[R] timeseries highlighting
I'd like to plot a given time series in a primary color but highlight a segment of it in a different color. Is there an elegant way to do it? A+ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rbind a heterogeneous row
I have a dataframe with many rows like this: df X1 X2 X3 X4 X5 X6 X7 week d sim1 FALSE TRUE TRUE TRUE TRUE TRUE TRUE1 0.3064985 sim1 is the rowname, X1..X7,week,d are the column names. X1..X7 are factors, booleans in this case. I need to add another row, represented by the following list: list(rep(T,7),5,0.0) -- i.e, TRUE in all boolean columns, 5 in the week column, 0.0 in d. The name of the new row is dreps. I used to add fully numeric rows as follows: df1 - rbind(df,dreps=c(all numbers)) But if I do this here, df1 - rbind(df,dreps=c(rep(T,7),5,0.0)) -- booleans are converted to 0/1, which is not what I want. What's the recommended way to specify and bind a heterogeneous row above? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] applying to dataframe rows
How do I apply a function to every row of a dataframe most naturally? Specifically, I'd like to filter out any row which contains an Inf in any column. Since all columns are numeric, I guess max should work on a row... -- Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Developing a web crawler
On Mar 3, 2011, at 4:22 AM, antujsrv wrote: I wish to develop a web crawler in R. As Rex said, there are faster languages, but R string processing got better due to the stringr package (R Journal 2010-2). When Hadley is done with it, it will be like having it all in R! -- Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] the features of the truth
This is really a statistics problem, so I wonder which R packages can be employed best to solve and visualize it. I run a lot of simulations to approach the truth. The truth is a result of very complex computations, and is a real number. The closer it is to 0, the truthier it is. Each simulations has a set of features, some of which are not available for all simulations. Some of the features are numeric (week), some boolean (utility), while others are factors. Each simulation has the final value, the dm column in the data frame. The names of the simulations are rownames of the data frame, and feature names are the column names. Here's the dataframe: http://dl.dropbox.com/u/9300701/Data/sf.dm.pos.r You read it in R with sf - read.table(sf.dm.pos.r) Seeking the truth questions: -- What kinds of GLM and other models can we run to determine which features are most contributing to the truth, i.e. making dm closer to 0? -- What kind of clustering can emphasize the most contributing features? -- What kind of visualizations can be used to make it clear which features affect the truth the most, and in which combinations? What kind of color visualizations are there to make the truth even clearer? Cheers, Alexy [[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] .libPaths(new) stopped working in 2.10
I used to have the following in my .Rprofile: if (length(.libPaths())==1) .libPaths(paste(Sys.getenv(HOME),/Library/R/,paste(R.version$major,as.integer(R.version$minor),sep='.'),/library,sep='')) -- and it added my user-defined library directory. Then I installed packages there, so during an upgrade, I'd know exactly which packages I installed and auto-upgrade with a script. However, in R 2.10's Mac OSX GUI, .libPaths(new) does nothing... Did its behavior change? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] .libPaths(new) stopped working in 2.10
I have the .libPaths() defined in my .Rprofile, and it stopped having any effect. Even if I try to do it in the REPL, as: x - paste(Sys.getenv(HOME),/Library/R/,paste(R.version$major,as.integer(R.version$minor),sep='.'),/library,sep='') x [1] /Users/alexyk/Library/R/2.10/library .libPaths(x) .libPaths() [1] /Library/Frameworks/R.framework/Resources/library Nothing GUI'sh. (Changing back to r-help as it's by no means obvious yet it's a Mac-only problem.) Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] .libPaths(new) stopped working in 2.10
On Sun, Dec 6, 2009 at 3:04 PM, Duncan Murdoch murd...@stats.uwo.ca wrote: Does that directory exist? .libPaths(foobar) silently does nothing, because (on my system) foobar is not a directory. (This is documented behaviour, though it would perhaps be friendlier if it gave a warning when it dropped a requested addition.) I don't think this is new behaviour... Indeed. Thanks for the clarification! After mkdir it does add it to the list. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] comma-separated thousands in numbers on plot axes?
How can I make R separate thousands, millions, etc., on the plot axes, with commas? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] compressing the plot's white space
I need to fit a graph into a column of a 2-column paper. I found that just specifying width and height parameters (3.2in x 3.5in) to plot doesn't decrease the fonts of the main title, axis titles, and labeling numbers, and tick sizes. So I have to add cex to all labels and titles and manage ticks. However, I can't decrease the space between axis label and numbers on ticks. Is there a way to place those numbers inside the plot, and/or explicitly remove most of the space between the numbers and the axis title? Also, how should I specify the margins to achieve best white space elimination? On Quartz, decreasing margins seem to squeeze the titles properly, on postscript device, the axis titles simply move outside the plot. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] sorting by creation time in ls()
When trying to remember what did I do in the session, especially after coming back to it after a few days, I'd like to mimic Unix's ls -ltrh -- does R retain the timing a certain variable is created? If not, would it make a useful addition, to have ls with an option to sort by creation time? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] factors to integers preserving value in a dataframe
I want to produce a dataframe with integer columns for elements of string pairs: pairs - c(10 21,23 45) pairs.split - lapply(pairs,function(x)strsplit(x, )) pdf - as.data.frame(pairs.split) names(pdf) - c(p,q) -- at this point things look good, except the columns are factors, as I didn't change the default stringsAsFactors parameter to the as.data.frame. Now if I want to convert columns to integers, I get typeof(pdf$p) [1] integer pdf$p [1] 10 21 Levels: 10 21 as.integer(pdf$p) [1] 1 2 -- being factor levels instead of the original values. I could have used stringsAsFactors=F and then convert the strings to integers with as.integer all the same; what other ways are there -- e.g., is there a way to convert integer-looking factors to integers directly, without substituting levels? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] accessing and preserving list names in lapply
Sometimes I'm iterating over a list where names are keys into another
data structure, e.g. a related list. Then I can't use lapply as it
does [[]] and loses the name. Then I do something like this:
do.one - function(ldf) { # list-dataframe item
key - names(ldf)
meat - ldf[[1]]
mydf - some.df[[key]] # related data structure
r.df - cbind(meat,new.column=computed)
r - list(xxx=r.df)
names(r) - key
r
}
then if I operate on the list L of those ldf's not as lapply(L,...), but
res - lapply(1:length(L),do.one)
Can this procedure be simplified so that names are preserved?
Specifically, can the xxx=..., xxx - key part be eliminated -- how
can we have a variable on the left-hand side of list(lhs=value)?
Cheers,
Alexy
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Re: [R] accessing and preserving list names in lapply
res - lapply(1:length(L),do.one) Actually, I do res - lapply(:length(L),function(x)do.one(L[x])) -- this is the price of needing the element's name, so I have to both make do.one extract the name and the meat separately inside, and lapply becomes ugly. Yet the obvious alternatives -- extracting the names separately, attaching them back into list elements, etc., -- are even uglier. Something pretty? :) Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] growing dataframes with rbind
I'm growing a large dataframe by composing new rows and then doing row - compute.new.row.somehow(...) d - rbind(d,row) Is this a fast/preferred way? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 1.095e+09 for integers
I've had a very long file written out by R with write.table, with fields of time values, converted from POSIXlt as.numeric. Among 2.5 million values, very few had 6 trailing zeroes, and those were output in scientific notation as in the subject. Is this the default behavior for long integers, and how can it be turned off (with all digits for any integer field in write.table)? This is important to interoperate with other languages through such text dumps, as some do not expect scientific notation for integers, only for floats. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] name scoping within dataframe index
Every time I have to prefix a dataframe column inside the indexing brackets with the dataframe name, e.g. df[df$colname==value,] -- I am wondering, why isn't there an R scoping rule that search starts with the dataframe names, as if we'd said with(df, df[colname==value,]) -- wouldn't that be a reasonable default to prepend to the name search path? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] name scoping within dataframe index
On 1/26/2009 1:46 PM, Alexy Khrabrov wrote: Every time I have to prefix a dataframe column inside the indexing brackets with the dataframe name, e.g. df[df$colname==value,] -- I am wondering, why isn't there an R scoping rule that search starts with the dataframe names, as if we'd said with(df, df[colname==value,]) -- wouldn't that be a reasonable default to prepend to the name search path? If you did that, it would be quite difficult to get at a colname variable that *isn't* the column of df. It would be something like df[get(colname, parent.frame()) == value,] Actually, what I propose is a special search rule which simply looks at the enclosing dataframe.name[...] outside the brackets and looks up the columns first. It would break legacy code which used the column names identical to variables in this context, but there's probably other ideas to enhance R readability which would break legacy code. Perhaps when the next major overhaul occurs, this is something folks can voice opinions about. I find the need for inner prefixing quite unnatural, FWIW. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] name scoping within dataframe index
On Jan 26, 2009, at 2:12 PM, Duncan Murdoch wrote: df[get(colname, parent.frame()) == value,] Actually, what I propose is a special search rule which simply looks at the enclosing dataframe.name[...] outside the brackets and looks up the columns first. Yes, I understood that, and I explained why it would be a bad idea. Well this is the case in all programming languages with scoping where inner-scope variables override the outer ones. Usually it's solved with prefixing with the outer scope, outercsope.name or outerscope::name or so. So it only underscores the need to improve scoping access in R. Dataframe column names belong to the dataframe object and the natural thing would be to enable easy access to naming; you'd need to apply an extra effort to access an overridden unrelated external variable. Again, just an analogy from other programming languages. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Functional pattern-matching in R
I found there's a very good functional set of operations in R, such as apply family, Hadley Wickham's lovely plyr, etc. There's even a Reduce (a.k.a. fold). Now I wonder how can we do pattern-matching? E.g., now I split dimensions like this: m - dim(V)[1] # R n - dim(V)[2] # still R While even Matlab allows for [m,n] = size(V) % MATLAB! Ideally I'd be able to say, x,y - dim(V) -- where .,. is some magic needed. Similarly, to break lists, we'd need, in a MLish notation, match L with | head::tail = ... | () = ; What can be done in R now to simulate it, and/or how Rish is it to add something like that? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] svm models in a loop
On Oct 12, 2008, at 2:26 AM, Prof Brian Ripley wrote:
You need to use substitute() on the call. Something like
sapply(1:5,function(i)
eval(substitute(svm(person_oid ~ ., data=zrr[1:N,]),
list(N=100*i))
)
Thanks!
On Sun, 12 Oct 2008, Alexy Khrabrov wrote:
I want to train svm models on increasingly large training data
subsets of some zrr as follows:
m - sapply(1:5,function(i)
svm(person_oid~.,data=zrr[1:100*i,]))# (*)
However, when I inspect m[1], it literally shows
m[1]
[[1]]
svm(formula = person_oid ~ ., data = zrr[1:N, ])
I suspect it shows '100*i' not 'N', but in the absence of a
reproducible example, I cannot check.
Exactly -- I've mixed in an attempt to define N in sapply(...,
function(i) { N - 100*i, ...}), but now see I need to do it in
substitute().
Cheers,
Alexy
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[R] subsetting dataframe by rownames to be excluded
Is there a way to select a subset of a dataframe consisting of all those rows with rownames *except* from a subset of rownames to be excluded? Example: a - data.frame(x=1:10,y=10:1) a - a[order(a$y),] # to make rownames differ visually a[8,] x y 3 3 8 a[8,] x y 8 8 3 a[-8,] x y 10 10 1 9 9 2 8 8 3 7 7 4 6 6 5 5 5 6 4 4 7 2 2 9 1 1 10 a[-8,] Error in -8 : invalid argument to unary operator -- is there a similar exclusion operator or simple way? So far the best I can do is a[setdiff(rownames(a),8),] x y 10 10 1 9 9 2 7 7 4 6 6 5 5 5 6 4 4 7 3 3 8 2 2 9 1 1 10 Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] svm models in a loop
I want to train svm models on increasingly large training data subsets of some zrr as follows: m - sapply(1:5,function(i) svm(person_oid~.,data=zrr[1:100*i,]))# (*) However, when I inspect m[1], it literally shows m[1] [[1]] svm(formula = person_oid ~ ., data = zrr[1:N, ]) -- as opposed to m1 - svm(person_oid~.,data=zrr[1:100,]) m1 m1 Call: svm(formula = person_oid ~ ., data = zrr[1:100, ]) ... -- actual parameters How do I force actual model evaluation in (*) ? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R/OCaml?
Did anyone try to write R extensions in OCaml? What would it entail to enable it? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] namespaces
I'd like to control my namespace thoroughly, separated by task. Is there a way, in R session, to introduce namespaces for tasks dynamically and switch them as needed? Or, is there a combination of load/save workspace steps which can facilitate this? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] namespaces
Yes, I could prefix everything with taskN$, but that's boring! Can I now attach and detach tasks to have one prefix-less, since they look like dataframes? What does proto buy us? To respond to Uwe here as well, I want dynamic task switching and *also* an ability to load and save task from their workspaces into their namespaces in the same R session. Cheers, Alexy On Oct 2, 2008, at 11:19 AM, Gabor Grothendieck wrote: You could have an environment for each task and place your objects for each task in its environment. Note that this is getting close to object oriented ideas where each enviroment/task is an object containing your R variables and methods and the proto package can be used to facilitate that: library(proto) task1 - proto(var = 0, addx = function(this, x) this$var - this $var + x) task1$var # 0 task1$addx(3) task1$var # 3 On Thu, Oct 2, 2008 at 11:03 AM, Alexy Khrabrov [EMAIL PROTECTED] wrote: I'd like to control my namespace thoroughly, separated by task. Is there a way, in R session, to introduce namespaces for tasks dynamically and switch them as needed? Or, is there a combination of load/save workspace steps which can facilitate this? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] partitioning vectors of intervals
I have two pairs of time intervals: coarse- and fine-grained. They're components of their respective dataframes, looking like, coarse:endtimestarttime 1t1_end t1_start 2 t2_end t2_start ... fine: is the same, except that its intervals presumably fall into the coarse's enclosing ones. The problem is to partition the fine intervals into the coarse ones, adding a list to each row showing which fine intervals fall in it, like coarse: ... fine 1[1,2] 2[3,4,5] Is there a functional way to do this? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 10-minute presentation of R as a machine learning platform
Greetings -- I'd like to present R to our university research group as a viable platform to do machine learning applications for human behavior modeling. The actual research will be further specialized, but general activities -- acquiring/interfacing with the data, specifying/learning a model, detecting mean behaviors vs outliers, and of course visualizing it all, are perfectly done using R base and add-on packages. I'm thinking of sticking some timeseries data into a MySQL database (real world), extracting it into an R session, and showing things emphasizing R strengths. Do folks have some similar sessions saved, and what would you recommend to do in just the 10 minutes I'll have? Especially an example of bedazzling graphics which can be produced from models of data, 3d, colorful, and rotatable with rgl! :) Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] creating horizontal dataframes with column names
Greetings -- in order to write back to SQL databases, one needs to create a dataframe with values. I can get column names of an existing table with sqlColumns. Say I have a vector of values (if they're all the same type), or a list (if different). How do I create a dataframe with column names given by my sqlColumns? To make it concrete, how do we make a dataframe A B C 1 2 3 out of column.names - LETTERS[1:3] values - 1:3 ? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] creating horizontal dataframes with column names
Exactly -- also found creating horizontal vector helps: df - data.frame(matrix(1:5,nrow=1)) colnames(df) - LETTERS[1:5] df A B C D E 1 1 2 3 4 5 Thanks, Alexy On Sep 17, 2008, at 1:17 AM, Moshe Olshansky wrote: If df is your data.frame, then colnames(df) - c(col1,Col2,COL3) --- On Wed, 17/9/08, Alexy Khrabrov [EMAIL PROTECTED] wrote: From: Alexy Khrabrov [EMAIL PROTECTED] Subject: [R] creating horizontal dataframes with column names To: [EMAIL PROTECTED] Received: Wednesday, 17 September, 2008, 1:52 PM Greetings -- in order to write back to SQL databases, one needs to create a dataframe with values. I can get column names of an existing table with sqlColumns. Say I have a vector of values (if they're all the same type), or a list (if different). How do I create a dataframe with column names given by my sqlColumns? To make it concrete, how do we make a dataframe A B C 1 2 3 out of column.names - LETTERS[1:3] values - 1:3 ? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] splitting time vector into days
Greetings -- I have a dataframe a with one element a vector, time, of POSIXct values. What's a good way to split the data frame into periods of a$time, e.g. days, and apply a function, e.g. mean, to some other column of the dataframe, e.g. a$value? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] dealing with NAs in time series
Certain timeseries I have had outliers, which I removed by assigning NA to their positions. Now acf() refuses to go to work. What's the right way to remove outliers from ts objects, and what are teh standard ways to interpolate NAs in them? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] annotating objects in workspace
Is there a way to associate descriptions with the objects in the workspace, and later retrieve them to know what the object was created for? Thanks, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] modeling interval data, a.k.a. irregular timeseries
Greetings -- I've got some sensor data of the form t1_1, t1_2 t2_1, t2_2 ... tN_1,tN_2 -- time intervals measuring starts and stops of sensor activity. I'd like to see whether there's any regularity in it. Seems natural to consider these data timeseries -- except most of the timeseries packages and models assume regular ones, with a fixed frequency. I wonder what's a good way to apply existing regular timeseries packages to these data, and perhaps try some others? I like David Stoffer's book a lot, yet he uses R's own ts methods (with some extras). I also like the zoo package, which allows for irregular timeseries, yet I'm not sure how to apply the usual models to zoo objects -- even though zoo strives to be compatible with ts... Is zoo directly usable for ts-like time domain and spectral analysis as per Stoffer? Another way I was pondering is to map the above to a an artificial index 1:n and consider it multivariate timeseries. Is it something done in irregular timeseries analysis? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] figure margins too large for a barplot in png, pdf ok
On May 6, 2008, at 10:30 PM, Prof Brian Ripley wrote: What were H W? For png() they are (by default) in pixels, for pdf() in inches. You haven't told us your OS, but I guess Mac OS. Please update to R 2.7.0: that offers you two new png() devices for higher-quality plots, and various other improvements. (If you want to use the cairo-based png() at other than 72dpi, use R-patched or remember that the pointsize is mistakenly in pixels.) For some reason, R 2.6.2 on Mac OSX (indeed) stopped doing png at all, even for plot(1:10). I've been using a postcard printer with A5 size in between, was wondering if that affected things -- and changed that in Page Setup to US Letter, to no avail. H an W were 600 x 800, resp., and most importantly this same code worked with R 2.6.0 before... In any case, simply went and installed the 2.7.0, recompiled littler, and it all works fine now, just as before. (Hope the 4/22 build for Mac OSX incorporates Simon's recentmost fixes.) Thanks! Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] figure margins too large for a barplot in png, pdf ok
I've used to have a script with a barplot command it in, preceded by a png: png(graph.file,height=H,width=W) barplot(t,names.arg=breaks[2:(length(t)+1)],tck=gridlines) -- worked before R 2.6.2. When I tried it in R 2.6.2, which I have for a while but didn't run with that script, it complained, the margins too large, and I've googled the messages from our list where neither height nor width had been specified. Yet here they are specified here. Calling same from R GUI draws the nice barplot in Quartz, and replacing png with pdf or postscript does fine. Other graphs work fine with png. Jpeg also complains; when I try various values for H or W, still the same -- how can I subdue the png? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] preallocating matrices and rda read-back objects
I've read in Phil Spector's new book that it's a good idea to preallocate a big matrix, like u - matrix(0,nrow,ncol) # (1) Now, I read contents of a huge matrix from a Fortran binary dump. u - readBin(con,what=double,n=nrow*ncol) # (2) If I do (1) and then (2), u is a vector, obviously it's either reallocated or its matrix nature is lost -- overridden? overwritten? Instead, I do it now as u - matrix(readBin(con,what=double,n=nrow*ncol),nrow=nrow,ncol=ncol) # (3) What's going on with memory management here and what's the right way to make it efficient -- and how to preallocate? After that, I'm saving u as R binary object in an rda file. Does it make sense to preallocate u before reading it back now from the rda file? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 in a Fortran binary array
Greetings -- I'd like to avoid converting a Fortran array of floats into ASCII and back reading it in R. Furthermore it's much faster to dump large arrays in binary, as they take up much less space with full precision -- many decimal points take up many bytes in ASCII versus four or eight per float in raw. Is there a way to read such a Fortran unformatted file back into R? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] exporting a split list
Using wk - with(d, split(word, kind)), I get the following class table: wk$`1` [1] a bra ... # (*) wk$`10` ca dabra ... Now I need to export it in the following format: classnum_members examples 1 23 a bra ... 104 ca dabra For each class C such as `1`, I need to print the number of members, length(wk[[C]]), and show N examples as sample(wk[[C]], N), space- separated. The columns themselves are tab-separated. What's the R way to export such as list? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] [:]
What are idioms for taking a head or a tail of a vector, either up to an index, or from an index to the end? Also -- is it necessary to use length(v) to refer to the last element? E.g., Python has v[:3] # indices 0,1,2 v[3:] # indices 3,4,... v[-1] # the last element of v v[:-1] # all but last Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ragged array with append
I wonder what's the right way in R to do the following -- placing objects of the same kind together in subarrays of varying length. Here's what I mean: word - c(a,b,c,d,e,f,g,h,i,j) kind - c(1,1,1,2,3,4,5,5,7,7) d - data.frame(word,kind) d word kind 1 a1 2 b1 3 c1 4 d2 5 e3 6 f4 7 g5 8 h5 9 i7 10j7 Now from this data frame, I want to assemble words of the same kind into lists. The result should look like (not R syntax): 1 = [a,b,c] 2 = [d] 3 = [e] 4 = [f] 5 = [g,h] 7 = [i,j] What is the most appropriate data structure in R for this result and growing these sublists most effectively with append? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] printing levels as tuples
I'm running rle() on a long vector, and get a result which looks like uc Run Length Encoding lengths: int [1:16753] 1 1 1 1 1 1 1 1 1 1 ... values : int [1:16753] 29462748 22596107 18322820 14323315 12684505 9909036 7296916 6857692 5884755 5883697 ... I can print uc$names or uc$levels separately. Is there any way to print them together as tuples, looking like (29462748, 1) (22596107, 1) ... (5883697, 1) ... ... Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] shrink a dataframe for plotting
I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row of those averages into the shrunk result Is there any existing package to do that in R? Otherwise, which R idioms are most effective to achieve that? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] shrink a dataframe for plotting
On Nov 21, 2007, at 1:24 PM, Thibaut Jombart wrote: Alexy Khrabrov wrote: I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row of those averages into the shrunk result Is there any existing package to do that in R? Otherwise, which R idioms are most effective to achieve that? Cheers, Alexy if you want to extract relevant information from such a table, splitting rows in arbitrary chuncks may not solve your problem. Ordinations in reduced space are designed for that kind of task, but hierachical clustering may also help. See Legendre Legendre (1998, Numerical Ecology, Elsevier) for examples of such methods in Ecology, and the R packages ade4, vegan and hclust. Well, in this case the function is monotonically decreasing, and so averages would do fine just to plot the curve. What I'm after is an R way -- preferably functional -- to split a vector into chunks of N elements and issue a new vector of the averages of those chunks. Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] uniq -c
Is there an R analog of the Unix command uniq -c: http://en.wikipedia.org/wiki/Uniq Given an array x, uniq -c replaces each contiguous subsequence of identical numbers with a tuple (count, number). E.g. $ cat usample 10 10 9 8 8 7 7 7 6 3 1 1 1 0 $ uniq -c usample 2 10 1 9 2 8 3 7 1 6 1 3 3 1 1 0 Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 graph metadata text from a file
I've tried tetxplot() but it fills the whole frame. I could either
use mfrow but it would devote unnecessarily large space to the text.
In fact I want it in a corner of my current plot, not occupied by the
curves. Here's what I ended up with -- it works, but I have to
manually move top text down as it's cut off by the upper boundary of
the graph. Any better/shorter/nicer ways?
First I fetch the dimensions of the current plot:
max.xy - function() {
p - par()
x.max - p$usr[2]
y.max - p$usr[4]
xy.coords(x=x.max, y=y.max)
}
Then, after plotting, I say
plot(...)
xy.max - max.xy()
# top-right -- need to move a bit down or letters are cut off on top:
text(xy.max$x,xy.max$y*0.99,story$text,adj=c(1,1),col=blue)
# bottom-right -- no cut-off, a small nice gap comes free:
# story.text is story$text with some more appended details
text(xy.max$x, 0, story.text,adj=c(1,0),col=blue)
As for the original question -- I ended up creating, in each data
directory, a file story.r, looking like this:
-
# R titles, labels, and story text for the plot
# when I assigned color=blue right in data.frame, it became an
integer level!
story - data.frame(title=,x=,y=,text=,color=)
story$title - graph title
story$x - x units
story$y - y units
story$text - story text -- this data has come long way. Once upon
a time there was R...
# we can separate colors of title, labels, and text like
# title.color, x.color, y.color, text.color
story$color - dark blue
-
First I create a data.frame and then assign to its components one by
one for readability. When I tried to assign color right in data.frame
(..., color=blue), it became integer levels! So I had to move it
out along with others. What's the logic here?
Cheers,
Alexy
On Nov 20, 2007, at 1:39 AM, Bert Gunter wrote:
... But is I understand correctly,this is certainly straightforward
without
textplot,too...
e.g.
mylegend - Some text...\n Some more text
mytitle - This is a title
plot(0:1,0:1, main = mytitle)
legend(.2,.2,leg=mylegend, bty=n)
Naturally, this could all be functionized and the various text
arguments
passed as arguments to the function (see ?plot.default or its
code); or they
could be components of a list, or ...
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On
Behalf Of Greg Snow
Sent: Monday, November 19, 2007 2:18 PM
To: Alexy Khrabrov; r-help@r-project.org
Subject: Re: [R] reading graph metadata text from a file
You may want to use the textplot function from the gplots package
rather
than the legend.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Alexy Khrabrov
Sent: Monday, November 19, 2007 1:17 PM
To: r-help@r-project.org
Subject: [R] reading graph metadata text from a file
I'd like to produce graphs with titles, axis labels, and
legend as parameters read from a separate text file.
Moreover, I'd like to use the legend for a short summary of
the data -- not necessarily for describing the line colors
per se. How do we do this?
Cheers,
Alexy
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[R] xy.coords and log10
Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xy.coords and log10
xy.coords can have a log=xy parameter which then plot interprets to use log scale. I wonder whether plot can be instructed in a similar way to use log10 scale instead of natural logs. Cheers, Alexy On Nov 20, 2007, at 7:01 PM, Duncan Murdoch wrote: On 11/20/2007 10:41 AM, Alexy Khrabrov wrote: Is there a way to teach xy.coords, when given log=xy, or just x or y separately, to do a decimal log10 instead of the natural log? xy.coords doesn't do any transformation other than setting non- positive values to NA. So your question doesn't make sense; could you elaborate on what you're seeing that you don't want to see? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] asymptote
I have a graph which looks like hyperbole. I'd like to fit a straight line to the lower segment going to infinity, approaching the X axis -- I'm interested in the angle. If I'd do it manually, I'd cut off a certain initial part of the range, [0..x_min], and then do an lm with the rest. Yet I wonder whether those curve fitting packages mentioned earlier do something similar automatically? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 graph metadata text from a file
I'd like to produce graphs with titles, axis labels, and legend as parameters read from a separate text file. Moreover, I'd like to use the legend for a short summary of the data -- not necessarily for describing the line colors per se. How do we do this? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] assign if not set
What's the idiom of assigning a default value to a variable if it's not set? In Ruby one can say v ||= default -- that's an or-assign, which triggers the assignment only if v is not set already. Is there an R shorthand? Cheers, Alexy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] assign if not set; stand-alone R script, source'able too?
Marc -- thanks, very interesting.
I was in fact tinkering at a very simple default arguments assignment
to a generic command-line R script header:
#!/bin/sh
# graph a fertility run
tail --lines=+4 $0 | R --vanilla --slave --args $*; exit
args - commandArgs()[-(1:4)]
# the krivostroi library
source(/w/ct/r/kriv/krivostroi.r)
# NB: vector assignment in R? defaults?
file- args[1]
maxruns - if (is.na(args[2])) 1 else args[2]
prefix - if (is.na(args[3])) file.basename(file) else args[3]
-- turns out, args[N] here are NA if not supplied on the command-
line. I'd like to see a nicer way to do it still, without repeating
args[N] twice for each assignment though.
Another thing from this snippet, unrelated to assignment, is that was
the only way to get R script to be packed in a single file runnable
from the command line in a stand alone way. Yet when I want to source
() it, R obviously chokes on the shell command tail. My previous
solution was to have a pair of files, script.r/script.sh for each R
script, where .sh would look like
echo argv - c('$1','$2'); source('main.r') | R --vanilla --slave
Wonder if there's a way to have a single file which is a stand-alone
command script, and can be source()'d in R.
Cheers,
Alexy
On Nov 20, 2007, at 4:03 AM, Marc Schwartz wrote:
On Tue, 2007-11-20 at 03:32 +0300, Alexy Khrabrov wrote:
What's the idiom of assigning a default value to a variable if it's
not set? In Ruby one can say
v ||= default
-- that's an or-assign, which triggers the assignment only if v is
not set already. Is there an R shorthand?
Cheers,
Alexy
If 'v' is not set, then it does not exist, hence you can use exists
() to
check for it. However, you need to [potentially] distinguish where the
variable might be located. Keep in mind that R uses lexical scoping,
hence the exists() function has other arguments to define where to
look.
A simple example:
v
Error: object v not found
if (!exists(v)) v - Not Set
v
[1] Not Set
v - Set
if (!exists(v)) v - Not Set
v
[1] Set
See ?exists for more information.
That being said, just as an example of extending R, you could do the
following, which is to create a new function %||=% (think %in% or %*%)
which can then take two arguments, one preceding it and one following
it, and then basically do the same thing as above. Again here, scoping
is critical.
%||=% - function(x, y)
{
Var - deparse(substitute(x))
if (!exists(Var))
assign(Var, y, parent.frame())
}
v
Error: object v not found
v %||=% Not Set
v
[1] Not Set
v - Set
v %||=% Not Set
v
[1] Set
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Re: [R] R as a programming language
On Nov 7, 2007, at 4:13 PM, Duncan Murdoch wrote:
And, still no option processing as in GNU long options, or python
or ruby's optparse.
What's the semantics of parameter passing -- by value or by
reference?
By value.
Thanks Duncan! So if I have a huge table t, and the idea was to
write a function t.xy(t, ...) to select slices of it, will parameter
passing copying waste forfeit all aesthetic savings from
refactoring? What I'm dreading is having to explicitly select x and
y from t,
if (t has some shape) {
plot(t$this, t$that, ...)
} else if (t has that shape) {
plot(t$smth_else, ...)
}
-- that way I do refer to parts of t and there's no copying except to
plot (?), yet if indeed passing parameters by value copies them, one
would have to refrain from writing functions! Is that the state of
things?
Cheers,
Alexy
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[R] R as a programming language
Greetings -- coming from Python/Ruby perspective, I'm wondering about
certain features of R as a programming language.
Say I have a huge table t of the form
run ord unitwords new
1 1 69391013641
1 2 275 1001518
1 3 33141008488
1 4 14154 1018463
1 5 29821006421
Alternatively, it may have a part column in front. For each run (in
a part if present), I select ord and new columns as x and y and plot
their functions in various ways. t is huge. So I want to select the
subset to plot, as follows:
t.xy - function(t,part=NA,run=NA) {
if (is.na(run)) {
# TODO does this entail a full copy -- or how do we do
references
in R?
r - t
} else if (is.na(part)) {
r - t[t$run == run,]
} else { # part present too
r - t[t$part == part t$run == run,]
}
x - r$ord
y - r$new
xy.coords(x,y)
}
What I'm wondering about is whether r -t will copy the complete t,
and how do I minimize copying in R. I heard it's a functional
language -- is there lazy evaluation in place here?
Additionally, tried to use --args command line arguments, and found a
way only due to David Brahm -- who helped with several important R
points (thanks Dave!):
#!/bin/sh
# graph a fertility run
tail --lines=+4 $0 | R --vanilla --slave --args $*; exit
args - commandArgs()[-(1:4)]
...
And, still no option processing as in GNU long options, or python or
ruby's optparse.
What's the semantics of parameter passing -- by value or by reference?
Is there anything less ugly than
print(paste(x=,x,y=,y))
-- for routine printing? Can [1] be eliminated from such simple
printing? What about formatted printing?
Is there a way to assign all of
a - args[1]
b - args[2]
c - args[3]
in one fell swoop, a lá Python's
a,b,c = args
What's the simplest way to check whether a filename ends in .rda?
Will ask more as I go programming...
(Will someone here please write an O'Reilly's Programming in R? :)
Cheers,
Alexy
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[R] running sum of a vector
I need a vector with sums of vectors up to each position in the
original. The imperative version is simple:
# running sum: the traditional imperative way
sumr.1 - function(x) {
s - c()
ss - 0
for (i in 1:length(x)) {
ss - ss + x[i]
s[i] - ss
}
s
}
Yet I want a functional way, which is shorter:
# running sum: functional way, but inefficient one!
sumr.2 - function(x) {
sapply(1:length(x), function(i) sum(x[1:i]))
}
-- the problem with the latter is, we need to create indices to run
over them, and the sum is recomputed anew for each position, while
the imperative version iterates without recomputing. Is there a
better functional solution?
Cheers,
Alexy
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Re: [R] R as a programming language
With all due respect to the great book -- of which I own 2 copies I bought new -- it's not an O'Reilly Programming in X book. The idea of a programming book like that is to thoroughly treat the language from a programmer's standpoint, in a fairly standard way, such as Ruby or Python. As I'm learning more of statistics with R, I prefer to do it with the book by Crawley. Looks like most of R books are written by statisticians who became programmers, not the other way. Through all those years I periodically follow R, I forget its programming spirit in between, and there's no Programming ... book to help. Statistics is hard to forget once you master it; syntax sugar melts away... Programming with Data is the closest to an O'Reilly, but more advanced and esoteric than that. Since R became a bona fide Open Source language with CRAN and all, an O'Reilly book by a [Python and Ruby] programmer-turn-statistician is long overdue! If it systematically compares R with Ruby and Python, its closest Open Source cousins, it would help even more. RPy and RRb are there to help, too. Just my $0.01... Cheers, Alexy On Nov 7, 2007, at 7:46 PM, Bert Gunter wrote: (Will someone here please write an O'Reilly's Programming in R? :) Someone already has ... see Venable and Ripley's S PROGRAMMING. **However** R is more than a general purpose programming language: it is a programming language specifically designed for data analysis -- including statistical graphics -- and statistics. So, IMHO anyway, it's really impossible to discuss it without reference to the data structures and procedures underlying such tasks. Because it is targeted to do those sorts of things well, it may handle poorly some things that general purpose languages do well (minimizing storage with the use of references, for example). My own experience is that one appreciates the power and beauty of the language and the wisdom of the designers the more one uses it in real applications. But I am not a computer scientist and have only a limited exposure to standard CS concepts and algorithms, to say nothing of real programming experience. So just my $.02. Best regards, Bert Gunter Genentech Nonclinical Statistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
