Re: [R] small negative values instead of zeros in nested loop
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Cristina Fdez. Aragón
Sent: Tuesday, September 25, 2012 4:40 PM
To: r-help@r-project.org
Subject: [R] small negative values instead of zeros in nested loop
Hi,I am trying to run a code with a series of nested for loops, here is a
simplified version of it:
J-seq(0,1,0.2) D-seq(0,1,0.2)
for (x in 1:10) {
for (j
in 1:length(J)) {
for (d
in 1:(length(D)-j+1)) {
x.end-x*(1-J[j]-D[d])
print(x)print(J[j])
print(D[d]) print(x.end)
}
}}
The problem is that whenever x.end should be zero it takes a small
negative value really close to zero instead. Any idea of why this might be
happening and how can I fix it?Thanks!
The reason for why this happens can be found in R FAQ 7.31.
Dan
Daniel Nordlund
Bothell, WA USA
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[R] Ask for help - how to change WHIRR.117.csv to WHIRR_117.csv
Hi,
I have a script below.
dat - read.table(file=pt.csv, header=T, sep=,, row.names=1,
col.names=1)
dat
for(which_col in seq_len(ncol(dat)))
{
subset_data - dat[,which_col:ncol(dat)]
file_name - sprintf('%s.csv', colnames(dat)[which_col])
write.csv(subset_data, file_name)
message(sprintf('Saving %s', file_name))
}
dput(head(dat))
structure(list(WHIRR.25 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.28 = c(0L,
0L, 1L, 0L, 0L, 0L), WHIRR.55 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.61 = c(0L,
0L, 1L, 0L, 0L, 0L), WHIRR.76 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.87 = c(0L,
0L, 0L, 0L, 0L, 0L), WHIRR.92 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.115 =
c(0L,
0L, 0L, 0L, 0L, 0L), WHIRR.117 = c(0L, 0L, 0L, 0L, 0L, 0L)), .Names = c(
WHIRR.25,
WHIRR.28, WHIRR.55, WHIRR.61, WHIRR.76, WHIRR.87, WHIRR.92,
WHIRR.115, WHIRR.117), row.names = c(Adrian Cole, Alison Wong,
Andrei Savu, Bruno Dumon, Edward J. Yoon, Eugene Koontz
), class = data.frame)
The script is able to save the file in the directory, but with the
following name:
WHIRR.25.csv
WHIRR.28.csv
WHIRR.55.csv
WHIRR.61.csv
WHIRR.76.csv
WHIRR.87.csv
WHIRR.92.csv
WHIRR.115.csv
WHIRR.117.csv
My first question is:
How can I change or convert the name above to WHIRR_25.csv, WHIRR_28.csv,
WHIRR_55.csv, etc?
My second question is:
The last column which is WHIRR.177.csv is not properly created, the output
for the last column is as below:
X1
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 1
15 0
Suppose, the last column should be properly created like this, as below:
WHIRR.117
Adrian Cole 0
Alison Wong 0
Andrei Savu0
Bruno Dumon 0
Edward J. Yoon 0
Eugene Koontz 0
Jakob Homan 0
Kelvin Kakugawa 0
Kirk True 0
Lars George0
Soren Macbeth0
Stu Hood0
Tibor Kiss 0
Tom White 1
Unassigned0
Appreciate your thought...
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Re: [R] Memory usage in R grows considerably while calculating word frequencies
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 25/09/12 01:29, mcelis wrote: I am working with some large text files (up to 16 GBytes). I am interested in extracting the words and counting each time each word appears in the text. I have written a very simple R program by following some suggestions and examples I found online. Just an idea (I have no experience with what you want to do, so it might not work): What about putting the text in a database (sqlite comes to mind) where each word is one entry. Then you could use sql to query the database, which should need much less memory. In addition, it should make further processing much easier. Cheers, Rainer If my input file is 1 GByte, I see that R uses up to 11 GBytes of memory when executing the program on a 64-bit system running CentOS 6.3. Why is R using so much memory? Is there a better way to do this that will minimize memory usage. I am very new to R, so I would appreciate some tips on how to improve my program or a better way to do it. R program: # Read in the entire file and convert all words in text to lower case words.txt-tolower(scan(text_file,character,sep=\n)) # Extract words pattern - (\\b[A-Za-z]+\\b) match - gregexpr(pattern,words.txt) words.txt - regmatches(words.txt,match) # Create a vector from the list of words words.txt-unlist(words.txt) # Calculate word frequencies words.txt-table(words.txt,dnn=words) # Sort by frequency, not alphabetically words.txt-sort(words.txt,decreasing=TRUE) # Put into some readable form, Name of word and Number of times it occurs words.txt-paste(names(words.txt),words.txt,sep=\t) # Results to a file cat(Word\tFREQ,words.txt,file=frequencies,sep=\n) -- View this message in context: http://r.789695.n4.nabble.com/Memory-usage-in-R-grows-considerably-while-calculating-word-frequencies-tp4644053.html Sent from the R help mailing list archive at Nabble.com. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://www.enigmail.net/ iEYEARECAAYFAlBitboACgkQoYgNqgF2egr1pgCgjHxE/E1qIwUbrYzB30qIk9cK z/oAoILCYn66+c9CF5tzkWeQH3E2utwi =ahI5 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help needed on parallel processing
Le mercredi 26 septembre 2012 à 13:04 +0530, Anindya Sankar Dey a
écrit :
Hi All,
If i have a vector say x-1:10 and then use
parLapply(cl,x,function(k){k=k*2; return(k);}
it works and will also parallel process depending on the number of cores
and the number of clusters I've built in cl.
My query is, if I want this function -
function(k1,k2){ s=k1+k2; return(s);}
to work using parallel processing what will be the procedure.
I think you should have a look at the clusterMap() function. It's the
parallel equivalent of mapply().
My two cents
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Re: [R] Simulating from probit
On 12-09-25 10:16 PM, Tjun Kiat Teo wrote: Is there anyway to simulate random deviates from probit ? Use pnorm() to calculate the probabilities, and rbinom() to simulate the random values. 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] Broken Links on http://www.r-project.org
I was not sure who I should contact about this, so I am posting this here. There are a few broken links on the R website. 1) http://www.r-project.org/search.html - link to the Nabble R Forum. I belive the correct/new URL should be: http://r.789695.n4.nabble.com/ 2) http://www.r-project.org/other-docs.html - link to Auswertung ökologischer Daten. Not sure if there is a new URL. 3) http://www.r-project.org/other-projects.html - link to Jim Lindsey's R page. I believe the correct/new URL should be: http://www.commanster.eu/rcode.html Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.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] map two names into one
Dear R user: I have got the following problem: I have imported two data sets into R: one set includes price information, another one includes volume information. but I noticed the wrong data order problem in the product name, for instance, in one data set, GALAXY ACE S 5830 in another one, it is S 5830 GALAXY ACE both represent same product. how do i map two name into one in R? there are so many product name having this problem. i hope there is some mechanism which can autimatically map those. thanks for your help.. Kind regards, Tammy [[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] map two names into one
It may be easy or difficult depending on what your data are like. GALAXY ACE S 5830 vs S 5830 GALAXY ACE One easy and reasonably general way would be to divide each such bit into 4 words and then compare if set 2 contains exactly all words in set 1 but possibly in different order. x1 - GALAXY ACE S 5830 x2 - S 5830 GALAXY ACE x3 - S 5830 GALAXY ZOMBIE divide - function(x) strsplit(x1, )[[1]] check - function(x, y) all(divide(x) %in% divide(y)) check(x1,x2) # [1] TRUE check(x1,x3) #FALSE Or you could try reading in your data in a different way so that S, GALAXY, ACE, and 5830 would be in different variables (if all product names have identical structure i.e 4 elements, or is S 5830 supposed to be the price?). Or build a catalogue of all possible product names and then compare each name to it. etc htmh On 9/26/12, Tammy Ma metal_lical...@live.com wrote: Dear R user: I have got the following problem: I have imported two data sets into R: one set includes price information, another one includes volume information. but I noticed the wrong data order problem in the product name, for instance, in one data set, GALAXY ACE S 5830 in another one, it is S 5830 GALAXY ACE both represent same product. how do i map two name into one in R? there are so many product name having this problem. i hope there is some mechanism which can autimatically map those. thanks for your help.. Kind regards, Tammy [[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] map two names into one
Hi Tammy, I think we need more information. Are the names always four parts? Does the fix always involve moving two parts from the back to the front? For that matter, which of the two you gave is correct? Or does it matter what order the parts are in as long as it's consistent? Sorting them would be easiest, and would work regardless of number of parts and how they were entered. That could be done, for instance, with strsplit(), sort() and paste(). Sarah On Wednesday, September 26, 2012, Tammy Ma wrote: Dear R user: I have got the following problem: I have imported two data sets into R: one set includes price information, another one includes volume information. but I noticed the wrong data order problem in the product name, for instance, in one data set, GALAXY ACE S 5830 in another one, it is S 5830 GALAXY ACE both represent same product. how do i map two name into one in R? there are so many product name having this problem. i hope there is some mechanism which can autimatically map those. thanks for your help.. Kind regards, Tammy [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[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] Ask for help - how to change WHIRR.117.csv to WHIRR_117.csv
Hello,
Maybe the code below answers to both your questions (Q1 and Q2)
cnames - colnames(dat)
cnames - sub(WHIRR\\., WHIRR_, cnames)
for(which_col in seq_len(ncol(dat)))
{
subset_data - dat[which_col:ncol(dat)] # change 1, Q2
file_name - sprintf('%s.csv', cnames[which_col]) # change 2, Q1
#write.csv(subset_data, file_name) # debug 1
message(sprintf('Saving %s', file_name))
if(which_col == ncol(dat)) print(subset_data) # debug 2
}
Em 26-09-2012 07:43, s.s.m. fauzi escreveu:
Hi,
I have a script below.
dat - read.table(file=pt.csv, header=T, sep=,, row.names=1,
col.names=1)
dat
for(which_col in seq_len(ncol(dat)))
{
subset_data - dat[,which_col:ncol(dat)]
file_name - sprintf('%s.csv', colnames(dat)[which_col])
write.csv(subset_data, file_name)
message(sprintf('Saving %s', file_name))
}
dput(head(dat))
structure(list(WHIRR.25 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.28 = c(0L,
0L, 1L, 0L, 0L, 0L), WHIRR.55 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.61 = c(0L,
0L, 1L, 0L, 0L, 0L), WHIRR.76 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.87 = c(0L,
0L, 0L, 0L, 0L, 0L), WHIRR.92 = c(0L, 0L, 0L, 0L, 0L, 0L), WHIRR.115 =
c(0L,
0L, 0L, 0L, 0L, 0L), WHIRR.117 = c(0L, 0L, 0L, 0L, 0L, 0L)), .Names = c(
WHIRR.25,
WHIRR.28, WHIRR.55, WHIRR.61, WHIRR.76, WHIRR.87, WHIRR.92,
WHIRR.115, WHIRR.117), row.names = c(Adrian Cole, Alison Wong,
Andrei Savu, Bruno Dumon, Edward J. Yoon, Eugene Koontz
), class = data.frame)
The script is able to save the file in the directory, but with the
following name:
WHIRR.25.csv
WHIRR.28.csv
WHIRR.55.csv
WHIRR.61.csv
WHIRR.76.csv
WHIRR.87.csv
WHIRR.92.csv
WHIRR.115.csv
WHIRR.117.csv
My first question is:
How can I change or convert the name above to WHIRR_25.csv, WHIRR_28.csv,
WHIRR_55.csv, etc?
My second question is:
The last column which is WHIRR.177.csv is not properly created, the output
for the last column is as below:
X1
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 1
15 0
Suppose, the last column should be properly created like this, as below:
WHIRR.117
Adrian Cole 0
Alison Wong 0
Andrei Savu0
Bruno Dumon 0
Edward J. Yoon 0
Eugene Koontz 0
Jakob Homan 0
Kelvin Kakugawa 0
Kirk True 0
Lars George0
Soren Macbeth0
Stu Hood0
Tibor Kiss 0
Tom White 1
Unassigned0
Appreciate your thought...
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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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] create new column in a DF according to values from another column
Hi everyone,
I have a small problem in my R-code.
Imagine this DF for example:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
I would like to add a new column Station in this DF. This new column must
be automatically filled with: V1 or V2 or V3.
The choice must be done on the numbers (1st column).
For example, I would like to have V1 in the column Station in the rows
where the numbers of the 1st column are: 1,7,11,16 ; then I would like to
have V2 in the rows where the numbers are: 4,14,20 and finally V3 in the
rows where the numbers are: 3,17,19.
I'm trying with if and something like this, but it's not working yet:
# For V1:
if(DF$number %in% c(1,7,11,16)) {test$Station==V1}
# For V2:
...
So my final DF should look like this:
FINALDF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10),
Station=c(V1,V2,V1,V3,V1,V1,V2,V3,V2,V3))
Could someone help me to finish this?
Thank you very much!!!
--
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] R for commercial use
cool, im none the wiser now, but thanks anyway -- View this message in context: http://r.789695.n4.nabble.com/R-for-commercial-use-tp4644027p4644204.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] Running different Regressions using for loops
Hi,
I am trying to run many different regressions using a FOR Loop.
The input data that is read into R has the following variables
· Volume
· Price1
· Price2
· Price3
· Price4
· Price5
· Trend
· Seasonality
I want to run 5 regressions, with the Volume as an dependent variable and
Price, Trend Seasonality as independent variables. I have read the above
mentioned variables in a variable called tryout
I am entering the following syntax in R
for(i in 1:5)
+ {
+ result[i]=lm(Volume~Price[i]+Trend+Seasonaliy,data=tryout)
+ summary(result[i])
+ }
After running these lines
I am getting the following error message
Error in eval(expr, envir, enclos) : object 'Price' not found
Can someone help me out with this error message. Appreciate for your time
and consideration.
Thanks Regards,
Krunal Nanavati
Solutions Manager - Cogitaas
9769-919198
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Re: [R] lattice dotplot reorder contiguous levels
sorry for my slow reply, this is what I worked out so far… my reproducible example and the code test-structure(list(site = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L), .Label = c(A, B, C, D, E), class = factor), conc = c(2.32, 0.902, 0.468, 5.51, 1.49, 0.532, 0.72, 0.956, 0.887, 20, 30, 2.12, 0.442, 10, 50, 110, 3.36, 2.41, 20, 70, 3610, 100, 4.79, 20, 0.0315, 30, 60, 1, 3.37, 80, 1.21, 0.302, 0.728, 1.29, 30, 40, 90, 30, 0.697, 6.25, 0.576, 0.335, 20, 10, 620, 40, 9.98, 4.76, 2.61, 3.39, 20, 4.59), samp.time = structure(c(2L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 8L, 8L, 8L, 8L, 8L, 9L, 8L, 7L, 8L, 8L, 8L, 8L, 3L, 3L, 2L, 4L, 4L, 4L, 4L, 4L, 1L, 4L, 6L, 4L, 8L, 4L, 8L, 4L, 3L, 8L, 4L, 8L, 4L, 8L, 4L, 9L, 3L, 8L, 8L, 8L, 8L, 8L, 8L, 1L), .Label = c(2, 4, 12, 24, 96, 135, 167, 168, 169), class = factor)), .Names = c(site, conc, samp.time), row.names = c(NA, 52L), class = data.frame) test$samp.time.new - with(test, reorder(samp.time:site, as.numeric(site))) m-match(unique(droplevels(test$samp.time.new)),test$samp.time.new) lab-as.character(test$samp.time[m]) dotplot(samp.time.new~conc|site, data=test, ylim=lab, scales=list(x=list(log=10), y = list(relation = free)), layout=c(1,5), strip=FALSE, strip.left=TRUE ) Now labels are correctly spaced and sorted out but still a “slight” problem persist: i.e. the reordering of samp.time.new within each site; in fact, I would like to have an ascending order of sampling time but for some reason I’m not able to work it out properly… any help much appreciated max -- View this message in context: http://r.789695.n4.nabble.com/lattice-dotplot-reorder-contiguous-levels-tp4643741p4644215.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] add a data frame to my data frame
Thanks to all of you. The three advices helped me a lot - solved my problem and thank you Sarah for the hint with rseek.org. Didn't know that one. Have a great day, Tagmarie -- View this message in context: http://r.789695.n4.nabble.com/add-a-data-frame-to-my-data-frame-tp4644122p4644206.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] average environmental data if AnimalID and Time is duplicated
Hello, I tried for about three hours now to solve this problem but I can't figure it out. I am sure someone knows how do it. At least I hope so. I have a data frame somewhat like this: myframe - data.frame (ID=c(Ernie, Ernie, Bert, Bert), Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00, 25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28) ) myframe As you can see for Ernie I do have different data for 24.09.2012 9:00. Now I would like to average the Hunger and Temp value for this timestamp to get a data frame without duplicated Times and the respective average Temp and Hunger. I tried something like Meanframe- by(myframe[, 3:4], duplicated(myframe$ID, Zusatzdaten3$Timestamp) == TRUE, mean) but it doesn't work and I guess that it is also totally crap ;-) Tagmarie -- View this message in context: http://r.789695.n4.nabble.com/average-environmental-data-if-AnimalID-and-Time-is-duplicated-tp4644218.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] Change in order of names after applying plyr package
Dear R helpers
I have following two data.frames viz. equity_data and param.
equity_data = data.frame(security_id = c(Air, Air, Air, Air, Air,
Air, Air, Air, Air, Air, Air, Air, AB, AB, AB, AB, AB,
AB, AB, AB, AB, AB, AB, AB, AD, AD, AD, AD, AD, AD,
AD, AD, AD, AD, AD, AD), ason_date =
c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 31-Dec-11,
30-Dec-11, 10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 31-Dec-11,
30-Dec-11, 10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12, 31-Dec-11,
30-Dec-11), security_rate = c(0.597,0.61,0.6,0.63,0.67,0.7,0.74,0.735,
7.61,0.795,0.796, 0.84, 8.5,8.1,8.9,8.9,8.9,9,9,9,9,9,9,9,3.21,3.22,3.12, 3.51,
3.5, 3.37, 3.25, 3, 3.07, 3, 2.94, 2.6))
param = data.frame(confidence_level = c(0.99), holding_period = c(10),
calculation_method = MC, no_simulation_mc = c(100))
library(plyr)
library(reshape2)
attach(equity_data)
attach(param)
security_names = unique(equity_data$security_id)
# (security_names are used further in R code not included here)
alpha = param$confidence_level
t = param$holding_period
n = param$no_simulation_mc
method = param$calculation_method
mc_VaR = function(security_id, ason_date, security_rate)
{
security_rate_returns - NULL
for (i
in(1:length(ason_date)-1))
{
security_rate_returns[i] = log(security_rate[i]/security_rate[i+1])
}
return_mean = mean(security_rate_returns)
return_sd = sd(security_rate_returns)
simulation = rnorm(n, return_mean, return_sd)
qq = sort(simulation, decreasing = TRUE)
VaR_mc = -qq[alpha * n]*sqrt(t)
return(VaR_mc)
}
result_method_other - dlply(.data = equity_data, .variables = security_id,
.fun = function(x)
mc_VaR(ason_date = x$ason_date, security_id =
x$security_id,
security_rate = x$security_rate))
result_method_other
$AB
[1] 0.2657424
$AD
[1] 0.212061
$Air
[1] 6.789733
attr(,split_type)
[1] data.frame
attr(,split_labels)
security_id
1 AB
2 AD
3 Air
MY PROBLEM :
My original data (i.e. equity_data) has the order of Air, AB and AD.
However, after applying plyr, my order (and corresponding result) has changed
to AB, AD Air.
I need to
maintain my original order of Air, AB and AD. How do I modify my R code
for this?
Kindly guide
Vincy
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Re: [R] create new column in a DF according to values from another column
On 26-09-2012, at 12:49, jeff6868 geoffrey_kl...@etu.u-bourgogne.fr wrote:
Hi everyone,
I have a small problem in my R-code.
Imagine this DF for example:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
I would like to add a new column Station in this DF. This new column must
be automatically filled with: V1 or V2 or V3.
The choice must be done on the numbers (1st column).
For example, I would like to have V1 in the column Station in the rows
where the numbers of the 1st column are: 1,7,11,16 ; then I would like to
have V2 in the rows where the numbers are: 4,14,20 and finally V3 in the
rows where the numbers are: 3,17,19.
I'm trying with if and something like this, but it's not working yet:
# For V1:
if(DF$number %in% c(1,7,11,16)) {test$Station==V1}
# For V2:
...
So my final DF should look like this:
FINALDF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10),
Station=c(V1,V2,V1,V3,V1,V1,V2,V3,V2,V3))
DF[DF$number %in% c(1,7,11,16),Station] - V1
DF[DF$number %in% c(4,14,20),Station] - V2
DF[DF$number %in% c(3,17,19),Station] - V3
DF
The Station column is of type character.
To make FINALDF identical you should add stringsAsFactors=FALSE to the
arguments of data.frame.
Berend
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Re: [R] lattice dotplot reorder contiguous levels
On Wed, Sep 26, 2012 at 3:36 PM, maxbre mbres...@arpa.veneto.it wrote: sorry for my slow reply, this is what I worked out so far… my reproducible example and the code test-structure(list(site = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L), .Label = c(A, B, C, D, E), class = factor), conc = c(2.32, 0.902, 0.468, 5.51, 1.49, 0.532, 0.72, 0.956, 0.887, 20, 30, 2.12, 0.442, 10, 50, 110, 3.36, 2.41, 20, 70, 3610, 100, 4.79, 20, 0.0315, 30, 60, 1, 3.37, 80, 1.21, 0.302, 0.728, 1.29, 30, 40, 90, 30, 0.697, 6.25, 0.576, 0.335, 20, 10, 620, 40, 9.98, 4.76, 2.61, 3.39, 20, 4.59), samp.time = structure(c(2L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 8L, 8L, 8L, 8L, 8L, 9L, 8L, 7L, 8L, 8L, 8L, 8L, 3L, 3L, 2L, 4L, 4L, 4L, 4L, 4L, 1L, 4L, 6L, 4L, 8L, 4L, 8L, 4L, 3L, 8L, 4L, 8L, 4L, 8L, 4L, 9L, 3L, 8L, 8L, 8L, 8L, 8L, 8L, 1L), .Label = c(2, 4, 12, 24, 96, 135, 167, 168, 169), class = factor)), .Names = c(site, conc, samp.time), row.names = c(NA, 52L), class = data.frame) test$samp.time.new - with(test, reorder(samp.time:site, as.numeric(site))) m-match(unique(droplevels(test$samp.time.new)),test$samp.time.new) lab-as.character(test$samp.time[m]) dotplot(samp.time.new~conc|site, data=test, ylim=lab, scales=list(x=list(log=10), y = list(relation = free)), layout=c(1,5), strip=FALSE, strip.left=TRUE ) Now labels are correctly spaced and sorted out but still a “slight” problem persist: i.e. the reordering of samp.time.new within each site; in fact, I would like to have an ascending order of sampling time but for some reason I’m not able to work it out properly… For that, it should be enough to just reorder again by samp.time. Your label code doesn't work then (I haven't tried to figure out why), but your earlier idea using strsplit() does: test$samp.time.new - with(test, reorder(reorder(samp.time:site, as.numeric(site)), as.numeric(samp.time))) lab - sapply(strsplit(levels(test$samp.time.new), :, fixed=TRUE), [, 1) dotplot(samp.time.new~conc|site, data=test, ylim=lab, scales=list(x=list(log=10), y = list(relation = free)), layout=c(1,5), strip=FALSE, strip.left=TRUE ) -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] average environmental data if AnimalID and Time is duplicated
On 09/26/2012 08:53 PM, Tagmarie wrote: Hello, I tried for about three hours now to solve this problem but I can't figure it out. I am sure someone knows how do it. At least I hope so. I have a data frame somewhat like this: myframe- data.frame (ID=c(Ernie, Ernie, Bert, Bert), Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00, 25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28) ) myframe As you can see for Ernie I do have different data for 24.09.2012 9:00. Now I would like to average the Hunger and Temp value for this timestamp to get a data frame without duplicated Times and the respective average Temp and Hunger. I tried something like Meanframe- by(myframe[, 3:4], duplicated(myframe$ID, Zusatzdaten3$Timestamp) == TRUE, mean) but it doesn't work and I guess that it is also totally crap ;-) Hi Tagmarie, Your problem is that both Hunger and Temp are read in as factors. If you try it like this: by(as.numeric(as.character(myframe[,3])),myframe[,ID],mean) by(as.numeric(as.character(myframe[,4])),myframe[,ID],mean) You might get what you want. The as.character call is necessary, otherwise you will get the wrong mean values. 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] Running different Regressions using for loops
Hello,
Try the following.
#cnames - names(tryout) # in your code, use this one
cnames - c(Volume, Price1, Price2, Price3, Price4, Price5,
Trend, Seasonaliy)
price - cnames[grep(Price, cnames)]
resp - cnames[1]
regr - cnames[7:8]
#lm.list - vector(list, 5)
for(i in 1:5){
regress - paste(price[i], paste(regr, collapse = +), sep = +)
fmla - paste(resp, regress, sep = ~)
print(fmla)
#lm.list[[i]] - lm(as.formula(fmla), data = tryout)
}
Hope this helps,
Rui Barradas
Em 26-09-2012 08:08, Krunal Nanavati escreveu:
Hi,
I am trying to run many different regressions using a FOR Loop.
The input data that is read into R has the following variables
· Volume
· Price1
· Price2
· Price3
· Price4
· Price5
· Trend
· Seasonality
I want to run 5 regressions, with the Volume as an dependent variable and
Price, Trend Seasonality as independent variables. I have read the above
mentioned variables in a variable called tryout
I am entering the following syntax in R
for(i in 1:5)
+ {
+ result[i]=lm(Volume~Price[i]+Trend+Seasonaliy,data=tryout)
+ summary(result[i])
+ }
After running these lines...I am getting the following error message
Error in eval(expr, envir, enclos) : object 'Price' not found
Can someone help me out with this error message. Appreciate for your time
and consideration.
Thanks Regards,
Krunal Nanavati
Solutions Manager - Cogitaas
9769-919198
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Re: [R] Creating x*y different contigency tables
On 26-09-2012, at 09:59, Loukia Spineli spinelilouki...@gmail.com wrote:
Dear all,
I am trying to construct 25x31 different matrices of 2x2 dimension. Here
is the problem:
we have the following matrix
matrix(c(54+s0,
43+s1, 56-s0, 67-s1), nrow=2, ncol=2, byrow=T)
the values for s0 and s1 are c(0:24) and c(0:31), respectively.
I wrote the following code without the desired results
x-0:24
y-0:30
results-array(matrix(0,nrow=2,ncol=2,byrow=T),dim=c(2,2,25*31))
for(i in 1:25){
for(j in 1:31){
for(k in
1:25*31){
results[,,k]-array(matrix(c(54+x[i], 43+y[j], 56-x[i],
67-y[j]),nrow=2,ncol=2,byrow=T),dim=c(2,2,25*31))
}
}
}
results
I am trying to figure out what I am missing.
You don't need the third loop for( k in …
With for loops you can do this
x-0:3
y-0:5
mat.start - matrix(c(54, 43, 56, 67), nrow=2, ncol=2, byrow=T)
mat.start
Nx - length(x)
Ny - length(y)
results-array(matrix(0,nrow=2,ncol=2,byrow=T),dim=c(2,2,Nx*Ny))
k - 1
for(i in 1:Nx){
for(j in 1:Ny){
results[,,k] - mat.start + matrix(c(x[i], y[j],
-x[i],-y[j]),nrow=2,ncol=2,byrow=T)
k - k+1
}
}
results
Berend
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Re: [R] average environmental data if AnimalID and Time is duplicated
Hello, Why do you have Hunger and Temp recorded as characters? Between double quotes? myframe - data.frame (ID=c(Ernie, Ernie, Bert, Bert), Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00, 25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28) ) str(myframe) myframe$Hunger - as.numeric(levels(myframe$Hunger)[myframe$Hunger]) myframe$Temp - as.numeric(levels(myframe$Temp)[myframe$Temp]) aggregate(cbind(Hunger, Temp) ~ ID, data = myframe, FUN = mean) Hope this helps, Rui Barradas Em 26-09-2012 11:53, Tagmarie escreveu: Hello, I tried for about three hours now to solve this problem but I can't figure it out. I am sure someone knows how do it. At least I hope so. I have a data frame somewhat like this: myframe - data.frame (ID=c(Ernie, Ernie, Bert, Bert), Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00, 25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28) ) myframe As you can see for Ernie I do have different data for 24.09.2012 9:00. Now I would like to average the Hunger and Temp value for this timestamp to get a data frame without duplicated Times and the respective average Temp and Hunger. I tried something like Meanframe- by(myframe[, 3:4], duplicated(myframe$ID, Zusatzdaten3$Timestamp) == TRUE, mean) but it doesn't work and I guess that it is also totally crap ;-) Tagmarie -- View this message in context: http://r.789695.n4.nabble.com/average-environmental-data-if-AnimalID-and-Time-is-duplicated-tp4644218.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] create new column in a DF according to values from another column
Here is another technique to use, especially if you have a long list
of replacement values:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
# create a list of replacement values; if you have a lot and
# you can create them automagically, then it is easier
replace - list(list(c(1, 7, 11, 16), V1)
+ , list(c(4, 14, 20), V2)
+ , list(c(3, 17, 19), V3)
+ )
for (i in replace){
+ DF$Station[DF$number %in% i[[1L]]] - i[[2L]]
+ }
DF
number data Station
1 11 V1
2 42 V2
3 73 V1
4 34 V3
5 115 V1
6 166 V1
7 147 V2
8 178 V3
9 209 V2
10 19 10 V3
On Wed, Sep 26, 2012 at 6:49 AM, jeff6868
geoffrey_kl...@etu.u-bourgogne.fr wrote:
Hi everyone,
I have a small problem in my R-code.
Imagine this DF for example:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
I would like to add a new column Station in this DF. This new column must
be automatically filled with: V1 or V2 or V3.
The choice must be done on the numbers (1st column).
For example, I would like to have V1 in the column Station in the rows
where the numbers of the 1st column are: 1,7,11,16 ; then I would like to
have V2 in the rows where the numbers are: 4,14,20 and finally V3 in the
rows where the numbers are: 3,17,19.
I'm trying with if and something like this, but it's not working yet:
# For V1:
if(DF$number %in% c(1,7,11,16)) {test$Station==V1}
# For V2:
...
So my final DF should look like this:
FINALDF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10),
Station=c(V1,V2,V1,V3,V1,V1,V2,V3,V2,V3))
Could someone help me to finish this?
Thank you very much!!!
--
View this message in context:
http://r.789695.n4.nabble.com/create-new-column-in-a-DF-according-to-values-from-another-column-tp4644217.html
Sent from the R help mailing list archive at Nabble.com.
__
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.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Change in order of names after applying plyr package
Here is one of the places that you need a 'factor' to create the
ordering you want; notice the statement that I added:
equity_data = data.frame(security_id = c(Air, Air, Air, Air
+ , Air, Air, Air, Air, Air, Air, Air, Air, AB
+ , AB, AB, AB, AB, AB, AB, AB, AB, AB, AB
+ , AB, AD, AD, AD, AD, AD, AD, AD, AD, AD
+ , AD, AD, AD)
+ , ason_date = c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12
+ , 6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12
+ ,1-Jan-12, 31-Dec-11, 30-Dec-11, 10-Jan-12,9-Jan-12
+ ,8-Jan-12, 7-Jan-12, 6-Jan-12,5-Jan-12,4-Jan-12
+ ,3-Jan-12,2-Jan-12,1-Jan-12, 31-Dec-11, 30-Dec-11
+ , 10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12, 6-Jan-12
+ ,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12
+ , 31-Dec-11, 30-Dec-11)
+ , security_rate = c(0.597,0.61,0.6,0.63,0.67,0.7,0.74,0.735
+ , 7.61,0.795,0.796, 0.84, 8.5,8.1,8.9,8.9,8.9,9,9,9,9,9,9,9
+ ,3.21,3.22,3.12, 3.51, 3.5, 3.37, 3.25, 3, 3.07, 3, 2.94, 2.6)
+ )
# create a factor with the specified ordering
equity_data$security_id - factor(equity_data$security_id
+ , levels = c(Air, AB, AD)
+ )
Here are the results:
result_method_other
$Air
[1] 6.229422
$AB
[1] 0.2355425
$AD
[1] 0.2918782
attr(,split_type)
[1] data.frame
attr(,split_labels)
security_id
1 Air
2 AB
3 AD
On Wed, Sep 26, 2012 at 4:55 AM, Vincy Pyne vincy_p...@yahoo.ca wrote:
Dear R helpers
I have following two data.frames viz. equity_data and param.
equity_data = data.frame(security_id = c(Air, Air, Air, Air, Air,
Air, Air, Air, Air, Air, Air, Air, AB, AB, AB, AB,
AB, AB, AB, AB, AB, AB, AB, AB, AD, AD, AD, AD,
AD, AD, AD, AD, AD, AD, AD, AD), ason_date =
c(10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,
31-Dec-11, 30-Dec-11, 10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,
31-Dec-11, 30-Dec-11, 10-Jan-12,9-Jan-12,8-Jan-12, 7-Jan-12,
6-Jan-12,5-Jan-12,4-Jan-12,3-Jan-12,2-Jan-12,1-Jan-12,
31-Dec-11,
30-Dec-11), security_rate = c(0.597,0.61,0.6,0.63,0.67,0.7,0.74,0.735,
7.61,0.795,0.796, 0.84, 8.5,8.1,8.9,8.9,8.9,9,9,9,9,9,9,9,3.21,3.22,3.12,
3.51, 3.5, 3.37, 3.25, 3, 3.07, 3, 2.94, 2.6))
param = data.frame(confidence_level = c(0.99), holding_period = c(10),
calculation_method = MC, no_simulation_mc = c(100))
library(plyr)
library(reshape2)
attach(equity_data)
attach(param)
security_names = unique(equity_data$security_id)
# (security_names are used further in R code not included here)
alpha = param$confidence_level
t = param$holding_period
n = param$no_simulation_mc
method = param$calculation_method
mc_VaR = function(security_id, ason_date, security_rate)
{
security_rate_returns - NULL
for (i
in(1:length(ason_date)-1))
{
security_rate_returns[i] = log(security_rate[i]/security_rate[i+1])
}
return_mean = mean(security_rate_returns)
return_sd = sd(security_rate_returns)
simulation = rnorm(n, return_mean, return_sd)
qq = sort(simulation, decreasing = TRUE)
VaR_mc = -qq[alpha * n]*sqrt(t)
return(VaR_mc)
}
result_method_other - dlply(.data = equity_data, .variables = security_id,
.fun = function(x)
mc_VaR(ason_date = x$ason_date, security_id =
x$security_id,
security_rate = x$security_rate))
result_method_other
$AB
[1] 0.2657424
$AD
[1] 0.212061
$Air
[1] 6.789733
attr(,split_type)
[1] data.frame
attr(,split_labels)
security_id
1 AB
2 AD
3 Air
MY PROBLEM :
My original data (i.e. equity_data) has the order of Air, AB and AD.
However, after applying plyr, my order (and corresponding result) has changed
to AB, AD Air.
I need to
maintain my original order of Air, AB and AD. How do I modify my R
code for this?
Kindly guide
Vincy
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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.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do 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] Extrapolating Cox predicted risk
On 09/26/2012 05:00 AM, r-help-requ...@r-project.org wrote: I generated predicted risk of death for each subject in the study by means of Cox proportional hazards model at 8 year of follow-up, a time point at which follow-up was more than 90% complete. It is possible to extrapolate to 10-year the predicted risk of each subjet by assuming an exponential distribution? Any help would be greatly appreciated. Thanks for your consideration. The ability to extrapolate over long distances is exactly why industrial reliability work uses parametric models (weibull or log-normal, see survreg) instead of the Cox model. If any of your data goes out to 10 years, then the predictions for coxph will go out that far, just like they would for a Kaplan-Meier. But, just like the KM, if there are only a handful of people out that far the extrapolated curve will be very noisy. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RV: problems for making grids from lmer models
Dear colleagues: I am working with binary mixed models using lme4 package and everything works fine until I try to spatialize the fitted models using grids predictors. I have used the predict function from RASTER package and the RSAGA functionalities, but always I have the same error: Error in object$xlevels : $ operator not defined for this S4 class. I think the problem comes from the slot (@) used in lme4 for values derived from fitted models. In other mixed models (gausssian) from nlme package, the slots are $ and the predict function works fine. How do you think can I solve this problem?' Is there any other function or package to make grid maps from fitted glmer models? These are the command lines and error message: fitted_glmer_geo-predict(grid_stack, fitted_glmer, type=response) Error in object$xlevels : $ operator not defined for this S4 class Thanks in advance, and my best regards, Olga Olga Viedma Sillero Profesora Ordenacion del Territorio Departamento Ciencias Ambientales Facultad Ciencias del Medio Ambiente Avd/ Carlos III, s/n 45071 Toledo (Spain) email: olga.vie...@uclm.es Tel: 925-268800 (ext. 5469) Tel movil: 675 880 297 Fax: 925 268844 De: MARIA OLGA VIEDMA SILLERO Enviado el: mié 26/09/2012 13:09 Para: ba...@stat.wisc.edu; bbol...@gmail.com; maech...@r-project.org Asunto: problems making grids from lmer models [[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] create new column in a DF according to values from another column
Yes this is it! Thank you for your help Berend! -- View this message in context: http://r.789695.n4.nabble.com/create-new-column-in-a-DF-according-to-values-from-another-column-tp4644217p4644225.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] Jointly distributed random variables in R
Dear all, is there a specific package and reference book for plotting Jointly distributed random variables? Kindly help. Kizito. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] gbinom function
Dear all, I have just downloaded a package 'prob' and also loaded it using library(prob). Whereas function 'tosscoin' works very well the other functions like 'gbinom' for graphing density functions does not work. I get the message: gbinom(20,0.3) Error: could not find function gbinom How do I go about it? Thanks. Kizito. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] create new column in a DF according to values from another column
Hello,
'if' is not vectorized, it only uses the first value of the multiple
condition. 'ifelse' is vectorized and in your case use nested ifelses.
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
v1 - c(1,7,11,16)
v2 - c(4,14,20)
v3 - c(3,17,19)
DF$Station - ifelse(DF$number %in% v1, V1,
ifelse(DF$number %in% v2, V2, V3))
Hope this helps,
Rui Barradas
Em 26-09-2012 11:49, jeff6868 escreveu:
Hi everyone,
I have a small problem in my R-code.
Imagine this DF for example:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
I would like to add a new column Station in this DF. This new column must
be automatically filled with: V1 or V2 or V3.
The choice must be done on the numbers (1st column).
For example, I would like to have V1 in the column Station in the rows
where the numbers of the 1st column are: 1,7,11,16 ; then I would like to
have V2 in the rows where the numbers are: 4,14,20 and finally V3 in the
rows where the numbers are: 3,17,19.
I'm trying with if and something like this, but it's not working yet:
# For V1:
if(DF$number %in% c(1,7,11,16)) {test$Station==V1}
# For V2:
...
So my final DF should look like this:
FINALDF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10),
Station=c(V1,V2,V1,V3,V1,V1,V2,V3,V2,V3))
Could someone help me to finish this?
Thank you very much!!!
--
View this message in context:
http://r.789695.n4.nabble.com/create-new-column-in-a-DF-according-to-values-from-another-column-tp4644217.html
Sent from the R help mailing list archive at Nabble.com.
__
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Re: [R] average environmental data if AnimalID and Time is duplicated
HI,
Just to add to Jim's solution with data.table()
myframe- data.frame (ID=c(Ernie, Ernie, Bert, Bert),
Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00,
25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28)
)
library(data.table)
myframe1-data.table(myframe)
myframe2-within(myframe1,{Hunger-as.numeric(as.character(Hunger));
Temp-as.numeric(as.character(Temp))})
myframe2[,list(meanHunger=mean(Hunger),meanTemp=mean(Temp)),list(ID,Timestamp)]
# ID Timestamp meanHunger meanTemp
#1: Ernie 24.09.2012 09:00 3 27.5
#2: Bert 24.09.2012 10:00 2 27.0
#3: Bert 25.09.2012 10:00 2 28.0
A.K.
- Original Message -
From: Jim Lemon j...@bitwrit.com.au
To: Tagmarie ramga...@gmx.net
Cc: r-help@r-project.org
Sent: Wednesday, September 26, 2012 7:29 AM
Subject: Re: [R] average environmental data if AnimalID and Time is duplicated
On 09/26/2012 08:53 PM, Tagmarie wrote:
Hello,
I tried for about three hours now to solve this problem but I can't figure
it out. I am sure someone knows how do it. At least I hope so.
I have a data frame somewhat like this:
myframe- data.frame (ID=c(Ernie, Ernie, Bert, Bert),
Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00,
25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28)
)
myframe
As you can see for Ernie I do have different data for 24.09.2012 9:00. Now I
would like to average the Hunger and Temp value for this timestamp to get a
data frame without duplicated Times and the respective average Temp and
Hunger.
I tried something like
Meanframe- by(myframe[, 3:4], duplicated(myframe$ID,
Zusatzdaten3$Timestamp) == TRUE, mean)
but it doesn't work and I guess that it is also totally crap ;-)
Hi Tagmarie,
Your problem is that both Hunger and Temp are read in as factors. If you
try it like this:
by(as.numeric(as.character(myframe[,3])),myframe[,ID],mean)
by(as.numeric(as.character(myframe[,4])),myframe[,ID],mean)
You might get what you want. The as.character call is necessary,
otherwise you will get the wrong mean values.
Jim
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[R] RCURL ftp upload - ASCII or Binary type?
I'm trying to upload a file using RCURL:s ftpUpload() to a ftp-server using the
following command:
ftpUpload('VERY.ODD.FILE.NAME(+1)',to=ftp://x.x.x.x/,;'
VERY.ODD.FILE.NAME(+1)',userpwd=USER:PASSWORD)
OK
0
The file I'm trying to upload is a very simple text-file but with a bit weird
filename. Note the ' on each side of the filename.
So the upload itself is successful but the receiver of the file tells me that
the file I uploaded was of Binary type and that his system only accepts
ASCII. So the receiver can see the file but it contains only weird characters.
Surfing the web I found this:
http://www.webweaver.nu/html-tips/ascii-binary.shtml
and indeed, when I try filezilla (http://filezilla-project.org/) to do the same
upload, there is a setting in filezilla: Default transfer type that can be
set to ASCII or Binary. The transfer works fine when using ASCII and has
same error as in R when using Binary.
My conclusion is that, for some reason, R uses Binary as Transfer type
here, but it should be using ASCII.
I have been looking at curlSetOpt() but .encoding is not the problem here.
Is there a way to change R:s Transfer Type from Binary to ASCII in this
case? How?
System: windows 7
R version: 2.15.0
Thanks for your help
Best regards
Magnus Eriksson
__
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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] create new column in a DF according to values from another column
HI,
Try this:
DF$Station[DF$number%in%c(1,7,11,16)]-V1
DF$Station[DF$number%in%c(4,14,20)]-V2
DF$Station[DF$number%in%c(3,17,19)]-V3
DF
# number data Station
#1 1 1 V1
#2 4 2 V2
#3 7 3 V1
#4 3 4 V3
#5 11 5 V1
#6 16 6 V1
#7 14 7 V2
#8 17 8 V3
#9 20 9 V2
#10 19 10 V3
#or if you have more replacement values, then:
library(car)
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
DF1-DF1
DF1$Station-recode(DF1$number,c(1,7,11,16)='V1';c(4,14,20)='V2';c(3,17,19)='V3')
DF1
# number data Station
#1 1 1 V1
#2 4 2 V2
#3 7 3 V1
#4 3 4 V3
#5 11 5 V1
#6 16 6 V1
#7 14 7 V2
#8 17 8 V3
#9 20 9 V2
#10 19 10 V3
A.K.
- Original Message -
From: jeff6868 geoffrey_kl...@etu.u-bourgogne.fr
To: r-help@r-project.org
Cc:
Sent: Wednesday, September 26, 2012 6:49 AM
Subject: [R] create new column in a DF according to values from another column
Hi everyone,
I have a small problem in my R-code.
Imagine this DF for example:
DF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10))
I would like to add a new column Station in this DF. This new column must
be automatically filled with: V1 or V2 or V3.
The choice must be done on the numbers (1st column).
For example, I would like to have V1 in the column Station in the rows
where the numbers of the 1st column are: 1,7,11,16 ; then I would like to
have V2 in the rows where the numbers are: 4,14,20 and finally V3 in the
rows where the numbers are: 3,17,19.
I'm trying with if and something like this, but it's not working yet:
# For V1:
if(DF$number %in% c(1,7,11,16)) {test$Station==V1}
# For V2:
...
So my final DF should look like this:
FINALDF - data.frame(number=c(1,4,7,3,11,16,14,17,20,19),data=c(1:10),
Station=c(V1,V2,V1,V3,V1,V1,V2,V3,V2,V3))
Could someone help me to finish this?
Thank you very much!!!
--
View this message in context:
http://r.789695.n4.nabble.com/create-new-column-in-a-DF-according-to-values-from-another-column-tp4644217.html
Sent from the R help mailing list archive at Nabble.com.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] average environmental data if AnimalID and Time is duplicated
Thank you! Am 26.09.2012 13:31, schrieb Jim Lemon [via R]: On 09/26/2012 08:53 PM, Tagmarie wrote: Hello, I tried for about three hours now to solve this problem but I can't figure it out. I am sure someone knows how do it. At least I hope so. I have a data frame somewhat like this: myframe- data.frame (ID=c(Ernie, Ernie, Bert, Bert), Timestamp=c(24.09.2012 09:00, 24.09.2012 09:00, 24.09.2012 10:00, 25.09.2012 10:00), Hunger=c(1,5,2,2), Temp=c(25,30,27,28) ) myframe As you can see for Ernie I do have different data for 24.09.2012 9:00. Now I would like to average the Hunger and Temp value for this timestamp to get a data frame without duplicated Times and the respective average Temp and Hunger. I tried something like Meanframe- by(myframe[, 3:4], duplicated(myframe$ID, Zusatzdaten3$Timestamp) == TRUE, mean) but it doesn't work and I guess that it is also totally crap ;-) Hi Tagmarie, Your problem is that both Hunger and Temp are read in as factors. If you try it like this: by(as.numeric(as.character(myframe[,3])),myframe[,ID],mean) by(as.numeric(as.character(myframe[,4])),myframe[,ID],mean) You might get what you want. The as.character call is necessary, otherwise you will get the wrong mean values. Jim __ [hidden email] /user/SendEmail.jtp?type=nodenode=4644224i=0 mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/average-environmental-data-if-AnimalID-and-Time-is-duplicated-tp4644218p4644224.html To unsubscribe from average environmental data if AnimalID and Time is duplicated, click here http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4644218code=UmFtZ2FkODJAZ214Lm5ldHw0NjQ0MjE4fDIwNzkwMzU2MDU=. NAML http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://r.789695.n4.nabble.com/average-environmental-data-if-AnimalID-and-Time-is-duplicated-tp4644218p4644231.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gbinom function
On 26-09-2012, at 13:24, Kizito Omala kizrom...@gmail.com wrote: Dear all, I have just downloaded a package 'prob' and also loaded it using library(prob). Whereas function 'tosscoin' works very well the other functions like 'gbinom' for graphing density functions does not work. I get the message: gbinom(20,0.3) Error: could not find function gbinom This error message is similar to what you got yesterday. Function gbinom is simply not in package prob. Did you look in the index of that package or in the table of contents? How do I go about it? You could put some effort in searching. Try googling on gbinom. You will see some hits. There is apparently something available. Berend __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] calculation of diversity confidence interval
Mike, You could use bootstrapping. See for example the function boot() in pacakge boot. library(boot) ?boot Jean Michael Eisenring michael.eisenr...@gmx.ch wrote on 09/25/2012 04:54:29 AM: Dear R-help members. Maybe this is not the right platform to ask this, but I'm looking desperately for a test which is calculating confidence intervals from diversity measurements (non-normaly distributed) (fishers alpha diversity). I was checking the package vegan but there seems to be nothing useful. Does anyone of you know with what package I easily could calculate such a confindence interval? Best, Mike [[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] Interaction scatterplots in ggplot with multiple regression lines
I'm trying to treat a continuous variable as discrete for plotting multiple regression lines in a scatterplot as a function of the level on the moderating variable. In the example below, there is only one regression line plotted to the whole data. I would like a separate regression line for each discrete level of the moderator. The moderator is continuous, so I'd like to treat it as discrete for plotting the regression lines. Here's an example (I would like 7 regression lines corresponding to the discrete levels of the moderator, as displayed in the legend, instead of just 1 regression line): ### library(ggplot2) set.seed(1234) predictor - rnorm(1000, 3) outcome - rnorm(1000, 10) moderator - rnorm(1000) mydata - data.frame(predictor, outcome, moderator) ggplot(mydata, aes(x=predictor, y=outcome, color=moderator)) + geom_point() + scale_colour_gradient2(low=blue, high=red) + stat_smooth(method=lm, se=TRUE, fullrange=T) ### Also, how can I set how many discrete levels to plot (e.g., 3 instead of 7)? Thanks in advance! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gbinom function
I have forwarded your message to the R-help list. You should also send your replies to the R-help list and not just to the person(s) who replied. Berend On 26-09-2012, at 15:44, Kizito Omala kizrom...@gmail.com wrote: Hello Berend, I got the code from google, pasted in the script editor run it and all is well. Thanks for the guidance. On 26 September 2012 16:17, Berend Hasselman b...@xs4all.nl wrote: On 26-09-2012, at 13:24, Kizito Omala kizrom...@gmail.com wrote: Dear all, I have just downloaded a package 'prob' and also loaded it using library(prob). Whereas function 'tosscoin' works very well the other functions like 'gbinom' for graphing density functions does not work. I get the message: gbinom(20,0.3) Error: could not find function gbinom This error message is similar to what you got yesterday. Function gbinom is simply not in package prob. Did you look in the index of that package or in the table of contents? How do I go about it? You could put some effort in searching. Try googling on gbinom. You will see some hits. There is apparently something available. Berend __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RCURL ftp upload - ASCII or Binary type?
Hi,
On Sep 26, 2012, at 8:07 AM, Magnus Eriksson wrote:
I'm trying to upload a file using RCURL:s ftpUpload() to a ftp-server using
the following command:
ftpUpload('VERY.ODD.FILE.NAME(+1)',to=ftp://x.x.x.x/,;'
VERY.ODD.FILE.NAME(+1)',userpwd=USER:PASSWORD)
OK
0
The file I'm trying to upload is a very simple text-file but with a bit weird
filename. Note the ' on each side of the filename.
So the upload itself is successful but the receiver of the file tells me that
the file I uploaded was of Binary type and that his system only accepts
ASCII. So the receiver can see the file but it contains only weird
characters.
Surfing the web I found this:
http://www.webweaver.nu/html-tips/ascii-binary.shtml
and indeed, when I try filezilla (http://filezilla-project.org/) to do the
same upload, there is a setting in filezilla: Default transfer type that
can be set to ASCII or Binary. The transfer works fine when using ASCII
and has same error as in R when using Binary.
My conclusion is that, for some reason, R uses Binary as Transfer type
here, but it should be using ASCII.
I have been looking at curlSetOpt() but .encoding is not the problem here.
Is there a way to change R:s Transfer Type from Binary to ASCII in this
case? How?
What happens if you explicitly set the asText argument to ftpUpload() to TRUE?
asText is defined by default based upon the 'what' argument.
what = 'VERY.ODD.FILE.NAME(+1)'
asText = inherits(what, AsIs) || is.raw(what)
asText
[1] FALSE
So, maybe you need to set it to TRUE explicitly. It's worth a try!
Cheers,
Ben
System: windows 7
R version: 2.15.0
Thanks for your help
Best regards
Magnus Eriksson
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Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine 04575-0475
http://www.bigelow.org
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[R] Retrieve regression summary results after rq
Hi all, I am using quantile regression with svy design. I want to retrieve summary regression statistics (std error, p-value), since I don't have any in my output: Commands: clus1_d- svydesign(id=~cd002_co, weights=~wtper, strata=~str, data=data) bclus1-as.svrepdesign(clus1_d,type=bootstrap,replicates=100) fit1- withReplicates(bclus1,quote(coef(rq(newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Output: coefficients(fit1) tau= 0.05 tau= 0.25 tau= 0.50 tau= 0.75 tau= 0.95 (Intercept) 2340 2980 3.30e+03 3750 4360. sch_new_2185 -30 -5.50e+01 -250 -360. sch_new_315520 5.032317e-16 -200 -245. sch_new_4 6520 -1.50e+01 -200 -309.9998 Any help will be appreciated. Best, 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] Interaction scatterplots in ggplot with multiple regression lines
Some like this help? mydata$modnew - cut(mydata$moderator, 7) ggplot(mydata, aes(x=predictor, y=outcome, color=modnew)) + geom_point() + stat_smooth(method=lm, se=TRUE, fullrange=T) John Kane Kingston ON Canada -Original Message- From: dadr...@gmail.com Sent: Wed, 26 Sep 2012 09:45:07 -0400 To: r-help@r-project.org Subject: [R] Interaction scatterplots in ggplot with multiple regression lines I'm trying to treat a continuous variable as discrete for plotting multiple regression lines in a scatterplot as a function of the level on the moderating variable. In the example below, there is only one regression line plotted to the whole data. I would like a separate regression line for each discrete level of the moderator. The moderator is continuous, so I'd like to treat it as discrete for plotting the regression lines. Here's an example (I would like 7 regression lines corresponding to the discrete levels of the moderator, as displayed in the legend, instead of just 1 regression line): ### library(ggplot2) set.seed(1234) predictor - rnorm(1000, 3) outcome - rnorm(1000, 10) moderator - rnorm(1000) mydata - data.frame(predictor, outcome, moderator) ggplot(mydata, aes(x=predictor, y=outcome, color=moderator)) + geom_point() + scale_colour_gradient2(low=blue, high=red) + stat_smooth(method=lm, se=TRUE, fullrange=T) ### Also, how can I set how many discrete levels to plot (e.g., 3 instead of 7)? Thanks in advance! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Plotting of regsubsets adjr2 values not correct
Does your dataset have any missing data? (without a reproducible example we can only guess). If it does then you may be fitting the same model to different subsets of the data between the 2 methods. On Tue, Sep 25, 2012 at 9:03 AM, Maximilian Lklweryc maxlklwe...@gmail.com wrote: Hi, I want to make model selection with regsubsets. My code is: a-regsubsets(Gesamt ~ CommunistSocialist + CountrySize + GNI + Lifeexp + Schoolyears + ExpMilitary + Mortality + PopPoverty + PopTotal + ExpEdu + ExpHealth, data=olympiadaten, nbest=2) summary(a) plot(a,scale=adjr2) (output attached) The problem is now, that I want to fit the best model again manually and have a look at it, but the value of the adjusted R squared is not the same as in the regsubsets output? This is also the case for the other models, e.g. when I do the simplest model in the graphic: summary(lm(Gesamt~ExpHealth)) I get an adj. R squared of 0.009202 but the plot says something abou 0.14, so it is not correct? I don't know how to solve this problem, any help would be nice, thanks. Also I do not understand, which models are shown there, e.g. the simple model just with an intercept and the variable GNI is not shown in the plot, why? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.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] Retrieve regression summary results after rq
summary(fit1) perhaps/ John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 11:39:30 -0300 To: r-help@r-project.org Subject: [R] Retrieve regression summary results after rq Hi all, I am using quantile regression with svy design. I want to retrieve summary regression statistics (std error, p-value), since I don't have any in my output: Commands: clus1_d- svydesign(id=~cd002_co, weights=~wtper, strata=~str, data=data) bclus1-as.svrepdesign(clus1_d,type=bootstrap,replicates=100) fit1- withReplicates(bclus1,quote(coef(rq(newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Output: coefficients(fit1) tau= 0.05 tau= 0.25 tau= 0.50 tau= 0.75 tau= 0.95 (Intercept) 2340 2980 3.30e+03 3750 4360. sch_new_2185 -30 -5.50e+01 -250 -360. sch_new_315520 5.032317e-16 -200 -245. sch_new_4 6520 -1.50e+01 -200 -309.9998 Any help will be appreciated. Best, 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. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rows extraction
subtest - subset(test, Name. %in% c(PKB123, PKB22, PKB23, PKB32, CTV19, CTV20, PKB11, PKB11)) subtest Name. Score performance Environment. 10 CTV19 2 0.52740797 0.53639048 11 CTV20 3 0.05298615 0.04856818 12 PKB11 4 0.90037809 0.79427806 13 PKB11 5 0.41806588 0.40839968 14 PKB123 5 0.16914593 0.17565094 15 PKB22 4 0.13450181 0.14681555 16 PKB23 3 0.05703352 0.04438428 17 PKB32 2 0.07606024 0.07606045 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Nico Met Sent: Wednesday, September 26, 2012 10:20 AM To: r-help Subject: [R] rows extraction Dear all, I want to extract rows from a data frame shown here as test. For example: rows with with sorting PKB123 PKB22 PKB23 PKB32 CTV19 CTV20 PKB11 PKB11 dput(test) structure(list(Name. = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 19L), .Label = c(CTV10, CTV11, CTV12, CTV13, CTV14, CTV15, CTV16, CTV17, CTV18, CTV19, CTV20, PKB11, PKB123, PKB22, PKB23, PKB32, PKB54, PKB55, PKB65 ), class = factor), Score = c(1, 3, 4, 5, 2, 3, 4, 5, 6, 2, 3, 4, 5, 5, 4, 3, 2, 5, 6, 6, 2), performance = c(0.1885092462, 0.0794777814, 0.2503300253, 0.0378809048, 0.7203585833, 0.0517920055, 0.2064060066, 0.5514853303, 0.2605452552, 0.5274079653, 0.0529861537, 0.9003780927, 0.4180658816, 0.1691459321, 0.1345018054, 0.0570335197, 0.0760602378, 0.2203198271, 0.2233031679, 0.030859, 0.6791582042 ), Environment. = c(0.1936732121, 0.1073581974, 0.2399158958, 0.0370952629, 0.6749189555, 0.0545192018, 0.2067554284, 0.4832804062, 0.2784950304, 0.5363904829, 0.0485681822, 0.7942780565, 0.4083996821, 0.175650937, 0.1468155515, 0.0443842831, 0.0760604527, 0.2029511384, 0.2486623715, 0.0362999435, 0.6409256796)), .Names = c(Name., Score, performance, Environment.), class = data.frame, row.names = c(NA, 21L)) regards Nico [[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] geom_line: How to plot two data sets having different maximum X-axis values in a single plot?
Clumsy but this should do it. aa$set - rep(a, length(aa$position)) bb$set - rep(b, length(bb$position)) (mydata - rbind(aa,bb)) p - ggplot( mydata , aes( position, count, colour = set )) + geom_line() p John Kane Kingston ON Canada -Original Message- From: jimmikes...@gmail.com Sent: Tue, 25 Sep 2012 09:07:24 -0400 To: r-help@r-project.org Subject: [R] geom_line: How to plot two data sets having different maximum X-axis values in a single plot? Hello, I just started to learn R and ggplot2. Can someone help? How to plot two data sets having different maximum X-axis values in a single plot? For example, I have two data sets showed below. Using position as X, and count as Y, how can I plot them out in different color lines within a single plot using ggplot2 geom_line? dataset a: position count 13 29 310 415 519 628 715 813 911 105 dataset b: position count 14 28 316 417 519 610 Thanks a lot! Jim [[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. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Retrieve regression summary results after rq
This does not work at all... On Wed, Sep 26, 2012 at 12:04 PM, John Kane jrkrid...@inbox.com wrote: summary(fit1) perhaps/ John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 11:39:30 -0300 To: r-help@r-project.org Subject: [R] Retrieve regression summary results after rq Hi all, I am using quantile regression with svy design. I want to retrieve summary regression statistics (std error, p-value), since I don't have any in my output: Commands: clus1_d- svydesign(id=~cd002_co, weights=~wtper, strata=~str, data=data) bclus1-as.svrepdesign(clus1_d,type=bootstrap,replicates=100) fit1- withReplicates(bclus1,quote(coef(rq(newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Output: coefficients(fit1) tau= 0.05 tau= 0.25 tau= 0.50 tau= 0.75 tau= 0.95 (Intercept) 2340 2980 3.30e+03 3750 4360. sch_new_2185 -30 -5.50e+01 -250 -360. sch_new_315520 5.032317e-16 -200 -245. sch_new_4 6520 -1.50e+01 -200 -309.9998 Any help will be appreciated. Best, 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. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Retrieve regression summary results after rq
Strange, I have never used it but presumably you are using the package ‘survey’? The manual suggests summary(xx) should work. What results or error messages do you get? John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 12:39:46 -0300 To: jrkrid...@inbox.com Subject: Re: [R] Retrieve regression summary results after rq This does not work at all... On Wed, Sep 26, 2012 at 12:04 PM, John Kane jrkrid...@inbox.com wrote: summary(fit1) perhaps/ John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 11:39:30 -0300 To: r-help@r-project.org Subject: [R] Retrieve regression summary results after rq Hi all, I am using quantile regression with svy design. I want to retrieve summary regression statistics (std error, p-value), since I don't have any in my output: Commands: clus1_d- svydesign(id=~cd002_co, weights=~wtper, strata=~str, data=data) bclus1-as.svrepdesign(clus1_d,type=bootstrap,replicates=100) fit1- withReplicates(bclus1,quote(coef(rq(newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Output: coefficients(fit1) tau= 0.05 tau= 0.25 tau= 0.50 tau= 0.75 tau= 0.95 (Intercept) 2340 2980 3.30e+03 3750 4360. sch_new_2185 -30 -5.50e+01 -250 -360. sch_new_315520 5.032317e-16 -200 -245. sch_new_4 6520 -1.50e+01 -200 -309.9998 Any help will be appreciated. Best, 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. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] boxplot of different colors
Shamelessly stealling Richard Heiberger's data set I'd suggest another way using ggplot2 which you would need to install library(ggplot2) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) p - ggplot(dataN , aes(Diet_B, GE_distance, colour = Diet_B )) + geom_boxplot() + xlab(Migration) + ylab(Distance) p John Kane Kingston ON Canada -Original Message- From: r...@temple.edu Sent: Mon, 24 Sep 2012 19:00:09 -0400 To: elaine.kuo...@gmail.com Subject: Re: [R] boxplot of different colors ## I would do this in lattice using the panel.bwplot.intermediate.hh ## function from the HH package. ## install.packages(HH) ## if necessary library(HH) dataN - data.frame(GE_distance=rnorm(260), Diet_B=factor(rep(1:13, each=20))) Diet.colors - c(forestgreen, darkgreen,chocolate1,darkorange2, sienna2,red2,firebrick3,saddlebrown,coral4, chocolate4,darkblue,navy,grey38) bwplot(GE_distance ~ Diet_B, data=dataN, xlab=list(Diet of Breeding Ground, cex = 1.4), ylab = list( Distance between Centers of B and NB Range (1000 km), cex = 1.4), panel=panel.bwplot.intermediate.hh, col=Diet.colors, pch=rep(|,13)) On Mon, Sep 24, 2012 at 6:23 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN -read.csv(H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv,header=T, row.names=1) dim(dataN) dataN[1,] str(dataN) # graph par(mai=c(1,1.03,0.4,0.4)) obs.group-dataN$Diet_B par(new=T) boxplot(GE_distance~Diet_B, data=dataN,xlab=Diet of Breeding Ground,ylab=, yaxt=n,type=p, pch=1,lwd=0.95, cex.lab=1.4, cex.axis=1.2, font.axis=2, cex=1.5, las=1, bty=l, col=c(forestgreen, darkgreen,chocolate1,darkorange2,sienna2, red2,firebrick3, saddlebrown,coral4,chocolate4,darkblue,navy,grey38)[obs.group])) op = par(mar = c(5,5,4,2) + 0.1) title(ylab = Distance between Centers of B and NB Range (1000 km), cex.lab = 1.4,line = 3) axis(side=2,yaxp=c(0,2,4),cex.lab=1.4, cex.axis=1.2,font.axis=2, las=1) [[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. [[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. Send any screenshot to your friends in seconds... Works in all emails, instant messengers, blogs, forums and social networks. TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if2 for FREE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Latitude Longitude to SPDF
I think I know considerably less than you do but have a look as the sp package.
I think you are referring to and object type SpatialPolygonsDataFrame from
the package
sp or which that package will produce.
Good luck. Now to install rgdal.
John Kane
Kingston ON Canada
-Original Message-
From: vickytha...@gmail.com
Sent: Mon, 24 Sep 2012 10:02:39 -0500
To: r-help@r-project.org
Subject: [R] Latitude Longitude to SPDF
Hi Team,
Need your guidance in building SPDF objects from Latitude, Longitude
Information available.
I am using package plotGoogleMaps which is really awesome but it
requires
SPDF objects to build the maps.
I have a data frame which have Latitude and Longitude information and
wanted to convert it in SPDF for making maps.
Please help me to find suitable package or function to convert it. Or if
I
am missing something. I am really sorry but have very less
experience when dealing with Spatial Data.
Best Regards,
Bhupendrasinh Thakre
*Disclaimer :*
The information contained in this communication is =\ ...{{dropped:15}}
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Re: [R] rows extraction
You need to use the match function if you want to specify result sort order or duplication. test[ match(c( PKB123, PKB22, PKB23,PKB32, CTV19, CTV20, PKB11, PKB11 ),test$Name.), ] --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. David L Carlson dcarl...@tamu.edu wrote: subtest - subset(test, Name. %in% c(PKB123, PKB22, PKB23, PKB32, CTV19, CTV20, PKB11, PKB11)) subtest Name. Score performance Environment. 10 CTV19 2 0.52740797 0.53639048 11 CTV20 3 0.05298615 0.04856818 12 PKB11 4 0.90037809 0.79427806 13 PKB11 5 0.41806588 0.40839968 14 PKB123 5 0.16914593 0.17565094 15 PKB22 4 0.13450181 0.14681555 16 PKB23 3 0.05703352 0.04438428 17 PKB32 2 0.07606024 0.07606045 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Nico Met Sent: Wednesday, September 26, 2012 10:20 AM To: r-help Subject: [R] rows extraction Dear all, I want to extract rows from a data frame shown here as test. For example: rows with with sorting PKB123 PKB22 PKB23 PKB32 CTV19 CTV20 PKB11 PKB11 dput(test) structure(list(Name. = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 19L), .Label = c(CTV10, CTV11, CTV12, CTV13, CTV14, CTV15, CTV16, CTV17, CTV18, CTV19, CTV20, PKB11, PKB123, PKB22, PKB23, PKB32, PKB54, PKB55, PKB65 ), class = factor), Score = c(1, 3, 4, 5, 2, 3, 4, 5, 6, 2, 3, 4, 5, 5, 4, 3, 2, 5, 6, 6, 2), performance = c(0.1885092462, 0.0794777814, 0.2503300253, 0.0378809048, 0.7203585833, 0.0517920055, 0.2064060066, 0.5514853303, 0.2605452552, 0.5274079653, 0.0529861537, 0.9003780927, 0.4180658816, 0.1691459321, 0.1345018054, 0.0570335197, 0.0760602378, 0.2203198271, 0.2233031679, 0.030859, 0.6791582042 ), Environment. = c(0.1936732121, 0.1073581974, 0.2399158958, 0.0370952629, 0.6749189555, 0.0545192018, 0.2067554284, 0.4832804062, 0.2784950304, 0.5363904829, 0.0485681822, 0.7942780565, 0.4083996821, 0.175650937, 0.1468155515, 0.0443842831, 0.0760604527, 0.2029511384, 0.2486623715, 0.0362999435, 0.6409256796)), .Names = c(Name., Score, performance, Environment.), class = data.frame, row.names = c(NA, 21L)) regards Nico [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Removing duplicates without a for loop
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date, and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers should be
unique but on occassion aren't because they get entered more than once. This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date but it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
--
View this message in context:
http://r.789695.n4.nabble.com/Removing-duplicates-without-a-for-loop-tp4644255.html
Sent from the R help mailing list archive at Nabble.com.
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[R] specifying arguments in functions and calling functions, within functions
Esteemed R UseRs,
Regarding specifying arguments in functions and calling functions
within functions:
## beginning ##
## some data
ex - rnorm(10)
ex[5] - NA
## example function
Scale - function(x, method=c(mean, median)) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median)
median(ex, na.rm=FALSE)
## both return the median
Scale(ex, method=median)
median(ex, na.rm=TRUE)
## 1. Why does the use of apostrophes have this effect when calling
## a fucntion within a function?
## 2. What's the canonical use of apostrophes in functions like the above:
## Scale - function(x, method=c(mean, median)) {
## or
## Scale - function(x, method=c(mean, median)) {
## 3. How does one specify the arguments of a function being called
## within a function? i.e. i thought the use of '...' might work in
## the following but i was wrong.
## '...' has no apparent effect
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median, na.rm=TRUE)
Scale(ex, method=median, na.rm=FALSE)
## end ##
I failed to comprehend anything google returned when trying to
understand this myself. Greatly appreciate any thoughts /or
examples on this.
Tia, Karl
--
Karl Brand
Dept of Cardiology and Dept of Bioinformatics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161
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Re: [R] map two names into one
HI, Try this: vec1-GALAXY ACE S 5830 vec2-S 5830 GALAXY ACE vec3-R GALAXY 5812 ACE vec11-paste(sort(unlist(strsplit(vec2, ))),collapse=_) vec22-paste(sort(unlist(strsplit(vec2, ))),collapse=_) vec11 #[1] 5830_ACE_GALAXY_S vec22 #[1] 5830_ACE_GALAXY_S identical(vec11,vec22) #[1] TRUE vec33-paste(sort(unlist(strsplit(vec3, ))),collapse=_) identical(vec11,vec33) #[1] FALSE A.K. - Original Message - From: Tammy Ma metal_lical...@live.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Wednesday, September 26, 2012 5:04 AM Subject: [R] map two names into one Dear R user: I have got the following problem: I have imported two data sets into R: one set includes price information, another one includes volume information. but I noticed the wrong data order problem in the product name, for instance, in one data set, GALAXY ACE S 5830 in another one, it is S 5830 GALAXY ACE both represent same product. how do i map two name into one in R? there are so many product name having this problem. i hope there is some mechanism which can autimatically map those. thanks for your help.. Kind regards, Tammy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reading multiple files
Hi,
I have 35 data files for reading. I would like get a program for
performing reading of 35 files at once.
All are of the type: Dados1.raw, Dados2.raw and so on.
If the files have the same number of columns, I can read with the
following commands:
rm(list=ls())
filenames = list.files(path=~/Silvano/Arq, pattern=Dados+.*raw)
names = substr(filenames, 1, 7)
for(i in names){
filepath = file.path(~/Silvano/Dados, paste(i, .raw, sep=))
assign(i, read.delim(filepath,
colClasses=c(rep(character, 5), rep(numeric, 5)),
sep = ))
}
It happens that the files have different number of columns. And I can't
solve the problem.
Any suggestions?
-
Silvano Cesar da Costa
Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística
Fone: (43) 3371-4346
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[R] averageif and looping
haiii i want to know, is there any script in R to measure looping averageif (like in the excel) ... for example: i have a vector rowvalue 10 22 3-3 4-2 51 6-2 i want to measure the average of the vector for negative value with window estimation 5 so first mean is (-3+-2)/2 second mean is (-3+-2+-2)/3 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 with R invoking
Hi, I encountered a very strange error with R (2.14.1). I tried to build an R package and eventually worked (passing all the checks etc.). Then, I tried this command R CMD INSTALL --binary pkg, which supposedly installs and produce a binary source archive (*.zip) for use on Windows only. Nothing happened, but I could not run R CMD check pkg anymore. Further, when I tried to invoke R, I had \ Warning message: In normalizePath(c(new, .Library.site, .Library), /) : path[1]=: No such file or directory I looked through all the document but could not find an answer. Could you please provide some hint? Thanks! Jianying Li Bionformatics Scientist, Contractor National Institute of Environmental Health Sciences l...@niehs.nih.govmailto:l...@niehs.nih.gov (919) 541 - 5736 [[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] Submit a new script after all parallel jobs have completed
Dear R experts, I have an R script that creates multiple scripts and submits these simultaneously to a computer cluster, and after all of the multiple scripts have completed and the output has been written in the respective folders, I would like to automatically launch another R script that works on these outputs. I haven't been able to figure out whether there is a way to do this in R: the function 'wait' is not what I want since the scripts are submitted as different jobs and each of them completes and writes its output file at different times, but I actually want to run the subsequent script after all of the outputs appear. Can you please help me find a solution? Thank you very much -fra __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] factor expansion
Thank you PIKAL Petr, This is used when you have a big data base of a national sample. So, this factor is a variable that uses the sample in order to obtain information about all the people of the country. Similar of getting a real approach about what's going on in the total population. I don't know how it is called in english (my first tonge is spanish). Perhaps, there's a function in R, but I have not idea. Hope it helps. Thanks in advance. José De: PIKAL Petr petr.pi...@precheza.cz l...@r-project.org Enviado: Miércoles 19 de septiembre de 2012 9:19 Asunto: RE: [R] factor expansion Hi I did not see any answer yet but can you explain what you mean by factor expansion? Something like expand.grid? Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Jose Bustos Melo Sent: Wednesday, September 12, 2012 4:16 PM To: r-help@r-project.org Subject: [R] factor expansion I'm trying to use a data base from SPSS and get all data representing the true data. I would like to use a variable as expansion data. In our data base we have the variable with the factor expansion, but we have not idea how to set it in R. Any idea? Thanks in advance! José [[alternative HTML version deleted]] [[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] Create an error logging text file
Hi, I am looking to run a script which calls other functions from other scripts. Such as in script 1 I may have function f1 which then calls functions f2, f3, f4 which are found in script 3 and then f4 also calls function f6 which can be found in script 3 etc. What I am looking to do is to create a text file that reports any errors or warnings that come about while running this script, and then also reporting which function and script that error/warning occurs. Any help would be greatly appreciated. Regards, Sam -- View this message in context: http://r.789695.n4.nabble.com/Create-an-error-logging-text-file-tp4644268.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] Specifying a response variable in a Bayesian network
I'm trying to teach myself about Bayesian Networks and am working with the following data and the bnlearn package. I understand the conceptual aspects of BNs, but I'm not sure how to specify the response variables in R when constructing a dag plot. I've cecked ?hc and done numerous google searches without luck. Can anyone help? library(bnlearn) library(Rgraphviz) dat=data.frame(won=c(1,0,0,1,0,0), sold=c(0,0,0,1,0,0), insured=c(0,0,1,0,0,1), credit=c(POOR,FAIR,GOOD,FAIR,FAIR,GOOD)) dat$won = factor(dat$won) dat$sold = factor(dat$sold) dat$insured = factor(dat$insured) dat$credit = factor(dat$credit) highlight.opts - list(nodes = c(won,sold,insured,credit), col = red, fill = grey) bn.hc - hc(dat, score = aic) graphviz.plot(bn.hc, highlight=highlight.opts) Thanks, Abraham -- *Abraham Mathew Statistical Analyst www.amathew.com 720-648-0108 @abmathewks* [[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] lme(y ~ ns(x, df=splineDF)) error
I would like to fit regression models of the form
y ~ ns(x, df=splineDF)
where splineDF is passed as an argument to a wrapper function.
This works fine if the regression function is lm(). But with lme(),
I get two different errors, depending on how I handle splineDF
inside the wrapper function.
A workaround is to turn the lme() command, along with the appropriate
value of splineDF, into a text string and then use
eval(parse(text=mystring)). Is there not a more elegant solution?
The function below demonstrates this. According to the value of
WhichApproach (1, 2, or 3), it attempts one of the approaches that
does not work or the workaround using the text string.
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
base
other attached packages:
[1] nlme_3.1-104 ggplot2_0.9.1
loaded via a namespace (and not attached):
[1] colorspace_1.1-1 dichromat_1.2-4digest_0.5.2
grid_2.15.1labeling_0.1
[6] lattice_0.20-6 MASS_7.3-18memoise_0.1
munsell_0.3plyr_1.7.1
[11] proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1
scales_0.2.1 stringr_0.6
[16] tools_2.15.1
wrapper -function(WhichApproach=1, splineDF=4 ){
# Create toy dataset
nID-25
IDnames-LETTERS[1:nID]
longdat-data.frame( x=rep(-10:10, nID) / 3 , ID= rep( IDnames , each=21)
)
set.seed(5)
longdat$x-longdat$x + rnorm(nrow(longdat))/10
IDeffect-rnorm(nID) * 20
names(IDeffect) - IDnames
longdat$IDeffect-IDeffect[as.character(longdat$ID)]
longdat$y- (longdat$x
+ longdat$x^3
+ (longdat$x-1)^4 / 5
+ 1/(abs(longdat$x/50) + 0.02)
+ longdat$IDeffect
+ rnorm(1:nrow(longdat)) * 2
)
longdat-longdat[order(longdat$x),]
library(splines)
# Calling ns within lm works fine:
mylm- lm( y ~ ns(x,df=splineDF), data=longdat)
longdat$lmfit-predict(mylm)
library(ggplot2)
print(
ggplot(longdat, aes(x, y))
+ geom_point(shape=1)
+ geom_line(aes(x=x, y=lmfit), color=red)
)
cat(Enter to attempt lme.)
readline()
library(nlme)
if(WhichApproach==1) {
# returns: Error in eval(expr, envir, enclos) : object 'splineDF' not found
#
# First make sure splineDF does not exist in .GlobalEnv, else we would be in
WhichApproach==2.
if(exists(splineDF, where=.GlobalEnv)) remove(list=splineDF,
pos=.GlobalEnv)
mylme-lme(fixed= y ~ ns(x, df=splineDF)
, random= ~ 1 | ID
, correlation = corAR1()
, data=longdat
)
} else if(WhichApproach==2) {
# returns: Error in model.frame.default(formula = ~ID + y + x + splineDF, data = list( :
# variable lengths differ (found for 'splineDF')
assign(x=splineDF, value=splineDF, pos=.GlobalEnv)
mylme-lme(fixed= y ~ ns(x, df=splineDF)
, random= ~ 1 | ID
, correlation = corAR1()
, data=longdat
)
} else if (WhichApproach==3) {
thecommandstring- paste(mylme-lme(fixed= y ~ ns(x, df=, splineDF, ) , random= ~
1 | ID , correlation = corAR1() , data=longdat))
thecommandstring
eval(parse(text=thecommandstring))
} else {
stop(paste(WhichApproach=, WhichApproach, not valid.))
}
mylme
longdat$fullfit-predict(mylme)
library(ggplot2)
print(
ggplot( longdat, aes(x,y))
+ geom_point(shape=1)
+ facet_wrap( ~ ID )
+ geom_line( aes(x, fullfit), color=red)
)
invisible(mylme)
}
Jacob A. Wegelin
Assistant Professor
Department of Biostatistics
Virginia Commonwealth University
830 E. Main St., Seventh Floor
P. O. Box 980032
Richmond VA 23298-0032
U.S.A.
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Re: [R] specifying arguments in functions and calling functions, within functions
Hi,
You have some basic confusion here, and a problem likely caused by an
object named scl that exists in your global environment.
On Wed, Sep 26, 2012 at 11:56 AM, K. Brand k.br...@erasmusmc.nl wrote:
Esteemed R UseRs,
Regarding specifying arguments in functions and calling functions
within functions:
## beginning ##
## some data
ex - rnorm(10)
ex[5] - NA
## example function
Scale - function(x, method=c(mean, median)) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median)
median(ex, na.rm=FALSE)
## both return the median
Scale(ex, method=median)
median(ex, na.rm=TRUE)
## 1. Why does the use of apostrophes have this effect when calling
## a fucntion within a function?
Those are double quotes, not apostrophes, and they don't have that effect:
Scale(ex, method=median)
[1] NA
Scale(ex, method=median)
Error in Scale(ex, method = median) : could not find function scl
You probably have something named scl in your global environment: you
can see that with ls().
Take a look at:
class(median)
[1] function
class(median)
[1] character
In your first example, you're passing a function to Scale(), which
gives it a new name then uses it. In the second you're passing a
character string that happens to be the name of a function, which
Scale() gives a new name and then tries but fails to use (because it
isn't a function).
See also:
Scale(ex, Nothing)
Error in Scale(ex, Nothing) : could not find function scl
## 2. What's the canonical use of apostrophes in functions like the above:
## Scale - function(x, method=c(mean, median)) {
## or
## Scale - function(x, method=c(mean, median)) {
Depends on whether you want to pass a function or the name of a function.
## 3. How does one specify the arguments of a function being called
## within a function? i.e. i thought the use of '...' might work in
## the following but i was wrong.
## '...' has no apparent effect
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x)
}
You can pass them explicitly as named arguments, or with ... as you
try. In either case you have to hand those off to the function you
want to use them:
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x, ...)
}
Scale - function(x, method=c(mean, median), na.rm=FALSE) {
scl - method
scl(x, na.rm=na.rm)
}
## both return NA
Scale(ex, method=median, na.rm=TRUE)
Scale(ex, method=median, na.rm=FALSE)
## end ##
I failed to comprehend anything google returned when trying to
understand this myself. Greatly appreciate any thoughts /or
examples on this.
Many functions that come with R are written purely in R and use these
capabilities so you can look at them for examples.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [R] Help with R invoking
On 26/09/2012 11:03 AM, Li, Jianying (NIH/NIEHS) [C] wrote: Hi, I encountered a very strange error with R (2.14.1). I tried to build an R package and eventually worked (passing all the checks etc.). Then, I tried this command R CMD INSTALL --binary pkg, which supposedly installs and produce a binary source archive (*.zip) for use on Windows only. Nothing happened, but I could not run R CMD check pkg anymore. Further, when I tried to invoke R, I had \ Warning message: In normalizePath(c(new, .Library.site, .Library), /) : path[1]=: No such file or directory I looked through all the document but could not find an answer. Could you please provide some hint? Please try to put together a reproducible example. It looks sort of like symptoms of having a bad package name in your DESCRIPTION file, which was fixed quite recently (after 2.15.1): * A malformed package name could cause |R CMD INSTALL| to write outside the target library. You can try a nightly build of R-patched if you can make the problem reproducible. If it's not fixed yet, please send me instructions on how to reproduce. (That probably means sending me a copy of your pkg source.) 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] how to know where you've been sourced from
Hello All, I need a script to perform different actions depending on the file from which it was source()'d. Thus, my script needs a way to figure out from whence it was sourced. There seems to be some relevant information in sys.calls() (see below). However, I need to get at the name of the file that directly source the file in question. That is, just one level above. For example, in the example below, test.r needs to know that it was called by source_test.r. In this example, the information is in sys.calls()[[4]]. But, if there are other calls in the stack, I don't imagine it will always be in sys.calls()[[4]]. Is there a consistent place in sys.calls() or elsewhere I can look for the sourcing file name? thanks, allie cat(print(sys.calls()),file=test.r) cat(source(\test.r\),file=source_test.r) cat(source(\source_test.r\),file=source_test_parent.r) source(source_test_parent.r) [[1]] source(source_test_parent.r) [[2]] eval.with.vis(ei, envir) [[3]] eval.with.vis(expr, envir, enclos) [[4]] source(source_test.r) [[5]] eval.with.vis(ei, envir) [[6]] eval.with.vis(expr, envir, enclos) [[7]] source(test.r) [[8]] eval.with.vis(ei, envir) [[9]] eval.with.vis(expr, envir, enclos) [[10]] print(sys.calls()) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rows extraction
On Sep 26, 2012, at 8:28 AM, David L Carlson wrote: subtest - subset(test, Name. %in% c(PKB123, PKB22, PKB23, PKB32, CTV19, CTV20, PKB11, PKB11)) subtest Name. Score performance Environment. 10 CTV19 2 0.52740797 0.53639048 11 CTV20 3 0.05298615 0.04856818 12 PKB11 4 0.90037809 0.79427806 13 PKB11 5 0.41806588 0.40839968 14 PKB123 5 0.16914593 0.17565094 15 PKB22 4 0.13450181 0.14681555 16 PKB23 3 0.05703352 0.04438428 17 PKB32 2 0.07606024 0.07606045 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 I read the request as calling for a subsequent ordering: subtest[match(subtest$Name., c(PKB123, PKB22, PKB23, PKB32, CTV19, CTV20, PKB11, PKB11) ), ] Name. Score performance Environment. 14 PKB123 5 0.16914593 0.17565094 15PKB22 4 0.13450181 0.14681555 16PKB23 3 0.05703352 0.04438428 16.1 PKB23 3 0.05703352 0.04438428 10CTV19 2 0.52740797 0.53639048 11CTV20 3 0.05298615 0.04856818 12PKB11 4 0.90037809 0.79427806 13PKB11 5 0.41806588 0.40839968 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Nico Met Sent: Wednesday, September 26, 2012 10:20 AM To: r-help Subject: [R] rows extraction Dear all, I want to extract rows from a data frame shown here as test. For example: rows with with sorting PKB123 PKB22 PKB23 PKB32 CTV19 CTV20 PKB11 PKB11 dput(test) structure(list(Name. = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 19L), .Label = c(CTV10, CTV11, CTV12, CTV13, CTV14, CTV15, CTV16, CTV17, CTV18, CTV19, CTV20, PKB11, PKB123, PKB22, PKB23, PKB32, PKB54, PKB55, PKB65 ), class = factor), Score = c(1, 3, 4, 5, 2, 3, 4, 5, 6, 2, 3, 4, 5, 5, 4, 3, 2, 5, 6, 6, 2), performance = c(0.1885092462, 0.0794777814, 0.2503300253, 0.0378809048, 0.7203585833, 0.0517920055, 0.2064060066, 0.5514853303, 0.2605452552, 0.5274079653, 0.0529861537, 0.9003780927, 0.4180658816, 0.1691459321, 0.1345018054, 0.0570335197, 0.0760602378, 0.2203198271, 0.2233031679, 0.030859, 0.6791582042 ), Environment. = c(0.1936732121, 0.1073581974, 0.2399158958, 0.0370952629, 0.6749189555, 0.0545192018, 0.2067554284, 0.4832804062, 0.2784950304, 0.5363904829, 0.0485681822, 0.7942780565, 0.4083996821, 0.175650937, 0.1468155515, 0.0443842831, 0.0760604527, 0.2029511384, 0.2486623715, 0.0362999435, 0.6409256796)), .Names = c(Name., Score, performance, Environment.), class = data.frame, row.names = c(NA, 21L)) regards Nico David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to know where you've been sourced from
On 26/09/2012 2:39 PM, Alexander Shenkin wrote: Hello All, I need a script to perform different actions depending on the file from which it was source()'d. Thus, my script needs a way to figure out from whence it was sourced. There seems to be some relevant information in sys.calls() (see below). However, I need to get at the name of the file that directly source the file in question. That is, just one level above. For example, in the example below, test.r needs to know that it was called by source_test.r. In this example, the information is in sys.calls()[[4]]. But, if there are other calls in the stack, I don't imagine it will always be in sys.calls()[[4]]. Is there a consistent place in sys.calls() or elsewhere I can look for the sourcing file name? Look in the global variable you created just before you sourced it, e.g. MyNameIs - foo.R source(bar.R) thanks, allie cat(print(sys.calls()),file=test.r) cat(source(\test.r\),file=source_test.r) cat(source(\source_test.r\),file=source_test_parent.r) source(source_test_parent.r) [[1]] source(source_test_parent.r) [[2]] eval.with.vis(ei, envir) [[3]] eval.with.vis(expr, envir, enclos) [[4]] source(source_test.r) [[5]] eval.with.vis(ei, envir) [[6]] eval.with.vis(expr, envir, enclos) [[7]] source(test.r) [[8]] eval.with.vis(ei, envir) [[9]] eval.with.vis(expr, envir, enclos) [[10]] print(sys.calls()) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] specifying arguments in functions and calling functions, within functions
Hello,
You define a 2nd version of Scale with the dots argument but do not use it.
Scale2 - function(x, method=c(mean, median),...) {
scl - match.fun(method)
scl(x, ...) # Here!
}
Scale2(ex, method=median, na.rm=TRUE) # both return
Scale2(ex, method=median, na.rm=TRUE) # the median
You could also use 'na.rm = TRUE' instead of '...', since both mean and
median use it. Anyway, if you define a function with certain arguments,
do try to use them in the function body. :)
As for the method argument, when the default value is a vector, it's
primary use is to check that one of those vector values and _only_ one
of those is passed to the function. More or less like this.
Scale3 - function(x, method=c(mean, median),...) {
method - match.arg(method)
scl - match.fun(method)
scl(x, ...)
}
Scale3(ex, method=median, na.rm=TRUE) # Error
Scale3(ex, method=median, na.rm=TRUE) # Right
Scale3(ex, method=var, na.rm=TRUE) # Other type of error
Hope this helps,
Rui Barradas
Em 26-09-2012 16:56, K. Brand escreveu:
Esteemed R UseRs,
Regarding specifying arguments in functions and calling functions
within functions:
## beginning ##
## some data
ex - rnorm(10)
ex[5] - NA
## example function
Scale - function(x, method=c(mean, median)) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median)
median(ex, na.rm=FALSE)
## both return the median
Scale(ex, method=median)
median(ex, na.rm=TRUE)
## 1. Why does the use of apostrophes have this effect when calling
## a fucntion within a function?
## 2. What's the canonical use of apostrophes in functions like the above:
## Scale - function(x, method=c(mean, median)) {
## or
## Scale - function(x, method=c(mean, median)) {
## 3. How does one specify the arguments of a function being called
## within a function? i.e. i thought the use of '...' might work in
## the following but i was wrong.
## '...' has no apparent effect
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median, na.rm=TRUE)
Scale(ex, method=median, na.rm=FALSE)
## end ##
I failed to comprehend anything google returned when trying to
understand this myself. Greatly appreciate any thoughts /or
examples on this.
Tia, Karl
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Re: [R] Retrieve regression summary results after rq
On Sep 26, 2012, at 8:50 AM, John Kane wrote: Strange, I have never used it but presumably you are using the package ‘survey’? The manual suggests summary(xx) should work. What results or error messages do you get? She didn't return a model object as fit1. She return only the results of the coef() on the rq(model) object. Perhaps: summ1 - withReplicates(bclus1, quote( summary( rq( newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Untested, and I've never used 'survey' and 'rq' packages together so this is based entirely on analogous reasoning.) -- David. John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 12:39:46 -0300 To: jrkrid...@inbox.com Subject: Re: [R] Retrieve regression summary results after rq This does not work at all... On Wed, Sep 26, 2012 at 12:04 PM, John Kane jrkrid...@inbox.com wrote: summary(fit1) perhaps/ John Kane Kingston ON Canada -Original Message- From: cacamende...@gmail.com Sent: Wed, 26 Sep 2012 11:39:30 -0300 To: r-help@r-project.org Subject: [R] Retrieve regression summary results after rq Hi all, I am using quantile regression with svy design. I want to retrieve summary regression statistics (std error, p-value), since I don't have any in my output: Commands: clus1_d- svydesign(id=~cd002_co, weights=~wtper, strata=~str, data=data) bclus1-as.svrepdesign(clus1_d,type=bootstrap,replicates=100) fit1- withReplicates(bclus1,quote(coef(rq(newm428b~sch_new_2+sch_new_3+sch_new_4, tau=c(0.05,0.25,0.5,0.75,0.95),weights=wtper Output: coefficients(fit1) tau= 0.05 tau= 0.25 tau= 0.50 tau= 0.75 tau= 0.95 (Intercept) 2340 2980 3.30e+03 3750 4360. sch_new_2185 -30 -5.50e+01 -250 -360. sch_new_315520 5.032317e-16 -200 -245. sch_new_4 6520 -1.50e+01 -200 -309.9998 Any help will be appreciated. Best, 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. FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] specifying arguments in functions and calling functions, within functions
Adding on to what Sarah has said, your function appears to limit the
functions that can be passed to it, but it does not. The character strings
mean and median will fail, but passing the function name directly will
work:
Scale - function(x, method=mean,...) {
scl - method
scl(x, ...)
}
The method=c(mean, median) is irrelevant to the function because you
never check to guarantee that only those strings are used in the function
call. This is fortunate since those strings will fail whereas passing any
function that requires a single vector as input will work just fine:
set.seed(42)
ex - runif(10)
ex[5] - NA
Scale(ex)
[1] NA
Scale(ex, na.rm=TRUE)
[1] 0.635653
Scale(ex, median)
Error in Scale(ex, median) : could not find function scl
Scale(ex, median)
[1] NA
Scale(ex, median, na.rm=TRUE)
[1] 0.7050648
Scale(ex, fivenum)
[1] 0.134 0.5190959 0.7050648 0.8304476 0.9370754
Scale(ex, hist)
--
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77843-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Sarah Goslee
Sent: Wednesday, September 26, 2012 1:26 PM
To: K. Brand
Cc: r-help@r-project.org
Subject: Re: [R] specifying arguments in functions and calling
functions, within functions
Hi,
You have some basic confusion here, and a problem likely caused by an
object named scl that exists in your global environment.
On Wed, Sep 26, 2012 at 11:56 AM, K. Brand k.br...@erasmusmc.nl
wrote:
Esteemed R UseRs,
Regarding specifying arguments in functions and calling functions
within functions:
## beginning ##
## some data
ex - rnorm(10)
ex[5] - NA
## example function
Scale - function(x, method=c(mean, median)) {
scl - method
scl(x)
}
## both return NA
Scale(ex, method=median)
median(ex, na.rm=FALSE)
## both return the median
Scale(ex, method=median)
median(ex, na.rm=TRUE)
## 1. Why does the use of apostrophes have this effect when calling
## a fucntion within a function?
Those are double quotes, not apostrophes, and they don't have that
effect:
Scale(ex, method=median)
[1] NA
Scale(ex, method=median)
Error in Scale(ex, method = median) : could not find function scl
You probably have something named scl in your global environment: you
can see that with ls().
Take a look at:
class(median)
[1] function
class(median)
[1] character
In your first example, you're passing a function to Scale(), which
gives it a new name then uses it. In the second you're passing a
character string that happens to be the name of a function, which
Scale() gives a new name and then tries but fails to use (because it
isn't a function).
See also:
Scale(ex, Nothing)
Error in Scale(ex, Nothing) : could not find function scl
## 2. What's the canonical use of apostrophes in functions like the
above:
## Scale - function(x, method=c(mean, median)) {
## or
## Scale - function(x, method=c(mean, median)) {
Depends on whether you want to pass a function or the name of a
function.
## 3. How does one specify the arguments of a function being called
## within a function? i.e. i thought the use of '...' might work in
## the following but i was wrong.
## '...' has no apparent effect
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x)
}
You can pass them explicitly as named arguments, or with ... as you
try. In either case you have to hand those off to the function you
want to use them:
Scale - function(x, method=c(mean, median),...) {
scl - method
scl(x, ...)
}
Scale - function(x, method=c(mean, median), na.rm=FALSE) {
scl - method
scl(x, na.rm=na.rm)
}
## both return NA
Scale(ex, method=median, na.rm=TRUE)
Scale(ex, method=median, na.rm=FALSE)
## end ##
I failed to comprehend anything google returned when trying to
understand this myself. Greatly appreciate any thoughts /or
examples on this.
Many functions that come with R are written purely in R and use these
capabilities so you can look at them for examples.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [R] Removing duplicates without a for loop
This might be quicker.
Para.5C.sorted - Para.5C[order(Para.5C[, 1]), ]
Para.5C.final - Para.5C.sorted[!duplicated(Para.5C.sorted$REQ.NR), ]
If your data are already sorted by date, then you can skip the first step
and just run
Para.5C.final - Para.5C[!duplicated(Para.5C$REQ.NR), ]
Jean
wwreith reith_will...@bah.com wrote on 09/26/2012 10:19:21 AM:
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date,
and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers
should be
unique but on occassion aren't because they get entered more than once.
This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date
but it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
[[alternative HTML version deleted]]
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Re: [R] Reading multiple files
Will your data be read in correctly if you do away with the colClasses
argument to read.delim (or read.table)?
Jean
Silvano Cesar da Costa silv...@uel.br wrote on 09/26/2012 09:11:33 AM:
Hi,
I have 35 data files for reading. I would like get a program for
performing reading of 35 files at once.
All are of the type: Dados1.raw, Dados2.raw and so on.
If the files have the same number of columns, I can read with the
following commands:
rm(list=ls())
filenames = list.files(path=~/Silvano/Arq, pattern=Dados+.*raw)
names = substr(filenames, 1, 7)
for(i in names){
filepath = file.path(~/Silvano/Dados, paste(i, .raw, sep=))
assign(i, read.delim(filepath,
colClasses=c(rep(character, 5), rep(numeric,
5)),
sep = ))
}
It happens that the files have different number of columns. And I can't
solve the problem.
Any suggestions?
-
Silvano Cesar da Costa
Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística
Fone: (43) 3371-4346
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[R] R and sell buy stock
Hi all, I have seen that R can be switched on to a Broker called IB. There is another one similar to IB that permits to make a code and send orders to broker to buy or sell stocks? Can be done trough R, writte in excel and trough API sell/buy to the broker? Can someone send me an example (easy example?) Many thanks. [[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] Removing duplicates without a for loop
Sorry, but in my previous post I've confused the columns. It's by
REQ.NR, not by date
REQ.NR - 1:4
REQ.NR - c(REQ.NR, sample(REQ.NR, 2))
dat - data.frame(date = Sys.Date() + 1:6, REQ.NR = REQ.NR, value =
rnorm(6))
aggregate(dat, by = list(dat$REQ.NR), FUN = tail, 1)
Rui Barradas
Em 26-09-2012 16:19, wwreith escreveu:
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date, and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers should be
unique but on occassion aren't because they get entered more than once. This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date but it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
--
View this message in context:
http://r.789695.n4.nabble.com/Removing-duplicates-without-a-for-loop-tp4644255.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Help with invoking R
Hi, I encountered a very strange error with R (2.14.1). I tried to build an R package and eventually worked (passing all the checks etc.). Then, I tried this command R CMD INSTALL --binary pkg, which supposedly installs and produce a binary source archive (*.zip) for use on Windows only. Nothing happened, but I could not run R CMD check pkg anymore. Further, when I tried to invoke R, I had \ Warning message: In normalizePath(c(new, .Library.site, .Library), /) : path[1]=: No such file or directory I looked through all the document but could not find an answer. Could you please provide some hint? Thanks! Jianying Li Bionformatics Scientist, Contractor National Institute of Environmental Health Sciences l...@niehs.nih.govmailto:l...@niehs.nih.gov (919) 541 - 5736 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing duplicates without a for loop
Hello,
If I understand it correctly, something like this will get you what you
want.
d - Sys.Date() + 1:4
d2 - sample(d, 2)
dat - data.frame(id = 1:6, date = c(d, d2), value = rnorm(6))
aggregate(dat, by = list(dat$date), FUN = tail, 1)
Hope this helps,
Rui Barradas
Em 26-09-2012 16:19, wwreith escreveu:
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date, and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers should be
unique but on occassion aren't because they get entered more than once. This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date but it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
--
View this message in context:
http://r.789695.n4.nabble.com/Removing-duplicates-without-a-for-loop-tp4644255.html
Sent from the R help mailing list archive at Nabble.com.
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[R] replace string values with numbers
Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3.Gene[Gene==GG]-3 It always give me: Warning in `[-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu [[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] Background color in a grid plot seems to interfere with plot()
Dear Paul,
Many thanks, that solved it.
Cheers,
Marius
Paul Murrell p.murr...@auckland.ac.nz writes:
Hi
On 25/09/2012 6:10 p.m., Marius Hofert wrote:
Dear Paul,
Thanks. Redrawing the points solves it for the minimal example, but
what happens if you have plot(.., type=b) like below?
You can use points(..., type=b)
Paul
Actually, originally I wanted to use just grid (without mixing it
with base graphics), but I couldn't find an equivalent for plot(..,
type=b). Also, later on, I would like to use eaxis() to draw nice
y-axes in log-scale. I guess that's easier with gridBase then.
Cheers,
Marius
require(grid) require(gridBase)
pdf(file=Rplot.pdf, width=8, height=8, onefile=FALSE)
## set up the grid layout plot.new() # start (empty) new page with
'graphics' gl- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8, 8, 0.8),
cm), heights=unit(c(0.8, 8, 0.8, 8, 1.5), cm))
pushViewport(viewport(layout=gl))
## plot data par.- par(no.readonly=TRUE) # save plot settings for(i
in 1:2) { # rows i.- if(i 1) i+2 else i+1 # jumping over gaps
for(j in 1:2) { # columns j.- if(j 1) j+2 else j+1 # jumping over
gaps pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
grid.rect(gp=gpar(col=NA, fill=gray90)) # background
par(plt=gridPLT()) ## plot par(new=TRUE) # always do this before each
new 'graphics' plot plot(runif(5), runif(5), type=b, log=y,
xlab=, ylab=, frame.plot=FALSE, xaxt=n, yaxt=n)
grid(col=white, lty=solid, lwd=1.6, equilogs=FALSE) # background
grid upViewport() } } par(par.) dev.off()
Paul Murrellp...@stat.auckland.ac.nz writes:
Hi
On 25/09/12 11:50, Marius Hofert wrote:
Dear Paul,
Thanks for helping. Is there a way to call grid() first? The
problem seems to be that everything drawn before grid() is
overplotted.
No, but you can redraw the points ...
require(grid) require(gridBase)
pdf(file=Rplot.pdf, width=8, height=8, onefile=FALSE)
## set up the grid layout plot.new() # start (empty) new page with
'graphics' gl- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8, 8,
0.8), cm), heights=unit(c(0.8, 8, 0.8, 8, 1.5), cm))
pushViewport(viewport(layout=gl))
## plot data par.- par(no.readonly=TRUE) # save plot settings
for(i in 1:2) { # rows i.- if(i 1) i+2 else i+1 # jumping over
gaps for(j in 1:2) { # columns j.- if(j 1) j+2 else j+1 #
jumping over gaps pushViewport(viewport(layout.pos.row=i.,
layout.pos.col=j.)) grid.rect(gp=gpar(col=NA, fill=gray90)) #
background par(plt=gridPLT()) ## plot par(new=TRUE) # always do
this before each new 'graphics' plot plot(1:5, if(i==1 j==2)
c(1, 1, 2, 3, 1) else 1:5, log=y, xlab=, ylab=,
frame.plot=FALSE, xaxt=n, yaxt=n) # background grid
grid(col=white, lty=solid, lwd=1.6, equilogs=FALSE) points(1:5,
if(i==1 j==2) c(1, 1, 2, 3, 1) else 1:5) upViewport() } }
par(par.) dev.off()
Paul
Cheers,
Marius
require(grid) require(gridBase)
pdf(file=Rplot.pdf, width=8, height=8, onefile=FALSE)
## set up the grid layout plot.new() # start (empty) new page
with 'graphics' gl- grid.layout(5, 5, widths=unit(c(1.8, 8, 0.8,
8, 0.8), cm), heights=unit(c(0.8, 8, 0.8, 8, 1.5), cm))
pushViewport(viewport(layout=gl))
## plot data par.- par(no.readonly=TRUE) # save plot settings
for(i in 1:2) { # rows i.- if(i 1) i+2 else i+1 # jumping over
gaps for(j in 1:2) { # columns j.- if(j 1) j+2 else j+1 #
jumping over gaps pushViewport(viewport(layout.pos.row=i.,
layout.pos.col=j.)) grid.rect(gp=gpar(col=NA, fill=gray90)) #
background par(plt=gridPLT()) ## plot par(new=TRUE) # always do
this before each new 'graphics' plot plot(1:5, if(i==1 j==2)
c(1, 1, 2, 3, 1) else 1:5, log=y, xlab=, ylab=,
frame.plot=FALSE, xaxt=n, yaxt=n) grid(col=white,
lty=solid, lwd=1.6, equilogs=FALSE) # background grid
upViewport() } } par(par.) dev.off()
Paul Murrellp...@stat.auckland.ac.nz writes:
Hi
On 24/09/12 18:06, Marius Hofert wrote:
Dear Paul,
Thank you for helping. This works great.
I then tried to put in a grid (via grid()). Why does that
fail?
Because grid() is used to add lines to an existing plot; just
put the grid() call AFTER the plot() call and it should work
ok.
Paul
Cheers,
Marius
require(grid) require(gridBase)
pdf(file=Rplot.pdf, width=8, height=8, onefile=FALSE)
## set up the grid layout plot.new() # start (empty) new page
with 'graphics' gl- grid.layout(5, 5, widths=unit(c(1.8, 8,
0.8, 8, 0.8), cm), heights=unit(c(0.8, 8, 0.8, 8, 1.5),
cm)) pushViewport(viewport(layout=gl))
## plot data par.- par(no.readonly=TRUE) # save plot
settings for(i in 1:2) { # rows i.- if(i 1) i+2 else i+1 #
jumping over gaps for(j in 1:2) { # columns j.- if(j 1)
j+2 else j+1 # jumping over gaps
pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
grid.rect(gp=gpar(fill=gray90)) # background
par(plt=gridPLT()) ## plot par(new=TRUE) # always do this
before each new 'graphics' plot grid(col=1) plot(1:10, 1:10,
log=y, xlab=, ylab=, xaxt=if(i==2) s else n,
yaxt=if(j==1) s
Re: [R] Removing duplicates without a for loop
?duplicated
Clint BowmanINTERNET: cl...@ecy.wa.gov
Air Quality Modeler INTERNET: cl...@math.utah.edu
Department of Ecology VOICE: (360) 407-6815
PO Box 47600FAX:(360) 407-7534
Olympia, WA 98504-7600
USPS: PO Box 47600, Olympia, WA 98504-7600
Parcels:300 Desmond Drive, Lacey, WA 98503-1274
On Wed, 26 Sep 2012, Rui Barradas wrote:
Sorry, but in my previous post I've confused the columns. It's by REQ.NR, not
by date
REQ.NR - 1:4
REQ.NR - c(REQ.NR, sample(REQ.NR, 2))
dat - data.frame(date = Sys.Date() + 1:6, REQ.NR = REQ.NR, value = rnorm(6))
aggregate(dat, by = list(dat$REQ.NR), FUN = tail, 1)
Rui Barradas
Em 26-09-2012 16:19, wwreith escreveu:
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date,
and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers should
be
unique but on occassion aren't because they get entered more than once.
This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date but
it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
--
View this message in context:
http://r.789695.n4.nabble.com/Removing-duplicates-without-a-for-loop-tp4644255.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Simple Question About Exporting Back to Excel
All, Relatively new R user so this is probably an easy question to answer. I am able to generate a cluster for my dataset using hclust() then ploting the data with plot(). This results in an image with a dendrogram with my sample names along the bottom. Great! However, I now need a way to get that sample order from the image into excel. i.e. sample 7 was on the far left, sample 19 was in position 2, sample 93 was in position 3, etc. As of now the only way for me to do this is to manually type the samples from the image into a worksheet. Very time consuming as I've got a couple hundred samples and several different dendrograms! Any thoughts? Thanks so much! -- View this message in context: http://r.789695.n4.nabble.com/Simple-Question-About-Exporting-Back-to-Excel-tp4644296.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing duplicates without a for loop
On Sep 26, 2012, at 11:23 AM, Rui Barradas wrote:
Hello,
If I understand it correctly, something like this will get you what you want.
d - Sys.Date() + 1:4
d2 - sample(d, 2)
dat - data.frame(id = 1:6, date = c(d, d2), value = rnorm(6))
aggregate(dat, by = list(dat$date), FUN = tail, 1)
If these are sorted by date, then the oldest date would come first any you
would want:
aggregate(dat, by = list(dat$date), FUN = head, 1)
--
David.
Hope this helps,
Rui Barradas
Em 26-09-2012 16:19, wwreith escreveu:
I have several thousand rows of shipment data imported into R as a data
frame, with two columns of particular interest, col 1 is the entry date, and
col 2 is the tracking number (colname is REQ.NR). Tracking numbers should be
unique but on occassion aren't because they get entered more than once. This
creates two or more rows of with the same tracking number but different
dates. I wrote a for loop that will keep the row with the oldest date but it
is extremely slow.
Any suggestions of how I should write this so that it is faster?
# Creates a vector of on the unique tracking numbers #
u-na.omit(unique(Para.5C$REQ.NR))
# Create Data Frame to rbind unique rows to #
Para.5C.final-data.frame()
# For each value in u subset Para.5C find the min date and rbind it to
Para.5C.final #
for(i in 1:length(u))
{
x-subset(Para.5C,Para.5C$REQ.NR==u[i])
Para.5C.final-rbind(Para.5C.final,x[which(x[,1]==min(x[,1])),])
}
--
David Winsemius, MD
Alameda, CA, USA
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Re: [R] replace string values with numbers
On Sep 26, 2012, at 12:52 PM, JiangZhengyu wrote: Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3. Gene[Gene==GG]-3 It always give me: Warning in `[-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? You are trying to replace a factor value with a level that it doesn't have. Hence that particular very informative error message. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] replace string values with numbers
On Sep 26, 2012, at 2:27 PM, David Winsemius wrote: On Sep 26, 2012, at 12:52 PM, JiangZhengyu wrote: Hi everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3. Gene[Gene==GG]-3 It always give me: Warning in `[-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? You are trying to replace a factor value with a level that it doesn't have. Hence that particular very informative error message. You probably could do this: Gene[] - lapply(Gene, as.character) Gene P1 P2 P3 1 CG CG GG 2 -- -- AC 3 -- AC CC 4 AC -- AC The use of the form `object[] -` preserves the original dimensions. You would otherwise have needed to use data.frame() around the result. Gene[Gene==GG] - 3 Gene P1 P2 P3 1 CG CG 3 2 -- -- AC 3 -- AC CC 4 AC -- AC and provide commented, minimal, self-contained, reproducible code. Your code was not really self-contained and reproducible, but what I did was this: Gene - read.table(text=P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC, header=TRUE) read.table will by default create factors when the input column contains character values unless you use stringsAsFactors=FALSE. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reading multiple files
On 26 Sep 2012, at 16:11 , Silvano Cesar da Costa wrote:
Hi,
I have 35 data files for reading. I would like get a program for
performing reading of 35 files at once.
All are of the type: Dados1.raw, Dados2.raw and so on.
If the files have the same number of columns, I can read with the
following commands:
rm(list=ls())
filenames = list.files(path=~/Silvano/Arq, pattern=Dados+.*raw)
names = substr(filenames, 1, 7)
for(i in names){
filepath = file.path(~/Silvano/Dados, paste(i, .raw, sep=))
assign(i, read.delim(filepath,
colClasses=c(rep(character, 5), rep(numeric, 5)),
sep = ))
}
It happens that the files have different number of columns. And I can't
solve the problem.
Any suggestions?
Dear Silvano Cesar da Costa,
You can read an entire folder by analysing the path.
I wrote this program to convert wave files, but it can be applied to any file
type.
Just change the few lines (if ywave... etc) into your own operations:
# select FOLDER with WAV-files
fnam = dirname(file.choose())
print(); print(FILES)
print(list.files(fnam))
print(); print(DIRS)
print(list.dirs(fnam, full.names=FALSE))
print(); print(RECURSIVE FILE LIST)
filist = list.files(fnam, recursive=TRUE, pattern=wav)
print(filist)
filist1 = paste(fnam,/,filist, sep=)
nfiles = length(filist1)
#
# filenames loop ===
for(i in 1:nfiles) {
inname=filist1[i]
ywave=readWave(inname)
ster=ywave@stereo
if (ster==stereo) {} # wat dan??
srate=yw...@samp.rate
ywave2=ywave
if (ywave2@bit==8) {
ywave2@left=(ywave2@left-128)*255
ywave2@bit - 16
}
if (ywa...@samp.rate10) {
ywa...@samp.rate - ywa...@samp.rate * 10
}
if (ywa...@samp.rate != 312500) {
ywave2 - resamp(ywave2,f=ywa...@samp.rate,g=312500,
output=Wave)
}
outname=paste(dirname(inname), /*,basename(inname), sep=)
writeWave(ywave2,outname)
}
Best wishes,
Franklin Bretschneider
Dept of Biology
Kruytgebouw W711
Padualaan 8
3584 CH Utrecht
The Netherlands
f.bretschnei...@uu.nl
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Re: [R] Reading multiple files
If your previously posted code worked with files all having the same
number of columns, and if your data is read in correctly without the
colClasses argument, then I think the following code should work.
for(i in names){
filepath = file.path(~/Silvano/Dados, paste(i, .raw, sep=))
assign(i, read.table(filepath))
}
If not, then my guess is the error (what is the error message???) is due
to the file referencing or naming. For example, it's not clear to me why
you take the substring of the file name, only to paste on the file type
suffix later.
Jean
Silvano Cesar da Costa silv...@uel.br wrote on 09/26/2012 04:31:48 PM:
Hi,
I didn't notice problems with this.
Will your data be read in correctly if you do away with the colClasses
argument to read.delim (or read.table)?
Jean
Silvano Cesar da Costa silv...@uel.br wrote on 09/26/2012 09:11:33
AM:
Hi,
I have 35 data files for reading. I would like get a program for
performing reading of 35 files at once.
All are of the type: Dados1.raw, Dados2.raw and so on.
If the files have the same number of columns, I can read with the
following commands:
rm(list=ls())
filenames = list.files(path=~/Silvano/Arq, pattern=Dados+.*raw)
names = substr(filenames, 1, 7)
for(i in names){
filepath = file.path(~/Silvano/Dados, paste(i, .raw, sep=))
assign(i, read.delim(filepath,
colClasses=c(rep(character, 5),
rep(numeric,
5)),
sep = ))
}
It happens that the files have different number of columns. And I
can't
solve the problem.
Any suggestions?
-
Silvano Cesar da Costa
Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística
Fone: (43) 3371-4346
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Re: [R] averageif and looping
Hello,
Try the following.
sapply(seq_len(nrow(dat) - 4), function(i){
w - window(dat$value, start = i, end = i + 4)
mean(w[w 0])})
Hope this helps,
Rui Barradas
Em 26-09-2012 16:38, Eko andryanto Prakasa escreveu:
haiii
i want to know, is there any script in R to measure looping averageif (like in
the excel) ...
for example:
i have a vector
rowvalue
10
22
3-3
4-2
51
6-2
i want to measure the average of the vector for negative value with window
estimation 5
so first mean is (-3+-2)/2
second mean is (-3+-2+-2)/3
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] averageif and looping
You could use filter(..., filter=rep(1,5)) to get running sums of length 5
to get your answer. The following calls filter once to get the sum of
the negative values in each window and once to get the number of negative
values in each window, then divides to get the means.
f - function(x, n=5) {
sumNeg - filter(pmin(x, 0), filter=rep(1,n)) # running sums of negative
values
numNeg - filter( x 0, filter=rep(1,n)) # running numbers of negative
values
as.vector(sumNeg/numNeg) # running means of negative values
}
E.g.,
s - c(0, 2, -3, -2, 1, -2)
cbind(s, meanNeg = f(s, n=5))
s meanNeg
[1,] 0NA
[2,] 2NA
[3,] -3 -2.50
[4,] -2 -2.33
[5,] 1NA
[6,] -2NA
It is quick for long vectors
ss - floor(sin(1:1e6)*5) # one million numbers
system.time(f(ss, 5))
user system elapsed
1.036 0.040 1.079
If you want results at the ends, append (n-1)/2 0's to each end of the series
and remove the NA's that appear at those positions in the output.
The 'as.vector' is there because filter always returns a 'ts' (a class of time
series
objects), even if the input is a simple vector.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Eko andryanto Prakasa
Sent: Wednesday, September 26, 2012 8:39 AM
To: r-help@R-project.org
Subject: [R] averageif and looping
haiii
i want to know, is there any script in R to measure looping averageif (like
in the excel)
...
for example:
i have a vector
rowvalue
10
22
3-3
4-2
51
6-2
i want to measure the average of the vector for negative value with window
estimation 5
so first mean is (-3+-2)/2
second mean is (-3+-2+-2)/3
__
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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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and provide commented, minimal, self-contained, reproducible code.
[R] Is there a way to source from a specific Git repository without hardcoding the location everywhere?
Folks, A small group of us are working together to develop a set of R functions to support data management and analysis using Eclipse/StatET in a Windows environment. We are using Git/EGit for version control. We work within our own repository and occasionally push to a common remote location. I'd like to have the code source files from the 'local' git repository without modification, where 'local' could mean c:\yada\ for one person, m:\my documents\wetlands\ for another, and l:\foo\bar\sharedRemote\wet\ to another user. The chdir argument to source() has been suggested for similar questions, but I have not been able to figure out how this helps without hardcoding the location in some manner. One option is for each repository to have an untracked file which sets the local working directory before sourcing another file that actually sources the function definitions. This file (projectStart.r below) would be read into the R session prior to use, at least during development. projectStart.r # untracked setwd(c:\yada\) # or setwd(L:\foo\bar\sharedRemote\wet\) -- this is the only difference among repository locations. source(projectStart2.r) projectStart2.r # tracked source(func1.r) source(func2.r) source(func3.r) ... func1.r # tracked func2.r # tracked func3.r # tracked ... Is there an easier or better accepted method? Thank you for your time, cur -- Curt Seeliger, Data Ranger Raytheon Information Services - Contractor to ORD seeliger.c...@epa.gov 541/754-4638 [[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] Is there a way to source from a specific Git repository without hardcoding the location everywhere?
On 12-09-26 8:25 PM, Curt Seeliger wrote: Folks, A small group of us are working together to develop a set of R functions to support data management and analysis using Eclipse/StatET in a Windows environment. We are using Git/EGit for version control. We work within our own repository and occasionally push to a common remote location. I'd like to have the code source files from the 'local' git repository without modification, where 'local' could mean c:\yada\ for one person, m:\my documents\wetlands\ for another, and l:\foo\bar\sharedRemote\wet\ to another user. The chdir argument to source() has been suggested for similar questions, but I have not been able to figure out how this helps without hardcoding the location in some manner. One option is for each repository to have an untracked file which sets the local working directory before sourcing another file that actually sources the function definitions. This file (projectStart.r below) would be read into the R session prior to use, at least during development. projectStart.r # untracked setwd(c:\yada\) # or setwd(L:\foo\bar\sharedRemote\wet\) -- this is the only difference among repository locations. source(projectStart2.r) projectStart2.r # tracked source(func1.r) source(func2.r) source(func3.r) ... func1.r # tracked func2.r # tracked func3.r # tracked ... Is there an easier or better accepted method? Yes. Use library(myProject) where myProject is a package containing all the scripts, written as functions. 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] Mac Text editors
Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Thanks! -Steve ___ Steven Wolf Research Associate CREATE for STEM Institute 115 H Erickson Hall Michigan State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a way to source from a specific Git repository without hardcoding the location everywhere?
Duncan Murdoch murdoch.dun...@gmail.com wrote on 09/26/2012 05:35:00 PM: ... I'd like to have the code source files from the 'local' git repository without modification, where 'local' could mean c:\yada\ for one person, m:\my documents\wetlands\ for another, and l:\foo\bar\sharedRemote\wet\ to another user. ... Yes. Use library(myProject) where myProject is a package containing all the scripts, written as functions. Yes, the eventual fate of these functions is expected to be a package. I'd like the pushed/pulled code to be runable as is without an intermediate step of package creation or gsub()ing hardcoded paths. Thanks for the quick reply, cur -- Curt Seeliger, Data Ranger Raytheon Information Services - Contractor to ORD seeliger.c...@epa.gov 541/754-4638 [[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] Comparing density plots using same axes or same axes scale
Good Evening-
I have a set of nine scenarios I want to plot to see how the distribution
is changing, if one tail is getting larger in certain scenario, currently I
am using this code
colnames-dimnames(sag_pdfs)[[2]]
par(mfrow=c(3,3))
for(i in 1:9) {
d-density(sag[,i])
plot(d,type=n, main=colnames[i])
polygon(d,col=red,border=grey)}
where sag is a 7305x9 double matrix and 9 different scenarios. I want to be
able to compare the distribution using the same axes scale.
Can anyone help?
Thanks
Meredith LaBeau
--
Doctoral Candidate
Department of Civil and Environmental Engineering
Michigan Technological University
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Re: [R] Mac Text editors
Have you looked at aquamacs? (emacs for the mac). its at aquamacs.org. albyn On 2012-09-26 17:48, Steven Wolf wrote: Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Thanks! -Steve ___ Steven Wolf Research Associate CREATE for STEM Institute 115 H Erickson Hall Michigan State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Mac Text editors
On Sep 26, 2012, at 5:48 PM, Steven Wolf wrote: Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Probably best in the future to post to R-SIG-Mac. The editor in the Mac-GUI works well. Has parenthesis, bracket and ellipsis matching which is very helpful. Also tab-completion thanks to the continuing effors to Simon Urbanek and Hans-Joerg Bibiko and probably others whose contributions are too subtle for for my aging brane. You can also get R-specific macro behaviors with TextWrangler. The default editor defined by options() is vi which has many powerful features as well. (I do not think I am interacting with 'vi' inside the editing panels that pop up from the GUI, although I would be happy to be corrected on this point.) Emacs is a UNIX standard and the Mac is yet-another-Unix-boxen. Many Mac users are also happy with R-Studio. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Random Forest - Extract
Hello, I have two Random Forest (RF) related questions. 1. How do I view the classifications for the detail data of my training data (aka trainset) that I used to build the model? I know there is an object called predicted which I believe is a vector. To view the detail for my testset I use the below-bind the columns together. I was trying to do something similar for my trainset but without putting it through the predict function. Instead taking directly from the randomForest which I stored in FOREST_model. I really need to get to this information to do some comparison of certain cases. RF_DTL-cbind(testset,predict(FOREST_model, testset, type=response)) 2. In the RF model in R the predict function has three possible arguments: response, vote or prob. I noticed vote and prob are identical for all records in my data set. Is this typical? If so then what is the point of having these two arguments? Ease of use? Dan [[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] Mac Text editors
On Sep 26, 2012, at 5:48 PM, Steven Wolf wrote: Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) Further point. Just as with Windoze, your dot-files are hidden by Finder.app. You can see them with terminal or do as I do and unhide them (and never trash any). Run this in a terminal session: defaults write com.apple.Finder AppleShowAllFiles YES # and pt-click-hold on Dock-Finder-icon, choose relaunch What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Thanks! -Steve ___ Steven Wolf Research Associate CREATE for STEM Institute 115 H Erickson Hall Michigan State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Comparing density plots using same axes or same axes scale
Hello,
Something like this?
sag - matrix(rnorm(1e3 * 9), ncol = 9)
d.list - apply(sag, 2, density)
xrange - range(sapply(d.list, function(d) range(d$x)))
ymax - max(sapply(d.list, function(d) max(d$y)))
op - par(mfrow=c(3,3))
for(i in 1:9)
plot(d.list[[i]], xlim = xrange, ylim = c(0, ymax))
par(op)
Hope this helps,
Rui Barradas
Em 27-09-2012 01:53, Meredith Ballard LaBeau escreveu:
Good Evening-
I have a set of nine scenarios I want to plot to see how the distribution
is changing, if one tail is getting larger in certain scenario, currently I
am using this code
colnames-dimnames(sag_pdfs)[[2]]
par(mfrow=c(3,3))
for(i in 1:9) {
d-density(sag[,i])
plot(d,type=n, main=colnames[i])
polygon(d,col=red,border=grey)}
where sag is a 7305x9 double matrix and 9 different scenarios. I want to be
able to compare the distribution using the same axes scale.
Can anyone help?
Thanks
Meredith LaBeau
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Mac Text editors
On Sep 26, 2012, at 6:06 PM, David Winsemius wrote: On Sep 26, 2012, at 5:48 PM, Steven Wolf wrote: Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) Further point. Just as with Windoze, your dot-files are hidden by Finder.app. You can see them with terminal or do as I do and unhide them (and never trash any). Run this in a terminal session: defaults write com.apple.Finder AppleShowAllFiles YES Sorry. I do not know how to relaunch in Snow Leopard. Those direction for relaunching Finder.app worked in Leopard but when I just checked, no longer seem to. # and pt-click-hold on Dock-Finder-icon, choose relaunch What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Thanks! -Steve ___ Steven Wolf Research Associate CREATE for STEM Institute 115 H Erickson Hall Michigan State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Comparing density plots using same axes or same axes scale
Hello, again.
I forgot, but the subject line also says same axes, not just same axes
scale.
If you want all densities on the same graph, use ?matplot (matrix plot).
Rui Barradas
Em 27-09-2012 02:08, Rui Barradas escreveu:
Hello,
Something like this?
sag - matrix(rnorm(1e3 * 9), ncol = 9)
d.list - apply(sag, 2, density)
xrange - range(sapply(d.list, function(d) range(d$x)))
ymax - max(sapply(d.list, function(d) max(d$y)))
op - par(mfrow=c(3,3))
for(i in 1:9)
plot(d.list[[i]], xlim = xrange, ylim = c(0, ymax))
par(op)
Hope this helps,
Rui Barradas
Em 27-09-2012 01:53, Meredith Ballard LaBeau escreveu:
Good Evening-
I have a set of nine scenarios I want to plot to see how the
distribution
is changing, if one tail is getting larger in certain scenario,
currently I
am using this code
colnames-dimnames(sag_pdfs)[[2]]
par(mfrow=c(3,3))
for(i in 1:9) {
d-density(sag[,i])
plot(d,type=n, main=colnames[i])
polygon(d,col=red,border=grey)}
where sag is a 7305x9 double matrix and 9 different scenarios. I want
to be
able to compare the distribution using the same axes scale.
Can anyone help?
Thanks
Meredith LaBeau
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Mac Text editors
My vote for R-Studio. Very elegant design and great functionality. However if coming from languages like Java and others then eclipse is better. R-Studio have dedicated section for Mac user which you will find useful. Best Regards, Bhupendrasinh Thakre Sent from my iPhone On Sep 26, 2012, at 7:48 PM, Steven Wolf wolfs...@msu.edu wrote: Hi everyone, I've recently moved from using a windows machine to a Mac (some might call it an upgrade, others not…I'll let you be the judge). Once I started using Notepad ++ on my windows machine, I really began to like it. Unfortunately, I'm not sure what the free text editor options are for the Mac (Notepad ++ is windows only). I've dabbled with Linux before and used Emacs/ESS there. However, I seem to remember fighting pretty hard to make that work and the OSX file structure isn't that intuitive to me yet. (For example, where is my .emacs file?) What text editors are best for the Mac, keeping in mind that I'm probably going to use them via the command line interface (e.g. X11 or Terminal). Thanks! -Steve ___ Steven Wolf Research Associate CREATE for STEM Institute 115 H Erickson Hall Michigan State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
