2 93 02 17 3981.2 93 02 18 3996.8 93 02 19 4028.2 93 02 20 4029.5 93 02 21 3953.4 93 02 22 3857.3 93 02 23 3848.3 93 02 24 3869.8 93 02 25 3898.1 93 02 26 3920.5 93 02 27 3936.7 93 02 28 3931.9 con - textConnection(txt) dat - read.table(con, header = TRUE) close(con) dat$date - as.Date(paste(dat$y, dat$m, dat$d), format = %y %m %d) library(pastecs) tp - turnpoints(dat$count) [[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] problem regarding the data
On 09/18/2009 04:10 PM, meghana kulkarni wrote:
Hi,
This is Meghana Kulkarni.
I have a problem regarding the data I am working with.
I have a data frame as follows:
x
V1 V2 V3V10
414 A
416 A
417 A
417 B
418 A
421 A
421 B
421 C
422 A
I want to conver this data frame in the following format.
x
V1 V2 V3V10
414 A
416 A
417 A
417 B
418 A
421 A
421 B
421 C
422 A
i.e. I want to insert a blank row after new entry in the 1st column. So that
it is easy for me to take readings in next columns when this data frame is
printed.
It would be great if you could tell me how this can be done.
Hi Meghana,
Try this:
spaceBlocks-function(x,spacevar) {
thisblock-x[1,spacevar]
for(row in 1:dim(x)[1]) {
if(thisblock != x[row,spacevar]) cat(\n)
for(col in 1:length(unlist(x[row,])))
cat(as.character(x[row,col]), )
cat(\n)
thisblock-x[row,spacevar]
}
}
Jim
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Re: [R] Datetime conversion
Seems to work alright for me. datetime -c( 01OCT1987:00:00:00.000, 12APR2004:00:00:00.000, 01DEC1987:00:00:00.000, 01OCT1975:00:00:00.000, 01AUG1979:00:00:00.000, 26JUN2003:00:00:00.000, 01JAN1900:00:00:00.000, 13MAY1998:00:00:00.000, 30SEP1998:00:00:00.000) date-strptime(datetime,%d%b%Y) date [1] 1987-10-01 2004-04-12 1987-12-01 1975-10-01 1979-08-01 2003-06-26 [7] 1900-01-01 1998-05-13 1998-09-30 cheers, -Girish premmad wrote: Thanks for your reply datetime 01OCT1987:00:00:00.000 12APR2004:00:00:00.000 01DEC1987:00:00:00.000 01OCT1975:00:00:00.000 01AUG1979:00:00:00.000 26JUN2003:00:00:00.000 01JAN1900:00:00:00.000 13MAY1998:00:00:00.000 30SEP1998:00:00:00.000 is in the test file and i have imported it in to R and created dataframe test with variable datetime for extracting only the datepart from it. By using the following function test$date-strptime(test$datetime,%d%b%Y) and i got the following error Error in `$-.data.frame`(`*tmp*`, rw, value = list(sec = c(0, 0, 0, : replacement has 9 rows, data has 14 Is there any other way to solve this, please do reply . David Winsemius wrote: On Sep 18, 2009, at 1:03 AM, premmad wrote: I'm relatively new to R .I tried converting the datetime column with values like 01apr1985:00:00:00.000 using strptime(datetime,%d%b%Y).Could anyone help me in this regard .Please reply ASAP i need . You will need to give us a more complete sample of your code, because I don't see a problem: strptime(01apr1985:00:00:00.000,%d%b%Y) [1] 1985-04-01 also works when hours, minutes and seconds format was used: strptime(01apr1985:00:00:00.000,%d%b%Y:%H:%M:%S) [1] 1985-04-01 strptime(01apr1985:00:00:00.000,%d%b%Y:%T) [1] 1985-04-01 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. -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25505915.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] Lattice barplot not wokring in for-loop?
Dear List-Members,
I am plotting a barplot with the lattice package. The code works, but
when I execute the same code in a for-loop
no plot is shown. Can't figure what the problem is.
(Maybe I am missing something here, but I tried it with plot device
pdf, calling windows() or X11(), testing on windows and linux, etc.)
INFO: R version 2.9.1 (2009-06-26) using Windows/RGui
require(lattice)
for( z in 1:3) {
## plot works when executed alone,
## however in a for loop no plot is shown...
barchart(yield ~ variety | site, data = barley,
groups = year, layout = c(1,6), stack = TRUE,
auto.key = list(points = FALSE, rectangles = TRUE, space = right),
ylab = Barley Yield (bushels/acre),
scales = list(x = list(rot = 45)))
}
I can't program any further without solving this.
So, thanks! Really!
Steve
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Re: [R] Lattice barplot not wokring in for-loop?
On 09/18/2009 11:44 AM, stvienna wiener wrote:
Dear List-Members,
I am plotting a barplot with the lattice package. The code works, but
when I execute the same code in a for-loop
no plot is shown. Can't figure what the problem is.
(Maybe I am missing something here, but I tried it with plot device
pdf, calling windows() or X11(), testing on windows and linux, etc.)
INFO: R version 2.9.1 (2009-06-26) using Windows/RGui
require(lattice)
for( z in 1:3) {
## plot works when executed alone,
## however in a for loop no plot is shown...
barchart(yield ~ variety | site, data = barley,
groups = year, layout = c(1,6), stack = TRUE,
auto.key = list(points = FALSE, rectangles = TRUE, space = right),
ylab = Barley Yield (bushels/acre),
scales = list(x = list(rot = 45)))
}
I can't program any further without solving this.
So, thanks! Really!
Steve
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
--
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Re: [R] A stat related question
Let's assume you have just three observations, and x-- = 1:3 for your observations. Predictor 1:y = x^2 Predictor 2:y = 1 if x=1 y = 4 if x=2 y = 9 if x=3 y = 0 elsewhere These predictors are obviously not the same, but will give the same Mean Squared Error for your data (whatever your observed y-values are). This should suffice as a counter example. Or did I misunderstand your question? HTH, Michael -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of RON70 Sent: Freitag, 18. September 2009 11:23 To: r-help@r-project.org Subject: [R] A stat related question Can I ask a small stat. related question here? Suppose I have two predictors for a time series processes and accuracy of predictor is measured from MSEs. My question is, if two predictors give same MSE then, necessarily they have to be identical? Can anyone provide me any counter example? Thanks. -- View this message in context: http://www.nabble.com/A-stat-related-question-tp25505618p25505618.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-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] SVM
Thank you again for your reply! What I would like to do is to class my sample into two group (0,1). I am not sure which method to apply and whether the svm is the correct one! However, when I apply the below R code I get two group the samples in TRUE and FALSE. Can I take this result to put TRUE samples in group A and FALSE samples in group B? Best wishes, Samuel PS: I will not give up to understand statistics! --- On Thu, 9/17/09, Steve Lianoglou mailinglist.honey...@gmail.com wrote: From: Steve Lianoglou mailinglist.honey...@gmail.com Subject: Re: [R] SVM To: Samuel Okoye samu...@yahoo.com Cc: r-h...@stat.math.ethz.ch Date: Thursday, September 17, 2009, 2:47 PM Hi, On Sep 17, 2009, at 5:34 PM, Samuel Okoye wrote: Thank you for your reply! Yes, I am using the svm and I do not have new data (how do you create new data?), all I have these 12 samples which I want to classify (predict) these into two group so that I do have six sample in each group? I'm not really sure where to begin ... what are you trying to do, exactly? Why do you think you want to build an SVM? What do you expect it to do for you? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]] __ 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] Datetime conversion
See if this is what you are looking for: dt - as.data.frame(datetime) date-strptime(as.character(dt$datetime),%d%b%Y) date [1] 1987-10-01 2004-04-12 1987-12-01 1975-10-01 1979-08-01 2003-06-26 [7] 1900-01-01 1998-05-13 1998-09-30 cheers, -Girish premmad wrote: Girish it works for me also if its a vector.I have problem if the data is stored as dataframe(rows and columns) please do help me in this Girish A.R. wrote: Seems to work alright for me. datetime -c( 01OCT1987:00:00:00.000, 12APR2004:00:00:00.000, 01DEC1987:00:00:00.000, 01OCT1975:00:00:00.000, 01AUG1979:00:00:00.000, 26JUN2003:00:00:00.000, 01JAN1900:00:00:00.000, 13MAY1998:00:00:00.000, 30SEP1998:00:00:00.000) date-strptime(datetime,%d%b%Y) date [1] 1987-10-01 2004-04-12 1987-12-01 1975-10-01 1979-08-01 2003-06-26 [7] 1900-01-01 1998-05-13 1998-09-30 cheers, -Girish premmad wrote: Thanks for your reply datetime 01OCT1987:00:00:00.000 12APR2004:00:00:00.000 01DEC1987:00:00:00.000 01OCT1975:00:00:00.000 01AUG1979:00:00:00.000 26JUN2003:00:00:00.000 01JAN1900:00:00:00.000 13MAY1998:00:00:00.000 30SEP1998:00:00:00.000 is in the test file and i have imported it in to R and created dataframe test with variable datetime for extracting only the datepart from it. By using the following function test$date-strptime(test$datetime,%d%b%Y) and i got the following error Error in `$-.data.frame`(`*tmp*`, rw, value = list(sec = c(0, 0, 0, : replacement has 9 rows, data has 14 Is there any other way to solve this, please do reply . David Winsemius wrote: On Sep 18, 2009, at 1:03 AM, premmad wrote: I'm relatively new to R .I tried converting the datetime column with values like 01apr1985:00:00:00.000 using strptime(datetime,%d%b%Y).Could anyone help me in this regard .Please reply ASAP i need . You will need to give us a more complete sample of your code, because I don't see a problem: strptime(01apr1985:00:00:00.000,%d%b%Y) [1] 1985-04-01 also works when hours, minutes and seconds format was used: strptime(01apr1985:00:00:00.000,%d%b%Y:%H:%M:%S) [1] 1985-04-01 strptime(01apr1985:00:00:00.000,%d%b%Y:%T) [1] 1985-04-01 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. -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506234.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] some irritation with heteroskedasticity testing
Dear all, Trying to test for heteroskedasticity I tried several test from the car package respectively lmtest. Now that they produce rather different results i am somewhat clueless how to deal with it. Here is what I did: 1. I plotted fitted.values vs residuals and somewhat intuitively believe, it isn't really increasing... 2. further I ran the following tests bptest (studentized and non-studentized), gqtest, ncv.test with the following results: ncv: Non-constant Variance Score Test Variance formula: ~ fitted.values Chisquare = 13.87429Df = 1 p = 0.00194580 Goldfeld-Quandt test data: reg GQ = 1.7092, df1 = 327, df2 = 327, p-value = 7.93e-07 studentized Breusch-Pagan test data: reg BP = 15.8291, df = 23, p-value = 0.92 Breusch-Pagan test data: reg BP = 377.5604, df = 23, p-value 2.8e-18 bptest and gq.test sport pretty straight forward examples saying the H0 = homoskedasticity. The ncv.test clarifies the same in its description. Thus the studentized bptest appears to be the only one to support my first intuition from the graphical solution. I am really disturbed what to do know and how to interpret my results... Can someone lead the way ? thx in advance matt __ 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] Errors and line numbers in scripts?
ws wrote: Is there a way to have R return the line number in a script when it errors out? I call my script like: $ R --vanilla script.R output.txt I seem to remember a long discussion about this at some point, but I can't remember the outcome. The current development version returns much more information about error locations. I don't know if it will handle this case (R doesn't get told the filename in case of input redirection, for example). Generally the goal is to report error lines during interactive use, batch use is assumed to already be debugged. 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.
Re: [R] Suppressing script commands in R console when executing long program
Ishwor wrote: Steve. Hi. I have a script composing of more than 1000 lines and would like suppress the R codes from the console when executing the script (to reduce the physical processing time) I have tried options(echo=T) but no luck.. *Q1. Are there any way of suppressing the commands in the R console?* Also, when importing spreadsheet consisting of numbers with 1,000 separator commas (i.e 1 as 10,000) into R and performing basic arithmetic, R does not seem to recognise these separators.. *Q2. Is R capable of reading numbers that are represented with 1,000 separator commas?* ** Many thanks for your expertise in resolving these problems. You can try putting this in your Rprofile options(keep.source=F) This will work in the R cmd but it will not work in the RGui The syntax is wrong there: that should be options(keep.source=F). But I don't think it addresses either question. The normal way to execute a script from the console is source(filename.R), which by default doesn't echo. I don't know the answer to Q2, but would guess that the answer is yes; just not sure if someone has already written the function to remove the commas. Duncan Murdoch Goodluck! :-) __ 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] Datetime conversion
I'm not able to replicate your problem. Here's what I get. See if this is what you want: dt$date-strptime(as.character(dt$datetime),%d%b%Y) dt datetime date 1 01OCT1987:00:00:00.000 1987-10-01 2 12APR2004:00:00:00.000 2004-04-12 3 01DEC1987:00:00:00.000 1987-12-01 4 01OCT1975:00:00:00.000 1975-10-01 5 01AUG1979:00:00:00.000 1979-08-01 6 26JUN2003:00:00:00.000 2003-06-26 7 01JAN1900:00:00:00.000 1900-01-01 8 13MAY1998:00:00:00.000 1998-05-13 9 30SEP1998:00:00:00.000 1998-09-30 cheers, -Girish === premmad wrote: It works but what i need is the result also as a column . I tried using the following code . dt$new-strptime(as.character(dt$datetime),%d%b%Y. It shows the following error Error in `$-.data.frame`(`*tmp*`, Sa_dt, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14. Please help me to solve this -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506493.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Datetime conversion
Girish it works for me also if its a vector.I have problem if the data is stored as dataframe(rows and columns) please do help me in this Girish A.R. wrote: Seems to work alright for me. datetime -c( 01OCT1987:00:00:00.000, 12APR2004:00:00:00.000, 01DEC1987:00:00:00.000, 01OCT1975:00:00:00.000, 01AUG1979:00:00:00.000, 26JUN2003:00:00:00.000, 01JAN1900:00:00:00.000, 13MAY1998:00:00:00.000, 30SEP1998:00:00:00.000) date-strptime(datetime,%d%b%Y) date [1] 1987-10-01 2004-04-12 1987-12-01 1975-10-01 1979-08-01 2003-06-26 [7] 1900-01-01 1998-05-13 1998-09-30 cheers, -Girish premmad wrote: Thanks for your reply datetime 01OCT1987:00:00:00.000 12APR2004:00:00:00.000 01DEC1987:00:00:00.000 01OCT1975:00:00:00.000 01AUG1979:00:00:00.000 26JUN2003:00:00:00.000 01JAN1900:00:00:00.000 13MAY1998:00:00:00.000 30SEP1998:00:00:00.000 is in the test file and i have imported it in to R and created dataframe test with variable datetime for extracting only the datepart from it. By using the following function test$date-strptime(test$datetime,%d%b%Y) and i got the following error Error in `$-.data.frame`(`*tmp*`, rw, value = list(sec = c(0, 0, 0, : replacement has 9 rows, data has 14 Is there any other way to solve this, please do reply . David Winsemius wrote: On Sep 18, 2009, at 1:03 AM, premmad wrote: I'm relatively new to R .I tried converting the datetime column with values like 01apr1985:00:00:00.000 using strptime(datetime,%d%b%Y).Could anyone help me in this regard .Please reply ASAP i need . You will need to give us a more complete sample of your code, because I don't see a problem: strptime(01apr1985:00:00:00.000,%d%b%Y) [1] 1985-04-01 also works when hours, minutes and seconds format was used: strptime(01apr1985:00:00:00.000,%d%b%Y:%H:%M:%S) [1] 1985-04-01 strptime(01apr1985:00:00:00.000,%d%b%Y:%T) [1] 1985-04-01 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. -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25505976.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] Maximum No.of code in R
I tried running 50 lines of ifelse statement in R and the system says context stack overflow at 50 line.Is it the limitation of R or is there any way around that can be done to overcome this.Thanks -- View this message in context: http://www.nabble.com/Maximum-No.of-code-in-R-tp25506024p25506024.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] Datetime conversion
It works but what i need is the result also as a column . I tried using the following code . dt$new-strptime(as.character(dt$datetime),%d%b%Y. It shows the following error Error in `$-.data.frame`(`*tmp*`, Sa_dt, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14. Please help me to solve this -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506438.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Datetime conversion
The same what you have worked out is my need but i'm getting the following error Error in `$-.data.frame`(`*tmp*`, date, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14 Please help me in this -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506705.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] Suppressing script commands in R console when executing long program
On Fri, Sep 18, 2009 at 03:46:27PM +1000, Steven Kang wrote:
*Q1. Are there any way of suppressing the commands in the R console?*
I think this has been answered already.
*Q2. Is R capable of reading numbers that are represented with 1,000
separator commas?*
I am not aware of an option to read.table and freinds that does this
but you can recover easily:
foo - read.delim('foo.tbl')
foo
A B
1 1 12,300
2 2 256,001.01
3 3 900.1
4 4 80
str(foo)
'data.frame': 4 obs. of 2 variables:
$ A: int 1 2 3 4
$ B: Factor w/ 4 levels 12,300,256,001.01,..: 1 2 4 3
foo$B - as.numeric(sub(',', '', as.character(foo$B)))
foo
AB
1 1 12300.0
2 2 256001.0
3 3900.1
4 4 80.0
str(foo)
'data.frame': 4 obs. of 2 variables:
$ A: int 1 2 3 4
$ B: num 12300 256001 900 80
cu
Philipp
--
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://webclu.bio.wzw.tum.de/~pagel/
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Re: [R] Datetime conversion
The same what you have worked out is my need but i'm getting the following error Error in `$-.data.frame`(`*tmp*`, date, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14 Please give more detail about what you did. This error is certainly not from the example used in previous postings, as the data fram eused there has 9 rows, not 14. Without the details (code) on what you did its all guesswork. Perhaps you are mixing two data.frames of differnt shape or ... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Datetime conversion
Can you post a reproducible code snippet, along with the output/error messages, and the output of sessionInfo(). That way other folks on R-help may be able to offer help. Here's myl output of sessionInfo() sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid splines stats graphics grDevices utils datasets methods [9] base other attached packages: [1] RWinEdt_1.8-1 gtools_2.6.1 gmodels_2.15.0 lme4_0.999375-31 [5] Matrix_0.999375-30 lattice_0.17-25ggplot2_0.8.3 reshape_0.8.3 [9] plyr_0.1.9 proto_0.3-8Design_2.2-0 Hmisc_3.7-0 [13] survival_2.35-4doBy_4.0.1 loaded via a namespace (and not attached): [1] cluster_1.12.0 Formula_0.1-3gdata_2.6.1 kinship_1.1.0-23 MASS_7.2-48 [6] nlme_3.1-93 plm_1.1-4sandwich_2.2-1 cheers, -Girish === premmad wrote: The same what you have worked out is my need but i'm getting the following error Error in `$-.data.frame`(`*tmp*`, date, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14 Please help me in this -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506979.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] Suppressing script commands in R console when executing long program
On Fri, Sep 18, 2009 at 12:59:16PM +0200, Philipp Pagel wrote:
foo$B - as.numeric(sub(',', '', as.character(foo$B)))
Thinking about it some more, you should use gsub instead of sub here.
Otherwise only the first occurrence of the thousands separator will be
removed.
cu
Philipp
--
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://webclu.bio.wzw.tum.de/~pagel/
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[R] Error: length(f1) == length(f2) is not TRUE
Dear R users, I am trying to fit an lmer model with only random effects which is giving me the following error: Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used I am trying to extract variance components for a phenotype 'peg.no', using the variable 'family' and a marker column 'P1L55' (which is categorical and has 2 levels- 0 and 1), as random effects. There are no fixed effects. The code I used is as follows: vc-read.table(...) vcdf-data.frame(vc) colms-(vc)[4:13] ##these are the markers lapply(colms,factor) try(fit-lmer(peg.no~1 + (1|family/P1L55), na.action=na.include, data=vcdf)) I thought that putting the data into a dataframe would help, along with the na.exclude command, because there is a lot of missing data in patches which I have replaced with NA's, but I don't know how to fix this error at all. Its a bit urgent, and any help is hugely appreciated. The data files are at: http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.html (excel) http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html (txt) Cheers, Aditi -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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] Maximum No.of code in R
On 9/18/2009 5:49 AM, premmad wrote: I tried running 50 lines of ifelse statement in R and the system says context stack overflow at 50 line.Is it the limitation of R or is there any way around that can be done to overcome this.Thanks You can always break it up into multiple lines. For example, the following are equivalent if we ignore the presence of the temp variable in the second case. x - ifelse(a, b, ifelse(c, d, e)) and temp - ifelse(c, d, e) x - ifelse(a, b, temp) 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.
Re: [R] lattice: How to display no box but only a y-axis on the left + Thicker lines
1.) How do I make lattice (e.g. barchart) to not draw a box but only a y-axis on the left hand side so that the plot looks like barplot with default settings? Does nobody have an idea? Or is the solution that obvious? __ 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] Datetime conversion
Your problem is that 'strptime' returns an object of POSIXlt type which is 9 elements; what you what is: ( you need a POSIXct type) dt$new-as.POSIXct(strptime(as.character(dt$datetime),%d%b%Y)) On Fri, Sep 18, 2009 at 6:26 AM, premmad mtechp...@gmail.com wrote: It works but what i need is the result also as a column . I tried using the following code . dt$new-strptime(as.character(dt$datetime),%d%b%Y. It shows the following error Error in `$-.data.frame`(`*tmp*`, Sa_dt, value = list(sec = c(0, 0, : replacement has 9 rows, data has 14. Please help me to solve this -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25506438.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] some irritation with heteroskedasticity testing
Dear matt, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Bunny, lautloscrew.com Sent: September-18-09 6:18 AM To: r-help@r-project.org Subject: [R] some irritation with heteroskedasticity testing Dear all, Trying to test for heteroskedasticity I tried several test from the car package respectively lmtest. Now that they produce rather different results i am somewhat clueless how to deal with it. Here is what I did: 1. I plotted fitted.values vs residuals and somewhat intuitively believe, it isn't really increasing... It's often difficult to judge whether the spread of the residuals changes with the fitted values; you might alternatively try to visualize the fit with the spread.level.plot() function in the car package. 2. further I ran the following tests bptest (studentized and non-studentized), gqtest, ncv.test with the following results: ncv: Non-constant Variance Score Test Variance formula: ~ fitted.values Chisquare = 13.87429Df = 1 p = 0.00194580 Goldfeld-Quandt test data: reg GQ = 1.7092, df1 = 327, df2 = 327, p-value = 7.93e-07 You don't show the function call to gqtest(). If you specified order.by=fitted(reg), then the two tests are similar, except that gqtest() by default uses a one-sided alternative hypothesis. If you used the default for order.by, then the test is probably nonsense. Both tests suggest heteroscedasticity. studentized Breusch-Pagan test data: reg BP = 15.8291, df = 23, p-value = 0.92 Breusch-Pagan test data: reg BP = 377.5604, df = 23, p-value 2.8e-18 bp.test() performs the same score test as ncv.test(), except that the default alternative hypothesis is different -- in bp.test() that the error variance is a function of a linear combination of the regressors and in ncv.test() that the error variance is a function of the fitted values (i.e., a *particular* linear combination of regressors). Testing against the fitted values with 1 df will have greater power if this is the real pattern of heteroscedasticity. That the chisquare is much greater for the general BP test suggests that the pattern is more complex. The studentized BP test is robust against non-normal errors. That you would get such a dramatically different result is surprising and would lead me to guess that the residual distribution is very heavy-tailed, perhaps with some bad outliers. Without the data, it's not possible to know. Regards, John bptest and gq.test sport pretty straight forward examples saying the H0 = homoskedasticity. The ncv.test clarifies the same in its description. Thus the studentized bptest appears to be the only one to support my first intuition from the graphical solution. I am really disturbed what to do know and how to interpret my results... Can someone lead the way ? thx in advance matt __ 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] Linear objective function with Quadratic constraints
I am new to R and I want to solve this following problem using R. My Objective function is a linear function with Quadratic constraints.I want to know how to solve this problem and which package will be helpful for me for solving such type of problems.Moreover my one constraint is linear and equality constraints and another quadratic constraint is inequality constraint. How to solve this problem ? Plz help Me Min z = 5 *x1 + 9*x2 + 7.15*x3 + 3.5 *x4 subject to following constraints. x1 + x2 + x3 + x4 = 9 x1 + x4 =6.55 x3(x3 - 3.6) = 0 -- View this message in context: http://www.nabble.com/Linear-objective-function-with-Quadratic-constraints-tp25507032p25507032.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] Datetime conversion
Thanks .I tried its working but when i tried to view the dataframe i got the following error Error in edit.data.frame(get(subx, envir = parent), title = subx, ...) : can only handle vector and factor elements -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25507734.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] Datetime conversion
Sorry for confusing you all with my inexperienced posting . I tried as u said if you have 9 rows in the data it is working fine but please try out the same example as you have suggested earlier with morethan 9 rows. I tried it as following datetime -c( + 01OCT1987:00:00:00.000, + 12APR2004:00:00:00.000, + 01DEC1987:00:00:00.000, + 01OCT1975:00:00:00.000, + 01AUG1979:00:00:00.000, + 26JUN2003:00:00:00.000, + 01JAN1900:00:00:00.000, + 13MAY1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000) dt - as.data.frame(datetime) dt$date-strptime(as.character(dt$datetime),%d%b%Y) and got the following error : Error in `$-.data.frame`(`*tmp*`, date, value = list(sec = c(0, 0, : replacement has 9 rows, data has 12. MY session info details are as follows: R version 2.9.2 (2009-08-24) 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] tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] sqldf_0-1.5 gsubfn_0.5-0proto_0.3-8 RSQLite_0.7-2 DBI_0.2-4 lattice_0.17-25 chron_2.3-30 loaded via a namespace (and not attached): [1] grid_2.9.2 tools_2.9.2 -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25507205.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] matching pairs regardless of order
Dear list, I am using match() to match pairs of locations, e.g. trip=loc1,loc2 from a list of such pairs, e.g. list=(loc1,loc2, loc1,loc3, loc2,loc3,loc2,loc1). In this example match() will match trip with the first element of list, but not the 4th, because the order is reversed. How can I get a match with both ? Many thanks for any help, Juliane __ 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] Maximum No.of code in R
Thanks for the reply and it is useful.What i want to know here is i'm going to try and write an automated procedure using batch processing in R by the way input of the next step is going to be this steps output .so one will not able to predict the lines please also do answer in taking consideration the above mentioned criteria in to consideration.Once again thanks for the help this community is providing actively -- View this message in context: http://www.nabble.com/Maximum-No.of-code-in-R-tp25506024p25507509.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] SVM
Thank you again for your reply! What I would like to do is to class my sample into two group (0,1). I am not sure which method to apply and whether the svm is the correct one! However, when I apply the below R code I get two group the samples in TRUE and FALSE. Can I take this result to put TRUE samples in group A and FALSE samples in group B? The SVM packages in R implement SVMs that need to be trained in a supervised setting, which means that you have to have data *with* labels. Is this what you have? The SVM will look at the features of each data point and its label, and return you a model that can look at *similar* data and predict its label (+1 or -1). Since you *already know* the labels of your data points, you can give the SVM some of your data that it didn't use for training and see how well it can predict their labels. Lastly, I'm not sure where FALSE and TRUE are coming from, sorry. PS: I will not give up to understand statistics! You shouldn't give up, but unfortunately a mailing list isn't the best place to learn statistics (or anything really) from. If you're interested in really learning more about SVMs and other machine learning approaches, you can watch Andrew Ng's intro to machine learning classes online. The relevant links are at the top of this page: http://ai.stanford.edu/~ang/courses.html -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-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] Updating R-code in own package
Hey everybody! We have created our own package, and need to do some corrections in the R-code of one of the function included in the package. How can I do that. I have read a manual how to create an R package, but I can't find anything about updating R-code in the package. Best regards, Katrine [[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] Compare a group of line slopes
The test that a slope differs by group is a test that the variable*group interaction equals zero (overall test). Maybe searching post-hoc comparisons in regression will give you some leads. On Tue, Sep 15, 2009 at 10:57 AM, Jun Shen jun.shen...@gmail.com wrote: Hi, all, I am thinking to compare a group of slopes from regression lines to see if they are different overall, and then make specific comparisons between groups. How can I achieve that in R? I searched the archives and there are only discussions about comparing two lines a time. Thanks. A sample data set is like the following. I would like to compare the regression slopes between the five groups. Thanks for your help. data-data.frame(x=rep(1:10,5),y=rnorm(50),group=rep(1:5,each=10)) Jun Shen [[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] Updating R-code in own package
Hi, On Sep 18, 2009, at 8:31 AM, Katrine Damgaard wrote: Hey everybody! We have created our own package, and need to do some corrections in the R-code of one of the function included in the package. How can I do that. I have read a manual how to create an R package, but I can't find anything about updating R-code in the package. I'm pretty sure the only correct thing to do is just fix the code in your package's source tree then reinstall the package wholesale to replace the bad code with the fixed 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-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: How to display no box but only a y-axis on the left + Thicker lines
No box is easy, bwplot(y~x, data=data.frame(y=rnorm(10),x=sample(letters[1:3],10,repl=T)), par.settings=list(axis.line=list(col=NA))) but that seems to remove all axis lines and ticks as well. You may have to define a custom panel.axis() function. An alternative is to use grid.remove() to remove the frame, bwplot(y~x, data=data.frame(y=rnorm(10),x=sample(letters[1:3],10,repl=T))) grid.remove(rect,grep=T,global=TRUE) HTH, baptiste 2009/9/18 lith minil...@gmail.com: 1.) How do I make lattice (e.g. barchart) to not draw a box but only a y-axis on the left hand side so that the plot looks like barplot with default settings? Does nobody have an idea? Or is the solution that obvious? __ 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] msm package - interpreting categorical results
Hi, I have a simple question on interpreting output results from your msm package in R when using a categorical model with hcovariates i.e. covariates on the parameters of the emission model. The interpretation is straightforward for normal distributions, etc. but when using categorical distributions I get results like these: prob P(1)0.8597657482 P(2)0.0001943636 P(3)0.0042761544 P(4)0.0002781397 P(5)0.0005549986 P(6)0.1349305955 DC_MAX_POSSIBLE_L1 0.4804758829 DC_MAX_POSSIBLE_L1 0.4216246143 DC_MAX_POSSIBLE_L1 -0.0552074714 DC_MAX_POSSIBLE_L1 0.1899573843 DC_MAX_POSSIBLE_L1 0.0963140485 at first glance I thought that 1 unit of DC_MAX_POSSIBLE_L1 was responsible for increasing the probability of outcome of factor 2 (P(2)) by 0.48 but that does not make sense given that DC_MAX_POSSIBLE_L1 is an integer ranging from -20 to +20. How do I interpret the results ? the original call was: msm_pc10 = msm( OUTCOME ~ TIME, data = myFrame, qmatrix = qmatrix ,hmodel = list (hmmDist_1,hmmDist_2) ,hcovariates = list ( ~ 1 + DC_MAX_POSSIBLE_L1, ~ 1 + DC_MAX_POSSIBLE_L1) ,control = list(reltol = 1e-03) ,method = BFGS, use.deriv = FALSE, hessian=FALSE, analyticp=FALSE , est.initprobs=TRUE ); with hmmDist_1 and hmmDist_2 being hmmCat distributions as specified in the msm manual. Thanks! -- This message is for the named person(s) use only. It may contain confidential proprietary or legally privileged information. No confidentiality or privilege is waived or lost by any mistransmission. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. You must not, directly or indirectly use, disclose, distribute, print, or copy any part of this message if you are not the intended recipient. Allston Trading LLC and its subsidiaries and affiliates each reserve the right to monitor all e-mail communications through its networks. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorized to state them to be the views of any such entity. -- [[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] Missing link(s) in documentation object
Hi,
I want to cross-reference from the documentation of pkg1 to pkg2, which
is imported in the NAMESPACE of pkg1, and under Depends in DESCRIPTION
of pkg1. According to Writing R extensions, this can be done by:
\code{\link{foo}}
when foo is an aliased function in the documentation of pkg2. This works
as it should when I install the package, but when I run R CMD check
pgk1, I get a warning:
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'fooPkg1.Rd'
foo
I have tried to change the link to
\code{\link[pkg2]{foo}}
\code{\link[pkg:pkg2]{foo}}
None of these works, the first gives a link that leads to an error page,
and the second one gives a link that does not work at all. I assume this
is as it should be; foo.Rd does not exist. However, R CMD check does not
complain about any of these links...
Why does R CMD check warn me against links that work? I think pkg2 is
not on the search path when looking for cross-references, but why? R CMD
check continues to run after the warning without any complaints, and all
tests rely on pkg2. I am quite sure there is something simple that I
have overlooked, but cannot figure out what it is.
Best wishes,
Jon
Platform etc:
XP SP3, R 2.9-2, Rtools210 (the problem was also there before upgrading
from R 2.9-1 and Rtools29 )
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Re: [R] matching pairs regardless of order
Try this: x[mapply(function(x, y)all(x %in% y), strsplit(x, ','), strsplit(trip, ','))] On Fri, Sep 18, 2009 at 9:47 AM, Juliane Struve juliane_str...@yahoo.co.uk wrote: Dear list, I am using match() to match pairs of locations, e.g. trip=loc1,loc2 from a list of such pairs, e.g. list=(loc1,loc2, loc1,loc3, loc2,loc3,loc2,loc1). In this example match() will match trip with the first element of list, but not the 4th, because the order is reversed. How can I get a match with both ? Many thanks for any help, Juliane __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] as.POSIXct(as.Date()) independent of timezone
Dear R users, I am struggling a bit with the converting dates to full POSIX timestamps, in particular, I would like to somehow force the timezone to be local, i.e. the output of as.POSIXct(as.Date(2008-07-01)) should always be equal to 2008-07-01 00:00:00, is that achievable ? I tried to set the origin and the timezone, neither of which seems to make a difference. On my Mac Book Pro (R version 2.9.1) which is set to Eastern US time zone, I obtain the shifted result: as.POSIXct(as.Date(2008-07-01)) [1] 2008-06-30 20:00:00 EDT And e.g. as.POSIXct( Sys.Date()) [1] 2009-09-17 20:00:00 EDT Sys.time() [1] 2009-09-18 10:10:48 EDT Any help would make life simpler for me. Thanks, Markus [[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] Within-group correlation confidence intervals
I'm trying to obtain within-group correlations on a subset of variables. I first selected my variables using the following command: mydata$x-mydata[c(iq,education,achievement)] I'd like to look at correlations among those variables separately for men and women. My gender variable in mydata is coded 1 (women) and 0 (men). I have successfully used the following to get within group correlations and p values: by(x,gender,function(x) rcorr(as.matrix(x))) However, I'm also interested in getting confidence intervals for the correlations as well, using cor.test. I tried the following without success. by(x,gender,function(x) cor.test(as.matrix(x))) Even if I just use 2 variables (e.g., IQ and education), I get exactly the same output for men and women with this command: by(x,gender,function(x) cor.test(iq,education)) I'm still in the learning stages with the by and cor.test functions, so I assume I'm using it incorrectly. Is it possible to get the correlation confidence intervals for each group using this approach? Many thanks in advance! John -- View this message in context: http://www.nabble.com/Within-group-correlation-confidence-intervals-tp25509629p25509629.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] Why S4 method is not visible from another package?
On Thu, Sep 17, 2009 at 5:59 PM, Martin Morgan mtmor...@fhcrc.org wrote:
Gábor Csárdi wrote:
Dear All,
maybe this is something obvious, I seem to be incapable of
understanding how S4 works.
So, in package 'A' I defined a summary method for my class:
setMethod(summary, signature(object=ListHyperGResult),
function(object, pvalue=pvalueCutoff(object), categorySize=NULL) {
whatever
})
ListHyperGResult has a subclass, GOListHyperGResult:
setClass(GOListHyperGResult,
representation=representation(conditional=logical),
contains=ListHyperGResult,
prototype=prototype(testname=GO))
The summary method is exported in the NAMESPACE:
exportMethods(summary)
Package 'B' depends on package 'A', this is stated in the
'DESCRIPTION' file. If I call 'summary' on a 'GOListHyperGResult' in
Hi Gabor
It is not S4 alone, but S4 + name spaces that are giving you problems.
You probably want to Import: A rather than depends, and importFrom(A,
summary).
As it stands, inside the B name space, you find base::summary, whereas
you've defined a method on summary that has been promoted to a generic
in one of the packages that A imports (probably AnnotationDbi).
This is a little bit of a guess; at some level it might seem more
appropriate to Import: AnnotationDbi and importFrom(AnnotationDbi,
summary) (or wherever the generic for summary that you are trying to use
is created).
Martin, thanks, this solved the problem.
But isn't this a bit weird? Suppose I am the author of package 'B' and
want to use the classes defined in package 'A'. I don't care about
exact details of the implementation of these classes, I don't want to
know that they are based on something in package 'C' (AnnotationDbi,
really). But I still have to import specific functions from 'C'.
Moreover, suppose the author of 'C' changes 'summary', e.g. puts it
into another package, 'D' and makes 'C' importing it from 'D'. This
will break my package, 'B' as well.
Anyway, thanks a lot for your help, Best Regards,
Gabor
Martin
--
Gabor Csardi gabor.csa...@unil.ch UNIL DGM
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Re: [R] matching pairs regardless of order
Here is an example:
x - c('loc1,loc2', 'loc2,loc3', 'loc2,loc1', 'loc3,loc1')
x.s - strsplit(x, ',')
# now sort them
x.s - sapply(x.s, sort)
# create new output
unique(apply(x.s, 2, paste, collapse=','))
[1] loc1,loc2 loc2,loc3 loc1,loc3
On Fri, Sep 18, 2009 at 8:47 AM, Juliane Struve
juliane_str...@yahoo.co.uk wrote:
Dear list,
I am using match() to match pairs of locations, e.g. trip=loc1,loc2 from a
list of such pairs, e.g. list=(loc1,loc2, loc1,loc3,
loc2,loc3,loc2,loc1).
In this example match() will match trip with the first element of list,
but not the 4th, because the order is reversed.
How can I get a match with both ?
Many thanks for any help,
Juliane
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--
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Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Updating R-code in own package
On 9/18/2009 9:05 AM, Steve Lianoglou wrote: Hi, On Sep 18, 2009, at 8:31 AM, Katrine Damgaard wrote: Hey everybody! We have created our own package, and need to do some corrections in the R-code of one of the function included in the package. How can I do that. I have read a manual how to create an R package, but I can't find anything about updating R-code in the package. I'm pretty sure the only correct thing to do is just fix the code in your package's source tree then reinstall the package wholesale to replace the bad code with the fixed code. Yes, that's the simplest way to do it. It also usually works for testing to just source the file containing the fix, to get a new copy in the global environment. This can sometimes fail if the function refers to other functions in the package that are not visible in the global environment, due to NAMESPACE hiding. It's possible to manipulate the environment of the sourced function (and it's even possible to place it into the right place so it just works), but those usually aren't worth the trouble. 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.
Re: [R] Why S4 method is not visible from another package?
Gábor Csárdi wrote:
On Thu, Sep 17, 2009 at 5:59 PM, Martin Morgan mtmor...@fhcrc.org wrote:
Gábor Csárdi wrote:
Dear All,
maybe this is something obvious, I seem to be incapable of
understanding how S4 works.
So, in package 'A' I defined a summary method for my class:
setMethod(summary, signature(object=ListHyperGResult),
function(object, pvalue=pvalueCutoff(object), categorySize=NULL) {
whatever
})
ListHyperGResult has a subclass, GOListHyperGResult:
setClass(GOListHyperGResult,
representation=representation(conditional=logical),
contains=ListHyperGResult,
prototype=prototype(testname=GO))
The summary method is exported in the NAMESPACE:
exportMethods(summary)
Package 'B' depends on package 'A', this is stated in the
'DESCRIPTION' file. If I call 'summary' on a 'GOListHyperGResult' in
Hi Gabor
It is not S4 alone, but S4 + name spaces that are giving you problems.
You probably want to Import: A rather than depends, and importFrom(A,
summary).
As it stands, inside the B name space, you find base::summary, whereas
you've defined a method on summary that has been promoted to a generic
in one of the packages that A imports (probably AnnotationDbi).
This is a little bit of a guess; at some level it might seem more
appropriate to Import: AnnotationDbi and importFrom(AnnotationDbi,
summary) (or wherever the generic for summary that you are trying to use
is created).
Martin, thanks, this solved the problem.
But isn't this a bit weird? Suppose I am the author of package 'B' and
want to use the classes defined in package 'A'. I don't care about
exact details of the implementation of these classes, I don't want to
know that they are based on something in package 'C' (AnnotationDbi,
really). But I still have to import specific functions from 'C'.
Moreover, suppose the author of 'C' changes 'summary', e.g. puts it
into another package, 'D' and makes 'C' importing it from 'D'. This
will break my package, 'B' as well.
Yes it seems a bit weird at first. But there really is a generic
C::summary that is different from base::summary, and could have, e.g., a
different signature, so you really are interested in C::summary and not
base::summary. Partly the (pleasant, in the long run) surprise here is
that R is separately managing both base::summary and C::summary, and
doing so in a way (via name spaces) that allows control over which will
be used. A second surprise, to the author of C, is that their package
has now become valuable enough to others that C can no longer be changed
at will.
Martin
Anyway, thanks a lot for your help, Best Regards,
Gabor
Martin
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Re: [R] Maximum No.of code in R
On Sep 18, 2009, at 7:58 AM, premmad wrote: Thanks for the reply and it is useful.What i want to know here is i'm going to try and write an automated procedure using batch processing in R by the way input of the next step is going to be this steps output .so one will not able to predict the lines please also do answer in taking consideration the above mentioned criteria in to consi Without your code it is difficult to know exactly what you mean. But one question (other than when will you show the code?) needs to be asked. Have you noted the 7-level nesting limit on ifelse statements on the ifelse help page? -- 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] as.POSIXct(as.Date()) independent of timezone
Try this: as.POSIXct(format(as.Date(2008-07-01))) [1] 2008-07-01 EDT See R News 4/1 for more. On Fri, Sep 18, 2009 at 10:19 AM, Markus Loecher markus.loec...@gmail.com wrote: Dear R users, I am struggling a bit with the converting dates to full POSIX timestamps, in particular, I would like to somehow force the timezone to be local, i.e. the output of as.POSIXct(as.Date(2008-07-01)) should always be equal to 2008-07-01 00:00:00, is that achievable ? I tried to set the origin and the timezone, neither of which seems to make a difference. On my Mac Book Pro (R version 2.9.1) which is set to Eastern US time zone, I obtain the shifted result: as.POSIXct(as.Date(2008-07-01)) [1] 2008-06-30 20:00:00 EDT And e.g. as.POSIXct( Sys.Date()) [1] 2009-09-17 20:00:00 EDT Sys.time() [1] 2009-09-18 10:10:48 EDT Any help would make life simpler for me. Thanks, Markus [[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] define a new family (and a new link function) for gam in gam package
I am using gam in gam package (not in mgcv) it is possible to force gam in mgcv to behave like gam in gam package? -- not *exactly*, no. But what do you want to do? (i.e. what feature of `gam' do you need?) -- Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ 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: length(f1) == length(f2) is not TRUE
I just wanted to know whether the chances of getting help with this would be greater if I posted this on the mixed models list, even though I would be cross-posting.. ? --On 18 September 2009 12:41 +0100 A Singh bz...@bristol.ac.uk wrote: Dear R users, I am trying to fit an lmer model with only random effects which is giving me the following error: Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used I am trying to extract variance components for a phenotype 'peg.no', using the variable 'family' and a marker column 'P1L55' (which is categorical and has 2 levels- 0 and 1), as random effects. There are no fixed effects. The code I used is as follows: vc-read.table(...) vcdf-data.frame(vc) colms-(vc)[4:13] ##these are the markers lapply(colms,factor) try(fit-lmer(peg.no~1 + (1|family/P1L55), na.action=na.include, data=vcdf)) I thought that putting the data into a dataframe would help, along with the na.exclude command, because there is a lot of missing data in patches which I have replaced with NA's, but I don't know how to fix this error at all. Its a bit urgent, and any help is hugely appreciated. The data files are at: http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.html (excel) http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html (txt) Cheers, Aditi -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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] matching pairs regardless of order
You are going to have to order your values for comparison. Use 'strsplit' to split on the comma, then rejoin the data items based on the sorting order. On Fri, Sep 18, 2009 at 8:47 AM, Juliane Struve juliane_str...@yahoo.co.uk wrote: Dear list, I am using match() to match pairs of locations, e.g. trip=loc1,loc2 from a list of such pairs, e.g. list=(loc1,loc2, loc1,loc3, loc2,loc3,loc2,loc1). In this example match() will match trip with the first element of list, but not the 4th, because the order is reversed. How can I get a match with both ? Many thanks for any help, Juliane __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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: length(f1) == length(f2) is not TRUE
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of A Singh Sent: Friday, September 18, 2009 4:42 AM To: r-help@r-project.org Subject: [R] Error: length(f1) == length(f2) is not TRUE Dear R users, I am trying to fit an lmer model with only random effects which is giving me the following error: Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used I am trying to extract variance components for a phenotype 'peg.no', using the variable 'family' and a marker column 'P1L55' (which is categorical and has 2 levels- 0 and 1), as random effects. There are no fixed effects. The code I used is as follows: vc-read.table(...) vcdf-data.frame(vc) colms-(vc)[4:13] ##these are the markers lapply(colms,factor) Note that you did not change columns 4:13 of vcdf to factors: you changed copies of them to factors. Do vcdf[4:13] - lapply(vcdf[4:13], factor) and lmer should be happier. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com try(fit-lmer(peg.no~1 + (1|family/P1L55), na.action=na.include, data=vcdf)) I thought that putting the data into a dataframe would help, along with the na.exclude command, because there is a lot of missing data in patches which I have replaced with NA's, but I don't know how to fix this error at all. Its a bit urgent, and any help is hugely appreciated. The data files are at: http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht ml (excel) http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html (txt) Cheers, Aditi -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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] Datetime conversion
use View to view the dataframe. On Fri, Sep 18, 2009 at 8:17 AM, premmad mtechp...@gmail.com wrote: Thanks .I tried its working but when i tried to view the dataframe i got the following error Error in edit.data.frame(get(subx, envir = parent), title = subx, ...) : can only handle vector and factor elements -- View this message in context: http://www.nabble.com/Datetime-conversion-tp25503138p25507734.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] T-test to check equality, unable to interpret the results.
It appears that you have a fundamental misunderstanding of what p-values do and do not say (though this misunderstanding is commom). The following article addresses this issue and could help with a better understanding: Murdock, D, Tsai, Y, and Adcock, J (2008) _P-Values are Random Variables_. The American Statistician. (62) 242-245. See also the Pvalue.norm.sim function in the TeachingDemos package for simulation examples demonstrating points from the article. 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 Robert Hall Sent: Wednesday, September 16, 2009 12:55 PM To: r-help Subject: [R] T-test to check equality, unable to interpret the results. Hi, I have the precision values of a system on two different data sets. The snippets of these results are as shown: sample1: (total 194 samples) 0.600238 0.800119 0.600238 0.200030 0.600238 ... ... sample2: (total 188 samples) 0.8001 0.2000 0.8001 0. 0.8001 0.4001 ... ... I want to check if these results are statistically significant? Intuitively, the similarity in the two results mean the results are statistically significant. I am using the t-test t.test(sample1,sample2)to check for similarity amongst the two results. I get the following output: --- Welch Two Sample t-test data: s1p5 and s2p5 t = 0.9778, df = 374.904, p-value = 0.3288 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -0.03170059 0.09441172 sample estimates: mean of x mean of y 0.5138298 0.4824742 I believe the t-test checks for difference amongst the two sets, and p- value 0.05 means both thesets are statistically different. Here while checking for dissimilarity the p-value is 0.3288, does it mean that higher the p-value (while t.test checks for dis-similarity) means more similar the results are (which is the case above as the means of the results are very close!) Please help me interpret the results.. thanks in advance! -- Rob Hall Masters Student ANU [[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] Writing Reports from R in Microsoft Office Open XML format (follow-up)
Dear Duncan and other R users, The department in which I work will soon make some decisions to improve our reporting. Since I hope that our solution will support R and Sweave-like functionality (otherwise it wouldn't be an improvement), I hope it's ok to repeat my question back from June if there are any news on an odfWeave-like package for weaving Microsoft Word documents? (in the Office Open XML format). Duncan, any news on the package? I am also asking on the list again because there might be developments by others in parallel to what Duncan has mentioned below? (For example, maybe someone is thinking of adapting Max Kuhn's excellent odfWeave package to support the XML format of Microsoft Word?) Kind regards, Tobias On Tue, Jun 9, 2009 at 4:22 PM, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Yes. We will release a version in the next few weeks when I have time to wrap it all up. There is also a Docbook-based version that uses R extensions to Docbook for authoring structured documents. D. Tobias Sing wrote: Dear all, has someone implemented functionality for writing reports from R in Office Open XML format (*), similar to what odfWeave does for the ODF format of OpenOffice? It would be great to have a kind of ooxmlWeave at least for those of us who are forced to work in an MS ecosystem. (*) Office Open XML is the default, XML-based, file format for MS Word: http://en.wikipedia.org/wiki/Office_Open_XML Kind regards, Tobias __ 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] T-test to check equality, unable to interpret the results.
Rolf,
I no longer claim to be young, the naïve part is still up for debate,
but I find that restricting the null to only include = to be more confusing
than to have it include the inequality. To have the alternative be and the
null be = implies that we are working on the assumption that is impossible, a
stronger assumption than = of the null hypothesis.
I prefer to have all three possibilities explicitly stated between the 2
hypotheses to cover all possibilities. An analogy that can be used to explain
why we do the computation using the = value instead of any or all of the
values in the = null is: If you wanted to prove that you are
smarter/stronger/richer/etc. than a group of people, then all you would need to
do is prove that you are smarter/stronger/richer/etc. than the
smartest/strongest/richest/etc.est of the group, not every individual. Using
the equality value of the null does the same, if you can find evidence against
that, then you have found evidence against all other possible values (within
the null) as well.
--
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 Rolf Turner
Sent: Wednesday, September 16, 2009 2:31 PM
To: Bert Gunter
Cc: 'r-help'
Subject: Re: [R] T-test to check equality, unable to interpret the
results.
On 17/09/2009, at 8:06 AM, Bert Gunter wrote:
snip
Furthermore, the null can be other than equality -- e.g. that the
mean of
the first population is less than the second.
snip
QUIBBLE: Some elementary texts will indeed state the null hypothesis
as
``mu_1 = mu_2'' when the alternative hypothesis is ``mu_1 mu_2''.
However it seems to me more perspicuous to keep the null hypothesis as
``='' and allow only the alternative to change (i.e. to be one of ``!
='',
``'', or ``'').
One calculates one's *test statistic* using the ``='' (which is the
``most extreme'' point of the null hypothesis, the point ``closest'' to
the alternative, i.e. the point least likely to lead one to reject
the null.
Thus confusion amongst the young and naive is minimized if one
insists that
the null hypothesis is always ``=''.
cheers,
Rolf Turner
##
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up)
Tobias Sing wrote: Dear Duncan and other R users, The department in which I work will soon make some decisions to improve our reporting. Since I hope that our solution will support R and Sweave-like functionality (otherwise it wouldn't be an improvement), I hope it's ok to repeat my question back from June if there are any news on an odfWeave-like package for weaving Microsoft Word documents? (in the Office Open XML format). Duncan, any news on the package? While I am starting a new quarter in a week, I expect that I will have a version of it packaged up before then. I am also asking on the list again because there might be developments by others in parallel to what Duncan has mentioned below? (For example, maybe someone is thinking of adapting Max Kuhn's excellent odfWeave package to support the XML format of Microsoft Word?) Kind regards, Tobias On Tue, Jun 9, 2009 at 4:22 PM, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Yes. We will release a version in the next few weeks when I have time to wrap it all up. There is also a Docbook-based version that uses R extensions to Docbook for authoring structured documents. D. Tobias Sing wrote: Dear all, has someone implemented functionality for writing reports from R in Office Open XML format (*), similar to what odfWeave does for the ODF format of OpenOffice? It would be great to have a kind of ooxmlWeave at least for those of us who are forced to work in an MS ecosystem. (*) Office Open XML is the default, XML-based, file format for MS Word: http://en.wikipedia.org/wiki/Office_Open_XML Kind regards, Tobias __ 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-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: length(f1) == length(f2) is not TRUE
Hi Bill, Thanks, I did try out what you suggested but it doesn't seem to work. I get the same error again. There's obviously something here that I don't get. Need to figure it out. Aditi --On 18 September 2009 08:34 -0700 William Dunlap wdun...@tibco.com wrote: From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of A Singh Sent: Friday, September 18, 2009 4:42 AM To: r-help@r-project.org Subject: [R] Error: length(f1) == length(f2) is not TRUE Dear R users, I am trying to fit an lmer model with only random effects which is giving me the following error: Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used I am trying to extract variance components for a phenotype 'peg.no', using the variable 'family' and a marker column 'P1L55' (which is categorical and has 2 levels- 0 and 1), as random effects. There are no fixed effects. The code I used is as follows: vc-read.table(...) vcdf-data.frame(vc) colms-(vc)[4:13] ##these are the markers lapply(colms,factor) Note that you did not change columns 4:13 of vcdf to factors: you changed copies of them to factors. Do vcdf[4:13] - lapply(vcdf[4:13], factor) and lmer should be happier. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com try(fit-lmer(peg.no~1 + (1|family/P1L55), na.action=na.include, data=vcdf)) I thought that putting the data into a dataframe would help, along with the na.exclude command, because there is a lot of missing data in patches which I have replaced with NA's, but I don't know how to fix this error at all. Its a bit urgent, and any help is hugely appreciated. The data files are at: http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht ml (excel) http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html (txt) Cheers, Aditi -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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. -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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] Suppressing script commands in R console when executing long program
Hi Duncan
You can try putting this in your Rprofile
options(keep.source=F)
This will work in the R cmd but it will not work in the RGui
The syntax is wrong there: that should be options(keep.source=F). But I
don't think it addresses either question.
I was working from my memory here. Glad you pointed out Duncan :-)
The normal way to execute a script from the console is source(filename.R),
which by default doesn't echo.
options(keep.source=F)
options(echo=F)
in RProf. Then doing R CMD -f filename.r (in the shell without )
does it for me but perhaps Duncan's answer is more 'standard' R-ish
way of doing it (i.e., source('filename.R') )
--
Regards,
Ishwor Gurung
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Re: [R] Missing link(s) in documentation object
Jon Olav Skoien wrote:
Hi,
I want to cross-reference from the documentation of pkg1 to pkg2, which
is imported in the NAMESPACE of pkg1, and under Depends in DESCRIPTION
of pkg1. According to Writing R extensions, this can be done by:
\code{\link{foo}}
when foo is an aliased function in the documentation of pkg2. This works
as it should when I install the package, but when I run R CMD check
pgk1, I get a warning:
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'fooPkg1.Rd'
foo
I have tried to change the link to
\code{\link[pkg2]{foo}}
\code{\link[pkg:pkg2]{foo}}
Hi Jon --
I think the current requirement is \link[pkg2;foo_Rd_file_name]{foo}
where foo_Rd_file_name is the name (without the .Rd extension) of the
FILE in which foo is documented. This would appear not to be foo.Rd,
because you say \link[pkg2]{foo} fails. This is as documented in Writing
R extensions.
None of these works, the first gives a link that leads to an error page,
and the second one gives a link that does not work at all. I assume this
is as it should be; foo.Rd does not exist. However, R CMD check does not
complain about any of these links...
Try building with R-devel, where the error messages are more detailed.
Why does R CMD check warn me against links that work? I think pkg2 is
I think the idea is that the cross-package links as you originally
specified work for some help formats, but not for others (e.g., pdf).
Martin
not on the search path when looking for cross-references, but why? R CMD
check continues to run after the warning without any complaints, and all
tests rely on pkg2. I am quite sure there is something simple that I
have overlooked, but cannot figure out what it is.
Best wishes,
Jon
Platform etc:
XP SP3, R 2.9-2, Rtools210 (the problem was also there before upgrading
from R 2.9-1 and Rtools29 )
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Re: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up)
The people who brought us rexcel are working on sword which is a sweave for ms word, the current version is at: http://rcom.univie.ac.at/download.html 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 Tobias Sing Sent: Friday, September 18, 2009 9:39 AM To: Duncan Temple Lang; r help; max.k...@pfizer.com Subject: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up) Dear Duncan and other R users, The department in which I work will soon make some decisions to improve our reporting. Since I hope that our solution will support R and Sweave-like functionality (otherwise it wouldn't be an improvement), I hope it's ok to repeat my question back from June if there are any news on an odfWeave-like package for weaving Microsoft Word documents? (in the Office Open XML format). Duncan, any news on the package? I am also asking on the list again because there might be developments by others in parallel to what Duncan has mentioned below? (For example, maybe someone is thinking of adapting Max Kuhn's excellent odfWeave package to support the XML format of Microsoft Word?) Kind regards, Tobias On Tue, Jun 9, 2009 at 4:22 PM, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Yes. We will release a version in the next few weeks when I have time to wrap it all up. There is also a Docbook-based version that uses R extensions to Docbook for authoring structured documents. D. Tobias Sing wrote: Dear all, has someone implemented functionality for writing reports from R in Office Open XML format (*), similar to what odfWeave does for the ODF format of OpenOffice? It would be great to have a kind of ooxmlWeave at least for those of us who are forced to work in an MS ecosystem. (*) Office Open XML is the default, XML-based, file format for MS Word: http://en.wikipedia.org/wiki/Office_Open_XML Kind regards, Tobias __ 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-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 Reports from R in Microsoft Office Open XML format (follow-up)
I believe that their approach is based on DCOM and the post was about Office Open XML. We have had the ability to do this via DCOM for at least 6 years, but unfortunately DCOM is limited to Windows. Greg Snow wrote: The people who brought us rexcel are working on sword which is a sweave for ms word, the current version is at: http://rcom.univie.ac.at/download.html hope this helps, __ 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] lapply - value changes as parameters to function?
Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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] Simple as.Date question dealing with a timezone offset
Took me a minute to grok the gsubfn solution, but that is sweet! very nice. thank you very much both for the suggestions, Landon -- View this message in context: http://www.nabble.com/Simple-as.Date-question-dealing-with-a-timezone-offset-tp25491955p25512218.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] Sum according observation
Hi listers, I have a simple doubt... I need to manipulate the data base as: var1 var2 7 0.1 7 0.1 8 0.12 100.15 120.18 200.31 I would like to aggregate the equal cases as var1 making the sum of var2... I would get... var1 var2 7 0.2 8 0.12 100.15 120.18 200.31 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Sum-according-observation-tp25510566p25510566.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] lapply - value changes as parameters to function?
Mark - The l in lapply refers to that fact that it will *return* a list, not that it wants a list for input. You could input a list, but then each element of the list would be one of the values you wanted processed. So I think you want x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) This will return a list whose elements are the result of calling the DoAvgCalcs function with each value contained in x. If they were all the same length, and you wanted them simplified to a matrix, you could use sapply (s for simplify) instead of lapply (l for list). - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 18 Sep 2009, Mark Knecht wrote: Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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] R on browser
Hi i can get sites that can r code on browser -- View this message in context: http://www.nabble.com/R-on-browser-tp25508719p25508719.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] Writing Reports from R in Microsoft Office Open XML format (follow-up)
I read the original post as asking if there is something like odfWeave that works for msword (I assumed windows, but I guess they could be asking about MSword on other platforms, it just sounds like a windows shop). But yes, sword only works on windows (and is in beta version still) and uses a different interface from the standard sweave and odfWeave (process from inside word rather than process a file through R). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: Duncan Temple Lang [mailto:dun...@wald.ucdavis.edu] Sent: Friday, September 18, 2009 11:00 AM To: Greg Snow Cc: Tobias Sing; r help Subject: Re: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up) I believe that their approach is based on DCOM and the post was about Office Open XML. We have had the ability to do this via DCOM for at least 6 years, but unfortunately DCOM is limited to Windows. Greg Snow wrote: The people who brought us rexcel are working on sword which is a sweave for ms word, the current version is at: http://rcom.univie.ac.at/download.html hope this helps, __ 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] Sum according observation
Try this: with(DF, tapply(var2, var1, sum)) On Fri, Sep 18, 2009 at 12:18 PM, MarcioRibeiro mes...@pop.com.br wrote: Hi listers, I have a simple doubt... I need to manipulate the data base as: var1 var2 7 0.1 7 0.1 8 0.12 10 0.15 12 0.18 20 0.31 I would like to aggregate the equal cases as var1 making the sum of var2... I would get... var1 var2 7 0.2 8 0.12 10 0.15 12 0.18 20 0.31 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Sum-according-observation-tp25510566p25510566.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] generating unordered combinations
The combn solution offered by Bill is great. It struck me that what you are
doing, in fact, is generating the null distribution of the two-sample Wilcoxon
test where the first group has size m and the second group has size n. In
general, the length of the array has size choose(n+m-1,m) which gets very big
very fast. For example,
choose(20+20-1,20)
[1] 68923264410
If, on the off chance that you are interested in *summing* the unordered
combinations across columns, there is a very slick way to do this that takes a
tiny fraction of the time and memory that generating huge arrays entails. If
not, obviously, you already have your solution.
Just in case, here is the code to generate the distribution of sums. It is
based on an algorithm due to Harding (1984).
f - function(m,n) {
umax - (m*n+1)
ifelse (umax%%2==0, umaxp - (umax/2)-1, umaxp - (umax-1)/2)
#umaxp is analagous to “M” from Harding (1984)
p - min((m+n),umaxp)
q - min(m,umaxp)
dis - c(1,numeric(umaxp))
if ((n+1)umaxp) {
for (i in 1:q) {#steps for denominator of generating
function
for (j in i:umaxp) {
dis[j+1] - (dis[j+1] + dis[(j-i)+1])
}
}
} else {
for (i in (n+1):(p)) { #steps for numerator of generating function
for (j in (umaxp):i) {
dis[j+1] - (dis[j+1] - dis[(j-i)+1])
}
}
for (i in 1:q) {#steps for denominator of generating
function
for (j in i:umaxp) {
dis[j+1] - (dis[j+1] + dis[(j-i)+1])
}
}
}
ldis - length(dis)
ifelse(umax%%2==0,dis - c(dis,dis[ldis:1]),dis - c(dis,dis[(ldis-1):1]))
dispr - dis/choose((n+m),n)
ws - sum(1:m):sum((n+1):(n+m))
lws - length(ws)
mat3 - cbind(ws,dis,dispr,numeric(lws),numeric(lws))
mat3[,4] - cumsum(mat3[,3])
mat3[,5] - cumsum(mat3[,3][lws:1])[lws:1]
colnames(mat3) - c(W,Freq,Probability,Sum up,Sum down)
print(mat3)
}
system.time(f(20,20))
user system elapsed
0.110.000.11
Bryan
That's brilliant - thanks.
On 17 Sep 2009, at 23:36, William Dunlap wrote:
There is a 1-1 correspondance between your n-sets
consisting of m possible element types (0 through m-1
in your example) and the number of n-subsets of a (n+m-1)-set.
E.g., your example had m=3 and n=3 and subtracting
1:3 from each column of combn(3+3-1,3) gives your result:
t(combn(3+3-1, 3)-(1:3))
[,1] [,2] [,3]
[1,]000
[2,]001
[3,]002
[4,]011
[5,]012
[6,]022
[7,]111
[8,]112
[9,]122
[10,]222
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Dan Halligan
Sent: Thursday, September 17, 2009 1:31 PM
To: r-help@r-project.org
Subject: [R] generating unordered combinations
Hi,
I am trying to generate all unordered combinations of a set of
numbers / characters, and I can only find a (very) clumsy way of
doing
this using expand.grid. For example, all unordered combinations of
the numbers 0, 1, 2 are:
0, 0, 0
0, 0, 1
0, 0, 2
0, 1, 1
0, 1, 2
0, 2, 2
1, 1, 1
1, 1, 2
1, 2, 2
2, 2, 2
(I have not included, for example, 1, 0, 0, since it is equivalent to
0, 0, 1).
I have found a way to generate this data.frame using expand.grid as
follows:
g - expand.grid(c(0,1,2), c(0,1,2), c(0,1,2))
for(i in 1:nrow(g)) {
g[i,] - sort(as.character(g[i,]))
}
o - order(g$Var1, g$Var2, g$Var3)
unique(g[o,]).
This is obviously quite clumsy and hard to generalise to a greater
number of characters, so I'm keen to find any other solutions. Can
anyone suggest a better (more general, quicker) method?
Cheers
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-
Bryan Keller, Doctoral Student/Project Assistant
Educational Psychology - Quantitative Methods
The University of Wisconsin - Madison
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Re: [R] Datetime conversion
On Fri, Sep 18, 2009 at 04:32:27AM -0700, premmad wrote: Sorry for confusing you all with my inexperienced posting . I tried as u said if you have 9 rows in the data it is working fine but please try out the same example as you have suggested earlier with morethan 9 rows. I tried it as following datetime -c( + 01OCT1987:00:00:00.000, + 12APR2004:00:00:00.000, + 01DEC1987:00:00:00.000, + 01OCT1975:00:00:00.000, + 01AUG1979:00:00:00.000, + 26JUN2003:00:00:00.000, + 01JAN1900:00:00:00.000, + 13MAY1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000, + 30SEP1998:00:00:00.000) dt - as.data.frame(datetime) dt$date-strptime(as.character(dt$datetime),%d%b%Y) and got the following error : Error in `$-.data.frame`(`*tmp*`, date, value = list(sec = c(0, 0, : replacement has 9 rows, data has 12. Oops - sorry you are right. There is a Problem with inserting the object. Try this instead: dt$date - as.Date(dt$datetime, %d%b%Y) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ 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] lapply - value changes as parameters to function?
Phil, Thanks for the reply. Your suggestion is actually the one I started with (assuming I'm understanding you) but I didn't seem to even get down into my function, or the error message is from other place within my function that I haven't discovered yet: x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in rep(NA, k) : invalid 'times' argument I should write some fake code that gives you all the depth so we could jsut run it. If no on eelse sees the answer then I'll be back later with more code that completely runs. Thanks, Mark On Fri, Sep 18, 2009 at 10:16 AM, Phil Spector spec...@stat.berkeley.edu wrote: Mark - The l in lapply refers to that fact that it will *return* a list, not that it wants a list for input. You could input a list, but then each element of the list would be one of the values you wanted processed. So I think you want x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) This will return a list whose elements are the result of calling the DoAvgCalcs function with each value contained in x. If they were all the same length, and you wanted them simplified to a matrix, you could use sapply (s for simplify) instead of lapply (l for list). - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 18 Sep 2009, Mark Knecht wrote: Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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] merging data frames with matrix objects when missing cases
This has something to do with your data.frame structure see str(df1) 'data.frame': 3 obs. of 2 variables: $ a : int 1 2 3 $ X1: 'AsIs' int [1:3, 1:2] 1 2 3 4 5 6 str(df2) 'data.frame': 2 obs. of 2 variables: $ a : int 1 2 $ X2: 'AsIs' int [1:2, 1:2] 11 12 13 14 This seems to work df1-data.frame(a=1:3, b = 1:3, c = 4:6) str(df1) 'data.frame': 3 obs. of 3 variables: $ a: int 1 2 3 $ b: int 1 2 3 $ c: int 4 5 6 df2-data.frame(a=1:2, d = 11:12, e = 13:14) str(df2) 'data.frame': 2 obs. of 3 variables: $ a: int 1 2 $ d: int 11 12 $ e: int 13 14 merge(df1,df2) a b c d e 1 1 1 4 11 13 2 2 2 5 12 14 merge(df1, df2, all=T) a b c d e 1 1 1 4 11 13 2 2 2 5 12 14 3 3 3 6 NA NA 2009/9/18 Kari Ruohonen kari.ruoho...@utu.fi: Hi, I have faced a problem with the merge() function when trying to merge two data frames that have a common index but the second one does not have cases for all indexes in the first one. With usual variables R fills in the missing cases with NA if all=T is requested. But if the variable is a matrix R seems to insert NA only to the first column of the matrix and fill in the rest of the columns by recycling the values. Here is a toy example: df1-data.frame(a=1:3,X1=I(matrix(1:6,ncol=2))) df2-data.frame(a=1:2,X2=I(matrix(11:14,ncol=2))) merge(df1,df2) a X1.1 X1.2 X2.1 X2.2 1 1 1 4 11 13 2 2 2 5 12 14 # no all=T, missing cases are dropped merge(df1,df2,all=T) a X1.1 X1.2 X2.1 X2.2 1 1 1 4 11 13 2 2 2 5 12 14 3 3 3 6 NA 13 # X2.1 set to NA correctly but X2.2 set to 13 by recycling. Can I somehow get the behaviour that the third row of the second matrix X2 in the above example would be filled with NA for all columns? None of the merge() options does not seem to provide a solution. regards, Kari __ 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] wilcox.test p-value = 0
Hello Thomas and Bryan, Thanks for the correction, sorry Murat I was mistaken. Actually your answers solved me a problem I was having using multiple fisher.test() on nucleic acid sequences, where we come up with hundreds of thousands of p values, a lot of which are 0's. Since we have to correct for multiple tests, even very, very small p's might end up not being significant, i had assumed the 0's were tied p values, but now I know I can use the numerator and the denominator to rank the 0's, even if I don't have the exact p value. Best, Keo. Marc Schwartz escribió: Once one gets past the issue of the p value being extremely small, irrespective of the test being used, the OP has asked the question of how to report it. Most communities will have standards for how to report p values, covering things like how many significant digits and a minimum p value threshold to report. For example, in medicine, it is common to report 'small' p values as 'p 0.001' or 'p 0.0001'. Thus, below those numbers, the precision is largely irrelevant and one need not report the actual p value. I just wanted to be sure that we don't lose sight of the forest for the trees... :-) The OP should consult a relevant guidance document or an experienced author in the domain of interest. HTH, Marc Schwartz On Sep 16, 2009, at 9:54 AM, Bryan Keller wrote: That's right, if the test is exact it is not possible to get a p-value of zero. wilcox.test does not provide an exact p-value in the presence of ties so if there are any ties in your data you are getting a normal approximation. Incidentally, if there are any ties in your data set I would strongly recommend computing the *exact* p-value because using the normal approximation on tied data sets will either inflate type I error rate or reduce power depending on how the ties are distributed. Depending on the pattern of ties this can result in gross under or over estimation of the p-value. I guess this is all by way of saying that you should always compute the exact p-value if possible. The package exactRankTests uses the algorithm by Mehta Patel and Tsiatis (1984). If your sample sizes are larger, there is a freely available .exe by Cheung and Klotz (1995) that will do exact p-values for sample sizes larger than 100 in each group! You can find it at http://pages.cs.wisc.edu/~klotz/ Bryan Hi Murat, I am not an expert in either statistics nor R, but I can imagine that since the default is exact=TRUE, It numerically computes the probability, and it may indeed be 0. if you use wilcox.test(x, y, exact=FALSE) it will give you a normal aproximation, which will most likely be different from zero. No, the exact p-value can't be zero for a discrete distribution. The smallest possible value in this case would, I think, be 1/choose(length(x)+length(y),length(x)), or perhaps twice that. More generally, the approach used by format.pvalue() is to display very small p-values as 2e-16, where 2e-16 is machine epsilon. I wouldn't want to claim optimality for this choice, but it seems a reasonable way to represent very small. -thomas Hope this helps. Keo. Murat Tasan escribi?: hi, folks, how have you gone about reporting a p-value from a test when the returned value from a test (in this case a rank-sum test) is numerically equal to 0 according to the machine? the next lowest value greater than zero that is distinct from zero on the machine is likely algorithm-dependent (the algorithm of the test itself), but without knowing the explicit steps of the algorithm implementation, it is difficult to provide any non-zero value. i initially thought to look at .mach...@double.xmin, but i'm not comfortable with reporting p .mach...@double.xmin, since without knowing the specifics of the implementation, this may not be true! to be clear, if i have data x, and i run the following line, the returned value is TRUE. wilcox.test(x)$p.value == 0 thanks for any help on this! __ 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] wilcox.test p-value = 0
Hello, Thanks for the correction, sorry Murat I was mistaken. Actually your answers solved me a problem I was having using multiple fisher.test() on nucleic acid sequences, where we come up with hundreds of thousands of p values, a lot of which are 0's. Since we have to correct for multiple tests, even very, very small p's might end up not being significant, i had assumed the 0's were tied p values, but now I know I can use the numerator and the denominator to rank the 0's, even if I don't have the exact p value. Best, Keo. Marc Schwartz escribió: Once one gets past the issue of the p value being extremely small, irrespective of the test being used, the OP has asked the question of how to report it. Most communities will have standards for how to report p values, covering things like how many significant digits and a minimum p value threshold to report. For example, in medicine, it is common to report 'small' p values as 'p 0.001' or 'p 0.0001'. Thus, below those numbers, the precision is largely irrelevant and one need not report the actual p value. I just wanted to be sure that we don't lose sight of the forest for the trees... :-) The OP should consult a relevant guidance document or an experienced author in the domain of interest. HTH, Marc Schwartz On Sep 16, 2009, at 9:54 AM, Bryan Keller wrote: That's right, if the test is exact it is not possible to get a p-value of zero. wilcox.test does not provide an exact p-value in the presence of ties so if there are any ties in your data you are getting a normal approximation. Incidentally, if there are any ties in your data set I would strongly recommend computing the *exact* p-value because using the normal approximation on tied data sets will either inflate type I error rate or reduce power depending on how the ties are distributed. Depending on the pattern of ties this can result in gross under or over estimation of the p-value. I guess this is all by way of saying that you should always compute the exact p-value if possible. The package exactRankTests uses the algorithm by Mehta Patel and Tsiatis (1984). If your sample sizes are larger, there is a freely available .exe by Cheung and Klotz (1995) that will do exact p-values for sample sizes larger than 100 in each group! You can find it at http://pages.cs.wisc.edu/~klotz/ Bryan Hi Murat, I am not an expert in either statistics nor R, but I can imagine that since the default is exact=TRUE, It numerically computes the probability, and it may indeed be 0. if you use wilcox.test(x, y, exact=FALSE) it will give you a normal aproximation, which will most likely be different from zero. No, the exact p-value can't be zero for a discrete distribution. The smallest possible value in this case would, I think, be 1/choose(length(x)+length(y),length(x)), or perhaps twice that. More generally, the approach used by format.pvalue() is to display very small p-values as 2e-16, where 2e-16 is machine epsilon. I wouldn't want to claim optimality for this choice, but it seems a reasonable way to represent very small. -thomas Hope this helps. Keo. Murat Tasan escribi?: hi, folks, how have you gone about reporting a p-value from a test when the returned value from a test (in this case a rank-sum test) is numerically equal to 0 according to the machine? the next lowest value greater than zero that is distinct from zero on the machine is likely algorithm-dependent (the algorithm of the test itself), but without knowing the explicit steps of the algorithm implementation, it is difficult to provide any non-zero value. i initially thought to look at .mach...@double.xmin, but i'm not comfortable with reporting p .mach...@double.xmin, since without knowing the specifics of the implementation, this may not be true! to be clear, if i have data x, and i run the following line, the returned value is TRUE. wilcox.test(x)$p.value == 0 thanks for any help on this! __ 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] lapply - value changes as parameters to function?
Change the order of the parameters in your function so that Lookback is the first one. The first parameter of the lapply is what is passed to the function as its first parameter. Now just have ResultList - lapply(x, DoAvgCalcs, IndexData=IndexData, SampleSize=TestSamples, Iteration=TestIterations) On Fri, Sep 18, 2009 at 1:32 PM, Mark Knecht markkne...@gmail.com wrote: Phil, Thanks for the reply. Your suggestion is actually the one I started with (assuming I'm understanding you) but I didn't seem to even get down into my function, or the error message is from other place within my function that I haven't discovered yet: x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in rep(NA, k) : invalid 'times' argument I should write some fake code that gives you all the depth so we could jsut run it. If no on eelse sees the answer then I'll be back later with more code that completely runs. Thanks, Mark On Fri, Sep 18, 2009 at 10:16 AM, Phil Spector spec...@stat.berkeley.edu wrote: Mark - The l in lapply refers to that fact that it will *return* a list, not that it wants a list for input. You could input a list, but then each element of the list would be one of the values you wanted processed. So I think you want x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) This will return a list whose elements are the result of calling the DoAvgCalcs function with each value contained in x. If they were all the same length, and you wanted them simplified to a matrix, you could use sapply (s for simplify) instead of lapply (l for list). - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 18 Sep 2009, Mark Knecht wrote: Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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 on browser
Hi, On Sep 18, 2009, at 9:32 AM, vinay basavanal wrote: Hi i can get sites that can r code on browser Oh don't mean to sound rude, but can you try to rephrase your question? I think a lot of people are having a hard time understanding what you're really asking, but we'd be happy to help. Thanks, -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-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: length(f1) == length(f2) is not TRUE (fwd)
-- Forwarded Message -- Date: 18 September 2009 19:24 +0100 From: A Singh bz...@bristol.ac.uk To: William Dunlap wdun...@tibco.com Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE Yup, they are all factors- and its still doesn't work. Getting to the stage where I can use 'summary()' is the problem- the error stalls the process before a summary can be output. I tried the same code, but using 'family' and P1L55 as independent random factors, and that works. (I actually tried this with a new marker P1L74) try(fit-lmer(peg.no~1 + (1|family) + (1|P1L74), na.action=na.exclude)) summary(fit) Linear mixed model fit by REML Formula: peg.no ~ 1 + (1 | family) + (1 | P1L74) AIC BIC logLik deviance REMLdev 2981 2997 -1487 29762973 Random effects: Groups NameVariance Std.Dev. family (Intercept) 87.86380 9.37357 P1L74(Intercept) 0.48815 0.69868 Residual 92.11681 9.59775 Number of obs: 390, groups: family, 57; P1L74, 2 Fixed effects: Estimate Std. Error t value (Intercept)96.40 1.49 64.71 ..but the nested random effect ..(1|family/P1L74).. is where the error occurs. And its the same error. Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used My design is a very unbalanced one. Do you think that can be the problem? --On 18 September 2009 09:11 -0700 William Dunlap wdun...@tibco.com wrote: Look at the output of summary(vcdf) and make sure that 'family' and 'P1L55' columns are factors. Perhaps columns 4:13 did not include them. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com -Original Message- From: A Singh [mailto:aditi.si...@bristol.ac.uk] Sent: Friday, September 18, 2009 9:03 AM To: William Dunlap; r-help@r-project.org Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE Hi Bill, Thanks, I did try out what you suggested but it doesn't seem to work. I get the same error again. There's obviously something here that I don't get. Need to figure it out. Aditi --On 18 September 2009 08:34 -0700 William Dunlap wdun...@tibco.com wrote: From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of A Singh Sent: Friday, September 18, 2009 4:42 AM To: r-help@r-project.org Subject: [R] Error: length(f1) == length(f2) is not TRUE Dear R users, I am trying to fit an lmer model with only random effects which is giving me the following error: Error : length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In P1L55:family : numerical expression has 390 elements: only the first used 2: In P1L55:family : numerical expression has 390 elements: only the first used I am trying to extract variance components for a phenotype 'peg.no', using the variable 'family' and a marker column 'P1L55' (which is categorical and has 2 levels- 0 and 1), as random effects. There are no fixed effects. The code I used is as follows: vc-read.table(...) vcdf-data.frame(vc) colms-(vc)[4:13] ##these are the markers lapply(colms,factor) Note that you did not change columns 4:13 of vcdf to factors: you changed copies of them to factors. Do vcdf[4:13] - lapply(vcdf[4:13], factor) and lmer should be happier. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com try(fit-lmer(peg.no~1 + (1|family/P1L55), na.action=na.include, data=vcdf)) I thought that putting the data into a dataframe would help, along with the na.exclude command, because there is a lot of missing data in patches which I have replaced with NA's, but I don't know how to fix this error at all. Its a bit urgent, and any help is hugely appreciated. The data files are at: http://www.4shared.com/file/131980362/460bdafe/Testvcomp10.ht ml (excel) http://www.4shared.com/file/131980512/dc7308b/Testvcomp10.html (txt) Cheers, Aditi -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ 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. -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol -- End Forwarded Message -- -- A Singh aditi.si...@bristol.ac.uk School of Biological Sciences University of Bristol __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
[R] Predicting the Present with R at Google
I thought some R-help readers might enjoy seeing the paper by Hal Varian on predicting the present using R and Google Trends that is linked via the following blog comment: http://googleresearch.blogspot.com/2009/04/predicting-present-with-google-trends.html Apologies in advance if this has already been mentioned, I didn't see it in the achives. -- View this message in context: http://www.nabble.com/Predicting-the-Present-with-R-at-Google-tp25513381p25513381.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] missing values at a combination of two factors
Dear All, I have two factors: GROUP and PATIENT, where PATIENT is nested within GROUP. levels(example$GROUP) [1] 0 1 2 3 4 levels(example$PATIENT) [1] 1 2 3 There are three observations at each combination of these factors. However, there are no observations for PATIENT = 3 and GROUP = 4. table(example$GROUP, example$PATIENT) 1 2 3 0 3 3 3 1 3 3 3 2 3 3 3 3 3 3 3 4 3 3 0 When I run an ANOVA on these factors fit - lm(ABUNDANCE ~ GROUP + GROUP/PATIENT, data = example) I receive an NA in the parameter estimate corresponding to missing combination. summary(fit) Call: lm(formula = ABUNDANCE ~ GROUP + GROUP/PATIENT, data = example) Residuals: Min 1Q Median 3Q Max -1.2985 -0.4284 0.1998 0.3663 0.8585 Coefficients: (1 not defined because of singularities) Estimate Std. Error t value Pr(|t|) (Intercept) 13.183200.37333 35.312 2e-16 *** GROUP1 0.618610.52797 1.1720.251 GROUP2 0.189930.52797 0.3600.722 GROUP3 0.271630.52797 0.5140.611 GROUP4 -0.281730.52797 -0.5340.598 GROUP0:PATIENT2 0.126430.52797 0.2390.812 GROUP1:PATIENT2 -0.726170.52797 -1.3750.180 GROUP2:PATIENT2 -0.263600.52797 -0.4990.621 GROUP3:PATIENT2 0.042930.52797 0.0810.936 GROUP4:PATIENT2 0.598120.52797 1.1330.267 GROUP0:PATIENT3 0.281470.52797 0.5330.598 GROUP1:PATIENT3 -0.364520.52797 -0.6900.496 GROUP2:PATIENT3 -0.347370.52797 -0.6580.516 GROUP3:PATIENT3 -0.551190.52797 -1.0440.305 GROUP4:PATIENT3 NA NA NA NA --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 0.6466 on 28 degrees of freedom Multiple R-squared: 0.1867, Adjusted R-squared: -0.191 F-statistic: 0.4943 on 13 and 28 DF, p-value: 0.9093 I need to perform a contrast on various levels of GROUP/PATIENT, and the NA prevents me from doing so. Is there a way to manipulate the levels of the factors so that an NA is not present in the parameter estimates? Thanks, Tim [[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] lapply - value changes as parameters to function?
Thanks Jim. That did the trick. I had wondered in passing about that as all the examples in the ?lapply page were pretty simple and each time it was the first argument. However I didn't read that this was a requirement so I didn't go there. Is this really stated and I just cannot see it or possibly should some extra verbiage be added. (Heck - it's Open Source - guess I could do it myself and submit it to who ever manages that stuff!) Again, thanks! Cheers, Mark On Fri, Sep 18, 2009 at 11:06 AM, jim holtman jholt...@gmail.com wrote: Change the order of the parameters in your function so that Lookback is the first one. The first parameter of the lapply is what is passed to the function as its first parameter. Now just have ResultList - lapply(x, DoAvgCalcs, IndexData=IndexData, SampleSize=TestSamples, Iteration=TestIterations) On Fri, Sep 18, 2009 at 1:32 PM, Mark Knecht markkne...@gmail.com wrote: Phil, Thanks for the reply. Your suggestion is actually the one I started with (assuming I'm understanding you) but I didn't seem to even get down into my function, or the error message is from other place within my function that I haven't discovered yet: x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in rep(NA, k) : invalid 'times' argument I should write some fake code that gives you all the depth so we could jsut run it. If no on eelse sees the answer then I'll be back later with more code that completely runs. Thanks, Mark On Fri, Sep 18, 2009 at 10:16 AM, Phil Spector spec...@stat.berkeley.edu wrote: Mark - The l in lapply refers to that fact that it will *return* a list, not that it wants a list for input. You could input a list, but then each element of the list would be one of the values you wanted processed. So I think you want x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) This will return a list whose elements are the result of calling the DoAvgCalcs function with each value contained in x. If they were all the same length, and you wanted them simplified to a matrix, you could use sapply (s for simplify) instead of lapply (l for list). - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 18 Sep 2009, Mark Knecht wrote: Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
[R] Ruuid missing Gtk glib.dylib
Hi,
I get an error indicating a missing library from the package 'Ruuid'.
I suppose this means I should install RGtk. I just thought I'd
document the error. Maybe a dependency entry is missing?
R 2.9.0
OS X 10.5.8
Thanks,
- chris
biocLite('Ruuid')
Using R version 2.9.0, biocinstall version 2.4.12.
Installing Bioconductor version 2.4 packages:
[1] Ruuid
Please wait...
Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
trying URL
'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib/2.9/Ruuid_1.22.0.tgz'
Content type 'application/x-gzip' length 66343 bytes (64 Kb)
opened URL
==
downloaded 64 Kb
The downloaded packages are in
/var/folders/n3/n3Xa3tJRED4hkXZd5y3QWk+++TI/-Tmp-//RtmpkHt9YC/downloaded_packages
library(Ruuid)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so,
6): Library not loaded:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/libglib-2.0.0.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so
Reason: image not found
Error: package/namespace load failed for 'Ruuid'
Error in args(getuuid) : no function to return from, jumping to top level
J. Christopher Bare
Institute for Systems Biology
__
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] Ruuid missing Gtk glib.dylib
We are in the same boat (which I think is caused in my case by never
having been successful in installing a 64 bit version of Gtk+ on my
Mac, if such a beast exists). My errors are a tad bit different than
yours. Are you attempting this from an R64 version? I get no error
when I install Ruuid from the BioConductor binary repository and then
execute:
library(Ruuid) # no errors
(This question should have gone to either the Bioconductor mailing
list or the Mac-sig.list)
--
David.
sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin9.8.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Ruuid_1.22.0
loaded via a namespace (and not attached):
[1] tools_2.9.2
This was what happend when I ran the following code in the R64 GUI
console:
source(http://bioconductor.org/biocLite.R;)
biocLite(Ruuid)
Using R version 2.9.2, biocinstall version 2.4.12.
Installing Bioconductor version 2.4 packages:
[1] Ruuid
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
argument 'lib' is missing: using '/Users/davidwinsemius/Library/R/
2.9/library'
Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.9
trying URL
'http://bioconductor.org/packages/2.4/bioc/bin/macosx/leopard/contrib/2.9/Ruuid_1.22.0.tgz'
Content type 'application/x-gzip' length 70572 bytes (68 Kb)
opened URL
==
downloaded 68 Kb
The downloaded packages are in
/var/folders/xS/xSUsVXTIHEiP7OLJg2OXmU+++TI/-Tmp-//RtmpoaE55s/
downloaded_packages
library(Ruuid)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Users/davidwinsemius/Library/R/2.9/
library/Ruuid/libs/x86_64/Ruuid.so':
dlopen(/Users/davidwinsemius/Library/R/2.9/library/Ruuid/libs/
x86_64/Ruuid.so, 6): Library not loaded: /Library/Frameworks/GTK
+.framework/Versions/2.14.X11/Resources/lib/libglib-2.0.0.dylib
Referenced from: /Users/davidwinsemius/Library/R/2.9/library/Ruuid/
libs/x86_64/Ruuid.so
Reason: no suitable image found. Did find:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/
libglib-2.0.0.dylib: no matching architecture in universal wrapper
Error: package/namespace load failed for 'Ruuid'
On Sep 18, 2009, at 2:58 PM, Christopher Bare wrote:
Hi,
I get an error indicating a missing library from the package 'Ruuid'.
I suppose this means I should install RGtk. I just thought I'd
document the error. Maybe a dependency entry is missing?
R 2.9.0
OS X 10.5.8
Thanks,
- chris
biocLite('Ruuid')
Using R version 2.9.0, biocinstall version 2.4.12.
Installing Bioconductor version 2.4 packages:
[1] Ruuid
Please wait...
Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
trying URL
'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib/2.9/Ruuid_1.22.0.tgz'
Content type 'application/x-gzip' length 66343 bytes (64 Kb)
opened URL
==
downloaded 64 Kb
The downloaded packages are in
/var/folders/n3/n3Xa3tJRED4hkXZd5y3QWk+++TI/-Tmp-//RtmpkHt9YC/
downloaded_packages
library(Ruuid)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/
Ruuid.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/
i386/Ruuid.so,
6): Library not loaded:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/
libglib-2.0.0.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/
Ruuid.so
Reason: image not found
Error: package/namespace load failed for 'Ruuid'
Error in args(getuuid) : no function to return from, jumping to top
level
J. Christopher Bare
Institute for Systems Biology
__
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] Error: length(f1) == length(f2) is not TRUE
Bill, It worked!!! lmer(data=vcdf, peg.no~1 + (1|family/P1L55)) Linear mixed model fit by REML Formula: peg.no ~ 1 + (1 | family/P1L55) Data: vcdf AIC BIC logLik deviance REMLdev 2981 2997 -1487 29762973 Random effects: Groups NameVariance Std.Dev. P1L55:family (Intercept) 4.6659e-11 6.8308e-06 family (Intercept) 8.7571e+01 9.3579e+00 Residual 9.2269e+01 9.6057e+00 Number of obs: 390, groups: P1L55:family, 82; family, 57 Fixed effects: Estimate Std. Error t value (Intercept) 96.577 1.37670.2 It seems as if all along it was the na.action=na.exclude that was working against me, because it probably threw out NAs in a way that made column lengths incompatible. It seemed to work with some other models I had tried, but here it was clearly a problem. Your example was brilliant for breaking it down. Thanks a huge bunch, and cheers! Aditi --On 18 September 2009 11:40 -0700 William Dunlap wdun...@tibco.com wrote: From: A Singh [mailto:aditi.si...@bristol.ac.uk] Sent: Friday, September 18, 2009 11:24 AM To: William Dunlap Subject: RE: [R] Error: length(f1) == length(f2) is not TRUE Yup, they are all factors- and its still doesn't work. Getting to the stage where I can use 'summary()' is the problem- the error stalls the process before a summary can be output. I meant to get a summary of the input, vcdf, not of the output of lmer. Make sure that vcdf$family and all the vcdf$P* things are factors. Here is a short example that gives an error like yours. Without seeing your data I can't say for sure yours is similar. You need to at least show the output of summary(vcdf). library(lme4) d - data.frame(y=log(1:36), expand.grid(g2=1:2,g3=11:13,g6=101:106)) sapply(d,class) yg2g3g6 numeric integer integer integer lmer(data=d, y~1 + (1|g2)) Linear mixed model fit by REML Formula: y ~ 1 + (1 | g2) Data: d AIC BIC logLikdeviance 98.784754747615 103.53531156298 -46.392377373808 90.735690977203 REMLdev 92.784754747615 Random effects: Groups NameVariance Std.Dev. g2 (Intercept) 0.000 0.000 Residual 0.748809753022119 0.865337941513094 Number of obs: 36, groups: g2, 2 Fixed effects: Estimate Std. Error t value (Intercept) 2.65888040394842 0.14422299035915 18.435898446754 lmer(data=d, y~1 + (1|g2/g6)) Error: length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In g6:g2 : numerical expression has 36 elements: only the first used 2: In g6:g2 : numerical expression has 36 elements: only the first used Now change the d$g* columns to be factors with d[2:4] - lapply(d[2:4],factor) # and check with summary(d) summary(d) # or sapply(d,class) y g2 g3 g6 Min. :0.000 1:18 11:12 101:6 1st Qu.:2.27624496408 2:18 12:12 102:6 Median :2.91740536853 13:12 103:6 Mean :2.65888040395 104:6 3rd Qu.:3.30492877705 105:6 Max. :3.58351893846 106:6 lmer(data=d, y~1 + (1|g2)) Linear mixed model fit by REML Formula: y ~ 1 + (1 | g2) Data: d AIC BIC logLikdeviance 98.784754747615 103.53531156298 -46.392377373808 90.735690977203 REMLdev 92.784754747615 Random effects: Groups NameVariance Std.Dev. g2 (Intercept) 0.000 0.000 Residual 0.748809753022119 0.865337941513094 Number of obs: 36, groups: g2, 2 Fixed effects: Estimate Std. Error t value (Intercept) 2.65888040394842 0.14422299035915 18.435898446754 lmer(data=d, y~1 + (1|g2/g6)) Linear mixed model fit by REML Formula: y ~ 1 + (1 | g2/g6) Data: d AIC BIC logLikdeviance 63.097147876589 69.431223630414 -27.548573938295 54.113964539198 REMLdev 55.097147876589 Random effects: Groups NameVariance Std.Dev. g6:g2(Intercept) 0.6928532833231706 0.832378089165717 g2 (Intercept) 0. 0.000 Residual 0.0955486486847417 0.309109444509128 Number of obs: 36, groups: g6:g2, 12; g2, 2 Fixed effects: Estimate Std. Error t value (Intercept) 2.6588804039484 0.2457461012621 10.819623954533 I tried the same code, but using 'family' and P1L55 as independent random factors, and that works. (I actually tried this with a new marker P1L74) try(fit-lmer(peg.no~1 + (1|family) + (1|P1L74), na.action=na.exclude)) summary(fit) Linear mixed model fit by REML Formula: peg.no ~ 1 + (1 | family) + (1 | P1L74) AIC BIC logLik deviance REMLdev 2981 2997 -1487 29762973 Random effects: Groups NameVariance Std.Dev. family (Intercept) 87.86380 9.37357 P1L74
Re: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up)
Thanks Duncan and Greg for the replies so far. Duncan, many thanks for your continued work on this; please let us (or at least me) know when your package will be available. Greg, the DCOM option sounds great, but we run R on a Linux cluster, and therefore it would be good to be able to write the reports in MS Word XML format from there without relying on Windows-specific functionality. Kind regards, Tobias On Fri, Sep 18, 2009 at 7:23 PM, Greg Snow greg.s...@imail.org wrote: I read the original post as asking if there is something like odfWeave that works for msword (I assumed windows, but I guess they could be asking about MSword on other platforms, it just sounds like a windows shop). But yes, sword only works on windows (and is in beta version still) and uses a different interface from the standard sweave and odfWeave (process from inside word rather than process a file through R). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: Duncan Temple Lang [mailto:dun...@wald.ucdavis.edu] Sent: Friday, September 18, 2009 11:00 AM To: Greg Snow Cc: Tobias Sing; r help Subject: Re: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up) I believe that their approach is based on DCOM and the post was about Office Open XML. We have had the ability to do this via DCOM for at least 6 years, but unfortunately DCOM is limited to Windows. Greg Snow wrote: The people who brought us rexcel are working on sword which is a sweave for ms word, the current version is at: http://rcom.univie.ac.at/download.html hope this helps, __ 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] Ruuid missing Gtk glib.dylib
Hi Chris --
Christopher Bare wrote:
Hi,
I get an error indicating a missing library from the package 'Ruuid'.
I suppose this means I should install RGtk. I just thought I'd
document the error. Maybe a dependency entry is missing?
R 2.9.0
OS X 10.5.8
Thanks,
- chris
biocLite('Ruuid')
Using R version 2.9.0, biocinstall version 2.4.12.
Installing Bioconductor version 2.4 packages:
[1] Ruuid
Please wait...
Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
trying URL
'http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib/2.9/Ruuid_1.22.0.tgz'
Content type 'application/x-gzip' length 66343 bytes (64 Kb)
opened URL
==
downloaded 64 Kb
The downloaded packages are in
/var/folders/n3/n3Xa3tJRED4hkXZd5y3QWk+++TI/-Tmp-//RtmpkHt9YC/downloaded_packages
library(Ruuid)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so':
dlopen(/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so,
6): Library not loaded:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/libglib-2.0.0.dylib
Referenced from:
/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/i386/Ruuid.so
Reason: image not found
Error: package/namespace load failed for 'Ruuid'
Error in args(getuuid) : no function to return from, jumping to top level
You're installing a binary (pre-built) package, and your system has to
play by the same rules as the system that was used to build the package.
So you'll need to follow the directions here
http://r.research.att.com/#other
or, as a more robust long-term solution, configure your system to build
packages from source (also on the page linked above) and use
biocLite(Ruuid, type=source)
Martin
J. Christopher Bare
Institute for Systems Biology
__
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] Emacs and ESS help
Hi, I decided to try emacs and ess with R, but to no avail. How are these things suppose to work with R - or work, period? I downloaded the latest windows versions of each and installed them as the documentation says. But then the documentation for ess says to add (require 'ess-site) to /.emacs and restart emacs. Where is /.emacs I opened the ess-site.el file and it also says to add the line to /.emacs. Can anyone help me on this? And once I get this problem fixed, how do I interact with R or any other package (S+, Stata, SAS, etc.)? I'm running Windows Vista on a Thinkpad. Any and all help is deeply appreciated. Thanks, Walt -- Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 dataanalyt...@earthlink.net www.dataanalyticscorp.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] Writing Reports from R in Microsoft Office Open XML format (follow-up)
That website says: Our components and applications for seamless integration allow to embed statistics software from the R project and data analysis and computation services from Scilab into applications on Microsoft Windows, MacOS X and Linux. Does anyone know if the claim to be supporting versions for Mac and Linux has substance? None of the applications that I attempted accessing from that download site appear to be *NIX compatible. They are all .exe files or require statconnDCOM, which I do not believe runs outside of WinXP. -- David On Sep 18, 2009, at 12:51 PM, Greg Snow wrote: The people who brought us rexcel are working on sword which is a sweave for ms word, the current version is at: http://rcom.univie.ac.at/download.html 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 Tobias Sing Sent: Friday, September 18, 2009 9:39 AM To: Duncan Temple Lang; r help; max.k...@pfizer.com Subject: [R] Writing Reports from R in Microsoft Office Open XML format (follow-up) Dear Duncan and other R users, The department in which I work will soon make some decisions to improve our reporting. Since I hope that our solution will support R and Sweave-like functionality (otherwise it wouldn't be an improvement), I hope it's ok to repeat my question back from June if there are any news on an odfWeave-like package for weaving Microsoft Word documents? (in the Office Open XML format). Duncan, any news on the package? I am also asking on the list again because there might be developments by others in parallel to what Duncan has mentioned below? (For example, maybe someone is thinking of adapting Max Kuhn's excellent odfWeave package to support the XML format of Microsoft Word?) Kind regards, Tobias On Tue, Jun 9, 2009 at 4:22 PM, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Yes. We will release a version in the next few weeks when I have time to wrap it all up. There is also a Docbook-based version that uses R extensions to Docbook for authoring structured documents. D. Tobias Sing wrote: Dear all, has someone implemented functionality for writing reports from R in Office Open XML format (*), similar to what odfWeave does for the ODF format of OpenOffice? It would be great to have a kind of ooxmlWeave at least for those of us who are forced to work in an MS ecosystem. (*) Office Open XML is the default, XML-based, file format for MS Word: http://en.wikipedia.org/wiki/Office_Open_XML Kind regards, Tobias __ 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-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] lapply - value changes as parameters to function?
It **IS** stated explicitly, though perhaps not so obviously, already in the help file, In the Note section at the end it says: ... This means that the recorded call is always of the form FUN(X[[0L]], ...), with 0L replaced by the current integer index. ... So you need to read more carefully ... Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Mark Knecht Sent: Friday, September 18, 2009 11:55 AM To: jim holtman Cc: r-help; Phil Spector Subject: Re: [R] lapply - value changes as parameters to function? Thanks Jim. That did the trick. I had wondered in passing about that as all the examples in the ?lapply page were pretty simple and each time it was the first argument. However I didn't read that this was a requirement so I didn't go there. Is this really stated and I just cannot see it or possibly should some extra verbiage be added. (Heck - it's Open Source - guess I could do it myself and submit it to who ever manages that stuff!) Again, thanks! Cheers, Mark On Fri, Sep 18, 2009 at 11:06 AM, jim holtman jholt...@gmail.com wrote: Change the order of the parameters in your function so that Lookback is the first one. The first parameter of the lapply is what is passed to the function as its first parameter. Now just have ResultList - lapply(x, DoAvgCalcs, IndexData=IndexData, SampleSize=TestSamples, Iteration=TestIterations) On Fri, Sep 18, 2009 at 1:32 PM, Mark Knecht markkne...@gmail.com wrote: Phil, Thanks for the reply. Your suggestion is actually the one I started with (assuming I'm understanding you) but I didn't seem to even get down into my function, or the error message is from other place within my function that I haven't discovered yet: x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in rep(NA, k) : invalid 'times' argument I should write some fake code that gives you all the depth so we could jsut run it. If no on eelse sees the answer then I'll be back later with more code that completely runs. Thanks, Mark On Fri, Sep 18, 2009 at 10:16 AM, Phil Spector spec...@stat.berkeley.edu wrote: Mark - The l in lapply refers to that fact that it will *return* a list, not that it wants a list for input. You could input a list, but then each element of the list would be one of the values you wanted processed. So I think you want x = seq(5:20) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) This will return a list whose elements are the result of calling the DoAvgCalcs function with each value contained in x. If they were all the same length, and you wanted them simplified to a matrix, you could use sapply (s for simplify) instead of lapply (l for list). - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Fri, 18 Sep 2009, Mark Knecht wrote: Hi, I'm trying to get better at things like lapply but it still stumps me. I have a function I've written, tested and debugged using individual calls to the function, ala: ResultList5 = DoAvgCalcs(IndexData, Lookback=5, SampleSize=TestSamples , Iterations=TestIterations ) ResultList8 = DoAvgCalcs(IndexData, Lookback=8, SampleSize=TestSamples , Iterations=TestIterations ) ResultList13 = DoAvgCalcs(IndexData, Lookback=13, SampleSize=TestSamples , Iterations=TestIterations ) ResultList21 = DoAvgCalcs(IndexData, Lookback=21, SampleSize=TestSamples , Iterations=TestIterations ) The function returns a list of numbers which I use for processing later. I'd like to run this on a longer list (100's of values for Lookback) so my thought was to try lapply but so far I cannot get the darn thing right. Let's say I want to run the function on a string of values: BarTestList = list(seq(5:20)) So my thought was something like: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) which fails down lower complaining that what it's receiving for Lookback isn't an integer: x = list(seq(5:20)) ResultList = lapply(x, DoAvgCalcs, IndexData, Lookback=x, SampleSize=TestSamples , Iterations=TestIterations ) Error in MyLag(df$Close, Lookback) : (list) object cannot be coerced to type 'integer' Can someone suggest how to do this correctly? Thanks, Mark __ 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
[R] Unable to install lme4
I am unable to install package lme4, after several attempts to do so using various repository URLs. Just to make sure everything works fine with proxy, connection, etc, I installed ggplot2 and it worked fine. I am using command install.packages(lme4, lib=/myRlibs), optionally using contrib argument with different URLs. Error message the I get is Warning message; In install.packages(lme4, lib=/myRlibs) package 'lme4' is not available Some other details, not sure how relevant are: getOption(repos) returns http://lib.stat.cmu.edu/R/CRAN; I tried setting contrib to various other URL, such as http://cran.mtu.edu/src/contrib; or Berkeley URL, but with no success. Actually, when I did available.packages() on this repos, I didn't see lme4 in the package indices. My machine has x86_64bit RedHat Linux. Would appreciate any tips or directions, Thanks Andre __ 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.
