Re: [R] Datapoints underneath datapoints Problem
> I would like to know if there is any > possible way in which I could view those datapoints that are layered on top > of each other You could use jitter() to add a little noise to the data. Of course that will slightly change the position of each point. If that is not an option you could possibly detect points with almost identical coordintes yourself and then change the color of the respective plotting symbol. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] plotting command trouble
On Thu, Apr 19, 2007 at 02:10:37PM +0200, Schmitt, Corinna wrote: >> Hi, the length of the coordinates are different. >> >> Try: >> plot(seq(0,60, l=100), seq(0,0.896, l=100), type="n", xlab="Zeit [min]", >> ylab="Absorptionsmessung >>bei 600nm",main="Zellwandstabilit?t" ) > I know, but it is needed. Any other idea? Read the reply again. Of course, the number of x and y values needs to be the same - how else would you plot the points? The problem is that 0:0.896 does not do what you assumed it does. Henrique actually provided the solution - did you try it? Also, in your plot command you are using type='n' which will cause R not to plot the actual data points. Without knowing the context of your command I can only guess what you are trying to accomplish. Are you plotting points into the empty plot later on? Maybe you are just trying to set the plotting range? In that case better use the xlim and ylim parameters of the plot function. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] categorical column to numeric column
> Let 'dd' be a data frame given as:
>
> dd=data.frame(aa=c("a","a","b","a","b","b"),bb=c(1,1,1,2,3,4))
>
> Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else
> dd$g= -1 .
You need to use ifelse instead of the if ... else construction:
dd$g = ifelse(dd$a=='a', 1, -1)
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
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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 Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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] legend/plotmath/substitute problem
On Thu, Dec 14, 2006 at 06:25:49PM -0500, Duncan Murdoch wrote:
> On 12/14/2006 5:05 PM, Philipp Pagel wrote:
> >My problem starts, when I want to put more than one series of data in
> >the plot and accordingly need one legend row per data series:
> >
> >year1 = 2001
> >year2 = 2005
> >g1 = 1.9
> >g2 = 1.7
> >plot(1)
> >legend('top',
> > legend=c(
> > substitute(paste(year, ': ', gamma, '=', g),
> > list(year=year1, g=g1)),
> > substitute(paste(year, ': ', gamma, '=', g),
> > list(year=year2, g=g2))
> > )
> >)
> >
> >This obviously does not produce the desired result. Apparently, I am not
> >generating a list of expressions, as intended. So I thought, maybe R uses a
> >variety of the recycling rule here and tried:
>
> The problem is that legend wants an expression, but substitute() isn't
> returning one, it's returning a call, and c(call1,call2) produces a list
> of two calls, not an expression holding two calls. So the following
> would work, but there might be something more elegant:
Thanks a lot! Learned something, again.
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
85350 Freising, Germany
http://mips.gsf.de/staff/pagel
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[R] legend/plotmath/substitute problem
Dear R Experts,
I am trying to produce a legend for a series of plots which are
generated in a loop. The legend is supposed to look like this:
2000: gamma=1.8
where gamma is replaced by the greek letter and both the year and the
value of gamma are stored in variables.
Everything works fine as long as I have only one data series:
year = 2001
g = 1.9
plot(1)
legend('top', legend=substitute(paste(year, ': ', gamma, '=', g),
list(year=year, g=g)) )
My problem starts, when I want to put more than one series of data in
the plot and accordingly need one legend row per data series:
year1 = 2001
year2 = 2005
g1 = 1.9
g2 = 1.7
plot(1)
legend('top',
legend=c(
substitute(paste(year, ': ', gamma, '=', g), list(year=year1,
g=g1)),
substitute(paste(year, ': ', gamma, '=', g), list(year=year2,
g=g2))
)
)
This obviously does not produce the desired result. Apparently, I am not
generating a list of expressions, as intended. So I thought, maybe R uses a
variety of the recycling rule here and tried:
year = c(2001, 2005)
g = c(1.9, 1.7)
plot(1)
legend('top',
legend=list(
substitute(paste(year, ': ', gamma, '=', g), list(year=year, g=g)),
)
)
No succes, either...
I have read and re-read the documentation for legend, expression, substitute
and plotmath but can't figure it out. Even drinking a cup of tea prepared from
fine-cut man page printouts didn't lead to satori.
I'm probably missing something simple. Any hints are highly appreciated.
Thanks
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
85350 Freising, Germany
http://mips.gsf.de/staff/pagel
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Re: [R] newbie: new_data_frame <- selected set of rows
Hi!
> distances <- order(distancevector(scaled_DB, scaled_DB['query',],
> d="euclid"))
Just compute the distances WITHOUT ordering, here. And then
> 1) create a small top_five frame
top = scaled_DB[rank(distances)<=5, ]
rank() is better for this than order() in case there are ties.
> 2) after I got top_five I woul like to get the index
> of my query entry, something along Pythons
> top_five.index('query_string')
You mean by row name?
which(row.names(scaled_DB)=='query_string')
But why would you need the index? If you want to get the respective row
use logical indexing:
my_dataframe['query_string', ]
> 3) possibly combine values in distances with row names
> from my_dataframe:
> row_1 distance_from_query1
> row_2 distance_from_query2
The easiest way to store the distances along with the original names and
data would be to simply make distances a column in your data frame,
which is what I would have done to begin with. The entire procedure
would then look like this:
my_dataframe = read.table( ... )
scaled_DB <- scale(my_dataframe, center=FALSE)
scaled_DB$dist1 = distancevector(scaled_DB, scaled_DB['query1',], ...)
scaled_DB$dist2 = distancevector(scaled_DB, scaled_DB['query2',], ...)
scaled_DB$dist3 = distancevector(scaled_DB, scaled_DB['query3',], ...)
...
top1 = scaled_DB[rank(scaled_DB$dist1)<=5, ]
...
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
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Re: [R] comma delimiter & comma in text
> 1, A, 24, The Red House > 2, A, 25, King's Home, by the Sea > ... > Is there a way i can specify to R that "King's Home, by the Sea" is one > word? Yes: It needs to be quoted in the file: 2, A, 25, "King's Home, by the Sea" cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich __ 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] How to increase decimal places
On Sun, Nov 12, 2006 at 07:32:49PM +0100, "Maja Schröter" wrote: > does anybody know how to increase the decimal places that R uses to > calculate something. > > I think that in default R uses 6 decimal places but I need 12. What you are experiencing is R PRINTING only a certain number of digits. All calcualtions are done at full precision, though. Example: > a=1/3 > a [1] 0.333 > print(a) [1] 0.333 > print(a, digits=12) [1] 0. For more details have a look at ?print and also at ?options and search for 'digits'. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] read file problem
On Fri, Nov 03, 2006 at 02:02:35PM +, Luis Ridao Cruz wrote: > DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL > MDBAR IPTS-68 PSS-78 OBS. > *** *** *** *** > 1 1.0 2999 > 2 2.0 5.9793 35.1629.10717 2221 > 3 3.0 5.9797 35.1631.10117 2221 > 4 4.0 5.9809 35.1631.11812 2221 > 5 5.1 5.9811 35.1629.11542 2221 > 6 6.1 5.9810 35.1631.11618 2221 > 7 7.1 5.9797 35.1631.11615 2221 > 8 8.1 5.9798 35.1630.10213 2221 > 9 9.1 5.9792 35.1629.11311 2221 > read.table(file, skip = 10) To me it looks like your data is in a fixed-width format. If that is the case you should use read.fwf() instead of read.table(). cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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] Read.csv
On Thu, Oct 26, 2006 at 09:41:25AM +0900, Wang, Joshua (EQS) wrote: > Are there ways to load a csv file without row.names by read.csv? Thanks. Have a look at ?read.csv. Somewhere in there you will find an explanation for the option row.name. In your case, you probably want to set it to NULL. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] one is not one
On Sat, Oct 21, 2006 at 11:04:13AM +0200, Patrick Giraudoux wrote: > Which means that actually sum(x) is NOT considered equal to 1... > > Any idea about what is going wrong? Others have already pointed out the problem and I would like to add a reference to a classical paper on this topic: David Goldberg What Every Computer Scientist Should Know About Floating-Point Arithmetic Computing Surveys, 1991 Reprints can be found in many places online - e.g. here: http://www.physics.ohio-state.edu/~dws/grouplinks/floating_point_math.pdf cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] Convert Contingency Table to Flat File
On Tue, Oct 17, 2006 at 03:08:49AM -0700, Marco LO wrote: > Is there any R function out there to turn a multi-way contingency > table back to a flat file table of individual rows and attribute > columns.? Are you looking for something like this? # generate some data x = sample(c(0,1), 100, replace=T) y = sample(c(0,1), 100, replace=T) z = sample(c(0,1), 100, replace=T) # contingency table mytab = table(x,y,z) # flat contingency table as.data.frame( mytab ) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] Help on direction of axis in R needed
> I'd like to plot things with axes going from the > highest to the lowest value You can use the xlim and ylim parameters of the plot function. E.g: x = 1:100 plot(x, x^2) # normal plot(x, x^2, xlim=c(100,0)) # reversed x axis cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] Reading data with blank elements
Hi!
On Fri, Jul 21, 2006 at 05:43:03AM -0700, Ahamarshan jn wrote:
> I have a dataset saved in *.csv format, that contains
[...]
> BS00,-0.084,0.0136,-0.1569,-0.6484,1.103,1.7859,0.40287,0.5368,0.08461,-0.1935,-0.147974,0.30685
> BS01,0.491270283,0.875826172,,
> BS02,0.090794476,0.225858954,,,0.32643,0.34317,0.133145295,,,0.115832599,0.47636458,
> BS03,0.019828221,-0.095735935,-0.122767219,-0.0676,0.002533,-0.1510361,0.736247,2.053192,-0.423658,0.4591219,1.1245015,
> BS04,-0.435189342,-0.041595955,-0.781281128,-1.923036,-3.2301671020.152322609,-1.495513519,,
> person.data<-read.table("datafile.csv",header=TRUE,sep=',',row.names=1)
>
> Error in scan (file = file, what = what, sep = sep,
> quote = quote, dec = dec, :
> line 1919 did not have 13 elements
> Execution halted "
R does handle empty elements fine. The error message you quote occurs if
a row does not contain the expected number of elements (empty or not.)
Did you have a look at row 1919? Does it really contain the same number
of separators (commas) as the other ones?
Some programs handle empty elements at the end of a row in a 'lazy' way
and simply ommit them. If this is the case you can use the option
'fill=TRUE' to tell read.table that you want it to silently pad short
rows with empty elements.
Another 'popular' reason for funny errors with read.table is the
unexpected occurence of quotation or comment characters in the data...
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
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Re: [R] Merge two dataframes of different column length and row length by two columns at a time
On Fri, Jul 21, 2006 at 09:33:56AM +0200, Gunther Höning wrote:
> I have two dataframes of the following structures:
[...]
> I want to merge these dataframes by V1 and V2 of a and b. The combination of
> V1, V2 is a unique key.
> Note that b is smaller than a.
>
> Any suggestions to solve this problem ?
Use merge()
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] how can I delete rows?
On Tue, Jul 18, 2006 at 12:25:47PM -0300, raul sanchez wrote:
> I have the Barro-Lee data set which contains 98 countries and I want
> to run the regressions only for the Latin America countries, so what
> do you recomend? How can I delete all the other countries or how can
> I select the countries of Lat. Am. thank you
> this is the list of countries
> SHCODE COUNTRY NAME WBCTRY (1) (2)
> _
>
> 1Algeria DZA + +
> 2Angola AGO - -
> 3BeninBEN - +
> 4Botswana BWA + +
> 5Burkina Faso HVO - -
> 6Burundi BDI + -
> 7Cameroon CMR + +
[...]
Assuming the data is stored in a data frame called bl you could do
something like this:
First you generate a list of all countries you are interested in - e.g.
> set = c('Benin', 'Congo', 'Mali')
And then you subset the data frame with it
> bl[bl$COUNTRY %in% set, ]
SHCODE COUNTRY NAME WBCTRY X.1. X.2.
3 3 Benin BEN -+ NA
12 12 Congo COG -+ NA
26 26Mali MLI -+ NA
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
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Re: [R] Way to convert data frame to matrix
On Fri, Jun 30, 2006 at 10:11:15AM -0400, Wade Wall wrote:
> I have a text file that I have imported into R. It contains 3 columns and
> 316940 rows. The first column is vegetation plot ID, the second species
> names and the third is a cover value (numeric). I imported using the
> read.table function.
>
> My problem is this. I need to reformat the information as a matrix, with
> the first column becoming the row labels and the second the column labels
> and the cover values as the matrix cell data.
I'm not 100% sure but I think you are looking for reshape().
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
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Re: [R] Extracting R plots from MS Word
On Thu, Jun 29, 2006 at 05:15:08PM +1200, [EMAIL PROTECTED] wrote: > I am revising a paper that I am a co-author of. The figures are plots > generated from R but at the moment I do not have the R code that generates > them. > > As this is time critical I would like to slightly abuse the list by asking > whether anyone knows how to extract from MS Word into a stand-alone > graphics file a plot that was pasted into Word from R (probably as a > Windows Metafile, but possibly as a bitmap). Open the doc file in OpenOffice, save in sxw format (openoffice's old native format), unpack the file with unzip and find the figure in the resulting directory. I'm not sure if and how this works with the new odt format used by openoffice now, but sxw will work. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] PowerPoint
On Fri, Jun 23, 2006 at 11:27:00AM -0500, Marc Schwartz (via MN) wrote: > On Fri, 2006-06-23 at 18:16 +0200, Philipp Pagel wrote: > > On Fri, Jun 23, 2006 at 09:21:37AM -0400, Gabor Grothendieck wrote: > > > Note that jpg, bmp and png are in less desirable bit mapped formats > > > whereas > > > eps is in a more desirable vector format (magnification and shrinking does > > > not involve loss of info) and so would be preferable from a quality > > > viewpoint. > > > > In addition to seconding the above statement I'd like to add that in > > cases where you are forced to use a bitmap format png tends to produce > > much better results than jpg where line drawings (e.g. most plots) are > > concerned. JPG format on the other hand is great for anyting which can be > > discirbed as photography-like. jpg images of plots tend to suffer from > > bad artifacts... > That is generally because png files are not compressed, whereas jpg > files are. In fact, png uses a combination of pre-filtering and lossless compression (in contrast to lossy compression algortihms use in jpg). Of course, lossy compression can achieve much smaller file sizes for most images. While even a substantial loss of information can go undetected by the observer in the case of photographic images with no sharp edges, line drawings suffer badly. Line drawings usually contain vast percentages of empty space (i.e. white) and thus can be compressed quite effectively by the pre-filteing/lossless compression used by png. Anyway - I totally agree that eps rules and pixel formats should be avoided at all cost for illustrations, plots, etc. ... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] PowerPoint
On Fri, Jun 23, 2006 at 09:21:37AM -0400, Gabor Grothendieck wrote: > Note that jpg, bmp and png are in less desirable bit mapped formats whereas > eps is in a more desirable vector format (magnification and shrinking does > not involve loss of info) and so would be preferable from a quality > viewpoint. In addition to seconding the above statement I'd like to add that in cases where you are forced to use a bitmap format png tends to produce much better results than jpg where line drawings (e.g. most plots) are concerned. JPG format on the other hand is great for anyting which can be discirbed as photography-like. jpg images of plots tend to suffer from bad artifacts... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] how to put the results of loop into a dataframe
On Tue, Jun 20, 2006 at 09:09:16AM +0800, zhijie zhang wrote: > suppose i want to do the following caulation for 100 times, how to put the > results of x , y and z into the same dataframe/dataset? > x<-runif(1) > y<-x+1 > z<-x+y Several possibilities: 1) Use rbind Before loop: d = NULL And in the loop: d = rbind(d, data.frame(x, y, z)) 2) Build empty data frame of desired size beforehand and fill by row E.g. for 10 rows: d = data.frame( x=rep(0, 10), y=rep(0,10), z=rep(0,10)) And in the loop (index i): d[i, ] = c(x, y, z) 3) Build vectors first, dataframe after the loop x = NULL y = NULL z = NULL in the loop: x = append(x, runif(1)) ... After loop: d = data.frame(x, y, z) Solutions 1&3 are slower but you don't need to know the final number of rows in advance. Solution 2 is cleaner, in my opinion, but requires that you know the final size. Of course, for the particular example calculation you don't need a loop at all: x = runif(100) y = x+1 z = x+y d = data.frame(x,y,z) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] managing data
On Sat, Jun 17, 2006 at 02:40:47PM +0100, yohannes alazar wrote: > Dear mailing list, may some one be kind to help me solve following problem. > > I am trying to write a code that will combine two tables "x" and "y". The > first columns of both tables are unique identification for the rows. The > first column of table "X" is a sub set of the first column of "Y". I need to > find the matching rows in both tables by looking on their unique > identification at the first columns. ?merge cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] relative frequency plot
On Thu, Apr 27, 2006 at 10:48:39AM -0700, [EMAIL PROTECTED] wrote: > Hi All, > > I want to use "hist" to get the relative frequency plot. But the range of > ylab is greater than 1,which I think it should be less than 1 since it > stands for the probability. > > I'm confused. Could you please help me with it? I was pretty confused by that, too at first. The solution is that freq=False cause hist to plot the DENSITY rather than frequency. And density is not necesssarily the same as relative frequency. Excerpt from ?hist: density: values f^(x[i]), as estimated density values. If 'all(diff(breaks) == 1)', they are the relative frequencies 'counts/n' and in general satisfy sum[i; f^(x[i]) (b[i+1]-b[i])] = 1, where b[i] = 'breaks[i]'. If you want relative distance try something like this: myhist = hist(x,breaks=52, plot=F) myhist$counts = myhist$counts / sum(myhist$counts) plot(myhist,main=NULL,border=TRUE,xlab="days",xlim=c(0,6),lty=2) Not exactly clean, though -- we are messing with the myhist object... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] string vector indices
On Sun, Apr 16, 2006 at 12:26:29AM -0400, Luke wrote: > > x <- "a", "aab" > y <- "a", "aa", "aab", "aabc". > > Is there any R function to get the indices of y for the elements of x, that > is, foo(x, y) will give me the index vector c(1, 3)? match(x, y) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] simple if statement
On Fri, Apr 07, 2006 at 09:55:47AM +0200, Philipp Pagel wrote: > On Fri, Apr 07, 2006 at 02:58:00AM -0400, Brian Quinif wrote: > > I tried this > > years <- "Freshmen" if i==1 > > years <- "Sophomores" if i==2 > > What you are looking for is not an if clause but logical indexing: > > years[years=="Freshmen"] <- 1 > years[years=="Sophomores"] <- 2 [...] OK - I'll have to comment myself: I misread your message and it does not make sense for you question. Others have given good answers in the meantime... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] simple if statement
On Fri, Apr 07, 2006 at 02:58:00AM -0400, Brian Quinif wrote:
>
> I have data on college students. I want to make a string variable
> that has the names of the years. That is, when the year variable i is
> equal to 1, I want to have a variable called years equal to
> "Freshmen".
>
> I tried this
> years <- "Freshmen" if i==1
> years <- "Sophomores" if i==2
What you are looking for is not an if clause but logical indexing:
years[years=="Freshmen"] <- 1
years[years=="Sophomores"] <- 2
Of course it's still a character vector so you will have to do
years = as.numeric(years)
Have a look at the manual (Introduciotn to R) for more details.
Another question is what you have in mind. To me it looks like what you
are trying to do is make a factor on your own. Maybe this is what you
want:
factor(years)
or maybe
factor(years, levels=c("Freshmen", "Sophomores"))
if you want more control over the coding.
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] load file RData which store in zip file
On Wed, Mar 29, 2006 at 11:44:03AM +0200, Muhammad Subianto wrote:
> How can I open/load "filename.zip"? Is there any function to open R
> workspace which it store in zip file?
I think you have two options:
1) use zip.file.extract() to unzip the file before loading
2) save your data with save.image(file="foo.RData", compress = True)
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Remove [1] ... from output
On Tue, Mar 28, 2006 at 01:21:59PM +0200, Gregor Gorjanc wrote:
>
> R> runif(20)
> [1] 0.653574 0.164053 0.036031 0.127208 0.134274 0.103252 0.506480 0.547759
> [9] 0.912421 0.584382 0.987208 0.996846 0.666760 0.053637 0.327590 0.370737
> [17] 0.505706 0.412316 0.887421 0.812151
>
> Any hints how to solve my task?
The indexes are generated by the print method for the vector. Use cat
instead:
> cat(runif(20))
0.01053970 0.7196873 0.08709377 0.2059949 0.9583586 0.7059125 0.8179168
0.2345666 0.4157858 0.0538792 0.4140722 0.5700817 0.7087922 0.4012365
0.6587029 0.2803821 0.7353465 0.4457628 0.09914006 0.8109087
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
__
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Re: [R] click on graph and select data points?
> Now I want to select the best clustered class, how can I click on the data > point, and the program returns the index of that cluster(its class number, > or color number)? Have a look at identify() cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] name of the graphics output
On Tue, Mar 14, 2006 at 01:03:22PM +0100, Philipp Pagel wrote:
> On Tue, Mar 14, 2006 at 12:55:47PM +0100, Arnau Mir Torres wrote:
>
> > All the outputs names are file.name.pdf but I want to put a different
> > name for each graphic.
>
> you can use paste() to put together the command:
>
> file ="foo"
> system( paste("mv Rplots.pdf ", file, ".name.pdf", sep='') )
Oops - of course it makes a lot more sense to put together the filename
when opening the pdf device:
pdf(file=paste(file, ".name.pdf", sep='') )
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] name of the graphics output
On Tue, Mar 14, 2006 at 12:55:47PM +0100, Arnau Mir Torres wrote:
> All the outputs names are file.name.pdf but I want to put a different
> name for each graphic.
you can use paste() to put together the command:
file ="foo"
system( paste("mv Rplots.pdf ", file, ".name.pdf", sep='') )
cu
Philipp
--
Dr. Philipp PagelTel. +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
GSF - National Research Center Fax. +49-89-3187 3585
for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] data import problem
On Wed, Mar 08, 2006 at 12:49:29PM +0100, [EMAIL PROTECTED] wrote: > Well, the data is generated by a perl script, and I could just > configure the perl script so that there is one file per data table, > but I though I'd probably must more efficent to have all records in a > single file rather than reading a thousands of small files ... . I guess I would make it a singe file and put the IDs in their own column: ID x y 123 89.17911.1024 123 90.57351.1024 123 92.56661.1024 123 95.07251.1024 123 101.20701.1024 321 60.16011.1024 321 64.80231.1024 321 70.05932.1502 ... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] data import problem
On Wed, Mar 08, 2006 at 12:32:28PM +0100, [EMAIL PROTECTED] wrote: > I'm trying to read a text data file that contains several records > separated by a blank line. Each record starts with a row that contains > it's ID and the number of rows for the records (two columns), then the > data table itself, e.g. > > 123 5 > 89.17911.1024 > 90.57351.1024 > 92.56661.1024 > 95.07251.1024 > 101.20701.1024 > > 321 3 > 60.16011.1024 > 64.80231.1024 > 70.05932.1502 That sound like a job for awk. I think it will be much easier to transform the data into a flat table using awk, python or perl an then just read the table with R. cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] Semi-log plot in R
On Sun, Mar 05, 2006 at 12:00:19AM +, christophe tournayre wrote: > Is it possible to create a semilog plot in R? If you mean a plot with one log-scale axis this is what you want: x = 1:100 y = x^2 plot(x,y, log="y") See ?plot for details cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] How to Import Data
On Tue, Feb 21, 2006 at 08:52:04AM -0500, Carl Klarner wrote: > x111 <-read.table(file='x111.csv', > sep="",header=T, > quote="",comment.char="",as.is=T) to make things easier for you you could do x111 <-read.table( file.choose(), ... ) Also: Why are you setting sep="" ? Your filename suggests that you have some kind of separator in your file... cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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
Re: [R] random samples
On Thu, Jan 13, 2005 at 01:50:38PM +0100, [EMAIL PROTECTED] wrote:
> I need to divide the array
>
> > A<-c(1:200)
>
> into two subsets at random. Therefore I use the function "sample" in R:
I suggest a slightly different approach which is probably faster than
using setdif() or %in% and friends:
a <- 1:200
i <- sample(1:200, 100)
s1 <- a[i]
s2 <- a[-i]
cu
Philipp
--
Dr. Philipp PagelTel. +49-89-3187-3675
Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel
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Re: [R] multiple plots problem
> for testing & learning purposes I create X11 device and specify layout like > layout(c(1,2,3), 3, 1), so I could play with parameters and see > several plots at the same time. That works fine until I try to create 4-th > plot - all other plots erased. That's expected behaviour: you asked for three plots to be present on your canvas. > Such behaviour isn't desirable for testing purposes and I'm asking > where to look to disable erasing other plots. Two possible solutions - depending on what exactly you'd like to get: Increase the size of the layout matrix to squeeze more plots on the canvas or open a new device whenever you want a new window. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can R be useful to me?
On Wed, Mar 31, 2004 at 08:32:49AM -0300, Luiz Rodrigo Tozzi wrote: > > My question is: can I generate graphics and tables in gif ou any graphical > format through shell script?? can I call R, run a package in my ascii data e > then export the results to a gif, png or whatever? Yes - R is well suited for such a task. Actually there even is a package called sweave which allows you to use LaTeX to format your results and create a perfectly fine report on the fly. If you need to generate such reports on a regular basis R is definitely a good way to appraoch the task. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems with postscript output
Hi!
> I have a little problem with saving plots to file. I use the command
> postscript() followed by the plotting command and a dev.off().
>
> When I then look at the resulting image saved to disk, some of the
> axis labels are missing (see attached image). Is there a way to fix
> this.
R is trying to be smart about labels getting too close/overlap. Specify the
graph to be a little wider and the labels will appear.
cu
Philipp
--
Dr. Philipp PagelTel. +49-89-3187-3675
Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585
GSF - National Research Center for Environment and Health
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Re: [R] Frequency table
On Wed, Mar 17, 2004 at 04:55:19PM +0200, Kai Hendry wrote: > I am trying to construct a frequency table. I guess this should be done with > table. Or perhaps factor and split. Or prop.table. cut? findInterval? Argh! > I got this far: > > table(cut(zz$x9, brk)) > > (40,50] (50,60] (60,70] (70,80] (80,90] (90,100] >2 19 21 1981 > > brk > [1] 40 50 60 70 80 90 100 > > > > t(table(cut(zz$x9, brk))) > (40,50] (50,60] (60,70] (70,80] (80,90] (90,100] > [1,] 2 19 21 19 8 1 > > Still feels a million miles off. Why? To me it looks like you figured it all out. You found out how to use cut() to get the appropriate factor and you used table() to compute the counts. Nothing wrong with that... The only difference to what you wanted to get is that your example looked more like a data frame. Try as.data.frame(yourtable) which will give you something like this: > as.data.frame(tbl) b Freq 1 (0,20] 17 2 (20,40] 28 3 (40,60] 19 4 (60,80] 15 5 (80,100] 21 Is that what you wanted? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] saving a data.frame to "\t" files
> could somebody please help with saving a data.frame with > column names into "\t" text files for later importing in other > programs? It seems an easy task, yet... it beats me. write.table(mydf, file="foo.tbl", sep="\t", col.names=T) Where mydf is your data frame. If you don't want quoting you can also add 'quote=FALSE' cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] recoding variables
Hi!
> using R, and I'm trying to figure out how to recode a continuous
> variable to make it into an ordinal variable with 3 categories.
You are looking for cut():
> a <- runif(15)
> a
[1] 0.19109987 0.78808597 0.78458256 0.31355035 0.02076274 0.82287287 0.75260382
0.82627690 0.14775167
[10] 0.59427620 0.12314764 0.44151537 0.05123785 0.88879744 0.25552054
> b = cut(a, breaks=c(0, 0.33, 0.66, 1), labels=c('low', 'medium', 'high'))
> b
[1] lowhigh high lowlowhigh high high low medium lowmedium
lowhigh low
Levels: low medium high
cu
Philipp
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Re: [R] Change the result data
Using stack() would be a possibility: > a <- stack(as.data.frame(hec.data)) > a$eye=rownames(hec.data) > a values ind eye 1 5 Black Green 2 15 Black Hazel 3 20 Black Blue 4 68 Black Brown 5 29 Brown Green 6 54 Brown Hazel 7 84 Brown Blue 8 119 Brown Brown 9 14 Red Green 10 14 Red Hazel 11 17 Red Blue 12 26 Red Brown 13 16 Blond Green 14 10 Blond Hazel 15 94 Blond Blue 16 7 Blond Brown Also have a look at reshape(). cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/~pagel __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interesting feature
Hi!
On Wed, Feb 18, 2004 at 10:45:23AM -0600, Svetlana Eden wrote:
> > d <- rbind(d, add)
> > d
> x y
> 1 1 99
> 2 10 55
> 11 14 99
> # it would be more natural to index the rows: 1,2,3 instead of
> #1,2,11 ?!
What you see in the first column are row-names not indexes. Since both
data frames had a row named '1' there was a conflict which R is trying
to resolve by appending '1'.
> # especially if index '11' is not functioning...
...
> # now I would think that the next index should be 21, BUT:
...
> # so what is the intuition of such indexing?
I think it all becomes clear if you try this:
> a <- data.frame(foo=1:5, bar=10:6, row.names=LETTERS[1:5])
> a
foo bar
A 1 10
B 2 9
C 3 8
D 4 7
E 5 6
> b <- data.frame(foo=c(9,10), bar=c(99,98), row.names=c('A','B'))
> b
foo bar
A 9 99
B 10 98
> rbind(a,b)
foo bar
A1 10
B2 9
C3 8
D4 7
E5 6
A1 9 99
B1 10 98
cu
Philipp
--
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Re: [R] Read In and Output Postscript file
On Wed, Jan 28, 2004 at 05:31:11PM -0600, Marc Schwartz wrote: > On Wed, 2004-01-28 at 14:19, Brad Holmes wrote: > > > > Would it be possible to read in a pre-existing postscript file, and > > output it "as is" through R? > > > > I have five plots, and I am placing them in a layout that is 2 X 3. I > > was hoping to "insert" the pre-existing postscript file made from > > Molscript in the last spot. > > Your e-mail header suggests that you are on a Mac. If you have access to > MS Word or an alternate document processing program like OpenOffice or a > functional equivalent, you can import EPS files into a table, with each > graphic going into a cell in the table. You can then "print" the > document to a PS file, using a PS printer driver. > > Others may have alternate ideas. Yes: I'd recommend Illustrator rather than Word/OOo for this. But actually, the original question got me curious. How difficult would it be to add EPS import to the postscript device? Other devices could just ignore it or simply read the bounding box and insert the usual empty box which says "EPS file". I guess I'll go for a litte walk in the source code when I have a little spare time to burn. ;-) I mean - this could be really usefull: Finally R would be capable of producing the wealth of chartjunk other software has offered for decades! Imagine using your corporate logo instead of boring circles or dots for plotting! (OK ok - ouch - don't beat me, please...) ;-) cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Legend text -- discrepancy between X11 and postscript
Hi!
On Wed, Jan 14, 2004 at 11:08:44PM -0800, Itay Furman wrote:
> When I place a legend on a plot it looks exactly as I intended
> on the screen. However, almost always, when I export this to
> postscript file, the legend's text protrudes through the legend's
> frame (the latter being placed correctly).
This routinely happens to me when using dev.copy2eps. If I use a
postscript device to begin with everything is fine.
cu
Philipp
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Re: [R] Easiest way to get the mean of a row of a data.frame?
On Wed, Dec 17, 2003 at 08:27:41AM +0100, Sven C. Koehler wrote: > I am kind of new to R. > I would like to calculate the mean of the numbers of this expression: > > data(USArrests) > USArrests[row.names(M) == "Alabama",] > > class() tells me it's a ``data.frame,'' what I actually desire is to get > all numbers of a row as a vector or a list to let mean() calculate the mean > of the whole row. (I know this doesn't make sense with USArrests, I just > used it here instead of my very own data.frame.) rowMeans(USArrest) does what you want. In case you want to do soemthing else but compute the mean you will find this handy: apply(USArrests, 1, mean) here you can substitute "mean" by whatever function you'd like to apply to each row. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] incorporating R into C
On Thu, Nov 20, 2003 at 02:38:35PM -0800, Amir Soofi wrote: > I've become somewhat decent with R over the last month, and I feel > confident that nothing online can help me with this question, http://cran.r-project.org/doc/manuals/R-exts.pdf is this online enough? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] reading data rows
On Thu, Nov 20, 2003 at 10:21:49AM -0800, forkusam wrote:
> I have problems reading a file with more than one row
> to carry out mathematical calculations
>
> I have a a file of the form
> mu1 mu2 alpha betaWsigma sigmaA b r
> 2515 .05 .05 22 3.3.5
> 3020 .1 .2 22 .3.3.5
>
> I intend to read one row , carry out the calculations
> and then the next row with which I intend to do the
> same calculations.
Although you can read the file line by line I guess you actually want to
read the whole table and then perform your calculations on the resulting
data frame.
> I do the following.
> p<-read.table(file="eingabe.csv", header=TRUE,sep=";")
Your file is not separated by ';'! From what you show above I guess it's
tab-separated - or maybe by variying numbers of spaces. Assuming tabs
this will read the entire file:
p <- read.table('eingabe.csv', header=T, sep='\t')
> data.frame(as.numeric(mu1<-p$mu1),as.numeric(mu2<-p$mu2),
> as.numeric(alpha<-p$alpha),as.numeric(beta<-p$beta),
> as.numeric(Wsigma<-p$Wsigma),as.numeric(sigmaA<-p$sigmaA),as.numeric(b<-p$b),as.numeric(r<-p$r))
I'm totally confused about this. First, p is already a data frame.
Second, the columns are already of type numeric or int after correctly
reading the file - so as.numeric is not needed here. You should
probably read 'An Introduction to R', especially the section on lists
and data frames and the one about reading data from files.
> I intend to use the variables stored in the the data
> frame for my caculations. but each time I try I get
> the followingerror message.
>
> Error in uniroot(function(n) eval(p.body) - power,
> c(2, 1e+07)) :
> invalid function value in 'zeroin'
> In addition: Warning message:
> the condition has length > 1 and only the first
> element will be used in: if (f(lower, ...) * f(upper,
> ...) >= 0) stop("f() values at end points not of
> opposite sign")
>
> ...which I do not get when I use just one row.
Since you didn't say what calculation you were attempting I can't even
guess, what is going on. Maybe you can tell us what the goal of all this
is and what commands you were using ...
cu
Philipp
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Re: [R] Find value in vector (or matrix)
On Thu, Nov 20, 2003 at 01:26:23PM +0100, Pascal A. Niklaus wrote:
> Is there a function to check if a particular value is contained in a
> vector?
> myvec <- c('foo','bar','duh','bonk')
> 'bonk' %in% myvec
[1] TRUE
> 'asdf' %in% myvec
[1] FALSE
> Also, is there a way to generate character sequences similar to numeric
> sequences, e.g. something like "A":"J" ?
> LETTERS[1:5]
[1] "A" "B" "C" "D" "E"
> letters[c(8,9,12,23)]
[1] "h" "i" "l" "w"
cu
Philipp
--
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Re: [R] read.table(..)..Help?
On Wed, Nov 19, 2003 at 11:11:27PM -0800, forkusam wrote: > p<-read.table(file="FILENAME ", header=TRUE,sep=";") > and later used the data.Frame() function. > It functions when the file has only a row of > variables. It is not at all clear to me what you are doing and what is going wrong. Please provide a (short) example of what exactly you do, what error messages and warnings you get and what your input file looks like. BTW: read.table returns a data frame so I'm not sure what you mean by using data.frame() later on. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Running R-program as queue jobs
Hi!
On Thu, Nov 13, 2003 at 09:59:48AM +, Arne Gjuvsland wrote:
> I have a problem with running my R programs as queue jobs. When I try
> to submit a batch file to the queue with qsub I get the following error
> message:
>
>
> /home/gjuvslan/kluster/R-1.7.1/bin/R.bin: error while loading shared
> libraries:
> libpcre.so.0: cannot load shared object file: No such file or directory
>
>
> When executed from the command prompt the batch file does its job.
Did you run the script on the same machine in both cases? I got burnt a
couple of times with different machines running different versions of
the OS, non-identical versions of shared libraries etc...
cu
Philipp
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Re: [R] postscript: font size in text(x,y,label)?
Hi! > I would like to just create my (point) labels [created by > text(x,y,labels)] in smaller font size, especially when I write out to > eps. all other point sizes should not change. is this possible? help I don't know how to define the point size exactly (since ps=something does not work in text()) but using the cex option is a workaround: plot(1:100, (1:100)^2) text(10,1000, "foo") text(10,2000, "foo", cex=2) cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] repeat until function
> I what to generate N random numbers(integer) that are different from each
> other.
> One suggestion:
>
> tabel <- rep(NULL, N)
> for (i in 1:N){
> temp <- as.integer(runif(1,1,max))
> if(temp in tabel) {
> repeat (?) (temp <- as.integer(runif(i,i,max)))
> until (?) ((temp in tabel) ==FALSE)
> }
> else{ tabel[i] <- temp}
>
> I can't use repeat/until - don't exist
repeat ... until loops can be rewritten as while loops.
The easiest way is this:
# n unique random numbers between min and max
sample(min:max, n)
But maybe you don't want to generate the array min:max for some reason
(because it is really large?). Then you can do the whole thing yourself:
# another way to the same result
left <- n
tab <- NULL
while (left > 0) {
new <- as.integer(runif(left, min, max))
tab <- unique(c(tab, new))
left <- n - length(tab)
}
If max-min is really large and n is not much smaller than max-min you
may want to generate more numbers than you actually need so unique()
leaves you with more results and you don't have to iterate so often...
cu
Philipp
--
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Re: [R] (no subject)
Hi! > I got information on the shares of some subgroups over time (summing > up to 1 in each year). The graph I want to create should display the > development of the individual shares over time by shading rectangulars > for each share in a different color. Maybe I'm missing the point but this sounds like a pretty simple barplot to me. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Barplots
On Fri, Nov 07, 2003 at 03:16:13PM -0500, Suzanne E. Blatt wrote: > Thanks for the suggestion below. I did one of my figures and it > worked perfectly. I tried it on my second figure and got > double-labelling on the first bar. I used the same code to create > both figures, and the same code to label. Well, maybe you should use the x values returned by barplot (your variable blocks) instead of computing x-positions yourself as I originally suggested. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Barplots
Hi!
On Fri, Nov 07, 2003 at 10:46:27AM -0500, Suzanne E. Blatt wrote:
> Can anyone tell me how to label individual bars on a barplot? I want
> to put an "*" or letter ABOVE the bar to denote statistical
> significance. Is this possible and how?
You can use text() to put arbitrary strings in your plot. So you only
need to add some offset to your y-values and work out the x-positions:
y <- c(10,12,15,8)
lab <- c('*','**','***','*')
barplot(y, ylim=c(0,20), space=0.5)
x <- (0:3*0.5)+1:4
text(x, y+1, lab, adj=0.5)
cu
Philipp
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Re: [R] Absolut newbie questions
Hi! > We have just measured dx and dt (d standing here for \Delta) on an inclined > plain and received some data thet are in two lists (x_list and t_list). The > theory says, that dx = a/2*(dt)^2 for a constant a. > > I should like to fit the data against the theoretical prediction. This > should deliver an estimate for a. You will find everyhing you want to know in the chapter on statistical models in the manual "Introduction to R". Also look at the online documentation for lm() and maybe nls(). > Then I should like to graph the data (as bullets) and the predicted > function into the same graph. Have a look at the documentation for plot(), line() and predict(). cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] weighted rank correlation test?
Hi R-gurus! Is there a package that implements corr.test with weights, or will I have to deal with this myself? I found corr() from the boot package which will calculate r for me and I could certainly do the ranking myself but it does not give me a p-value... Thanks for any hints. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Writing and running a R program
On Thu, Oct 23, 2003 at 09:29:46AM -0400, Subramanian Karthikeyan wrote: > Is there a way I can combine multiple lines of R commands (see below) into > a little code snippet or a program in a text file, and run it in R to do my > analysis? It's quite easy: Write your R code with your favorite text editor and run it in R using source(). cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] r-ish ? how can i improve my code?
On Wed, Oct 15, 2003 at 10:06:36AM +0100, Sean O'Riordain wrote:
> n <- 900; # number of valid items required...
>
> x <- numeric(n);
> y <- numeric(n);
> z <- numeric(n);
>
> c <- 1; # current 'array' pointer
> tc <- 0; # total items actually looked at...
>
> while (c <= n) {
> x[c] = runif(1, 0, 1);
> y[c] = runif(1, 0, 1);
>
> z[c] = sqrt(x[c]^2 + y[c]^2);
> if (z[c] < 1)
> c <- c + 1;
> tc <- tc + 1;
> }
>
> print("'overwork' ratio");
> print(tc/(c-1));
> plot(x,y);
If I read this correctly you want to find the frequency of the event
"sqrt(x^2 + y^2) < 1" where 0 <= x, y <= 1
right?
How about this:
n <- 1000
z <- sqrt(runif(n,0,1)^2 + runif(n,0,1)^2)
ratio <- (length(z)-1) / (length( z[z<1] ))
The main difference of course is that I uses a fixed number of "total
items" rather than "valid items". If that's a problem and you need
exactly 900 "valid items" things get a bit more complicated...
cu
Philipp
--
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Re: [R] Getting rows from a dataframe
> Sorry if this is a silly question. I'm trying to extract all elements > of a dataframe at a particular row. How about df[12, ] to get row number 12? > I can find no mention of this in any documentation You must have different documentation than me Subsetting is described on the first couple of pages of pretty much every introducory manual. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] startup file and lambda
On Thu, Oct 09, 2003 at 07:39:58AM -0700, christoff pale wrote: > Hi,s there a .Rrc file? so that when R starts up > it automatically loads this file? ?Startup will tell you everything you want to know - especially bout the .Rprofile file. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] data.frame with duplicated id's
Hi! > is there a exstisting function (..i found nothing until now.) > what makes it possible transfrom a dataset: > > ID AGE V.MAI V.JUNE > 11 20 100 120 > 12 30 200 90 > > into > > IDAGEV > 1120 100 > 1120 120 > 1230200 > 123090 I think reshape() will do what you want. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] extracting the levels of a subset of data
Hi! > > tmpdata<-subset(myd, TYPE=="A") > > levels(tmpdata$TYPE) > > [1] "A" "B" "C" > > I'd like to get only "A" as output... rebuild the factor after subsetting: tmpdata$TYPE <- factor(tmp$TYPE) If you want the levels of all factors in your data frame to be adjusted you could also use: tmpdata <- data.frame(as.matrix( subset(myd, TYPE=='A') )) cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to convert a Rd file into multi html files?
Hi! On Tue, Sep 09, 2003 at 04:17:25AM -0700, Yiming Zhou wrote: > The command I used was ' R > CMD Rdconv -t html foo.Rd'. It just converted the document of first > object in .Rd into html format. I'm not exactly an expert in writing R documentation but while playing arround with package building I initially had the same problem. By looking at other peoples *.Rd files I discovered that you need to separate individual sections of documentation by \eof. "Writing R Extensions" doesn't seem to mention this, though. hope it helps Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] big data file geting truncated
Hi!
> I used the following commands
> mydata<-read.table("dataALLAMLtrain.txt", header=TRUE, sep
> ="\t",row.names=NULL)
> It reads data without any error
> Now if I use
> edit(mydata)
> It shows only 3916 entries, whereas the actual file contains 7129 entries)
[...]
> So it seems R is truncating the data. How can I load the complete file?
Others have already recommended checking the length of the data.frame
using dim() and the file using wc. If it turns out that there really is
a difference in size the next thing would be to get an idea what lines
are affected: Are "random" lines missing or is everything ok up to line
3916 and then it stops? In either case - have a close look at the lines
missing or the last line present plus the first one missing: Is there
anything special about them?
But actually I have a feeling that this may be your problem:
read.table uses both '"' and "'" for quoting by default. Gene
descriptions love to contain things like "5'" and "3'".
=> Try quote='' in the read.table call.
cu
Philipp
--
Dr. Philipp PagelTel. +49-89-3187-3675
Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg, Germany
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Re: [R] hi
Hi!
> I have no clue what i am doing/ meant to do with R. i have just begun
> statistics for uni and all commands don't seem to work, they say
> syntax error, we are meant to put a hist.r in but ?
I guess you should have a look at the manuals. You can find them at the
R-Project web site:
http://www.r-project.org
In addition to the official manuals I found the "Simple R" manual very
helpful. It's under contributed documentation.
cu
Philipp
--
Dr. Philipp PagelTel. +49-89-3187-3675
Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg, Germany
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[R] bug plotting dates?
Hello R-experts! I am using R Version 1.7.1 (2003-06-16) on a Debian Linux box and I have discovered an odd result when plotting data involving dates. Please try this minimal example: a = seq(ISOdate(2000,1,1), ISOdate(2001,1,1), "months") b = 1:13 plot(a,b, col="red") What I get is a plot that looks as expected except the x-axis is mostly red. Can anyone reproduce this behaviour? I have tried the same thing on R 1.6.0 on a machine in the institute and everything looked fine there (i.e. axis is black). Also, if I set the ylim in the plot command: plot(a,b, col="red", ylim=c(0,20)) R gives me a warning 'parameter "ylim" couldn't be set in high-level plot() function' but sets the limit as requested, anyway. Any ideas what I'm doing wrong? Is this a bug? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] convert factor to numeric
Hi R-experts! Every once in a while I need to convert a factor to a vector of numeric values. as.numeric(myfactor) of course returns a nice numeric vector of the indexes of the levels which is usually not what I had in mind: > v <- c(25, 3.78, 16.5, 37, 109) > f <- factor(v) > f [1] 25 3.78 16.5 37 109 Levels: 3.78 16.5 25 37 109 > as.numeric(f) [1] 3 1 2 4 5 > What I really want is a function "unfactor" that returns v: > unfactor(f) [1] 25.00 3.78 16.50 37.00 109.00 Of course I could use something like > as.numeric(levels(f)[as.integer(f)]) But I just can't believe there is no R function to do this in a more readable way. Actually, the behaviour of as.numeric() doesn't strike me as very intuitive. I'm sure it has been implemented that way for a reason - but what is it? cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
