[R] percent sign in plot annotation

Hello, I would like to annotate a graph with the expression 'alpha = 5%' (the alpha should be displayed as the greek letter). I tried text(1,1,expression(alpha == 5%)) which gives a syntax error. escaping the percent sign (\%) or doubling (%%) does not help. What do I do? Thanks, Martin

Re: [R] parallel coordinates plot

Marco Helbich wrote: Dear List, I want to make a parallel coordinates plot with the specific variables on the abscissa and the cases on the ordinate should be dyed dependent on another nominal variable from the data frame. I use the parcoord function. Hi Marco, If I understand your

Re: [R] percent sign in plot annotation

Martin Keller-Ressel wrote: Hello, I would like to annotate a graph with the expression 'alpha = 5%' (the alpha should be displayed as the greek letter). I tried text(1,1,expression(alpha == 5%)) Try text(1,1,expression(alpha == 5*%)) Best, Bettina

Re: [R] percent sign in plot annotation

you can try text(1, 1, expression(paste(alpha, = 5%))) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015

Re: [R] percent sign in plot annotation

On Wed, Jan 17, 2007 at 09:57:49AM -, Martin Keller-Ressel wrote: I would like to annotate a graph with the expression 'alpha = 5%' (the alpha should be displayed as the greek letter). I tried text(1,1,expression(alpha == 5%)) text(1,1, expression(paste(alpha == 5, '%')) ) cu

Re: [R] percent sign in plot annotation

On Wed, 2007-01-17 at 09:57 +, Martin Keller-Ressel wrote: Hello, I would like to annotate a graph with the expression 'alpha = 5%' (the alpha should be displayed as the greek letter). I tried text(1,1,expression(alpha == 5%)) which gives a syntax error. escaping the percent

Re: [R] percent sign in plot annotation

Thanks to Bettina, Dimitris and Gavin for their help. All their solutions work nicely. For future reference, here are three ways to draw a percent sign in R plots: plot(0:10, 0:10, type = n) text(5,7,expression(paste(alpha == 5, %, sep = ))) text(5, 5, expression(paste(alpha, = 5%)))

[R] sleep data

When reading the documentation for the sleep data set in R, the impression is clear, this is an independent groups kind of design (two groups of 10 subjects each). However, when browsing the original article (referred to in the help file), my impression is quite clear, this is really a

Re: [R] nested hierarchical design

1. The first I used to do in SPSS and I would like to be able to do it in R as well. This is the hierarchical model I would like to use: a continuous variable explained by factor A(fixed) + factor B(random) nested in A + factor C (random) nested in factor B (which is nested in A). You

[R] problem with unlist POSIX date at midnight

Dear R-users, I use unlist of POSIX dates to extract the year, hour etc. With that I can search for files in my database which are in the form 'mmddhh_synops.txt' However, I get stucked during midnight where unlist just gives NA's. The script is given below, the problem accurs at

[R] Repeated measures

I am having a hard time understanding how to perform a repeated measures type of ANOVA with R. When reading the document found here: http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html I find that there is a reference to a function make.rm () that is supposed to rearrange a

[R] lmer or glm with family=binomial : probability variable

Dear all, We are dealing with a variable (BA) which indicates the overlap between small mammal home ranges. It varies between 0 and 1 and it can be interpreted as the probability of two home ranges to overlap, therefore we would have modelled it with the binomial family, also supported by the

Re: [R] problem with unlist POSIX date at midnight

On Wed, 17 Jan 2007, Hanneke Schuurmans wrote: Dear R-users, I use unlist of POSIX dates to extract the year, hour etc. With that I can search for files in my database which are in the form 'mmddhh_synops.txt' However, I get stucked during midnight where unlist just gives NA's. The

Re: [R] lmer or glm with family=binomial : probability variable

We are dealing with a variable (BA) which indicates the overlap between small mammal home ranges. It varies between 0 and 1 and it can be interpreted as the probability of two home ranges to overlap, therefore we would have modelled it with the binomial family, also supported by the

[R] Does R implement DBSCAN , ROCK, BIRCH?

I saw that R language has a cluster package which has in built PAM, CLARA and Kmeans (and many more) Clustering Algorithms. But, I couldnot find DBSCAN, ROCK, BIRCH algorithms (which I feel are standard ones). Aren't these implemented as well? Bhanu Kalyan K B.Tech Final Year, CSE Tel:

Re: [R] curious about dimension of 'apply' output when MARGIN=1

A logical reason for the phenomenon is that matrices are stored down their columns. For example: matrix(1:15,5) [,1] [,2] [,3] [1,]16 11 [2,]27 12 [3,]38 13 [4,]49 14 [5,]5 10 15 When an 'apply' across rows is done, it will be the values

Re: [R] Repeated measures

Tom Backer Johnsen wrote: I am having a hard time understanding how to perform a repeated measures type of ANOVA with R. When reading the document found here: http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html I find that there is a reference to a function make.rm ()

Re: [R] percent sign in plot annotation

Martin Keller-Ressel wrote: Thanks to Bettina, Dimitris and Gavin for their help. All their solutions work nicely. For future reference, here are three ways to draw a percent sign in R plots: plot(0:10, 0:10, type = n) text(5,7,expression(paste(alpha == 5, %, sep = ))) text(5, 5,

Re: [R] curious about dimension of 'apply' output when MARGIN=1

2007/1/17, Patrick Burns [EMAIL PROTECTED]: A logical reason for the phenomenon is that matrices are stored down their columns. For example: matrix(1:15,5) [,1] [,2] [,3] [1,]16 11 [2,]27 12 [3,]38 13 [4,]49 14 [5,]5 10 15 When an

[R] Effect size in GLIM models

Dear All, I wonder if anyone can advise me as to whether there is a consensus as to how the effect size should be calculated from GLIM models in R for any specified significant main effect or interaction. In investigating the causes of variation in infection in wild animals, we have fitted 4-way

Re: [R] Help on variable ranking

Thanks for quick responses. My dataset consists of 213 independent variables (disease related costs) and the depedent variable is the total medical + pharmacy cost of the member. As you had suggested, I tried to use hier.part function in R, but the current implementation does not seem to allow

[R] problem with unlist POSIX date at midnight

Dear R-users, I use unlist of POSIX dates to extract the year, hour etc. With that I can search for files in my database which are in the form 'mmddhh_synops.txt' However, I get stucked during midnight where unlist just gives NA's. The script is given below; the problem accurs at

Re: [R] Help on variable ranking

Rupendra Chulyadyo wrote: Hello all, I want to assign relative score to the predictor variables on the basis of its influence on the dependent variable. But I could not find any standard statistical approach appropriate for this purpose. Please suggest the possible approaches. Thanks in

Re: [R] problem with unlist POSIX date at midnight

[Unstated, but a near repeat of a posting earlier today with the same subject, in response to unacknowledged help.] The problem is not with unlist (as in your subject line) but your input to strptime. strptime() is intended to convert character strings, and as.character(acc.period[16]) [1]

Re: [R] Effect size in GLIM models

On Wed, 17 Jan 2007, Behnke Jerzy wrote: Dear All, I wonder if anyone can advise me as to whether there is a consensus as to how the effect size should be calculated from GLIM models in R for any specified significant main effect or interaction. I think there is consensus that effect sizes

[R] Fwd: model simplification in repeated anova

Hi, I tried to do a model simplification in repeated anovas. obviously it's not possible to use the function anova straight away. I got the suggestion to do it with proj (see below). In my data, however, I have in block not the third order interaction (n:p:k), but to factors and their

Re: [R] Effect size in GLIM models

Dear All Thanks very much for the rapid reply Prof Ripley. I had been looking at this anaysis for my colleague (Prof Behnke) and suggested that he contact the R mailing list because I couldn't answer his question. I think some of the detail got lost in translation (he grew up with the GLIM

[R] Row limit for read.table

I have been trying to read in a large data set using read.table, but I've only been able to grab the first 50,871 rows of the total 122,269 rows. f - read.table(http://www.cs.odu.edu/~fmccown/R/Tchange_rates_crawled.dat;, header=TRUE, nrows=123000, comment.char=, sep=\t)

[R] add non-linear line

I am trying to plot a non-linear trend line along with my data. I am sure the solution is simple; any help greatly appreciated. Recent and historic attempts: fit = nls((sd~a+b*exp(-c/time)+d*geology), start=list(a=1, b=1, c=10, d=-1), model=TRUE) plot(time, sd, col=3, main = Regression,

[R] How to annotate a graph with non-transparent math labels?

I do not know the precise language to describe the situation. But here it is what I want to do. I need to annotate a graph that contains two or more curves with labels that contain math symbols. The label must go on top of the curve. The problem is that when I annotate the plot, I can see the

[R] Correlation to a Single Gene

I am trying to find a way to perform pairwise correlations against one gene in a matrix rather than computing every pairwise correlation. I am interested in how 1 transcription factor correlates to every gene in a matrix of 55 experiments (columns) by 23,000 genes (rows), performing the

[R] sort dataframe by field

Hi there, How can I sort (order?) a data.frame using a dataframe field (evidence) as classifyer? My data.frame looks like: record model evidence 1 areatotha 6638.32581 2 areatotha_ca000 8111.01860 3 areatotha_ca000_Pais 1721.41828 4 areatotha_ca020

[R] Fwd: model simplification in repeated anova

Hi, I tried to do a model simplification in a repeated anova with 3 factors (population,treatment,site). I tried to get rid of some interactions. Obviously it's not possible to use the function anova straight away to compare the different models. I got the suggestion to use the function

Re: [R] sort dataframe by field

say your data.frame is called df df[order(df$evidence),] or df[order(df$evidence, decreasing=T),] # if you want the other way around. b On Jan 17, 2007, at 11:21 AM, Milton Cezar Ribeiro wrote: Hi there, How can I sort (order?) a data.frame using a dataframe field (evidence) as

[R] sp: proj4string has no impact

Hi all, I'm faced with a problem applying the sp package: The projection argument in readShapePoly(Shapefile,proj4string=CRS class argument) e.g.: CRS(+proj=aea +lat_1=46 +lat_2=73 +lat_0=60 +lon_0=84 +x_0=0 +y_0=0 +ellps=clrk66 +units=m +no_defs) doesn't have any impact on the plotted

Re: [R] Row limit for read.table

Frank McCown wrote: I have been trying to read in a large data set using read.table, but I've only been able to grab the first 50,871 rows of the total 122,269 rows. f - read.table(http://www.cs.odu.edu/~fmccown/R/Tchange_rates_crawled.dat;, header=TRUE, nrows=123000, comment.char=,

Re: [R] Row limit for read.table

Frank McCown schrieb: I have been trying to read in a large data set using read.table, but I've only been able to grab the first 50,871 rows of the total 122,269 rows. f - read.table(http://www.cs.odu.edu/~fmccown/R/Tchange_rates_crawled.dat;, header=TRUE, nrows=123000, comment.char=,

Re: [R] Effect size in GLIM models

Folks: I think this and several other recent posts on ranking predictors are nice illustrations of a fundamental conundrum: Empirical models are fit as good *predictors*; meaningful interpretation of separate parameters/components of the predictors may well be difficult or impossible, especially

Re: [R] Row limit for read.table

The problem is somewhere in the file, probably with tab characters, as removing sep= from your call does the job. dfr-read.table(Tchange_rates_crawled.dat,header=TRUE) str(dfr) 'data.frame': 122271 obs. of 5 variables: [skipped] dfr-

Re: [R] Row limit for read.table

In your case, read.table behaves as documented. The ' - character is one of the standard quoting characters. Some (but very few) of the entrys contain single ' chars, so sometimes more than ten thousand lines are just treated as a single entry. Try using quote= to disable quoting, as

Re: [R] add non-linear line

On 1/17/2007 10:42 AM, Matt Sakals wrote: I am trying to plot a non-linear trend line along with my data. I am sure the solution is simple; any help greatly appreciated. Recent and historic attempts: fit = nls((sd~a+b*exp(-c/time)+d*geology), start=list(a=1, b=1, c=10, d=-1),

Re: [R] add non-linear line

On 1/17/2007 12:24 PM, Duncan Murdoch wrote: On 1/17/2007 10:42 AM, Matt Sakals wrote: I am trying to plot a non-linear trend line along with my data. I am sure the solution is simple; any help greatly appreciated. Recent and historic attempts: fit = nls((sd~a+b*exp(-c/time)+d*geology),

Re: [R] Help on variable ranking

I suggest using permutation on each predictor and see how much the accuracy drops, no matter what modeling approach you used. HTH, weiwei On 1/17/07, Rupendra Chulyadyo [EMAIL PROTECTED] wrote: Hello all, I want to assign relative score to the predictor variables on the basis of its

Re: [R] Effect size in GLIM models

Dear All (apologies if some of you have received this twice) Thanks very much for the rapid reply Prof Ripley. I had been looking at this anaysis for my colleague (Prof Behnke) and suggested that he contact the R mailing list because I couldn't answer his question. I think some of the detail

Re: [R] sleep data

Yes, you refer to Cushny, A. R. and Peebles, A. R. The action of optical isomers: II hyoscines. The Journal of Physiology, 1905, 32: 501.510. which was used by 'Student' to illustrate the paired t-test. This is indeed a crossover design. On Wed, 17 Jan 2007, Tom Backer Johnsen

Re: [R] Correlation to a Single Gene

On Wed, 17 Jan 2007, Damion Colin Nero wrote: I am trying to find a way to perform pairwise correlations against one gene in a matrix rather than computing every pairwise correlation. I am interested in how 1 transcription factor correlates to every gene in a matrix of 55 experiments

Re: [R] sp: proj4string has no impact

On Wed, 17 Jan 2007, Albrecht Kauffmann wrote: Hi all, I'm faced with a problem applying the sp package: The projection argument in readShapePoly(Shapefile,proj4string=CRS class argument) e.g.: CRS(+proj=aea +lat_1=46 +lat_2=73 +lat_0=60 +lon_0=84 +x_0=0 +y_0=0 +ellps=clrk66 +units=m

Re: [R] Correlation to a Single Gene

In the package genefilter, from www.bioconductor.org there is a function to do this (genefinder, if I recall correctly) best wishes Robert Charles C. Berry wrote: On Wed, 17 Jan 2007, Damion Colin Nero wrote: I am trying to find a way to perform pairwise correlations against one gene in

[R] tapply, data.frame problem

Hi R-users, I'm quite new to R and trying to learn the basics. I have a following problem concerning the convertion of array object into data frame. I have made following data sets tmp1 - rnorm(100) tmp2 - gl(10,2,length=100) tmp3 - as.data.frame(cbind(tmp1,tmp2)) tmp3.sum -

Re: [R] tapply, data.frame problem

Lauri Nikkinen wrote: Hi R-users, I'm quite new to R and trying to learn the basics. I have a following problem concerning the convertion of array object into data frame. I have made following data sets tmp1 - rnorm(100) tmp2 - gl(10,2,length=100) tmp3 - as.data.frame(cbind(tmp1,tmp2))

Re: [R] eval(parse(text vs. get when accessing a function

(I overlooked the reply). Thanks, Gabor. That is neat and easy! (and I should have been able to see it on my own :-( Best, R. On 1/8/07, Gabor Grothendieck [EMAIL PROTECTED] wrote: The S4 is not essential. You could do it in S3 too: f.a - function(x) x+1 f.b - function(x) x+2 f -

[R] Memory leak with character arrays?

Hi - When I'm trying to read in a text file into a labeled character array, the memory stamp/footprint of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is

Re: [R] How to annotate a graph with non-transparent math labels?

try using strwidth strheight x-c(0,1) plot(x,x,type='l') dimensions-matrix(c(strwidth(expression(theta),cex=5),strheight(expression(theta), cex=5)),nrow=1) symbols(0.5,0.5 ,rectangle=dimensions,bg='white',fg='white',add=TRUE,inches=FALSE) text(0.5,0.5,expression(theta),cex=5) On 1/17/07,

[R] Coefficient of determination when intercept is zero

I am curious as to the lm calculation of R2 (multiple coefficient of determination, I assume) when intercept is zero. I have 18 data points, two independent variables: First, a model with an intercept: mod0=lm(Div~Rain+Evap,data=test) summary(mod0)$r.squared [1] 0.6257541

Re: [R] Fast Removing Duplicates from Every Column

Hi, Working further on this dataframe : my_data Col1 Col2 Col3 ... Col 159 Col 160 Row 1 0 0 LD ... 0 VD Row 2 HD0 0 0 MD Row 3 0 HDHD 0 LD Row 4 LDHDHD 0 0 ......

[R] R.oo Destructors

Has anyone figured out how to create a destructor in R.oo? How I'd like to use it: I have an object which opens a connection thru RODBC (held as a private member) It would be nice if the connection closes automatically (inside the destructor) when an object gets gc()'ed. Thanks in advance.

[R] help with regexpr in gsub

I have a very long vector of character strings of the format GO:0008104.ISS and need to strip off the dot and anything that follows it. There are always 10 characters before the dot. The actual characters and the number of them after the dot is variable. So, I would like to return in the format

Re: [R] help with regexpr in gsub

Try this: gsub([.].*, , GO:0008104.ISS) [1] GO:0008104 On 1/17/07, Kimpel, Mark William [EMAIL PROTECTED] wrote: I have a very long vector of character strings of the format GO:0008104.ISS and need to strip off the dot and anything that follows it. There are always 10 characters before the

Re: [R] help with regexpr in gsub

Kimpel, Mark William [EMAIL PROTECTED] writes: I have a very long vector of character strings of the format GO:0008104.ISS and need to strip off the dot and anything that follows it. There are always 10 characters before the dot. The actual characters and the number of them after the dot is

Re: [R] help with regexpr in gsub

On Wed, 2007-01-17 at 16:46 -0800, Seth Falcon wrote: Kimpel, Mark William [EMAIL PROTECTED] writes: I have a very long vector of character strings of the format GO:0008104.ISS and need to strip off the dot and anything that follows it. There are always 10 characters before the dot. The

Re: [R] Fast Removing Duplicates from Every Column

Here is one way of doing it by 'padding' all the elements to the same length: x - Col1 Col2 Col3 Col159 Col160 + Row1 0 0 LD 0 VD + Row2 HD0 0 0 MD + Row3 0 HDHD 0 LD + Row4 LDHDHD 0 0 + LastRow

Re: [R] R.oo Destructors

Hi, I'm about the head out of the office next 48 hours, but the short answer is to override the finalize() method in your subclass of Object. This will be called when R garbage collects the object. From ?finalize.Object: setConstructorS3(MyClass, function() { extend(Object(), MyClass)

Re: [R] help with regexpr in gsub

Thanks for 6 ways to skin this cat! I am just beginning to learn about the power of regular expressions and appreciate the many examples of how they can be used in this context. This knowledge will come in handy the next time the number of characters is variable both before and after the dot. On

Re: [R] Memory leak with character arrays?

What does the FASTA header look like. You are using 'gene' to access things in the array and if (for example) 'gene' is a character vector of 10, then for every element of vectors that you are using (I count about 4-5 that use this index) then you are going to have at least 550 * 6000 * 5 * 10

Re: [R] Memory leak with character arrays?

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Coefficient of determination when intercept is zero

This is documented on ?summary.lm. It is not that 'intercept is zero' or 'zero intercept', it is that there is no intercept term in the model. On Wed, 17 Jan 2007, endeitz wrote: I am curious as to the lm calculation of R2 (multiple coefficient of determination, I assume) when intercept is

[R] how to get the index of entry with max value in an array?

Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of the maxium value: 3. is there a neat expression to get this index? Thank you! Best, Feng [[alternative HTML version deleted]]

Re: [R] how to get the index of entry with max value in an array?

In R language, one solution is: a-c(3,4,6,2,3) which(a==max(a)) On 1/18/07, Feng Qiu [EMAIL PROTECTED] wrote: Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of the maxium value: 3. is

Re: [R] how to get the index of entry with max value in an array?

Or which.max(a) -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of talepanda Sent: Wednesday, January 17, 2007 11:45 PM To: Feng Qiu Cc: r-help@stat.math.ethz.ch Subject: Re: [R] how to get the index of entry with max value in an array? In R

Re: [R] help with regexpr in gsub

One thing to watch with experiments like this is that the locale will matter. Character operations will be faster in a single-byte locale (as used here) than in a variable-byte locale (and I suspect Seth and Marc used UTF-8), and the relative speeds may alter. Also, the PCRE regexps are

Re: [R] how to get the index of entry with max value in an array?

?which.max ?which.is.min On Wed, 17 Jan 2007, Feng Qiu wrote: Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of the maxium value: 3. is there a neat expression to get this index?

Re: [R] how to get the index of entry with max value in an array?

which.max a - sample(1:10,10) a [1] 3 4 5 7 2 8 9 6 10 1 which.max(a) [1] 9 On 1/17/07, Feng Qiu [EMAIL PROTECTED] wrote: Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of

Re: [R] help with regexpr in gsub

Thanks Brian, that advice may help speed up my regexp operations in the future. The computer science advice offered by those of you who are more expert is appreciated by we biologists who are primarily working more at the level of bioinformatics. Mark Mark W. Kimpel MD (317) 490-5129 Work,

Re: [R] how to get the index of entry with max value in an array?

which.max() b On Jan 17, 2007, at 11:20 PM, Feng Qiu wrote: Hi all: A short question: For example, a=[3,4,6,2,3], obviously the 3rd entry of the array has the maxium value, what I want is index of the maxium value: 3. is there a neat expression to get this index?

Re: [R] Coefficient of determination when intercept is zero

Thanks for the guidance. With the help of your explanation, I was able to find this reference that provides a good explanation of why the definition may be different in the no intercept or regression through origin case. For future readers of this list, the reference is: Joseph G. Eisenhauer

[R] 3D Plot

Hi all R users, I want to draw a 3D plot, where the Z-axis will represent the normal densities each with zero mean but different volatilities, Y-axis will represent the SD [volatilities), and X-axis will represent time at which these SD are calculated. Can anyone give me any clue? Your help will

[R] selecting rows for inclusion in lm

I am having trouble selecting rows of a dataframe that will be included in a regression. I am trying to select those rows for which the variable Meno equals PRE. I have used the code below: difffitPre-lm(data[,diff]~data[,Age]+data[,Race],data=data[data[,Meno]==PRE,]) summary(difffitPre) The

Re: [R] Memory leak with character arrays?

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.