[R] numerical summaries across variables.
Hi Every one, I have a dataframe class with name, sex, age, height, Weight. if i caluclate summary statistics with the below code numSummary(class[,c(Height, Weight)], groups=class$Name, statistics=c(mean, sd, quantiles), quantiles=c(0, .25,.5,.75,1)) iam getting output like this Variable: Height mean sd 0% 25% 50% 75% 100% n Alfred 69.0 NA 69.0 69.0 69.0 69.0 69.0 1 Alice 56.5 NA 56.5 56.5 56.5 56.5 56.5 1 Barbara 65.3 NA 65.3 65.3 65.3 65.3 65.3 1 Carol 62.8 NA 62.8 62.8 62.8 62.8 62.8 1 Variable: Weight mean sd0% 25% 50% 75% 100% n Alfred 112.5 NA 112.5 112.5 112.5 112.5 112.5 1 Alice84.0 NA 84.0 84.0 84.0 84.0 84.0 1 Barbara 98.0 NA 98.0 98.0 98.0 98.0 98.0 1 Carol 102.5 NA 102.5 102.5 102.5 102.5 102.5 1 now my question is i want output like this height weight Alfred mean sd 0% 25% 50% 75% 100% n Alice mean sd 0% 25% 50% 75% 100% n Barbara mean sd 0% 25% 50% 75% 100% n it is nothing but a numerical summaries across varibales. is it possible. Thanks in Advance. -- View this message in context: http://www.nabble.com/numerical-summaries-across-variables.-tp25234915p25234915.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] numerical summaries across variables.
Hi here, may be you can play with reshape, or may be aggregate and reshape... good luck milton On Tue, Sep 1, 2009 at 2:17 AM, rajclinasia r...@clinasia.com wrote: Hi Every one, I have a dataframe class with name, sex, age, height, Weight. if i caluclate summary statistics with the below code numSummary(class[,c(Height, Weight)], groups=class$Name, statistics=c(mean, sd, quantiles), quantiles=c(0, .25,.5,.75,1)) iam getting output like this Variable: Height mean sd 0% 25% 50% 75% 100% n Alfred 69.0 NA 69.0 69.0 69.0 69.0 69.0 1 Alice 56.5 NA 56.5 56.5 56.5 56.5 56.5 1 Barbara 65.3 NA 65.3 65.3 65.3 65.3 65.3 1 Carol 62.8 NA 62.8 62.8 62.8 62.8 62.8 1 Variable: Weight mean sd0% 25% 50% 75% 100% n Alfred 112.5 NA 112.5 112.5 112.5 112.5 112.5 1 Alice84.0 NA 84.0 84.0 84.0 84.0 84.0 1 Barbara 98.0 NA 98.0 98.0 98.0 98.0 98.0 1 Carol 102.5 NA 102.5 102.5 102.5 102.5 102.5 1 now my question is i want output like this height weight Alfred mean sd 0% 25% 50% 75% 100% n Alice mean sd 0% 25% 50% 75% 100% n Barbara mean sd 0% 25% 50% 75% 100% n it is nothing but a numerical summaries across varibales. is it possible. Thanks in Advance. -- View this message in context: http://www.nabble.com/numerical-summaries-across-variables.-tp25234915p25234915.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. [[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] decimal sign
Hello! Is it possible to change the decimal sign in the histogram created by hist() from dot to comma? Thanks for any help! Alexandros __ 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] permutation and reshuffling
Hi, I'm looking for an efficient code that will enable me to reshuffle data (phenotype) for certain number of individuals and creating a loop that will randomly simulate it for 1 times *(permutation)*. I also need to find how I keep the information (p value for each SNP) gathered for all the 1 iterations. My data set looks like this (n=500): Individual # Phenotype SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 1 0 T T G G A C G T A A T C 2 1 A T C G A C G T A G T C Many thanks, Jonathan [[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] Function for all 2^N subsets of N
Greetings all! I have been searching the Site for a function, say subsets, such that for instance subsets(10) would return a (say) matrix of indices to the 2^10 subsets of N items -- perhaps in the form of 2^10 rows each of which is 10 entries each either TRUE or FALSE. Or 1 or 0. Or ... I can of course write my own, using good old looping technology or similar, but it would be good to find one which did it quick and snappy, at the compiled level. A Site Search in Function on all subsets didn't seem to yield anything of the kind, which surprised me. Maybe I overlooked something ... (This is prompted by the recent OT discussion on HT vs. HH, to which I want to respond later). With thanks, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 01-Sep-09 Time: 09:09:09 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Function for all 2^N subsets of N
Maybe expand.grid( rep( list( 0:1), 10)) does what you want. Best regards -- Gerrit - AOR Dr. Gerrit Eichner Mathematical Institute, Room 305 E gerrit.eich...@math.uni-giessen.de Justus-Liebig-University Giessen Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany Fax: +49-(0)641-99-32109 http://www.uni-giessen.de/~gcb7 - On Tue, 1 Sep 2009, ted.hard...@manchester.ac.uk wrote: Greetings all! I have been searching the Site for a function, say subsets, such that for instance subsets(10) would return a (say) matrix of indices to the 2^10 subsets of N items -- perhaps in the form of 2^10 rows each of which is 10 entries each either TRUE or FALSE. Or 1 or 0. Or ... I can of course write my own, using good old looping technology or similar, but it would be good to find one which did it quick and snappy, at the compiled level. A Site Search in Function on all subsets didn't seem to yield anything of the kind, which surprised me. Maybe I overlooked something ... (This is prompted by the recent OT discussion on HT vs. HH, to which I want to respond later). With thanks, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 01-Sep-09 Time: 09:09:09 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] data frame
HI, R user,
I generate the vectors with the same length. I want to put each vector into
each column of data frame. Why it doesnt work`?
rm-data.frame()
for(a in 1:6){
rm[,a]-getmeasure(p1,a,speech)
}
thanks a lot
Tammy
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Re: [R] Function for all 2^N subsets of N
On 01-Sep-09 08:33:41, Gerrit Eichner wrote: Maybe expand.grid( rep( list( 0:1), 10)) does what you want. Best regards -- Gerrit Thanks! That does seem to do the job. I hadn't thought of expand.grid(). Ted. On Tue, 1 Sep 2009, ted.hard...@manchester.ac.uk wrote: Greetings all! I have been searching the Site for a function, say subsets, such that for instance subsets(10) would return a (say) matrix of indices to the 2^10 subsets of N items -- perhaps in the form of 2^10 rows each of which is 10 entries each either TRUE or FALSE. Or 1 or 0. Or ... I can of course write my own, using good old looping technology or similar, but it would be good to find one which did it quick and snappy, at the compiled level. A Site Search in Function on all subsets didn't seem to yield anything of the kind, which surprised me. Maybe I overlooked something ... (This is prompted by the recent OT discussion on HT vs. HH, to which I want to respond later). With thanks, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 01-Sep-09 Time: 09:09:09 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 01-Sep-09 Time: 09:42:18 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? Thanks -- 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] List of tags in roxygen and use for S4 classes?
Hi is there a list of all roxygen tags which are available? I couldn't find them. I am asking specifically towards the use of roxygen in documenting S4 classes - is that implemented yet (i am using roxygen 0.1 from CRAN at the moment)? Thanks Rainer -- Rainer M. Krug, Centre of Excellence for Invasion Biology, Stellenbosch University, South Africa __ 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] Offtopic, HT vs. HH in coin flips
On 31-Aug-09 19:16:33, Erik Iverson wrote:
Dear R-help,
Could someone please try to explain this paradox to me? What is
more likely to show up first in a string of coin tosses, Heads
then Tails, or Heads then Heads?
##generate 2500 strings of random coin flips
ht - replicate(2500,
paste(sample(c(H, T), 100, replace = TRUE),
collapse = ))
## find first occurrence of HT
mean(regexpr(HT, ht))+1#mean of HT position, 4
## find first occurrence of HH
mean(regexpr(HH, ht))+1#mean of HH position, 6
FYI, this is not homework, I have not been in school in years.
I saw a similar problem posed in a blog post on the Revolutions R
blog, and although I believe the answer, I'm having a hard time
figuring out why this should be?
Thanks,
Erik Iverson
Be very careful about the statement of the problem!
[1] The probability that HH will occur first (i.e. before HT)
is the same as the probability that HT will occur first (i.e.
before HH).
[2] However, the probability that the first occurrence of HT
will be on a given position of the H is generally not the same
as the probability that the first occurrence of HH will be on
the same position of the first H.
[1]: At the first occurrence of (either HH or HT), there is
an initial string S, ending in an H, followed by either an H
(for HH) or a T (for HT). Both are equally likely.
So the probability that the first occurrence of (either HH or HT)
is an HH is the same as the probability that it is an HT.
[2]: (A) the first occurrence of an HH is in a sequence of
any collection of H and T provided there is no HH in the
sequence, and the last is H, followed by H.
However, HT is allowed to occur in the sequence.
But (B) the first occurrence of an HT is in a sequence of
(zero or more T) followed by (1 or more H) followed by T.
This is the only pattern in which HT does not occur prior to
the final HT.
Similarly, HH is allowed to pccur in the sequence.
The reason that, in general, the probability of HH first occuring
at a given position is different from the probability if HT first
occurring at that position lies in the differences between the
number of possible sequences satisfying (A), and the number of
possible sequences satisfying (B).
The first few cases (HH or HT first occurring at (k+1), so
that the position of the first H in HH or HT is at k) are,
with their probabilities:
k=1: HH HT
1/41/4
K=2: THH HHT
THT
1/8 2/8
k=3: TTHH HHHT
HTHH THHT
TTHT
2/16 3/16
k=4:TTTHH T
THTHH THHHT
HTTHH TTHHT
TTTHT
3/32 4/32
The HT case is simple:
P.HT[k] = Prob(1st HT at (k+1)) = k/(2^(k+1))
Exercise for the reader: Sum(P.HT) = 1
The HH case is more interesting. Experimental scribblings on
parer threw up an hypothesis, which I decided to explore in R.
Thanks to Gerrit Eichner for suggestion the use of expand.grid()!
## Function to count sequences giving 1st HH on throw k+1
countHH - function(k){
M - as.matrix(expand.grid(rep(list(0:1),k)))
ix - (M[,k]==1) ## k must be an H (then k+1 will be H)
for(i in (1:(k-1))){ ix-ix( !((M[,i]==1)(M[,i+1]==1)) ) }
sum(ix)
## list(Count=sum(ix),Which=M[ix,])
}
Now, ignoring the case k=1:
HHcounts - NULL
for(i in (2:12)){ HHcounts-c(HHcounts,countHH(i)) }
rbind((3:13),HHcounts)
# [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
#3456789 10 111213
#HHcounts12358 13 21 34 5589 144
Lo and Behold, we have a Fibonnaci sequence! Another exercise for
the reader ...
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 01-Sep-09 Time: 10:38:58
-- XFMail --
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Re: [R] Google style
Duncan Murdoch wrote:
On 8/31/2009 11:50 AM, Mark Knecht wrote:
On Mon, Aug 31, 2009 at 6:36 AM, Terry Therneauthern...@mayo.edu
wrote:
SNIP
The authors borrowed so much else from C, the semicolon would have been
good too.
Something I have thought myself.
I know real R coders will chuckle
I'd say cringe, rather than chuckle. This is going to make you waste
a lot of time some day, when you stare and stare at code like Terry's
and can't figure out what's wrong with it:
zed - function(x,y,z) {
x + y
+z;
}
The value of the function is +z, not x+y+z, even though the C part of
your brain made you type it that way and reads it as one statement in
the body, not two.
This is getting interesting. One habit I have developed in R to
emphasize a line continuation is to always write the above as:
zed-function(x,y,z) {
x+y+
z
}
The trailing operator signalling to me and the interpreter that there's
more to come. A semicolon after the z would be innocuous. Now I know
that this marks me as a crabby old fart who learned to program on
Hollerith cards where there had to be firm conventions on when a line of
code ended. Still, given the moiety of global warming attributable to
endless discussions about how many spaces should be used for
indentation, I think the use of the semicolon as a personal aid to
interpretation is at worst a harmless affectation.
Jim
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[R] Odp: data frame
Hi
r-help-boun...@r-project.org napsal dne 01.09.2009 10:39:42:
HI, R user,
I generate the vectors with the same length. I want to put each vector
into
each column of data frame. Why it doesnt work`?
rm-data.frame()
for(a in 1:6){
rm[,a]-getmeasure(p1,a,speech)
}
Well, couldn't it be because function getmeasure does not exist?
Error: could not find function getmeasure
and you get another error
rm[,a]
Error in `[.data.frame`(rm, , 1:2) : undefined columns selected
If you need to put a vector to data frame you shall preassign the
structure, columns and rows.
Or you can use list and as.data.frame
Regards
Petr
thanks a lot
Tammy
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Re: [R] numerical summaries across variables.
rajclinasia wrote: Hi Every one, I have a dataframe class with name, sex, age, height, Weight. if i caluclate summary statistics with the below code numSummary(class[,c(Height, Weight)], groups=class$Name, statistics=c(mean, sd, quantiles), quantiles=c(0, .25,.5,.75,1)) iam getting output like this Variable: Height mean sd 0% 25% 50% 75% 100% n Alfred 69.0 NA 69.0 69.0 69.0 69.0 69.0 1 Alice 56.5 NA 56.5 56.5 56.5 56.5 56.5 1 Barbara 65.3 NA 65.3 65.3 65.3 65.3 65.3 1 Carol 62.8 NA 62.8 62.8 62.8 62.8 62.8 1 Variable: Weight mean sd0% 25% 50% 75% 100% n Alfred 112.5 NA 112.5 112.5 112.5 112.5 112.5 1 Alice84.0 NA 84.0 84.0 84.0 84.0 84.0 1 Barbara 98.0 NA 98.0 98.0 98.0 98.0 98.0 1 Carol 102.5 NA 102.5 102.5 102.5 102.5 102.5 1 now my question is i want output like this height weight Alfred mean sd 0% 25% 50% 75% 100% n Alice mean sd 0% 25% 50% 75% 100% n Barbara mean sd 0% 25% 50% 75% 100% n it is nothing but a numerical summaries across varibales. is it possible. Hi Raj, I think you may have to write a print function for this. Assign the result of numSummary to an object, use str to find out the structure and then use cat to display the bits in the format you want. I don't have Rcmdr on my system and haven't been able to install it as R refuses to believe that I have Tcl-Tk available. Thus I can't tell you exactly how to do this. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Corrado wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? I don't think I can answer that. I'd recommend planning to spend some serious time on the decision, and then go by your personal impression. S4 is definitely harder to learn but richer, so don't make the decision too quickly. Take a look at John Chamber's new book, try small projects in each style, etc. 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? S3 is much more limited than S4. It dispatches on just one argument, S4 can dispatch on several. S3 allows you to declare things to be of a certain class with no checks that anything will actually work; S4 makes it easier to be sure that if you say something is of a certain class, it really is. S4 hides more under the hood: if you understand how regular R functions work, learning S3 is easy, but there's still a lot to learn before you'll be able to use S4 properly. 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] Google style
Jim Lemon wrote:
Duncan Murdoch wrote:
On 8/31/2009 11:50 AM, Mark Knecht wrote:
On Mon, Aug 31, 2009 at 6:36 AM, Terry Therneauthern...@mayo.edu
wrote:
SNIP
The authors borrowed so much else from C, the semicolon would have been
good too.
Something I have thought myself.
I know real R coders will chuckle
I'd say cringe, rather than chuckle. This is going to make you waste
a lot of time some day, when you stare and stare at code like Terry's
and can't figure out what's wrong with it:
zed - function(x,y,z) {
x + y
+z;
}
The value of the function is +z, not x+y+z, even though the C part of
your brain made you type it that way and reads it as one statement in
the body, not two.
This is getting interesting. One habit I have developed in R to
emphasize a line continuation is to always write the above as:
zed-function(x,y,z) {
x+y+
z
}
That's a good habit. An alternative is to put parentheses around the
expression:
(x + y
+ z)
will work.
The trailing operator signalling to me and the interpreter that there's
more to come. A semicolon after the z would be innocuous. Now I know
that this marks me as a crabby old fart who learned to program on
Hollerith cards where there had to be firm conventions on when a line of
code ended. Still, given the moiety of global warming attributable to
endless discussions about how many spaces should be used for
indentation, I think the use of the semicolon as a personal aid to
interpretation is at worst a harmless affectation.
I think it's worse. To me, it's like putting in a comment that is
wrong, or writing code like this:
one - 2
x - x + one
Code has meaning, it's not just a bunch of binary instructions to the
computer. If the meaning and the look of the code clash, it is going to
lead to problems.
Duncan Murdoch
Jim
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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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Re: [R] Google style
On 01-Sep-09 10:25:53, Duncan Murdoch wrote:
Jim Lemon wrote:
Duncan Murdoch wrote:
On 8/31/2009 11:50 AM, Mark Knecht wrote:
On Mon, Aug 31, 2009 at 6:36 AM, Terry Therneauthern...@mayo.edu
wrote:
SNIP
The authors borrowed so much else from C, the semicolon would have
been good too.
Something I have thought myself.
I know real R coders will chuckle
I'd say cringe, rather than chuckle. This is going to make you waste
a lot of time some day, when you stare and stare at code like Terry's
and can't figure out what's wrong with it:
zed - function(x,y,z) {
x + y
+z;
}
The value of the function is +z, not x+y+z, even though the C part of
your brain made you type it that way and reads it as one statement in
the body, not two.
This is getting interesting. One habit I have developed in R to
emphasize a line continuation is to always write the above as:
zed-function(x,y,z) {
x+y+
z
}
That's a good habit. An alternative is to put parentheses around the
expression:
(x + y
+ z)
will work.
The trailing operator signalling to me and the interpreter that
there's more to come. A semicolon after the z would be innocuous.
Now I know that this marks me as a crabby old fart who learned
to program on Hollerith cards where there had to be firm
conventions on when a line of code ended. Still, given the moiety
of global warming attributable to endless discussions about how
many spaces should be used for indentation, I think the use of
the semicolon as a personal aid to interpretation is at worst a
harmless affectation.
I think it's worse. To me, it's like putting in a comment that is
wrong, or writing code like this:
one - 2
x - x + one
Code has meaning, it's not just a bunch of binary instructions to the
computer. If the meaning and the look of the code clash, it is going
to lead to problems.
Duncan Murdoch
And surely that is precisely the point of Jim's use of ;!
It is, in effect, ignored by R; but to Jim it means This marks the
end of a command. Surely useful, and surely not in the same league
as a comment that is wrong. You may see it as noise, but then
you can filter it out.
As one COF to another, I have to say that Jim's posting took me
back to the early days of my own evolution. That was dandy!
(Dinosaurs are not dead yet).
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 01-Sep-09 Time: 11:37:52
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[R] Article on teaching R
I've written a short article on my experiences with teaching R to computational biology graduate students: http://www.ploscompbiol.org/doi/pcbi.1000482 My lecture notes are available as supplementary material, along with the beamer/latex sources (from my web page: http://www.damtp.cam.ac.uk/user/sje30/downloads.html) Stephen -- Stephen Eglen, DAMTP, Centre for Mathematical Sciences Wilberforce Road, Cambridge CB3 0WA, U.K. Tel +44 (0)1223 765 761 s.j.eg...@damtp.cam.ac.uk Fax +44 (0)1223 760 419 http://www.damtp.cam.ac.uk/user/eglen __ 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] decimal sign
On Sep 1, 2009, at 3:25 AM, Alexandros Droseltis wrote: Hello! Is it possible to change the decimal sign in the histogram created by hist() from dot to comma? ?options options(OutDec = ,) Seems to work as described, at least with hist. -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Computer Modern and Sweave
Hello, I have a small but nasty problem with the Computer Modern fonts in connection with Sweave. Instead of giving my own code, it's probably better to look at a well established example. There is a nice introduction to using Sweave at Paul Murrell's website which can be found at: http://www.stat.auckland.ac.nz/~paul/R/CM/CMR.html Essentially, what I need from this page are the following 4 files for creating my final pdf: http://www.stat.auckland.ac.nz/~paul/R/CM/cmTutorial.Rnw ( This example needs the according Tex-package and the files for the symbol faces found at (the links are also given on the site): http://www.ctan.org/tex-archive/help/Catalogue/entries/cm-lgc.html http://www.stat.auckland.ac.nz/~paul/R/CM/cmsyase.afm http://www.stat.auckland.ac.nz/~paul/R/CM/cmsyase.pfb ) Creating the tex-file with R CMD Sweave cmTutorial.Rnw and compiling it with pdflatex cmTutorial.tex yields a perfect plot. BUT, if minus signs appear in the plot, it does not work poperly anymore! Just change the endpoints in the 'histogram' function to 'c(-59.5, 76.5)' ( instead of 'c(59.5, 76.5)' ) and run the two upper commands again. Then, I see a minus sign in the file 'cmTutorial-latticeShow.pdf' but NOT in the 'cmTutorial.pdf'. Very strange is also, that using sth. like mtext(text=-1.987,...) will give me a nice minus-sign in the pdf. ### Did anybody encounter this problem and could possibly help me with this question? How can pdflatex change something in the included pdf? Cheers, Frank -- für nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02 __ 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] Google style
On 9/1/2009 6:37 AM, (Ted Harding) wrote:
On 01-Sep-09 10:25:53, Duncan Murdoch wrote:
Jim Lemon wrote:
Duncan Murdoch wrote:
On 8/31/2009 11:50 AM, Mark Knecht wrote:
On Mon, Aug 31, 2009 at 6:36 AM, Terry Therneauthern...@mayo.edu
wrote:
SNIP
The authors borrowed so much else from C, the semicolon would have
been good too.
Something I have thought myself.
I know real R coders will chuckle
I'd say cringe, rather than chuckle. This is going to make you waste
a lot of time some day, when you stare and stare at code like Terry's
and can't figure out what's wrong with it:
zed - function(x,y,z) {
x + y
+z;
}
The value of the function is +z, not x+y+z, even though the C part of
your brain made you type it that way and reads it as one statement in
the body, not two.
This is getting interesting. One habit I have developed in R to
emphasize a line continuation is to always write the above as:
zed-function(x,y,z) {
x+y+
z
}
That's a good habit. An alternative is to put parentheses around the
expression:
(x + y
+ z)
will work.
The trailing operator signalling to me and the interpreter that
there's more to come. A semicolon after the z would be innocuous.
Now I know that this marks me as a crabby old fart who learned
to program on Hollerith cards where there had to be firm
conventions on when a line of code ended. Still, given the moiety
of global warming attributable to endless discussions about how
many spaces should be used for indentation, I think the use of
the semicolon as a personal aid to interpretation is at worst a
harmless affectation.
I think it's worse. To me, it's like putting in a comment that is
wrong, or writing code like this:
one - 2
x - x + one
Code has meaning, it's not just a bunch of binary instructions to the
computer. If the meaning and the look of the code clash, it is going
to lead to problems.
Duncan Murdoch
And surely that is precisely the point of Jim's use of ;!
It is, in effect, ignored by R; but to Jim it means This marks the
end of a command. Surely useful, and surely not in the same league
as a comment that is wrong. You may see it as noise, but then
you can filter it out.
I think you're missing the point. Using C-like syntax in R is
misleading because you will think it has C-like meaning. You will read
x + y
+ z;
as one statement, not two. (Actually you could argue that in R there are
three statements there, but the third one is empty).
This is harmful in the same way using misleading variable names is
harmful: as long as you're paying attention you'll get it right, but
when you are working on a hard problem and can't devote enough neurons
to this particular task, you'll get it wrong, and have a hard-to-spot
bug in your code. You'll decide you need to split a statement across
two lines, and write it in C style like the statements above, instead of
in correct R syntax.
Duncan Murdoch
As one COF to another, I have to say that Jim's posting took me
back to the early days of my own evolution. That was dandy!
(Dinosaurs are not dead yet).
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 01-Sep-09 Time: 11:37:52
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] R functions that count lines of a files
hi, everyone, do you know if there is a R function that can count the lines of a file without open it? something like wc -l in Unix. Thanks, Xue [[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] R functions that count lines of a files
length(count.fields(foo.txt)) ? xue dong wrote: hi, everyone, do you know if there is a R function that can count the lines of a file without open it? something like wc -l in Unix. Thanks, Xue [[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. -- View this message in context: http://www.nabble.com/R-functions-that-count-lines-of-a-files-tp25239480p25239578.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] Function for all 2^N subsets of N
My first thought was the odometer() function, which is often useful for tasks like this. To my surprise it is not a part of the current R. I wonder why? It shouldn't be an Splus copyright issue as this was a part of my original S distribution (before Splus even existed), and used in an example in one of the early books. Terry T __ 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] Syntax for crossed random effects in nlme
Hello R users, I've read the posts on this topic, and had a look at the R documentation for nlme, but I can't seem to make this work. I'd like to be able to fit a mixed effects model with crossed random effects, but also be able to specify the covariance matrix structure for the residuals. Here's the syntax using the lmer function in lme4 (which doesn't currently allow alternate error covariance structures). Does anybody know how to transform this to work with nlme? fit = lmer(data$DV ~ X + time + (X*time) + (1|Item_Number) + (1|Subject), data) Much appreciated, Ben Amsel -- View this message in context: http://www.nabble.com/Syntax-for-crossed-random-effects-in-nlme-tp25239714p25239714.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] Google's R Style Guide
Corrado wrote:
Thanks Duncan, Spencer,
To clarify, the situation is:
1) I have no reasons to choose S3 on S4 or vice versa, or any other coding
convention
2) Our group has not done any OO developing in R and I would be the first, so
I
can set up the standards
3) I am starting from scratch with a new package, so I do not have any code I
need to re-use.
One consideration might be the domain in which you are doing
development; Bioconductor for instance makes extensive use of S4 and
your efforts at learning to develop S4 would pay off both in your own
code and in understanding other packages.
4) I am an R OO newbie, so whatever I can learn from the beginning what is
better and good for me.
So the questions would be two:
1) What coding style guide should we / I follow? Is the google style guide
good, or is there something better / more prescriptive which makes our
research group life easier?
2) What class type should I use? From what you two say, I should use S3
because is easier to use what are the disadvantages? Is there an
advantages / disadvantages table for S3 and S4 classes?
It seems relevant to compare S3 and S4 code for doing S3-style
programming, leaving more 'advanced' S4 for another day. In S3 I might
define a simple class and method as
makeS3Foo -
function(x=numeric(), y=numeric())
{
if (class(x) != numeric)
stop('x' must be numeric)
if (class(y) != numeric)
stop('y' must be numeric)
l - list(x=x, y=y)
class(l) - S3Foo
l
}
doS3 - function(x, ...) NextMethod(doS3)
doS3.default - function(x, ...) doS3 default
doS3.S3Foo - function(x, ...) doS3 of S3Foo
with an example of use being
doS3(makeS3Foo())
[1] doS3 of S3Foo
I use 'makeS3Foo' as a constructor, so that whenever I make an instance
of what I'm calling class S3Foo, I have some guarantees about its structure.
The S4 implementation might be
setClass(S4Foo, representation(x=numeric, y=numeric))
makeS4Foo -
function(x = numeric(), y=numeric(), ...)
{
new(S4Foo, x=x, y=y, ...)
}
setGeneric(doS4, function(x, ...) standardGeneric(doS4),
useAsDefault=function(x, ...) do default)
setMethod(doS4, S4Foo, function(x, ...) doS4 of S4Foo)
and use with
doS4(makeS4Foo())
[1] doS4 of S4Foo
It seems like the translation between the two is really quite
transparent, and equally arcane to someone new to R.
Some things I get from S4 are a level of automatic type checking
makeS4Foo(x=bar)
Error in validObject(.Object) :
invalid class S4Foo object: invalid object for slot x in class
S4Foo: got class character, should be or extend class numeric
a way of knowing that my 'S4Foo' conforms to expectations -- in S3 I can say
l = list(a=1, b=2)
class(l) - S3Foo
and have no way of knowing whether this is 'valid' or not; in S4 I would
not use this method of creating a class (I'd use my constructor, or
perhaps 'new' if I were being undisciplined, and get type checking as
above) but if I did I'd be able to find
class(l) - S4Foo
validObject(l)
Error in validObject(l) :
invalid class S4Foo object: slots in class definition but not in
object: x, y
an error when I try and access data not in the class (normally I'd have
made a constructor, and not use slot access @ directly)
makeS3Foo()$z
NULL
makeS4Foo()@z
Error: no slot of name z for this object of class S4Foo
and reflection on the class
getClass(S4Foo)
Class “S4Foo” [in .GlobalEnv]
Slots:
Name:x y
Class: numeric numeric
Some of the tools for documenting S3 classes and methods are more mature
than for S4 (e.g., package.skeleton does a better job of making a
package containing my existing S3 code objects, but I usually use
package.skeleton to start a project, not to move existing objects into a
new project). The fact that the class has been declared explicitly means
that I'm expected to document it explicitly (in contrast to, say, the
result of lm(), which is documented only as the return value of the
function) and this then requires decisions about how to group class and
method documentation.
Using more complicated S4 features can be, well, more complicated. But
then these features are not readily available with S3, so...
To touch on a couple of other themes in this thread... Using a '.' in a
variable name seems like a very bad idea, given the way S3 dispatch
works. I like to think of objects as nouns and functions as verbs, and
so prefer to capitalize class names (as though they were proper nouns)
and lower-case function names (so they have a more dynamic sense). And
there are many S4 style issues that are not addressed by the google doc
-- setMethod and setGeneric indentation in particular.
A great feature of emacs-ESS that I've recently discovered (thanks
Deepayan for pointing this out, and also for command completion) is the
C-c C-p command when looking at an Rd file during package development;
it very nicely returns the formatted help page to emacs.
Martin
Re: [R] R2 for SAR and validation
Did you read the posting guide? Your posting is not comprehensible to most of the readers of this list, and you have not explained whether this has anything to do with R, or any of its contributed packages; there are no clues in included code or code snippets illustrating the problem. Your TLA is capable of many interpretations. Finally, if you are asking about spatial autoregression, you might have posted to the R-sig-geo list instead. If you are asking why lagsarlm() in the spdep package does not provide an R2 value in its summary, try using its log likelihood value, and comparing that with logLik() of the equivalent lm() model - this is reported in the summary() of the fitted object. You can calculate a pseudo-R2 by correlating the observed and fitted values, but the likelihood ratio (or comparisons of the AIC) are perhaps better founded. The same measures are found in other implementations (GeoDa, Matlab spatial econometrics toolbox). It is not obvious what you mean by validate in this context. Roger Bivand saniye keser wrote: Hi everyone, How can i obtain R2 for SAR model? and how can i validate the results, can i use the coefficients directly in a simple formula like y=b0+b1*x1+... or do i have to use the complicated formula for SAR (the one with the weight matrix and rho and...)? Thanks for any help! [[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. -- View this message in context: http://www.nabble.com/R2-for-SAR-and-validation-tp25225433p25239901.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 coefficients
Hi, A long time I have some problems to run a SVM - regression. Here an example with the Ozone data that represents very well my own data. data(Ozone, package = mlbench) #I cut the three first variables and splite the data in two parts Ozone- na.omit(Ozone[, -(1:3)]) index - 1:nrow(Ozone) testset - Ozone[104:203,] trainset - Ozone[1:103, ] names(Ozone) # library(e1071) # train svm with RBF kernel and without scale tuneobj = tune.svm(V4 ~ ., data = trainset, gamma = 10^(-6:-3), cost = 10^(1:3)) summary(tuneobj)$best.parameters svm.noscale - svm(V4 ~ ., data = trainset, cost = 1000, gamma = 0.001,scale=FALSE) Parameters: SVM-Type: eps-regression SVM-Kernel: radial cost: 1000 gamma: 0.001 epsilon: 0.1 Number of Support Vectors: 101 # I get 101 support vectors wich seems to be bad because I have 103 training observations. #When I test with the trainset I have good results but when I use the testset my prediction are pretty bad. pred.noscale1 - predict( svm.noscale, newdata=trainset, decision.values=T) crossprod(pred.noscale1 - trainset$V4)/103 #[1,] 0.009827706 pred.noscale2- predict( svm.noscale, newdata=testset, decision.values=T) crossprod(pred.noscale2 - testset$V4)/100 #[1,] 82.97046 # primal parameters w - t(svm.noscale$coefs) %*%svm.noscale$SV V5V6 V7 V8 V9 V10 V11 V12 V13 [1,] 44187.34 -265.8382 3741.839 6359.768 5455.063 -646352.6 317.6211 6456 -23256.67 b=svm.noscale$rho [1] -10.46065 #It seems that I have overfitting. I suppose that the problem comes from not use scale data #(V5 and V10 are very high). #Now scaling the data svm.scale - svm(V4 ~ ., data = trainset, cost = 1000, gamma = 0.001) Parameters: SVM-Type: eps-regression SVM-Kernel: radial cost: 1000 gamma: 0.001 epsilon: 0.1 Number of Support Vectors: 86 # It seems better svm.pred1 - predict( svm.scale, newdata=trainset, decision.values=T) crossprod( svm.pred1 - trainset$V4)/103 #[1,] 9.459279 svm.pred2 - predict( svm.scale, newdata=testset, decision.values=T) crossprod( svm.pred2 - testset$V4)/100 # 26.51138 # primal parameters w - t(svm.scale$coefs) %*%svm.scale$SV V5V6 V7 V8 V9 V10 V11 V12 V13 [1,] -89.03491 -22.88782 146.8991 56.09881 217.0120 43.01645 -8.27661 50.2729 -60.78473 b= svm.model$rho #[1] 18.42264 Looking only to prediction purpose the scale model is good but Im mainly interested in w. Is it possible to improve this model to get lower values to w? Actually Im trying to run the SVM-GARCH and one condition to the model is that the sum of ws 1 (in my model I have only two independent variables). If you have any idea how to improve the model or if you find any problem with it please let me now. Thanks in advance, Marlene. 2009/8/31 Noah Silverman n...@smartmediacorp.com Thanks, I just remember with RapidMiner, there was always a screen showing the effective weights assigned to each input variable by the SVM. These numbers themselves weren't good for much, except they really helped to visualize the data. It is rather useful to see how much relative weight (significance.) the SVM assigned to each variable. On 8/31/09 12:54 AM, Achim Zeileis wrote: On Mon, 31 Aug 2009, Noah Silverman wrote: Steve, That doesn't work. I just trained an SVM with 80 variables. svm_model$coefs gives me a list of 10,000 items. My training set is 30,000 examples of 80 variables, so I have no idea what the 10,000 items represent. Presumably, the coefficients of the support vectors times the training labels, see help(svm, package = e1071). See also http://www.jstatsoft.org/v15/i09/ for some background information and the different formulations available. There should be some attribute that lists the weights for each of the 80 variables. Not sure what you are looking for. Maybe David, the author auf svm() (and now Cc), can help. Z -- Noah On 8/30/09 7:47 PM, Steve Lianoglou wrote: Hi, On Sun, Aug 30, 2009 at 6:10 PM, Noah Silvermann...@smartmediacorp.com wrote: Hello, I'm using the svm function from the e1071 package. It works well and gives me nice results. I'm very curious to see the actual coefficients calculated for each input variable. (Other packages, like RapidMiner, show you this automatically.) I've tried looking at attributes for the model and do see a coefficients item, but printing it returns an NULL result. Hmm .. I don't see a coefficients attribute, but rather a coefs attribute, which I guess is what you're looking for (?) Run example(svm) to its end and type: R m$coefs [,1] [1,] 1.00884130 [2,] 1.27446460 [3,] 2. [4,] -1. [5,] -0.35480340 [6,] -0.74043692 [7,]
Re: [R] Google's R Style Guide
On 9/1/2009 8:58 AM, Martin Morgan wrote:
Corrado wrote:
Thanks Duncan, Spencer,
To clarify, the situation is:
1) I have no reasons to choose S3 on S4 or vice versa, or any other coding
convention
2) Our group has not done any OO developing in R and I would be the first, so I
can set up the standards
3) I am starting from scratch with a new package, so I do not have any code I
need to re-use.
One consideration might be the domain in which you are doing
development; Bioconductor for instance makes extensive use of S4 and
your efforts at learning to develop S4 would pay off both in your own
code and in understanding other packages.
4) I am an R OO newbie, so whatever I can learn from the beginning what is
better and good for me.
So the questions would be two:
1) What coding style guide should we / I follow? Is the google style guide
good, or is there something better / more prescriptive which makes our
research group life easier?
2) What class type should I use? From what you two say, I should use S3
because is easier to use what are the disadvantages? Is there an
advantages / disadvantages table for S3 and S4 classes?
It seems relevant to compare S3 and S4 code for doing S3-style
programming, leaving more 'advanced' S4 for another day. In S3 I might
define a simple class and method as
makeS3Foo -
function(x=numeric(), y=numeric())
{
if (class(x) != numeric)
stop('x' must be numeric)
if (class(y) != numeric)
stop('y' must be numeric)
l - list(x=x, y=y)
class(l) - S3Foo
l
}
doS3 - function(x, ...) NextMethod(doS3)
doS3.default - function(x, ...) doS3 default
doS3.S3Foo - function(x, ...) doS3 of S3Foo
with an example of use being
doS3(makeS3Foo())
[1] doS3 of S3Foo
That looks as though it was written by an S4 user. I would write it
this way (with some differences in behaviour):
S3Foo - function(x=numeric(), y=numeric()) {
structure(list(x=as.numeric(x), y=as.numeric(y)), class=S3Foo)
}
The rest of my code would be pretty similar to yours, though I think it
should use UseMethod(doS3) rather than NextMethod(doS3).
Duncan Murdoch
I use 'makeS3Foo' as a constructor, so that whenever I make an instance
of what I'm calling class S3Foo, I have some guarantees about its structure.
The S4 implementation might be
setClass(S4Foo, representation(x=numeric, y=numeric))
makeS4Foo -
function(x = numeric(), y=numeric(), ...)
{
new(S4Foo, x=x, y=y, ...)
}
setGeneric(doS4, function(x, ...) standardGeneric(doS4),
useAsDefault=function(x, ...) do default)
setMethod(doS4, S4Foo, function(x, ...) doS4 of S4Foo)
and use with
doS4(makeS4Foo())
[1] doS4 of S4Foo
It seems like the translation between the two is really quite
transparent, and equally arcane to someone new to R.
Some things I get from S4 are a level of automatic type checking
makeS4Foo(x=bar)
Error in validObject(.Object) :
invalid class S4Foo object: invalid object for slot x in class
S4Foo: got class character, should be or extend class numeric
a way of knowing that my 'S4Foo' conforms to expectations -- in S3 I can say
l = list(a=1, b=2)
class(l) - S3Foo
and have no way of knowing whether this is 'valid' or not; in S4 I would
not use this method of creating a class (I'd use my constructor, or
perhaps 'new' if I were being undisciplined, and get type checking as
above) but if I did I'd be able to find
class(l) - S4Foo
validObject(l)
Error in validObject(l) :
invalid class S4Foo object: slots in class definition but not in
object: x, y
an error when I try and access data not in the class (normally I'd have
made a constructor, and not use slot access @ directly)
makeS3Foo()$z
NULL
makeS4Foo()@z
Error: no slot of name z for this object of class S4Foo
and reflection on the class
getClass(S4Foo)
Class “S4Foo” [in .GlobalEnv]
Slots:
Name:x y
Class: numeric numeric
Some of the tools for documenting S3 classes and methods are more mature
than for S4 (e.g., package.skeleton does a better job of making a
package containing my existing S3 code objects, but I usually use
package.skeleton to start a project, not to move existing objects into a
new project). The fact that the class has been declared explicitly means
that I'm expected to document it explicitly (in contrast to, say, the
result of lm(), which is documented only as the return value of the
function) and this then requires decisions about how to group class and
method documentation.
Using more complicated S4 features can be, well, more complicated. But
then these features are not readily available with S3, so...
To touch on a couple of other themes in this thread... Using a '.' in a
variable name seems like a very bad idea, given the way S3 dispatch
works. I like to think of objects as nouns and functions as verbs, and
so prefer to capitalize class names (as though they were proper nouns)
and lower-case function names (so they have a more dynamic
Re: [R] interactions and stall or memory shortage
The short answer is that you're trying to make a categorical interaction out of continuous variables, so that the resulting factors i2 and i3 have 1050 and 7200 levels respectively. (Note to people trying to reproduce this example: you'll need library(emdbook); library(bbmle); data(Lily_sum) ...) It'll take me a little longer to come up with a more satisfactory answer, but the bottom line is that interactions in a continuous context are generally *products* rather than all combinations of levels ... alexander russell-2 wrote: Hello, After putting together interaction code that worked for a single pair of interactions, when I try to evaluate two pairs of interactions( flowers*gopher, flowers*rockiness) my computer runs out of memory, and the larger desktop I use just doesn't go anywhere after about 20 minutes. Is it really that big a calculation? to start: mle2(minuslogl = Lily_sum$seedlings ~ dnbinom(mu = a, size = k), start = list(a = 10, k = 1)) then: i2-interaction(Lily_sum$flowers, Lily_sum$gopher) i3-interaction(Lily_sum$flowers, Lily_sum$rockiness) mle2(Lily_sum$seedlings ~ dnbinom(mu = a, size = k), start=list(a=10,k=1) ,parameters=list(a~i3+i2+Lily_sum$flowers)) (the last run leads to a stalled calculation) regards, R [[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. -- View this message in context: http://www.nabble.com/interactions-and-stall-or-memory-shortage-tp25221662p25240372.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] Google's R Style Guide
On Tue, Sep 1, 2009 at 8:58 AM, Martin Morganmtmor...@fhcrc.org wrote:
It seems relevant to compare S3 and S4 code for doing S3-style
programming, leaving more 'advanced' S4 for another day. In S3 I might
define a simple class and method as
makeS3Foo -
function(x=numeric(), y=numeric())
{
if (class(x) != numeric)
stop('x' must be numeric)
if (class(y) != numeric)
stop('y' must be numeric)
l - list(x=x, y=y)
class(l) - S3Foo
l
}
This shorter version would suffice:
makeS3Foo - function(x = numeric(), y = numeric()) {
stopifnot(inherits(x, numeric), inherits(y, numeric))
structure(list(x = x, y = y), class = S3Foo)
}
doS3 - function(x, ...) UseMethod(doS3)
doS3.S3Foo - function(x, ...) doS3 of S3Foo
doS3.default - function(x, ...) doS3 default
doS3 - function(x, ...) NextMethod(doS3)
doS3.default - function(x, ...) doS3 default
doS3.S3Foo - function(x, ...) doS3 of S3Foo
with an example of use being
doS3(makeS3Foo())
[1] doS3 of S3Foo
I use 'makeS3Foo' as a constructor, so that whenever I make an instance
of what I'm calling class S3Foo, I have some guarantees about its structure.
The S4 implementation might be
setClass(S4Foo, representation(x=numeric, y=numeric))
makeS4Foo -
function(x = numeric(), y=numeric(), ...)
{
new(S4Foo, x=x, y=y, ...)
}
setGeneric(doS4, function(x, ...) standardGeneric(doS4),
useAsDefault=function(x, ...) do default)
setMethod(doS4, S4Foo, function(x, ...) doS4 of S4Foo)
and use with
doS4(makeS4Foo())
[1] doS4 of S4Foo
It seems like the translation between the two is really quite
transparent, and equally arcane to someone new to R.
Some things I get from S4 are a level of automatic type checking
makeS4Foo(x=bar)
Error in validObject(.Object) :
invalid class S4Foo object: invalid object for slot x in class
S4Foo: got class character, should be or extend class numeric
This is also the case for S3 (despite the use of less code for S3).
makeS3Foo(x = bar)
Error: inherits(x, numeric) is not TRUE
a way of knowing that my 'S4Foo' conforms to expectations -- in S3 I can say
l = list(a=1, b=2)
class(l) - S3Foo
and have no way of knowing whether this is 'valid' or not; in S4 I would
not use this method of creating a class (I'd use my constructor, or
perhaps 'new' if I were being undisciplined, and get type checking as
above) but if I did I'd be able to find
Its not too likely that one will do the above if they are given a
constructor like makeS3Foo. On the other hand the ability
to work at a lower level means that one can create variations
of objects which were not originally anticipated thus avoiding
having to design the system for every possible eventuality.
class(l) - S4Foo
validObject(l)
Error in validObject(l) :
invalid class S4Foo object: slots in class definition but not in
object: x, y
an error when I try and access data not in the class (normally I'd have
made a constructor, and not use slot access @ directly)
makeS3Foo()$z
NULL
makeS4Foo()@z
Error: no slot of name z for this object of class S4Foo
and reflection on the class
getClass(S4Foo)
Class “S4Foo” [in .GlobalEnv]
Slots:
Name: x y
Class: numeric numeric
But overall its easier to access the methods and objects in
S3 so discovering what is going on is easier.
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[R] Strange error returned or bug in gam in mgcv????
Dear friends,
what is this error message in gam I cannot understand what it means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec - array
In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
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
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Re: [R] Strange error returned or bug in gam in mgcv????
On Sep 1, 2009, at 9:51 AM, Corrado wrote:
Dear friends,
what is this error message in gam I cannot understand what it
means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
If the code was as posted, you have entered where you probably
wanted -.
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec -
array
In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
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
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] Strange error returned or bug in gam in mgcv????
Nope Of course, it was just a copy and paste problem
On Tuesday 01 September 2009 15:00:34 David Winsemius wrote:
On Sep 1, 2009, at 9:51 AM, Corrado wrote:
Dear friends,
what is this error message in gam I cannot understand what it
means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
If the code was as posted, you have entered where you probably
wanted -.
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec -
array
In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
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
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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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
--
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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Google's R Style Guide (has become S3 vs S4, in part)
Looks like the discussion is no longer about R Style, but S3 vs S4? To that end, I asked more or less the same question a few weeks ago, arising from the much the same motivations. The discussion was helpful, here's the link: http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S 3-to-S4-tc24901482.html#a24904049 For what it's worth, I decided, but with some ambivalence, to stay with S3 for now and possibly move to S4 later. In the spirit of S4, I did write a function that is nearly the equivalent of validObject for my S3 object of interest. Overall, it looked like I would have to spend a lot of time moving to S4, while staying with S3 would allow me to get the project done and get results going much faster (see Frank Harrell's comment in the thread above). As a concrete example (concrete for us non-programmers, non-statisticians), I recently decided that I wanted to add a descriptive piece of text to a number of my plots, and it made sense to include the text with the object. So I just added a list element to the existing S3 object, e.g. Myobject$descrip No further work was necessary, I could use it right away. If instead, if I had made Myobject an S4 object, then I would have to go back, redefine the object, update validObject, and possibly write some new accessor and definitely constructor functions. At least, that's how I understand the way one uses S4 classes. Back to trying to get something done! Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA On 9/1/09 6:16 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Corrado wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? I don't think I can answer that. I'd recommend planning to spend some serious time on the decision, and then go by your personal impression. S4 is definitely harder to learn but richer, so don't make the decision too quickly. Take a look at John Chamber's new book, try small projects in each style, etc. 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? S3 is much more limited than S4. It dispatches on just one argument, S4 can dispatch on several. S3 allows you to declare things to be of a certain class with no checks that anything will actually work; S4 makes it easier to be sure that if you say something is of a certain class, it really is. S4 hides more under the hood: if you understand how regular R functions work, learning S3 is easy, but there's still a lot to learn before you'll be able to use S4 properly. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] Strange error returned or bug in gam in mgcv???? - additional information
Here I pasted the code from when I opened the R shell, so that it possible to see what is going on: http://scsys.co.uk:8002/33309?hl=onsubmit=Format+it! Thanks in advance -- 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.
Re: [R] SVM coefficients
Hi Marlene, I'm going to cut out much of your post and just cut to the chase: On Sep 1, 2009, at 9:03 AM, marlene marchena wrote: Looking only to prediction purpose the scale model is good but Im mainly interested in w. Is it possible to improve this model to get lower values to w? Actually Im trying to run the SVM-GARCH and one condition to the model is that the sum of ws 1 (in my model I have only two independent variables). If you have any idea how to improve the model or if you find any problem with it please let me now. In principle you should be able to do what you're after (of course :-), but I'm pretty sure you won't be able to do this using the e1071 package since you're imposing a linear constraint on w (this is almost like an l1 w/o using absolute vals of w's components, no?), while e1071::svm is solving a convex constraint (l2 on w). You say you're mainly interested in w, so are you looking for a means of doing feature selection? You can stick with e1071 and try doing recursive feature elimination (google it, you'll find mucho (aka SVM RFE)), or you can rig up an l1-svm which is already implemented for you in the penalized svm package (haven't used it myself): cran: http://cran.r-project.org/web/packages/penalizedSVM/index.html publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/13/1711 Does that help? -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] data frame
Well the data frame has dimensions 0,0, to start with.
Try dim(rm)
What is getmeasure and what is it supposed to do?
# btw rm is NOT a good name since it also is a reserved word in R. It removes
objects.
To create a data.frame of your six vectors why not just say
mydata - data.frame(V1, V2, V3, V4, V5, V6)
--- On Tue, 9/1/09, Tammy Ma metal_lical...@live.com wrote:
From: Tammy Ma metal_lical...@live.com
Subject: [R] data frame
To: r-help@r-project.org
Received: Tuesday, September 1, 2009, 4:39 AM
HI, R user,
I generate the vectors with the same length. I want to put
each vector into each column of data frame. Why it doesnt
work`?
rm-data.frame()
for(a in 1:6){
rm[,a]-getmeasure(p1,a,speech)
}
thanks a lot
Tammy
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Re: [R] Plot several graphs in the same window
Thank you very much it works well. Henrique Dallazuanna wrote: Try this: par(mfrow = c(8,5), mar = c(1, 1, 1, 1)) replicate(40, plot(10)) On Mon, Aug 31, 2009 at 4:39 PM, swertie v_coudr...@voila.fr wrote: Hello, I would like to plot a large number of graphs (43) in a same window. I tried wit par(mfrow=c(8,5)), but when I give the code for the plots I receive a error message saying that the margins are to wide. Can someone help me? Is it possible to put so many graphs in a single window? Thank you -- View this message in context: http://www.nabble.com/Plot-several-graphs-in-the-same-window-tp25229263p25229263.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 [[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. -- View this message in context: http://www.nabble.com/Plot-several-graphs-in-the-same-window-tp25229263p25235251.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] Exclude 0 values from plot
Hello, I have a matrix of species abundance with a lot of 0 values. I would like to plot the species abundance vs date, but I don't want that the 0 values appear as points on my graph. Do you know how I could represent only non-0 values? Thank you very much -- View this message in context: http://www.nabble.com/Exclude-0-values-from-plot-tp25235290p25235290.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] data frame
Try doing somthing like this :
#your vector1 2
vect1 - 2:5
vect2 - c(3,1,6,4)
# put both vectors in data.frame
combVect - data.frame(vect1=vect1, vect2=vect2)
Note :
1) I suggest to avoid naming objects with names of already existing
functions like rm
2) In R it is usually helpful to see your data as vetors and this way
you can avoid for for() loop
3) Have also a look at the R-Wiki (
http://wiki.r-project.org/rwiki/doku.php ) and the other documents on
www.r-project.org : There are some very good tutorials about the
different types of data-structures and objects in R (and their use) !!!
Wolfgang
Tammy Ma a écrit :
HI, R user,
I generate the vectors with the same length. I want to put each vector into
each column of data frame. Why it doesnt work`?
rm-data.frame()
for(a in 1:6){
rm[,a]-getmeasure(p1,a,speech)
}
thanks a lot
Tammy
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC,
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger (a t) igbmc.fr
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[R] Mantel test least square line
Hello, I performed a Mantel test and plotted communitiy similarities. I would like to add a least square line. I thought about using abline taking as slope the r-statistic of the Mantel test and calculating the y-intercept analytically. Is this method correct? Is there any function for this calculation? Thank you -- View this message in context: http://www.nabble.com/Mantel-test-least-square-line-tp25235402p25235402.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] Function to find angle between coordinates?
Dear all, I was doing some self study and was wondering if a function already exists which allows one to determine the angle between points. e.g. given the following (x,y) coordinates input: (0,1); (0,0); (1,0) would result in: output: 90 degrees Best regards C.C. __ 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] Exclude 0 values from plot
test[test==0]-NA see previous post: http://www.nabble.com/Replacing-0s-with-NA-td23995885.html#a23996183 swertie wrote: Hello, I have a matrix of species abundance with a lot of 0 values. I would like to plot the species abundance vs date, but I don't want that the 0 values appear as points on my graph. Do you know how I could represent only non-0 values? Thank you very much -- View this message in context: http://www.nabble.com/Exclude-0-values-from-plot-tp25235290p25241485.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] permutation and reshuffling
Look at ?sample for how to shuffle/permute a single vector (or rows of a data frame/matrix) and ?replicate for a way to do it a bunch of times and return the results in a nice form. 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 Yonatan Nissenbaum Sent: Tuesday, September 01, 2009 1:35 AM To: r-help@r-project.org Subject: [R] permutation and reshuffling Hi, I'm looking for an efficient code that will enable me to reshuffle data (phenotype) for certain number of individuals and creating a loop that will randomly simulate it for 1 times *(permutation)*. I also need to find how I keep the information (p value for each SNP) gathered for all the 1 iterations. My data set looks like this (n=500): Individual # Phenotype SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 1 0 T T G G A C G T A A T C 2 1 A T C G A C G T A G T C Many thanks, Jonathan [[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] Function to find angle between coordinates?
That is if they have length 1 as is the case here. Normalize them to length 1, if not. On Tue, Sep 1, 2009 at 11:06 AM, Gabor Grothendieckggrothendi...@gmail.com wrote: Since the inner product of two vectors if the cos of the angle between them: A - c(0,1); O - c(0,0); B - c(1,0) acos((A-O) %*% (B-O)) * 180 / pi [,1] [1,] 90 On Tue, Sep 1, 2009 at 9:08 AM, clair.crossup...@googlemail.comclair.crossup...@googlemail.com wrote: Dear all, I was doing some self study and was wondering if a function already exists which allows one to determine the angle between points. e.g. given the following (x,y) coordinates input: (0,1); (0,0); (1,0) would result in: output: 90 degrees Best regards C.C. __ 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] Best option for exporting data frame to SPSS?
Dear list,
I am leaving my old position and now need to convert my R data frames
into a format that can be used by an SPSS user replacing me, without
running into conversion problems.
The data set consists of strings in UTF8 encoding and values in double
precision floats. The data set is not terribly large, but I had bit
problems getting it into R due to the large number of unfortunate
characters in the strings (', #, and so on) so I was just wondering
if there is any way to get the data into a SPSS friendly format (other
than tab-separated files) so that a minimum of conversion is done in
between the two systems.
A data base file (SQLite) would be ideal, but unfortunatelly, I don't
think the recieving end would be able to handle it, i.e. get the data
into SPSS.
Sorry for asking this on the list, but I have found lots of
information about getting data safelly _into_ R in the archive, but
far les about exporting data out of R.
Please give me your best tip.
/Fredrik
--
Life is like a trumpet - if you don't put anything into it, you don't
get anything out of it.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide (has become S3 vs S4, in part)
Bryan Hanson wrote: Looks like the discussion is no longer about R Style, but S3 vs S4? To that end, I asked more or less the same question a few weeks ago, arising from the much the same motivations. The discussion was helpful, here's the link: http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S 3-to-S4-tc24901482.html#a24904049 For what it's worth, I decided, but with some ambivalence, to stay with S3 for now and possibly move to S4 later. In the spirit of S4, I did write a function that is nearly the equivalent of validObject for my S3 object of interest. Overall, it looked like I would have to spend a lot of time moving to S4, while staying with S3 would allow me to get the project done and get results going much faster (see Frank Harrell's comment in the thread above). As a concrete example (concrete for us non-programmers, non-statisticians), I recently decided that I wanted to add a descriptive piece of text to a number of my plots, and it made sense to include the text with the object. So I just added a list element to the existing S3 object, e.g. Myobject$descrip No further work was necessary, I could use it right away. If instead, if I had made Myobject an S4 object, then I would have to go back, redefine the object, update validObject, and possibly write some new accessor and definitely constructor functions. At least, that's how I understand the way one uses S4 classes. It doesn't stop there: If you keep the same name for your redefined S4 class, I don't know what happens when you try to access stored objects of that class created before the change, but it might not be pretty. If you give your redefined S4 class a different name, then you have a lot more code to change before you can use the redefined class like you want. By contrast, with S3, if you have any code that tests the number of components in a list, that will have to be changed. Spencer Back to trying to get something done! Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA On 9/1/09 6:16 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Corrado wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? I don't think I can answer that. I'd recommend planning to spend some serious time on the decision, and then go by your personal impression. S4 is definitely harder to learn but richer, so don't make the decision too quickly. Take a look at John Chamber's new book, try small projects in each style, etc. 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? S3 is much more limited than S4. It dispatches on just one argument, S4 can dispatch on several. S3 allows you to declare things to be of a certain class with no checks that anything will actually work; S4 makes it easier to be sure that if you say something is of a certain class, it really is. S4 hides more under the hood: if you understand how regular R functions work, learning S3 is easy, but there's still a lot to learn before you'll be able to use S4 properly. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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. -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ 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] Re gression - cluster option in STATA
Hello In STATA there is command which has regression with clustering option. Can anyone tell me what is the command for the same in R for example in STATA its regress Height Weight, cluster(id) Thanks in Advance Regards Sunita -- View this message in context: http://www.nabble.com/Regression---cluster-option-in-STATA-tp25241948p25241948.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] Function to find angle between coordinates?
?atan2 is a possible starting point. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of clair.crossup...@googlemail.com Sent: Tuesday, September 01, 2009 8:09 AM To: r-help@r-project.org Subject: [R] Function to find angle between coordinates? Dear all, I was doing some self study and was wondering if a function already exists which allows one to determine the angle between points. e.g. given the following (x,y) coordinates input: (0,1); (0,0); (1,0) would result in: output: 90 degrees Best regards C.C. __ 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] ggplot2: geom_smooth and legend
Hi! simple word thank you Hadley! an answer bringing a new question... is that possible to mix the colour and linetype representation with geom_smooth()? I tried the following code, though it hasn't worked. I have three different datasets due to non even x-axis (Temp) values I guess I should handle the matter from this point...no? CODE # air_N2_desorb_plot-ggplot() + geom_smooth(data=DATA.NC60_N2_v1, aes(Temp,-DrTGA*100,colour=N2_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v2, aes(Temp,-DrTGA*100,colour=N2_v2),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_air_v1, aes(Temp,-DrTGA*100,colour=Air_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v1, aes(Temp,-DrTGA*100,linetype=N2_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v2, aes(Temp,-DrTGA*100,linetype=N2_v2),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_air_v1, aes(Temp,-DrTGA*100,linetype=Air_v1),span=0.05,size=1.6,se=F) + scale_colour_hue(name=Desorption\n Condition) + labs(x=Temp~(degree*C),y=Weight~Derivative~(%/*degree*C)) + opts(panel.grid.minor = theme_line(colour = grey94)) print(air_N2_desorb_plot) Regards/Cordialement Benoit Boulinguiez -Message d'origine- De : hadley wickham [mailto:h.wick...@gmail.com] Envoyé : mercredi 26 août 2009 19:58 À : Benoit Boulinguiez Cc : r-help@r-project.org Objet : Re: [R] ggplot2: geom_smooth and legend Hi Benoit, You could turn the standard errors off with se = F. Then they'll be removed from the legend as well. Hadley On Tue, Aug 18, 2009 at 7:43 AM, Benoit Boulinguiezbenoit.boulingu...@ensc-rennes.fr wrote: Sorry I forgot the code that goes with **CODE desorb_plot-ggplot() + geom_smooth(data=DATA.B1_SA_N2, aes(Temp,DrTGA*100,colour=B1),span=0.1,size=1.6) + geom_smooth(data=DATA.FM30K_SA_N2, aes(Temp,DrTGA*100,colour=FM30K),span=0.2,size=1.6) + geom_smooth(data=DATA.NC60_SA_N2, aes(Temp,-DrTGA*100,colour=NC60),span=0.1,size=1.6) + geom_smooth(data=DATA.THC515_SA_N2, aes(Temp,DrTGA*100,colour=THC515),span=0.2,size=1.6) + scale_colour_hue(name=Adsorbent) + labs(x=Temp~(degree*C),y=Weight~Derivative~(%/*degree*C)) + opts(panel.grid.minor = theme_line(colour = grey94)) print(desorb_plot) Cordialement / Regards --- Benoit Boulinguiez Ecole de Chimie de Rennes (ENSCR) Bureau 1.20 Equipe CIP UMR CNRS 6226 Sciences Chimiques de Rennes Avenue du Général Leclerc CS 50837 35708 Rennes CEDEX 7 Tel 33 (0)2 23 23 80 83 Fax 33 (0)2 23 23 81 20 http://www.ensc-rennes.fr/ Quoting Benoit Boulinguiez benoit.boulingu...@ensc-rennes.fr: Hi all, Is that possible to remove the grey colour in the legend key that goes with the geom_smooth? In my case it doesn't ease the reading of the legend. http://www.4shared.com/file/125864977/e10644f8/desorb.html Cordialement / Regards --- Benoit Boulinguiez Ecole de Chimie de Rennes (ENSCR) Bureau 1.20 Equipe CIP UMR CNRS 6226 Sciences Chimiques de Rennes Avenue du Général Leclerc CS 50837 35708 Rennes CEDEX 7 Tel 33 (0)2 23 23 80 83 Fax 33 (0)2 23 23 81 20 http://www.ensc-rennes.fr/ __ 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. -- http://had.co.nz/ __ 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] Function to find angle between coordinates?
Since the inner product of two vectors if the cos of the angle between them: A - c(0,1); O - c(0,0); B - c(1,0) acos((A-O) %*% (B-O)) * 180 / pi [,1] [1,] 90 On Tue, Sep 1, 2009 at 9:08 AM, clair.crossup...@googlemail.comclair.crossup...@googlemail.com wrote: Dear all, I was doing some self study and was wondering if a function already exists which allows one to determine the angle between points. e.g. given the following (x,y) coordinates input: (0,1); (0,0); (1,0) would result in: output: 90 degrees Best regards C.C. __ 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] Google's R Style Guide
On Tue, 01 Sep 2009 10:47:36 +0200, Corrado ct...@york.ac.uk wrote: Thanks Duncan, Spencer, To clarify, the situation is: 1) I have no reasons to choose S3 on S4 or vice versa, or any other coding convention 2) Our group has not done any OO developing in R and I would be the first, so I can set up the standards 3) I am starting from scratch with a new package, so I do not have any code I need to re-use. 4) I am an R OO newbie, so whatever I can learn from the beginning what is better and good for me. From my experience I can recommend tree things: 1) If hierarchy of your classes is complicated ( i.e. at least 3 levels of inheritance) and/or you intend to merge functionality of several classes into one (multiple inheritance), it's better to use S4, otherwise use S3. Majority of statistical models in R seem not to require even 2 levels of inheritance and OO is used mainly for method dispatch, so S3 is quite sufficient. 2) If your classes are meant to provide functionality for fundamental objects that you intend to use latter to build more complex structures, then use S4 (example could be super.data.frame or super.matrix, or implementation of sets etc). Usually this fundamental objects are derived from basic pseudo-classes in R like function and numeric. You can use S4 object to build your S3 objects latter without any trouble. Though starting R 2.8 one can integrate quite happily S3 objects into S4 and even inherit S4 from S3, that is somewhat artificial and generally not encouraged. 3) If you start with S4 try to avoid writing validity and initialization methods at the beginning. Put everything in the constructors, pretty much as in S3 style. Vitalie. So the questions would be two: 1) What coding style guide should we / I follow? Is the google style guide good, or is there something better / more prescriptive which makes our research group life easier? 2) What class type should I use? From what you two say, I should use S3 because is easier to use what are the disadvantages? Is there an advantages / disadvantages table for S3 and S4 classes? Thanks -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re gression - cluster option in STATA
A guess, as I don't know STATA: ?lme (library(nlme) first) (also perhaps anova with an Error term -- ?anova) But: R is not STATA R is not SAS R is not SPSS ... R is R So do not expect the same paradigms to hold; but because R IS R, one can always program ways to make them hold. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sunita22 Sent: Tuesday, September 01, 2009 8:03 AM To: r-help@r-project.org Subject: [R] Re gression - cluster option in STATA Hello In STATA there is command which has regression with clustering option. Can anyone tell me what is the command for the same in R for example in STATA its regress Height Weight, cluster(id) Thanks in Advance Regards Sunita -- View this message in context: http://www.nabble.com/Regression---cluster-option-in-STATA-tp25241948p252419 48.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] Google's R Style Guide
On Tue, Sep 1, 2009 at 6:29 AM, Duncan Murdochmurd...@stats.uwo.ca wrote:
On 9/1/2009 8:58 AM, Martin Morgan wrote:
Corrado wrote:
Thanks Duncan, Spencer,
To clarify, the situation is:
1) I have no reasons to choose S3 on S4 or vice versa, or any other
coding convention
2) Our group has not done any OO developing in R and I would be the
first, so I can set up the standards
3) I am starting from scratch with a new package, so I do not have any
code I need to re-use.
One consideration might be the domain in which you are doing
development; Bioconductor for instance makes extensive use of S4 and
your efforts at learning to develop S4 would pay off both in your own
code and in understanding other packages.
4) I am an R OO newbie, so whatever I can learn from the beginning what
is better and good for me.
So the questions would be two:
1) What coding style guide should we / I follow? Is the google style
guide good, or is there something better / more prescriptive which makes our
research group life easier? 2) What class type should I use? From what you
two say, I should use S3 because is easier to use what are the
disadvantages? Is there an advantages / disadvantages table for S3 and S4
classes?
It seems relevant to compare S3 and S4 code for doing S3-style
programming, leaving more 'advanced' S4 for another day. In S3 I might
define a simple class and method as
makeS3Foo -
function(x=numeric(), y=numeric())
{
if (class(x) != numeric)
stop('x' must be numeric)
if (class(y) != numeric)
stop('y' must be numeric)
l - list(x=x, y=y)
class(l) - S3Foo
l
}
doS3 - function(x, ...) NextMethod(doS3)
doS3.default - function(x, ...) doS3 default
doS3.S3Foo - function(x, ...) doS3 of S3Foo
with an example of use being
doS3(makeS3Foo())
[1] doS3 of S3Foo
That looks as though it was written by an S4 user. I would write it this
way (with some differences in behaviour):
S3Foo - function(x=numeric(), y=numeric()) {
structure(list(x=as.numeric(x), y=as.numeric(y)), class=S3Foo)
}
The rest of my code would be pretty similar to yours, though I think it
should use UseMethod(doS3) rather than NextMethod(doS3).
Duncan Murdoch
I use 'makeS3Foo' as a constructor, so that whenever I make an instance
of what I'm calling class S3Foo, I have some guarantees about its
structure.
The S4 implementation might be
setClass(S4Foo, representation(x=numeric, y=numeric))
makeS4Foo -
function(x = numeric(), y=numeric(), ...)
{
new(S4Foo, x=x, y=y, ...)
}
In S3 using R.methodsS3/R.oo utility functions:
library(R.oo);
setConstructorS3(S3Foo, function(x=numeric, y=numeric) {
# Validate arguments
stopifnot(inherits(x, numeric));
stopifnot(inherits(y, numeric));
extend(list(x=x, y=y), S3Foo); # similar to structure().
})
Naming guideline: Name the *constructor* function the same as your
class; this will make things consistent and help you and the user.
Note, you don't want to use class(x) != numeric, because class(x)
may return a vector; always use inherits().
Then, to setup methods for this class, do:
setMethodS3(print, S3Foo, function(object, ...) {
...
})
setMethodS3(plot, S3Foo, function(object, ...) {
...
})
Generic functions are created automagically when missing; no need for
you to specify that explicitly.
Dispatching in S3 is on the first argument only. FYI, it is extremely
rare that you want to dispatch on other arguments although you hear
that in the context of S4; I only know of one use case with formulas.
One purpose of R.methodsS3/R.oo is to ease any transitions to S4.
/Henrik
setGeneric(doS4, function(x, ...) standardGeneric(doS4),
useAsDefault=function(x, ...) do default)
setMethod(doS4, S4Foo, function(x, ...) doS4 of S4Foo)
and use with
doS4(makeS4Foo())
[1] doS4 of S4Foo
It seems like the translation between the two is really quite
transparent, and equally arcane to someone new to R.
Some things I get from S4 are a level of automatic type checking
makeS4Foo(x=bar)
Error in validObject(.Object) :
invalid class S4Foo object: invalid object for slot x in class
S4Foo: got class character, should be or extend class numeric
a way of knowing that my 'S4Foo' conforms to expectations -- in S3 I can
say
l = list(a=1, b=2)
class(l) - S3Foo
and have no way of knowing whether this is 'valid' or not; in S4 I would
not use this method of creating a class (I'd use my constructor, or
perhaps 'new' if I were being undisciplined, and get type checking as
above) but if I did I'd be able to find
class(l) - S4Foo
validObject(l)
Error in validObject(l) :
invalid class S4Foo object: slots in class definition but not in
object: x, y
an error when I try and access data not in the class (normally I'd have
made a constructor, and not use slot access @ directly)
makeS3Foo()$z
NULL
makeS4Foo()@z
Error: no slot of name z for this object of
Re: [R] ggplot2: geom_smooth and legend
I cleared out the data frame, I have now one data frame with all the values in as a function of the experimental condition. + successfully mix the linestyle and colour_hue representation of the geom_smooth though it doesn't look good NEW CODE air_N2_desorb_plot-ggplot(DATA,aes(Temp,-DrTGA*100,colour=Cond)) + geom_smooth(span=0.05,size=1.6,se=F,alpha=0.8) + geom_smooth(aes(linetype=Cond),span=0.05,size=1.6,se=F) + scale_colour_hue(name=Desorption\n Condition) + scale_linetype(name=Desorption\n Condition) + labs(x=Temp~(degree*C),y=Weight~Derivative~(%/*degree*C)) + opts(panel.grid.minor = theme_line(colour = grey94)) print(air_N2_desorb_plot) Regards/Cordialement Benoit Boulinguiez -Message d'origine- De : r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] De la part de Benoit Boulinguiez Envoyé : mardi 1 septembre 2009 17:20 À : r-help@r-project.org Objet : Re: [R] ggplot2: geom_smooth and legend Hi! simple word thank you Hadley! an answer bringing a new question... is that possible to mix the colour and linetype representation with geom_smooth()? I tried the following code, though it hasn't worked. I have three different datasets due to non even x-axis (Temp) values I guess I should handle the matter from this point...no? CODE # air_N2_desorb_plot-ggplot() + geom_smooth(data=DATA.NC60_N2_v1, aes(Temp,-DrTGA*100,colour=N2_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v2, aes(Temp,-DrTGA*100,colour=N2_v2),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_air_v1, aes(Temp,-DrTGA*100,colour=Air_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v1, aes(Temp,-DrTGA*100,linetype=N2_v1),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_N2_v2, aes(Temp,-DrTGA*100,linetype=N2_v2),span=0.05,size=1.6,se=F) + geom_smooth(data=DATA.NC60_air_v1, aes(Temp,-DrTGA*100,linetype=Air_v1),span=0.05,size=1.6,se=F) + scale_colour_hue(name=Desorption\n Condition) + labs(x=Temp~(degree*C),y=Weight~Derivative~(%/*degree*C)) + opts(panel.grid.minor = theme_line(colour = grey94)) print(air_N2_desorb_plot) Regards/Cordialement Benoit Boulinguiez -Message d'origine- De : hadley wickham [mailto:h.wick...@gmail.com] Envoyé : mercredi 26 août 2009 19:58 À : Benoit Boulinguiez Cc : r-help@r-project.org Objet : Re: [R] ggplot2: geom_smooth and legend Hi Benoit, You could turn the standard errors off with se = F. Then they'll be removed from the legend as well. Hadley On Tue, Aug 18, 2009 at 7:43 AM, Benoit Boulinguiezbenoit.boulingu...@ensc-rennes.fr wrote: Sorry I forgot the code that goes with **CODE desorb_plot-ggplot() + geom_smooth(data=DATA.B1_SA_N2, aes(Temp,DrTGA*100,colour=B1),span=0.1,size=1.6) + geom_smooth(data=DATA.FM30K_SA_N2, aes(Temp,DrTGA*100,colour=FM30K),span=0.2,size=1.6) + geom_smooth(data=DATA.NC60_SA_N2, aes(Temp,-DrTGA*100,colour=NC60),span=0.1,size=1.6) + geom_smooth(data=DATA.THC515_SA_N2, aes(Temp,DrTGA*100,colour=THC515),span=0.2,size=1.6) + scale_colour_hue(name=Adsorbent) + labs(x=Temp~(degree*C),y=Weight~Derivative~(%/*degree*C)) + opts(panel.grid.minor = theme_line(colour = grey94)) print(desorb_plot) Cordialement / Regards --- Benoit Boulinguiez Ecole de Chimie de Rennes (ENSCR) Bureau 1.20 Equipe CIP UMR CNRS 6226 Sciences Chimiques de Rennes Avenue du Général Leclerc CS 50837 35708 Rennes CEDEX 7 Tel 33 (0)2 23 23 80 83 Fax 33 (0)2 23 23 81 20 http://www.ensc-rennes.fr/ Quoting Benoit Boulinguiez benoit.boulingu...@ensc-rennes.fr: Hi all, Is that possible to remove the grey colour in the legend key that goes with the geom_smooth? In my case it doesn't ease the reading of the legend. http://www.4shared.com/file/125864977/e10644f8/desorb.html Cordialement / Regards --- Benoit Boulinguiez Ecole de Chimie de Rennes (ENSCR) Bureau 1.20 Equipe CIP UMR CNRS 6226 Sciences Chimiques de Rennes Avenue du Général Leclerc CS 50837 35708 Rennes CEDEX 7 Tel 33 (0)2 23 23 80 83 Fax 33 (0)2 23 23 81 20 http://www.ensc-rennes.fr/ __ 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. -- http://had.co.nz/ __ 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] Package NP; npregbw; selective bandwidth selection
Dear R-users, I am fitting a kernel regression model of the form y ~ x1 + factor(x2) + factor(x3) and am using the function npregbw in the np-package to find the optimal bandwidths. My dataset is relatively large and the optimization takes quite long. When testing different specifications I have noticed that the optimal bw for x3 is always very close to zero (around 10^-12 or so). I am wondering whether it is possible to hard code the bandwidth related to x3 to 0 and limit npregbw's choice of bw's those related to x1 and x2? My intuition suggests that this would reduce the number of parameters to be optimized from 3 to 2 and thus make the computations quicker. Furthermore the theoretical literature (e.g. [1]) seems to suggest that this might be a good idea with categorical variables and big datasets. Any comments? [1] Racine, J.S. and Q. Li (2004), Nonparametric estimation of regression functions with both categorical and continuous Data, Journal of Econometrics, 119, 99-130. Best regards, Otto Kassi University of Helsinki Dept. of Economics __ 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] Simple question about error on CSV import
I have a substantial CSV to import but can't seem to import even the simplest CSV. I'm running the latest stable REvolution R on OS X if that is pertinent. Here's the contents of a simple test2.csv CSV file: #,Status,Project 5842,New,Test snortalerts = read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=#) Error in data[[rowvar]] : attempt to select less than one element I can't see how it could get any more simple, yet it doesn't work. I'm obviously missing something basic, but based on the error, I can't see what it is. Landon -- View this message in context: http://www.nabble.com/Simple-question-about-error-on-CSV-import-tp25242899p25242899.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] X11 plot window sizes
Hi, I'm not understanding how the width height parameters are supposed to work. When I execute the following 4 commands: X11() X11(width=20, height=20) X11(width=20, height=10) X11(width=40, height=40) I get the following *approximate* physical sizes on my screen: 6 x 6 8 x 8 12 x 6 8 x 8 For now I'm assuming that my pointsize isn't quite the same as expected (1/72) which probably accounts for why I'm getting 6 windows instead of the default 7 window, but why does 20x20 == 40x40, and why on the 20x10 version do I get a 6 height? 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] Google's R Style Guide (has become S3 vs S4, in part)
spencerg wrote:
Bryan Hanson wrote:
Looks like the discussion is no longer about R Style, but S3 vs S4?
yes nice topic rename!
To that end, I asked more or less the same question a few weeks ago,
arising
from the much the same motivations. The discussion was helpful,
here's the
link:
http://www.nabble.com/Need-Advice%3A-Considering-Converting-a-Package-from-S
3-to-S4-tc24901482.html#a24904049
For what it's worth, I decided, but with some ambivalence, to stay
with S3
for now and possibly move to S4 later. In the spirit of S4, I did
write a
function that is nearly the equivalent of validObject for my S3 object of
interest.
Overall, it looked like I would have to spend a lot of time moving to S4,
while staying with S3 would allow me to get the project done and get
results
going much faster (see Frank Harrell's comment in the thread above).
Bryan's original post started me thinking about this, but I didn't
respond. I'd classify myself as an 'S4' 'expert', with my ignorance of
S3 obvious from Duncan's corrections to my earlier post. It's hard for
me to make a comparative statement about S3 vs. S4, and hard really to
know what is 'hard' for someone new to S4, to R, to programming, ... I
would have classified most of the responses in that thread as coming
from 'S3' 'experts'.
As a concrete example (concrete for us non-programmers,
non-statisticians),
I recently decided that I wanted to add a descriptive piece of text to a
number of my plots, and it made sense to include the text with the
object.
So I just added a list element to the existing S3 object, e.g.
Myobject$descrip No further work was necessary, I could use it right
away.
If instead, if I had made Myobject an S4 object, then I would have to go
back, redefine the object, update validObject, and possibly write some
new
accessor and definitely constructor functions. At least, that's how I
understand the way one uses S4 classes.
This is a variant of Gabor's comment, I guess, that it's easy to modify
S3 on an as-needed basis. In S3, forgoing any pretext of 'best
practices', one might
s3 - structure(list(x=1:10, y=10:1), class=MyS3Object)
## some lines of code...
if (aTest)
s3$descraption - A description
(either 'description' or 'discraption' is a typo, uncaught by S3).
In S4 I'd have to change my class definition from
setClass(MyS4Object, representation(x=numeric, y=numeric))
to
setClass(MyS4Object, representation(x=numeric, y=numeric,
description=character))
but the body of the code would look surprising similar
s4 - new(MyS4Object, x=1:10, y=10:1)
## some lines of code...
if (aTest)
s...@description - A description
(no typo, because I'd have been told that the slot 'discraption' didn't
exist). In the S3 case the (implicit) class definition is a single line,
perhaps nested deep inside a function. In S4 the class definition is in
a single location.
Best practices might make me want to have a validity method (x and y the
same dimensions? 'description' of length 1?), to use a constructor and
accessors (to provide an abstraction to separate the interface from its
implementation), etc., but those issues are about best practices.
A downstream consequence is that s4 always has a 'description' slot
(perhaps initialized with an appropriate default in the 'prototype'
argument of setClass, but that's more advanced), whereas s3 only
sometimes has 'description'. So I'm forced to check
is.null(s3$description) whenever I'm expecting a character vector.
It doesn't stop there: If you keep the same name for your
redefined S4 class, I don't know what happens when you try to access
stored objects of that class created before the change, but it might not
be pretty. If you give your redefined S4 class a different name, then
Actually, the old object is loaded in R. It is not valid
(validObject(originalS4) would complain about 'slots in class definition
not in object'). One might write an 'updateObject' generic and method
that detects and corrects this. This contrasts with S3, where there is
no knowing whether the object is consistent with the current (implicit)
class definition.
you have a lot more code to change before you can use the redefined
class like you want.
For slot addition, this is not true -- old code works fine. For slot
removal / renaming, this is analogous to S3 -- code needs reworking; use
of accessors might help isolate code using the class from the
implementation of the class.
A couple of comments on Duncan's
S3Foo - function(x=numeric(), y=numeric()) {
structure(list(x=as.numeric(x), y=as.numeric(y)), class=S3Foo)
}
I used makeS3Foo to emphasize that it was a constructor, but in my own
code I use S3Foo(). Realizing that, as Henrik has now also pointed out,
I'm far from perfect, the use of as.numeric() combines validity checking
and coercion, which I think is not usually a good thing (even when
efficient). In particular this
as.numeric(factor(c(one, two, three)))
Re: [R] Simple question about error on CSV import
esawdust wrote: Here's the contents of a simple test2.csv CSV file: #,Status,Project 5842,New,Test snortalerts = read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=#) Error in data[[rowvar]] : attempt to select less than one element Landon Figured out the answer, though it wasn't obvious (to me anyway). The symbol # used as the first column label was the problem. I changed that to be id and changed the read.table to be: snortalerts - read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=id) and it worked fine. -- View this message in context: http://www.nabble.com/Simple-question-about-error-on-CSV-import-tp25242899p25243159.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] pls package
Thank you so very much. Yes, a statistician friend expressed his certainty that NAs cannot be handled by such algorithms, and you just answered the R specific questions. I will prune the data more and feed them into pls as matrices. I am, in fact, following the examples your provide with the package and the Vol 6 no. 3 issue of the R Newsletter. Payam __ Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 +1 805 388 9911 ext. 159 +1 805 388 5948 fax payam.minoo...@meissner.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] Simple question about error on CSV import
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of esawdust Sent: Tuesday, September 01, 2009 8:53 AM To: r-help@r-project.org Subject: [R] Simple question about error on CSV import I have a substantial CSV to import but can't seem to import even the simplest CSV. I'm running the latest stable REvolution R on OS X if that is pertinent. Here's the contents of a simple test2.csv CSV file: #,Status,Project 5842,New,Test snortalerts = read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=#) Error in data[[rowvar]] : attempt to select less than one element I can't see how it could get any more simple, yet it doesn't work. I'm obviously missing something basic, but based on the error, I can't see what it is. Using '#' for the initial column name presents 2 problems: (a) # is the default comment character so that line is ignored. Add the read.table argument comment.char= to take care of that. (b) It looks like the column names are converted to legal R names before the row.names=name is processed and the # is not legal so it becomes something random like X.. If you turn off this conversion to legal names with check.names=FALSE then things will work. It might be better to use the index of the row.names column instead of the name, as in row.names=1. E.g., t-#,Status,Project\n5842,New,Test\n read.table(textConnection(t), header=TRUE, sep=,, comment.char=, check.names=FALSE, row.names=#) Status Project 5842NewTest read.table(textConnection(t), header=TRUE, sep=,, comment.char=, row.names=1) Status Project 5842NewTest Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com Landon -- View this message in context: http://www.nabble.com/Simple-question-about-error-on-CSV-impor t-tp25242899p25242899.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] Simple question about error on CSV import
By default for read.table, comment.char = # so the first line was being treated as a comment line, and when you specified row.names=#, read.table couldn't find that column. On Tue, Sep 1, 2009 at 12:07 PM, esawdust lan...@360vl.com wrote: esawdust wrote: Here's the contents of a simple test2.csv CSV file: #,Status,Project 5842,New,Test snortalerts = read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=#) Error in data[[rowvar]] : attempt to select less than one element Landon Figured out the answer, though it wasn't obvious (to me anyway). The symbol # used as the first column label was the problem. I changed that to be id and changed the read.table to be: snortalerts - read.table( /Users/lcox/Documents/test2.csv, header=TRUE, sep=,, row.names=id) and it worked fine. -- View this message in context: http://www.nabble.com/Simple-question-about-error-on-CSV-import-tp25242899p25243159.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. -- Levi Waldron post-doctoral fellow Jurisica Lab, Ontario Cancer Institute Division of Signaling Biology TMDT 9-304D 101 College Street Toronto, Ontario M5G 1L7 (416)581-7453 [[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] Combining: R + Condor in 2009 ? (+foreach maybe?)
There's no explicit link between foreach and Condor right now (although foreach is designed to work with any backend, so someone could write one if they wanted). If you use the NetworkSpaces back end (registerDoNWS in REvolutionR Enterprise), and can access members of the Condor cluster directly, you could always just set up a sleigh manually -- instructions are in the ParallelR manual. I expect you can do the same with snow (via the doSNOW package for foreach). Hope this helps, # David Smith On Sun, Aug 30, 2009 at 3:28 PM, Tal Galili tal.gal...@gmail.com wrote: Hello dear R-help group (and David Smith from REvolution), I would like to perform parallel computing using R with Condor (hopefully using foreach or other recommended solutions, if available) for some Embarrassingly parallel problem. I will start by listing what I found so far, and then go on asking for help. So far I found the a manual by Xianhong Xie from Rnews_2005-2 (see page 13) Talking about R and condor: http://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf I also found several references for R and condor in the task views of High Performance Computinghttp://cran.r-project.org/web/views/HighPerformanceComputing.html : http://cran.r-project.org/web/views/HighPerformanceComputing.html Stating that: The GridRhttp://cran.r-project.org/web/packages/GridR/index.html package by Wegener et al. can be used in a grid computing environment via a web service, via ssh or via Condor or Globus. I then found a 2008 lecture slides on the subject here: http://www.statistik.uni-dortmund.de/useR-2008/tutorials/GridR.pdf And an articles showing it was already done: http://www.ecmlpkdd2008.org/files/pdf/workshops/ubiqkd/3.pdf (But without code examples to my dismay) What I wish from you is some guidance. Is there a more updated (formal) material on condor and R then Xianhong Xie article from 2005? Is GridR a good way of making the connection? Is using the foreach package relevant or useful here? I am not a UNIX person. I never ran R in batch, and any step by step instructions (either by referring to links or explaining here) would be of great help. Thanks in advance, Tal -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (San Francisco, USA) Check out our upcoming events schedule at www.revolution-computing.com/events [[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] Strange error returned or bug in gam in mgcv???? - yet more additional information
I am using mgcv 1.4-1.1 on Fedora 9 64 bit on an Opteron server with 8Gb of RAM. On Tuesday 01 September 2009 15:19:28 Corrado wrote: Here I pasted the code from when I opened the R shell, so that it possible to see what is going on: http://scsys.co.uk:8002/33309?hl=onsubmit=Format+it! Thanks in advance -- 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] Plotting point text-labels with lattice splom
I have read the thread re: Plotting text with lattice but can't seem to get from there to what I need. . . would appreciate any advice. . . I have used splom to plot data of the first three principle components from a pca analysis. Here is the code I have thus far: mydata.pr-prcomp(mydata) grps - substr(rownames(mydata),1,4) super.sym=trellis.par.get(superpose.symbol) splom(data.frame(mydata.pr$x[,1:3]), groups = grps, panel = panel.superpose, key = list (title = Four Items in PCA space, text = list(c(G, H, N, Il)), points=list(pch=super.sym$pch[1:4], col=super.sym$col[1:4]))) I would now like to append text labels to each point in the plot that will identify the item based on its rowname in the original data set. so, something like this gets me the labels I want labs-substr(rownames(mydata),1,6) My trouble then comes in figuring out how to get these labels to attach to the corresponding points in the plot. Thanks. Matt -- Matthew Jockers Stanford University http://www.stanford.edu/~mjockers __ 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] Strange error returned or bug in gam in mgcv????
The basic problem is that you have requested a 10 dimensional thin plate
spline, with a basis dimension of 196830. In reality it will not be possible
to compute this, even if you have more than 196830 data. In any case it would
be unlikely to provide a very useful model --- the simplest function that
it can theoretically represent will have 3003 degrees of freedom.
That said the error message is obviously rather unhelpful... Can you tell me
how many data you are actually trying to fit, and I'll try and track down
exactly where it's failing, and put in a more informative message.
best,
Simon
On Tuesday 01 September 2009 14:51, Corrado wrote:
Dear friends,
what is this error message in gam I cannot understand what it means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec - array
In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
+44 1225 386603 www.maths.bath.ac.uk/~sw283
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Strange error returned or bug in gam in mgcv????
Dear Simon,
I have stored all information at the link:
http://scsys.co.uk:8002/33309?hl=onsubmit=Format+it!
I have the same problem if I do
s(PC1) + . + s(PC10) or
s(Pc1,PC2,PC3,PC4,PC5)+s(PC6,PC7,PC8,PC9,PC10) or
s(PC1,PC2,PC3,PC6,PC7,PC8) .
I have renamed PC1.1,PC2.1,PC3.1,PC4.1,PC5.1 to PC6,PC7,PC8,PC9,PC10 for
simplicity.
Regards
On Tuesday 01 September 2009 17:31:04 Simon Wood wrote:
The basic problem is that you have requested a 10 dimensional thin plate
spline, with a basis dimension of 196830. In reality it will not be
possible to compute this, even if you have more than 196830 data. In any
case it would be unlikely to provide a very useful model --- the simplest
function that it can theoretically represent will have 3003 degrees of
freedom.
That said the error message is obviously rather unhelpful... Can you tell
me how many data you are actually trying to fit, and I'll try and track
down exactly where it's failing, and put in a more informative message.
best,
Simon
On Tuesday 01 September 2009 14:51, Corrado wrote:
Dear friends,
what is this error message in gam I cannot understand what it means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec -
array In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
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.
Re: [R] online classes or online eduction in statistics? esp. time series analysis and cointegration?
Luna Laurent luna.laurent.ucb at gmail.com writes: Hi all, I am looking for low cost online education in statistics. I am thinking of taking online classes on time series analysis and cointegration, etc. Of course, if there are free video lectures, that would be great. However I couldn't find any free video lectures at upper-undergraduate and graduate level which formally going through the whole timeseries education... That's why I would like to enroll in some sort of online degree classes. However, I don't want to earn the certificate or the degree; I just want to audit the online class specifically in time series analysis and cointegration. Could anybody recommend such online education in statistics esp. in time series and cointegration, at low cost? Hopefully it's not going to be like a few thousand dollars for one class. Thanks a lot for your pointers in advance! [[alternative HTML version deleted]] Luna, You are welcome to use my time series course materials at chrisbilder.com/ts. While there are no videos, the course notes (schedule web page) are complete along with all of the R programs used for the course. I do have video lectures available for some other courses through my chrisbilder.com portal. Chris Christopher R. Bilder, Ph.D. Associate Professor University of Nebraska-Lincoln Department of Statistics Lincoln, NE 68583 Phone: (402) 472-2903 Fax: (402) 472-5179 E-mail: cbild...@unl.edu or ch...@chrisbilder.com Website: www.chrisbilder.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] Function to find angle between coordinates?
Thank you very much, these were exactly what i needed! :-) C.C. On 1 Sep, 14:08, clair.crossup...@googlemail.com clair.crossup...@googlemail.com wrote: Dear all, I was doing some self study and was wondering if a function already exists which allows one to determine the angle between points. e.g. given the following (x,y) coordinates input: (0,1); (0,0); (1,0) would result in: output: 90 degrees Best regards C.C. __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] Exclude 0 values from plot
Thank you it worked well -- View this message in context: http://www.nabble.com/Exclude-0-values-from-plot-tp25235290p25244045.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] Strange error returned or bug in gam in mgcv????
On Tue, 2009-09-01 at 17:55 +0100, Corrado wrote:
Dear Simon,
I have stored all information at the link:
http://scsys.co.uk:8002/33309?hl=onsubmit=Format+it!
You could have included that in your mail to the list - it is just plain
text after all.
I have the same problem if I do
s(PC1) + . + s(PC10) or
s(Pc1,PC2,PC3,PC4,PC5)+s(PC6,PC7,PC8,PC9,PC10) or
s(PC1,PC2,PC3,PC6,PC7,PC8) .
I have renamed PC1.1,PC2.1,PC3.1,PC4.1,PC5.1 to PC6,PC7,PC8,PC9,PC10 for
simplicity.
What does
str(dist_scot24_vector_with_climate)
show? I seem to recall getting similar errors when I'd done something
silly in a data prep routine and had data in a data frame that wasn't
numeric but looked like it was - a factor for example.
If you can't do some quite simple things like the first of your three
alternatives above, that suggests something amiss with the data. That'd
be the first thing to check.
HTH
G
Regards
On Tuesday 01 September 2009 17:31:04 Simon Wood wrote:
The basic problem is that you have requested a 10 dimensional thin plate
spline, with a basis dimension of 196830. In reality it will not be
possible to compute this, even if you have more than 196830 data. In any
case it would be unlikely to provide a very useful model --- the simplest
function that it can theoretically represent will have 3003 degrees of
freedom.
That said the error message is obviously rather unhelpful... Can you tell
me how many data you are actually trying to fit, and I'll try and track
down exactly where it's failing, and put in a more informative message.
best,
Simon
On Tuesday 01 September 2009 14:51, Corrado wrote:
Dear friends,
what is this error message in gam I cannot understand what it means
is it a bug?
gam_bray_scot24_pc_0505gam(bray~s(PC1,PC2,PC3,PC4,PC5,
PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
Error in if (length(data) != vl) { :
missing value where TRUE/FALSE needed
Calls: gam ... smooth.construct - smooth.construct.tp.smooth.spec -
array In addition: Warning message:
In array(0, n * k) : NAs introduced by coercion
Execution halted
Thanks in advance,
Best regards
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Basic population dynamics
Hello, For insect mortality data I'm trying to get an R script that will take the data from the raw form and convert it to Lx (% survival) for a number of treatments. The raw data has the number of days lived for each individual for the respective treatment. Thus, for example, when R selects the data for a single treatment I end up with the following vectors: day=seq(from=0,to=6) deaths=c(0,0,2,0,0,1,6) where deaths is the number of deaths on a given day. Now I need to create a new vector with the number alive for each day and this is where I'm stuck... I've tried to work various for and while loops but haven't had success. The vector should be: Alive=c(9,9,7,7,7,6,0) I realize it is a very basic problem that is easily accomplished in one's head or on a spreadsheet but in the context of the size of the data set I wish to have R do it for me. I would welcome any suggestions please. Best regards. __ 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] cbind objects using character vectors
Dear list,
I have a character vector such vec.names- c(a, b)
It happens that I have also two R objects called a and b that I would
like to merge. Is it possible to
do something like cbind(vec.names[1], vec.names[2]) ending up with the same
result as cbind(a,b)
Bellow is a reproducible example of what I need to to:
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
cbind(vec.names[1], vec.names[2])
[,1] [,2]
[1,] a b
But I was looking after the following result (using vec.names):
cbind(a,b)
a b
[1,] 0 5
[2,] 1 6
[3,] 2 7
[4,] 3 8
[5,] 4 9
Thanks in advance
Jonas
[[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] Basic population dynamics
Try ths: Alive - sum(deaths) - cumsum(deaths) On Tue, Sep 1, 2009 at 3:48 PM, Frostygoat frostyg...@gmail.com wrote: Hello, For insect mortality data I'm trying to get an R script that will take the data from the raw form and convert it to Lx (% survival) for a number of treatments. The raw data has the number of days lived for each individual for the respective treatment. Thus, for example, when R selects the data for a single treatment I end up with the following vectors: day=seq(from=0,to=6) deaths=c(0,0,2,0,0,1,6) where deaths is the number of deaths on a given day. Now I need to create a new vector with the number alive for each day and this is where I'm stuck... I've tried to work various for and while loops but haven't had success. The vector should be: Alive=c(9,9,7,7,7,6,0) I realize it is a very basic problem that is easily accomplished in one's head or on a spreadsheet but in the context of the size of the data set I wish to have R do it for me. I would welcome any suggestions please. Best regards. __ 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 [[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] Date format in plot
Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format standard in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have 06.05. I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have any clue? thank you -- View this message in context: http://www.nabble.com/Date-format-in-plot-tp25244066p25244066.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] cbind objects using character vectors
Not tested:
Instead of:
cbind(vec.names[1], vec.names[2])
cbind(get(vec.names[1]), get(vec.names[2]))
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of jonas garcia
Sent: Tuesday, September 01, 2009 12:53 PM
To: r-help@r-project.org
Subject: [R] cbind objects using character vectors
Dear list,
I have a character vector such vec.names- c(a, b)
It happens that I have also two R objects called a and b that I would
like to merge. Is it possible to
do something like cbind(vec.names[1], vec.names[2]) ending up with the same
result as cbind(a,b)
Bellow is a reproducible example of what I need to to:
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
cbind(vec.names[1], vec.names[2])
[,1] [,2]
[1,] a b
But I was looking after the following result (using vec.names):
cbind(a,b)
a b
[1,] 0 5
[2,] 1 6
[3,] 2 7
[4,] 3 8
[5,] 4 9
Thanks in advance
Jonas
[[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] Date format in plot
We will need a reproducible example! Please give us R commands that display the behavior you're observing: For example, I am having trouble understanding the as.Date function. When I input 39939, I would like to get 06.05.2009, but when I try it, I get as.Date(39939) Error in as.Date.numeric(39939) : 'origin' must be supplied I looked up what origin Excel uses for its' dates, and it seems like it might be January 1, 1900, so I tried as.Date(39939, origin = 1900-01-01) [1] 2009-05-08 Then we will much better be able to help you, because we will be able to paste your commands into R and see the results and make changes. But this still seems to be off by two days. So did you really mean 06.05, or 08.05? -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of swertie Sent: Tuesday, September 01, 2009 12:59 PM To: r-help@r-project.org Subject: [R] Date format in plot Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format standard in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have 06.05. I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have any clue? thank you __ 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] cbind objects using character vectors
Try this:
sapply(vec.names, get)
But for this example, you don't need for, try:
dat - 1
On Tue, Sep 1, 2009 at 2:52 PM, jonas garcia
garcia.jona...@googlemail.comwrote:
Dear list,
I have a character vector such vec.names- c(a, b)
It happens that I have also two R objects called a and b that I would
like to merge. Is it possible to
do something like cbind(vec.names[1], vec.names[2]) ending up with the same
result as cbind(a,b)
Bellow is a reproducible example of what I need to to:
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
cbind(vec.names[1], vec.names[2])
[,1] [,2]
[1,] a b
But I was looking after the following result (using vec.names):
cbind(a,b)
a b
[1,] 0 5
[2,] 1 6
[3,] 2 7
[4,] 3 8
[5,] 4 9
Thanks in advance
Jonas
[[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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[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] Date format in plot
On Sep 1, 2009, at 1:58 PM, swertie wrote: Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format standard in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have 06.05. I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have any clue? thank you You may need to do some jiggling around because R doesn't agree with that number of days since the beginning of the last century: as.Date(39939, origin=1900-01-01) [1] 2009-05-08 Then you need to look at docs re: the formating of date objects. Some code might move this process along. -- 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] GLM contrasting question
sodiumfish wrote: I have run a glm with a final formula of : (dependent variable = parasite load, main effects are sex, month, length and weight, with sex:month and length:weight first order interactions). I am using the summary(mod) command to give me the contrasts, which I believe use the contr.treatment command. I do not have a treatment group as such as I am comparing data from a wild system so I use the relevel command to reorder my factors in order to check the difference between each level and every other. I then use the coefficients and their related p-values to assess whether each level of my factors is significantly different from the next. This is fine for most things but what I really want to do is to assess whether there is a significant difference of between males and females in any particular month. However, because of my interaction term the male and female for any particular month are always the missing coefficients and so I can't contrast them with one another. Is there a way (preferably a relatively simple way) for me to do this. You will probably realise from my description above that I am a biologist not a statistician, so if anyone can help me in plain English that would be an enormous help. It would be a little easier if you gave us a reproducible example. It sounds like the easiest thing to do would be to partition your data set by month and run separate models in each month. If you were running lm() rather than glm() you could use lmList from the nlme package, but instead you should look at: http://finzi.psych.upenn.edu/Rhelp08/2008-February/154519.html for a solution. -- View this message in context: http://www.nabble.com/GLM-contrasting-question-tp25226439p25244287.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] Simple question about error on CSV import
thank you all for the quick responses and helpful explanations. I'm just getting started with R, so I'll get tripped up by some of this until I get in the groove. Thanks again, Landon -- View this message in context: http://www.nabble.com/Simple-question-about-error-on-CSV-import-tp25242899p25244282.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] Date format in plot
On Sep 1, 2009, at 3:13 PM, Erik Iverson wrote: We will need a reproducible example! Please give us R commands that display the behavior you're observing: For example, I am having trouble understanding the as.Date function. When I input 39939, I would like to get 06.05.2009, but when I try it, I get as.Date(39939) Error in as.Date.numeric(39939) : 'origin' must be supplied I looked up what origin Excel uses for its' dates, and it seems like it might be January 1, 1900, so I tried as.Date(39939, origin = 1900-01-01) [1] 2009-05-08 Then we will much better be able to help you, because we will be able to paste your commands into R and see the results and make changes. But this still seems to be off by two days. So did you really mean 06.05, or 08.05? One of the two day discrepancy is because the real date on which Excel dates are based is NOT 1900-01-01: http://support.microsoft.com/default.aspx?scid=kb;en-us;214058 They claim that fixing this would be too difficult and doesn't caus very many difficulties anyway, but apparently refuse to publish the correct starting date in their documents. Where the other missing day went I cannot say. It may have something to do with different definitions for where a date is supposed to start. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] On Behalf Of swertie Sent: Tuesday, September 01, 2009 12:59 PM To: r-help@r-project.org Subject: [R] Date format in plot Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format standard in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have 06.05. I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have any clue? thank you __ 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] Date format in plot
See R News 4/1. The article on dates there discusses how they work and discusses Excel's dates as well. On Tue, Sep 1, 2009 at 1:58 PM, swertiev_coudr...@voila.fr wrote: Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format standard in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have 06.05. I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have any clue? thank you -- View this message in context: http://www.nabble.com/Date-format-in-plot-tp25244066p25244066.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] package installation error
Hi, This also happens in 2.9.1 and 2.9.2. My personal solution is to look under 'C:\Program Files\R\R-2.9.0\library' for a bizarre-named directory (starts with an 'f' and has numbers and letters mixed) , which contains the package directory (in this case 'robustbase') and move it up one level (like the other packages). This is annoying, but so far is the only solutions I have found. On 31 Aug 2009 at 9:32, Duncan Murdoch wrote: On 31/08/2009 8:53 AM, Haynes, Maurice (NIH/NICHD) [E] wrote: On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? There have been two patch releases since 2.9.0. Have you tried 2.9.2? 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. -- Héctor Villalobos hvill...@ipn.mx CICIMAR - IPN A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34 ext. 82425 Fax. (+52 612) 122 53 22 [[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] understanding the output from gls
I'd like to compare two models which were fitted using gls, however I'm having trouble interpreting the results of gls. If any of you could offer me some advice, I'd greatly appreciate it. Short explanation of models: These two models have the same fixed-effects structure (two independent, linear effects), and differ only in that the second model includes a corExp structure for spatial autocorrelation. (more detailed explanation of the models at end). Specific questions: 1. The second model estimates two additional parameters in the process of fitting the corSpatial object - the range and nugget of the spatial autocorrelation. Based on this, I would expect the second model to have two fewer residual degrees of freedom. However, the summary function reports that both models have the same number of residual degrees of freedom. Why is this? (Interestingly, the difference in AIC between the two models reflects this difference in the number of model parameters) 2. In the model summary, what is the meaning of the small correlation matrix under the heading Correlation:? At first, I thought that this was describing possible correlations among the predictor variables, but then I saw that it also included the model intercept. What do these correlation value mean? ##More detailed information ##function calls: sppl.i.xx = gls(all.all.rch~l10area+newx, data = gtemp, method=ML) sppl.i.ex = gls(all.all.rch~l10area+newx, data = gtemp, method=ML, correlation = corExp(c(20,.8), form=~x+y|area, nugget=TRUE)) ##model summaries summary(sppl.i.xx) Generalized least squares fit by maximum likelihood Model: all.all.rch ~ l10area + newx Data: gtemp AIC BIClogLik 567.4893 578.572 -279.7446 Coefficients: Value Std.Error t-value p-value (Intercept) 6.891867 0.3295097 20.915522 0e+00 l10area 6.586182 0.3048870 21.602046 0e+00 newx0.047901 0.0117281 4.084307 1e-04 Correlation: (Intr) l10are l10area -0.364 newx 0.577 -0.007 Standardized residuals: Min Q1 Med Q3 Max -3.34307266 -0.57949890 -0.07214605 0.64309760 2.66409931 Residual standard error: 2.590313 Degrees of freedom: 118 total; 115 residual summary(sppl.i.ex) Generalized least squares fit by maximum likelihood Model: all.all.rch ~ l10area + newx Data: gtemp AIC BIClogLik 559.167 575.7911 -273.5835 Correlation Structure: Exponential spatial correlation Formula: ~x + y | area Parameter estimate(s): range nugget 15.4448835 0.3741476 Coefficients: Value Std.Error t-value p-value (Intercept) 7.621306 0.7648135 9.964921 0. l10area 6.400442 0.5588160 11.453576 0. newx0.066535 0.0204417 3.254857 0.0015 Correlation: (Intr) l10are l10area -0.592 newx 0.358 0.014 Standardized residuals: Min Q1Med Q3Max -3.0035983 -0.5990432 -0.2226852 0.5113270 2.263 Residual standard error: 2.820337 Degrees of freedom: 118 total; 115 residual Tim Handley Fire Effects Monitor Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr. Thousand Oaks, CA 91360 805-370-2347 __ 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] Read multiple files into dataframe?
Hello, I am fairly new to R programming and am stuck with the following problem. I am trying to read in multiple files (see attached file or at end of email), the files all have the same general header information and different precipitation (avgppt) and area (areasqmi) values. Some times the number of records are different in the files. I want to read in all files (.stdsummary), and create a dataframe that contains the area and precipitation for each file (files are different duration), and supply a header name that represents the duration (sixth line down in header information or extracted from data file da_zone1_15hr_1166.stdsummary). For example, this is what the final dataframe would look like for 1hr, 3hr, and 15hr datafiles: 1hrppt 1hrarea3hrppt 3hrarea15hrppt 15hrarea 3.806.8607.670 3.7116.7817.61 3.6956.7257.525 3.56106.55107.3210 3.33206.17206.9120 2.87505.25505.950 2.451004.351005.02100 1.942003.342004.09200 1.673002.783003.55300 The end result is to perform QC statistics and then plot each set of data. Also, is there away to create a dataframe that has different # of records? Datafile example of file below: Storm number: 1166 Zone number: 1 (ALL zones) Number of stations: 172 Total analyzed area (sq mi): 5360.8 Average station density (stns per 1000 sq mi): na Duration window (hours): 15 CPP beg hour index: 1 CPP end hour index: 15 Ishohyet interval step (inches): 0.2 Standard area size summary Begin run date/time: Tue Aug 25 01:17:43 2009 avgppt, areasqmi 7.67,000.00 7.60,001.00 7.52,005.00 7.32,010.00 6.91,020.00 5.90,050.00 5.02,100.00 4.09,200.00 3.55,300.00 2.96,500.00 2.27,0001000.00 1.64,0002000.00 0.82,0005000.00 0.77,0005360.00 -- - Douglas M. Hultstrand, MS Senior Hydrometeorologist Metstat, Inc. Windsor, Colorado voice: 970.686.1253 email: dmhul...@metstat.com web: http://www.metstat.com - Storm number: 1166 Zone number: 1 (ALL zones) Number of stations: 172 Total analyzed area (sq mi): 5360.8 Average station density (stns per 1000 sq mi): na Duration window (hours): 15 CPP beg hour index: 1 CPP end hour index: 15 Ishohyet interval step (inches): 0.2 Standard area size summary Begin run date/time: Tue Aug 25 01:17:43 2009 avgppt, areasqmi 7.67,000.00 7.60,001.00 7.52,005.00 7.32,010.00 6.91,020.00 5.90,050.00 5.02,100.00 4.09,200.00 3.55,300.00 2.96,500.00 2.27,0001000.00 1.64,0002000.00 0.82,0005000.00 0.77,0005360.00 __ 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] simple 3-dimensional plots?
dear R experts: I am trying to plot an empirical likelihood function in 3d. The values are not over a regular grid---I just searched the likelihood function to find the optimal value, and then computed a few values around it. (each point in the likelihood function takes a very long time to compute.) the likelihood values now sit in a csv file that has three columns, mu, sd, and v. I would like to look at my 3d plots to find out how well or badly behaved my likelihood function is (and then compute a Hessian, my next task). Is persp() the correct function for this task? something else? is there a wrapper that takes my x, y, and z values (which come in almost random order), and puts them into the format that persp() needs? pointers appreciated. sincerely, /iaw [[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] Loading file in MAC-Syntax Error
Hi, If any body can help me regarding a basic problem using R? I am starting with R and I have problem in loading my file. File is on Desktop of my MAC and I use code as follows to access it /Users/username/Desktop/test.txt/ It always gives me Syntax error message. Thanks for your help -- View this message in context: http://www.nabble.com/Loading-file-in-MAC-Syntax-Error-tp25244312p25244312.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] Read multiple files into dataframe?
I would put the data into a 'long' instead of 'wide' format since you
say you have files of different lengths. I took you data and
replicated it 3 time and changed the file name for the duration:
fileNames - Sys.glob('/da_zone*') # files to process
result - lapply(fileNames, function(.file){
+ # read in data after skipping 11 lines
+ .input - read.csv(.file, skip=11)
+ # extract the duration from file name
+ .dur - sub(.*_([[:digit:]]+)hr_.*, \\1, .file, perl=TRUE)
+ # add to the data frame
+ .input$dur - .dur
+ .input
+ })
# put into a single data.frame
do.call(rbind, result)
avgppt areasqmi dur
17.670 15
27.601 15
37.525 15
47.32 10 15
56.91 20 15
65.90 50 15
75.02 100 15
84.09 200 15
93.55 300 15
10 2.96 500 15
11 2.27 1000 15
12 1.64 2000 15
13 0.82 5000 15
14 0.77 5360 15
15 7.670 1
16 7.601 1
17 7.525 1
18 7.32 10 1
19 6.91 20 1
20 5.90 50 1
21 5.02 100 1
22 4.09 200 1
23 3.55 300 1
24 2.96 500 1
25 2.27 1000 1
26 1.64 2000 1
27 0.82 5000 1
28 0.77 5360 1
29 7.670 3
30 7.601 3
31 7.525 3
32 7.32 10 3
33 6.91 20 3
34 5.90 50 3
35 5.02 100 3
36 4.09 200 3
37 3.55 300 3
38 2.96 500 3
39 2.27 1000 3
40 1.64 2000 3
41 0.82 5000 3
42 0.77 5360 3
On Tue, Sep 1, 2009 at 4:24 PM, Douglas M.
Hultstranddmhul...@metstat.com wrote:
Hello,
I am fairly new to R programming and am stuck with the following problem.
I am trying to read in multiple files (see attached file or at end of
email), the files all have the same general header information and different
precipitation (avgppt) and area (areasqmi) values. Some times the number of
records are different in the files.
I want to read in all files (.stdsummary), and create a dataframe that
contains the area and precipitation for each file (files are different
duration), and supply a header name that represents the duration (sixth line
down in header information or extracted from data file
da_zone1_15hr_1166.stdsummary).
For example, this is what the final dataframe would look like for 1hr, 3hr,
and 15hr datafiles:
1hrppt 1hrarea 3hrppt 3hrarea 15hrppt 15hrarea 3.8 0
6.86 0 7.67 0
3.71 1 6.78 1 7.6 1
3.69 5 6.72 5 7.52 5
3.56 10 6.55 10 7.32 10
3.33 20 6.17 20 6.91 20
2.87 50 5.25 50 5.9 50
2.45 100 4.35 100 5.02 100
1.94 200 3.34 200 4.09 200
1.67 300 2.78 300 3.55 300
The end result is to perform QC statistics and then plot each set of data.
Also, is there away to create a dataframe that has different # of records?
Datafile example of file below:
Storm number: 1166
Zone number: 1 (ALL zones)
Number of stations: 172
Total analyzed area (sq mi): 5360.8
Average station density (stns per 1000 sq mi): na
Duration window (hours): 15
CPP beg hour index: 1
CPP end hour index: 15
Ishohyet interval step (inches): 0.2
Standard area size summary
Begin run date/time: Tue Aug 25 01:17:43 2009
avgppt, areasqmi
7.67,000.00
7.60,001.00
7.52,005.00
7.32,010.00
6.91,020.00
5.90,050.00
5.02,100.00
4.09,200.00
3.55,300.00
2.96,500.00
2.27,0001000.00
1.64,0002000.00
0.82,0005000.00
0.77,0005360.00
--
-
Douglas M. Hultstrand, MS
Senior Hydrometeorologist
Metstat, Inc. Windsor, Colorado
voice: 970.686.1253
email: dmhul...@metstat.com
web: http://www.metstat.com
-
Storm number: 1166
Zone number: 1 (ALL zones)
Number of stations: 172
Total analyzed area (sq mi): 5360.8
Average station density (stns per 1000 sq mi): na
Duration window (hours): 15
CPP beg hour index: 1
CPP end hour index: 15
Ishohyet interval step (inches): 0.2
Standard area size summary
Begin run date/time: Tue Aug 25 01:17:43 2009
avgppt, areasqmi
7.67,000.00
7.60,001.00
7.52,005.00
7.32,010.00
6.91,020.00
5.90,050.00
5.02,100.00
4.09,200.00
3.55,300.00
2.96,500.00
2.27,0001000.00
1.64,0002000.00
0.82,0005000.00
0.77,0005360.00
__
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
Re: [R] Loading file in MAC-Syntax Error
Hi, On Tue, Sep 1, 2009 at 4:40 PM, Awais77khan_awai...@yahoo.com wrote: Hi, If any body can help me regarding a basic problem using R? I am starting with R and I have problem in loading my file. File is on Desktop of my MAC and I use code as follows to access it /Users/username/Desktop/test.txt/ 1. Where's your code? 2. Try to remove the trailing slash of your filename It always gives me Syntax error message. What is the error message? -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] Loading file in MAC-Syntax Error
On Sep 1, 2009, at 4:40 PM, Awais77 wrote: Hi, If any body can help me regarding a basic problem using R? I am starting with R and I have problem in loading my file. File is on Desktop of my MAC and I use code as follows to access it /Users/username/Desktop/test.txt/ Are you expecting R to read your mind? Where is a function to do something with that file? Read some more introductory material and also read the R Import/Export Manual. There is a treasure trove of contributed documentation at the r-project website. It always gives me Syntax error message. Thanks for your help -- 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] Syntax for crossed random effects in nlme
Hi Ben, Pinheiro and Bates 2000 is the real documentation for nlme. See the Cell Culture Bioassay example starting on pg 163 for a demonstration of fitting crossed random effects using pdIdent and pdBlocked objects. hth, Kingsford On Tue, Sep 1, 2009 at 6:44 AM, bamselbenam...@gmail.com wrote: Hello R users, I've read the posts on this topic, and had a look at the R documentation for nlme, but I can't seem to make this work. I'd like to be able to fit a mixed effects model with crossed random effects, but also be able to specify the covariance matrix structure for the residuals. Here's the syntax using the lmer function in lme4 (which doesn't currently allow alternate error covariance structures). Does anybody know how to transform this to work with nlme? fit = lmer(data$DV ~ X + time + (X*time) + (1|Item_Number) + (1|Subject), data) Much appreciated, Ben Amsel -- View this message in context: http://www.nabble.com/Syntax-for-crossed-random-effects-in-nlme-tp25239714p25239714.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] Loading file in MAC-Syntax Error
Thanks for useful replies. It is working now.
I was typing only read.table(/Users/username/Desktop/test.txt/) without
surrounding the filename with quotes. It works when i use it as
read.table('/Users/khan_awais77/Desktop/test2.txt').
Cheers
Awais77 wrote:
Hi,
If any body can help me regarding a basic problem using R?
I am starting with R and I have problem in loading my file. File is on
Desktop of my MAC and I use code as follows to access it
/Users/username/Desktop/test.txt/
It always gives me Syntax error message.
Thanks for your help
--
View this message in context:
http://www.nabble.com/Loading-file-in-MAC-Syntax-Error-tp25244312p25248604.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.
[R] how to merge the fitted values from a linear model?
Hi All, I would like to run a linear model where the response is the duration of relief in days and the regressor is the drug dosage in mg. Then I would like compute the predicted values of the duration of relief from the model and merge it into the original data. I am not sure how the merge happens since if I have missing values in the data, R runs the resgression model but fitted values for some observations are not being calculated. Below is my R script Mydata-read.csv(file=”file1.csv”, header=T) Model-lm(y ~ x, data=Mydata) f-fitted(Model) Newdata-cbind(f , Mydata) Is Newdata merged correctly? Thanks for your help -- View this message in context: http://www.nabble.com/how-to-merge-the-fitted-values-from-a-linear-model--tp25248552p25248552.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.
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Re: [R] Simple question about data.frame reduction
Dear Ronaldo, You were almost there! Here is a suggestion: with(test, tapply(var3, var2, length)) # a b c d e # 2 1 1 1 1 HTH, Jorge 2009/9/1 Ronaldo Reis Júnior Hi, this is a simple question I have this data.frame: test - data.frame(var1=c(1,1,1,1,1,1),var2=c(a,a,b,c,d,e),var3=c(a1,a1,b1,a1,c1,d1)) test var1 var2 var3 11a a1 21a a1 31b b1 41c a1 51d c1 61e d1 Then I need to calculate the number of var3 excluding the repeated measure of var2. With tapply I have this: tapply(test$var1,test$var3,sum) a1 b1 c1 d1 3 1 1 1 But the correct result is: a1 b1 c1 d1 2 1 1 1 because on factor a1 in var3 I have 2 repeated factor a in var2. I try a simple solution for it but without success. aggregate function dont work with factors (var3 by var1). Anybody have an idea? Thanks Ronaldo -- It's men like him that give the Y chromosome a bad name. -- Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | chrys...@gmail.com | http://www.ppgcb.unimontes.br/lecc | ICQ#: 5692561 | LinuxUser#: 205366 -- Favor NÃO ENVIAR arquivos do Word ou Powerpoint Prefira enviar em PDF, Texto, OpenOffice (ODF), HTML, or RTF. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
