[R] data formatting: from rows to columns
At 09:11 29/08/07 Jim Holtman wrote Here is a way using sprintf: x - read.table(textConnection( V2 V3 27 2032567 19 28 2035482 19 126 2472826 19 132 2473320 19 136 2035480 135 145 2062458 135 148 2074927 135 151 2102395 142 156 2027252 142 158 2473082 142)) # output the data cat(sprintf(%d\n%d\n\n, x$V2, x$V3), sep='', file='tempxx.txt') How about write.table(x,clipboard,sep=\n,eol=\n\n,col.names = FALSE, row.names = FALSE) 2032567 19 2035482 19 2472826 19 2473320 19 2035480 135 2062458 135 2074927 135 2102395 142 2027252 142 2473082 142 Regards Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: [EMAIL PROTECTED] Ph 02 67729794 __ 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] background color in strip.custom()
One way is to use the argument par.settings get the right name names(trellis.par.get()) or str(trellis.par.get()) to find the list names to change then xyplot(y ~ x | f, par.settings = list(strip.background = list(col = c(your colours)) ) Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England ARMIDALE NSW 2351 Email: [EMAIL PROTECTED] home: [EMAIL PROTECTED] Phone: 02 6772 9794 At 20:01 04/12/06, you wrote: Hi all, how can I change the background color in lattice strips according to a factor level, eg: library(lattice) x - rnorm(100) y - sqrt(x) f - gl(2, 50, c(A, B)) xyplot(y ~ x | f) I like to change the background color of the strips according to the levels in f and tried several things like this with no success: xyplot(y ~ x | f, strip=strip.custom(bg=c(red, green))) Is this possible? Thanks, Sven __ 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. __ 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] R2.4 xyplot + panel.number problem
Hi
Try ?panel.number
As you have not specified R version I cannot be more specific but for 2.4
there have been changes to lattice
including panel.number to panel.number()
At 14:10 29/11/06, you wrote:
Hi all;
I'm trying to display a 2 panel plot for the Puromycin data from R
with 2 different non-linear models fitted to each group. The problem
is that as far as I know panel.number doesn't work in the latest
version of R. Can anyone give a hint how to solve this?
Here is the code that I used before and now doesn't work
xyplot(rate ~conc| state,Puromycin,
panel=function(x,y,panel.number,...){
panel.xyplot(x,y,...)
x.temp-seq(0, 1.2, len = 101)
if (panel.number==1) {
y.temp-(coef(m2.nls)[1]+coef(m2.nls)[2]) * x.temp/
(coef(m2.nls)[3] + x.temp)
panel.lines(x.temp,y.temp,col=2)}
if (panel.number==2) {
y.temp-coef(m2.nls)[1] * x.temp/
(coef(m2.nls)[3] + x.temp)
panel.lines(x.temp,y.temp,col=2)}
},
ylab=Rate of reaction,
xlab=Substrate concentration,
main = Puromycin---comparison bt. treated and untreated
)
thanks for any idea
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Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email: [EMAIL PROTECTED]
home: [EMAIL PROTECTED]
Phone: 02 6772 9794
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Re: [R] RGui: windows-record and command history
Hi all, On the subject of histories, how about changing the default value of max.show from 25 to Inf? I find that the line of code I'm looking for is ALWAYS on the 26th line back from the end of the default history!! Also, re changing the amount of history saved, Prof Ripley replied to an earlier query of mine on this list (04 Mar 2005) with info about the R_HISTSIZE environment variable that can be changed to save more or less history. And it wouldn't it be great if the history mechanism had the option of storing the session date??!! Cheers, Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html [[alternative HTML version deleted]] __ 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
[R] Justification of dendrogram labels
Hi all, Can someone tell me how to justify (right or left) the labels on the branches of a dendrogram tree? I have produced a dendrogram via agnes and plotted it with pltree. The dendrogram terminal branch labels seem to be centre-justified by default and I was hoping to change this to left justification. Thanks, Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html [[alternative HTML version deleted]] __ 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
[R] [Rd] bug in windows GUI/script editor (PR#8288)
Here's how I can reproduce this bug, running under MDI under WinXP 1) start Rgui 2) open a script window using FileNew script 3) click back in the console window and open a help window (e.g. by typing ?merge) in the console window 4) click in the close box of the help window 5) click in the close box of the script window (which was visible even though the script window was largely behind the console window) 6) click on the File menu ..CRASH!!! R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. Cheers, Duncan version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor2.0 year 2005 month10 day 06 svn rev 35749 language R * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ 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
[R] [Rd] bug in windows GUI/script editor (PR#8288)
P.S. I should have added that this crash occurred when the MDI toolbar was OFF. Here's how I can reproduce this bug, running under MDI under WinXP 1) start Rgui 2) open a script window using FileNew script 3) click back in the console window and open a help window (e.g. by typing ?merge) in the console window 4) click in the close box of the help window 5) click in the close box of the script window (which was visible even though the script window was largely behind the console window) 6) click on the File menu ..CRASH!!! R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. Cheers, Duncan version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor2.0 year 2005 month10 day 06 svn rev 35749 language R * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ 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] Stacked Area chart
At 16:03 16/08/05, Mike Saunders wrote:
I wish to do a stacked area chart to show how relative proportions of
species within a stand have changed over time.
I know this is simple, but can someone point me to the right function (if
it exists). I have not had any luck finding it in the R-help, but maybe I
am searching using the wrong keywords.
Thanks,
Mike
Mike Saunders
Research Assistant
Forest Ecosystem Research Program
Department of Forest Ecosystem Sciences
University of Maine
Orono, ME 04469
207-581-2763 (O)
207-581-4257 (F)
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I recently did some graphs using xyplot in lattice where I had the data
ordered by days,
the groups argument and possibly by condition.
I have slightly reduced the code for general use and re run it
The process is to create a matrix of cumulative data (xy) and to make a
filled polygon for each of the
groups using the previous group value as the lower limit of the polygon.
For the first group there has to be a dummy lower limit in these cases of zero
ie rep(0,5) in the single panel graph in the rbind sequence
Plotting of a group line is referred to as j+1 row due to the fact that
there is a dummy
line for the lower polygon of the first group
The first script is for a single graph where there were the groups (codeno)
were 4 species.
The days were 1,2,4,6,9 and the y values (comp ) were percentages.
All groupings and conditions are numeric for both datasets
Any NAs were converted to 0s so as not to give error messages etc.
The second script is for a conditioned graph of similar data
but is generalised.
The maximum y limit can cause problems in setting.
In these cases I had a good idea of what they would be.
For count data it would be necessary to first do a calculation to find it.
# Single panel
xyplot(comp ~ days, data = stackln,
as.table = T,
groups = codeno,
subscripts = T,
panel= function(x,y,subscripts,groups)
{
xy - rbind(rep(0,5), apply(sapply(1:4, function(j)
y[groups[subscripts]==j]),1,cumsum))
for(j in 1:4){
grid.polygon(x = c(c(1,2,4,6,9), rev(c(1,2,4,6,9)) ),
y = c(xy[(j+1),],rev(xy[(j),]) ),
gp = gpar(col = 0, fill = c(1,2,6,8)[j]),
default.units = native)
}
}
)
# Conditioned panel
xyplot(comp ~ days|grps3, data = in1,
as.table = T,
groups = codeno,
subscripts = T,
panel = function(x,y,subscripts,groups,panel.number)
{
grp.no - sort(unique(groups[subscripts]) )
x.vals - sort(unique(x))
xy - rbind(rep(0,length(x.vals) ),
apply(sapply(1:length(grp.no), function(j)
y[groups[subscripts]==grp.no[j]]),1,cumsum))
for (j in 1:length(grp.no))
{
grid.polygon(x = c(x.vals, rev(x.vals) ),
y = c(xy[(j+1),], rev(xy[(j),]) ),
gp = gpar(col = 0, fill = c(6,1,2,5,3,4,7,8)[j]),
default.units = native)
} # for (j in 1:length(grp.no))
} # panel
)
Regards
Duncan Mackay
(The other Duncan Mackay)
Duncan Mackay
Dept of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email: [EMAIL PROTECTED]
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[R] RGUI crash when opening script in XP Home enviroment
I can duplicate this problem under WinXP Professional 5.1.2600 Service Pack 2 Build 2600 on a Toshiba Satellite A10. Thanks to Knut for identifying just what was causing this problem - I was having this error repeatedly but couldn't track down the cause. Duncan version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor1.1 year 2005 month06 day 20 language R * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html [[alternative HTML version deleted]] __ 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
[R] Digest reading is tedious
Any prospects of getting R-news delivered as an RSS feed??? Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html [[alternative HTML version deleted]] __ 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
[R] RGUI crash when opening script in XP Home enviroment
__ 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
[R] Digest reading is tedious
__ 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
[R] RGUI crash when opening script in XP Home enviroment
I can duplicate this problem under WinXP Professional 5.1.2600 Service Pack 2 Build 2600 on a Toshiba Satellite A10. Thanks to Knut for identifying just what was causing this problem - I was having this error repeatedly but couldn't track down the cause. Duncan version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor1.1 year 2005 month06 day 20 language R * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ 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
[R] Digest reading is tedious
Any prospects of getting R-news delivered as an RSS feed??? Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ 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
[R] Rconsole wishlist
Hi all, Wouldn't it be nice (??!!) if R automatically issued a warning message when the R console buffer was about to fill so that you could save all your output into a text file? (I know about sink(), but I think it would be good to have an easier mechanism to save a complete record of messages and function output). And on a similar vein, wouldn't it also be nice if R automatically entered a date stamp into the history file?? Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html [[alternative HTML version deleted]] __ 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] Rconsole wishlist
Sorry, yes, Rgui under WinXP (SP2). But while Windows date stamps the
history file
file.info(.Rhistory)
size isdir mode mtime ctime
.Rhistory 5377 FALSE 666 2005-03-04 10:37:52 2005-03-04 10:37:52
atime
.Rhistory 2005-03-04 13:54:11
the problem is that there can be multiple sessions stored in .Rhistory and
the session dates aren't stored there. Moreover, it seems to me that the
history buffer can also overflow without warning after long sessions or many
repeated sessions and so that you can inadvertently lose parts of your
command log. (Is this right, anyone?) Perhaps it would be preferable for R
to save each session's command history in a separate history file, along the
lines of
.Last - function() {
savefilename - paste(Rhistory,date())
savefilename - gsub( ,_,savefilename)
savefilename - gsub(:,.,savefilename)
savefilename - paste(savefilename,.txt,sep=)
if(interactive()) try(savehistory(savefilename))
cat(Current history saved in file: ,savefilename,\n)
}
but this doesn't address any overflow issues.
Duncan
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: Friday, 4 March 2005 11:14 AM
To: 'Duncan Mackay'; R-news
Subject: RE: [R] Rconsole wishlist
I'm guessing you're talking about Rgui on Windows, but please don't leave us
guessing.
If you run R under Ess/(X)Emacs, you have the entire session that can be
saved in a (transcript) file.
Does your OS not put date stamps on file?
file.info(.Rhistory)
size isdir mode mtime ctime
.Rhistory 1025 FALSE 666 2005-03-03 19:27:31 2004-08-13 10:45:09
atime
.Rhistory 2005-03-03 19:27:31
Andy
From: Duncan Mackay
Hi all,
Wouldn't it be nice (??!!) if R automatically issued a
warning message when
the R console buffer was about to fill so that you could save all your
output into a text file? (I know about sink(), but I think it
would be good
to have an easier mechanism to save a complete record of messages and
function output). And on a similar vein, wouldn't it also be nice if R
automatically entered a date stamp into the history file??
Duncan
*
Dr. Duncan Mackay
School of Biological Sciences
Flinders University
GPO Box 2100
Adelaide
S.A.5001
AUSTRALIA
Ph (08) 8201 2627FAX (08) 8201 3015
http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html
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[R] package dependency error on loading lme4
Hi all, I recently (today) updated the Matrix package and installed the latticeExtra package, but then when I tried to load the lme4 package, I got the following error message:- library(lme4) Loading required package: Matrix Loading required package: latticeExtra Error in importIntoEnv(impenv, impnames, ns, impvars) : object(s) '.__C__lmeRep' are not exported by 'namespace:Matrix' Error in library(lme4) : package/namespace load failed for 'lme4' ??? I'm running R 2.0.1 under WinXP as follows R.Version() $platform [1] i386-pc-mingw32 $arch [1] i386 $os [1] mingw32 $system [1] i386, mingw32 $status [1] $major [1] 2 $minor [1] 0.1 $year [1] 2004 $month [1] 11 $day [1] 15 $language [1] R Cheers, Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ 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
[R] RGUI Console settings
Hi all, Would someone like to comment on the relation between the buffer bytes and lines settings in the console settings? Are they interdependent? If so, how? And why allow both to be tweaked? If not, what is the effect of changing lines, but leaving buffer bytes the same? I wanted to be able to see more of some large outputs in my console, as I was losing the beginning of the outputs under the default console settings. I changed the lines setting from 8000 to 16000, but that didn't seem to change the no. of lines that would display (checked with for(i in 1:9000) print(i)). So then I changed the buffer bytes setting to 13 and now the console will display what I want. But clearly I don't really understand what is going on here Thanks, Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ [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] Generate a sequence of random integer values
Hello, Have a look at the sample command. E.g. sample(20) [1] 3 2 18 6 10 5 9 20 19 13 8 15 17 7 4 14 11 1 12 16 Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Brian Davenhall Sent: Friday, 28 May 2004 10:24 AM To: [EMAIL PROTECTED] Subject: [R] Generate a sequence of random integer values I'm trying to generate a sequence of random integer values. I've tried to combine the random (r) and the sequence (seq) functions but this approach does not work. For example, if I use the following command: a - seq(1:100) a [1] 1 2 3 4 5 6 7 8 9 etc. This is a good start, but what I really want is something that would look like this instead [1] 3 96 45 67 8 24 99 63 8, etc. where the integer numbers between 1 and 100 are randomly chosen. Any help would be great, I've found workarounds in other stat packages, but would prefer to do this in R. __ [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 __ [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
[R] se.contrast ....too hard??? .... Too easy????? .....too trivial???? ...... Too boring.....too????????
Hi all,
Regular and avid readers of this column will know that Don Driscoll and
I have recently posted two messages requesting assistance concerning an
apparent failure of se.contrast to produce an se for a contrast. So
far, an ominous silence rings in our ears, but read on Gentle Reader,
and see if even the machinations of debug doesn't stimulate you to
respond with a revelatory epistle.
Thanks!!!
Duncan
Here is my first message :-
Just to follow up Don Driscoll's earlier post, can anyone please explain
why se.contrast fails here??
shp-factor(rep(c(reserve,strip),each=96))
site-factor(rep(c(1g,1p,1t,2g,2p,2t,3g,3p,3t,4g,4p
,4t),each=16))
pit-factor(rep(1:16,12))
reptsp-c(4,5,6,4,6,6,6,7,3,5,2,2,4,8,5,4,2,4,2,2,4,5,2,4,4,4,3,2,3,2,5,
3,5,3,4,4,4,3,4,
+
3,4,4,4,3,4,3,6,3,3,5,4,6,4,4,2,4,2,6,5,5,5,7,4,4,5,1,4,5,6,5,5,2,6,3,5,
6,4,5,
+
4,8,2,4,2,4,2,4,3,3,4,4,3,2,1,3,4,4,2,2,3,2,4,1,2,2,3,4,5,5,3,5,5,4,1,1,
2,1,3,
+
1,4,1,6,1,2,3,2,2,2,1,1,2,2,6,5,3,2,3,5,3,2,3,2,1,3,2,4,4,3,3,3,1,2,4,3,
4,5,6,
+
5,2,3,2,2,5,5,5,2,2,5,2,4,4,3,2,2,3,2,2,2,2,5,4,3,3,5,2,5,4,3,2,2,2,1,2)
ddata-data.frame(shp,pit,site,reptsp)
repmod2-aov(reptsp~shp/site+ Error(shp/site))
summary(repmod2)
Error: shp
Df Sum Sq Mean Sq
shp 1 53.13 53.13
Error: shp:site
Df Sum Sq Mean Sq
shp:site 10 61.885 6.189
Error: Within
Df Sum Sq Mean Sq F value Pr(F)
Residuals 180 318.561.77
table(ddata$shp)
reserve strip
96 96
se.contrast(repmod2, list(shp==strip, shp==reserve),data=ddata)
Error in qr.qty(strata$qr, scontrast) : qr and y must have the same
number of rows
?
Thanks,
Duncan
...and here is what debug says:-
debug(qr.qty)
se.contrast(repmod2, list(shp==strip, shp==reserve),data=ddata)
debugging in: qr.qty(e.qr, contrast)
debug: {
if (!is.qr(qr))
stop(argument is not a QR decomposition)
if (is.complex(qr$qr)) {
y - as.matrix(y)
if (!is.complex(y))
y[] - as.complex(y)
return(.Call(qr_qy_cmplx, qr, y, 1, PACKAGE = base))
}
a - attr(qr, useLAPACK)
if (!is.null(a) is.logical(a) a)
return(.Call(qr_qy_real, qr, as.matrix(y), 1, PACKAGE =
base))
n - nrow(qr$qr)
k - as.integer(qr$rank)
ny - NCOL(y)
if (NROW(y) != n)
stop(qr and y must have the same number of rows)
storage.mode(y) - double
.Fortran(dqrqty, as.double(qr$qr), n, k, as.double(qr$qraux),
y, ny, qty = y, PACKAGE = base)$qty
}
Browse[1]
debug: if (!is.qr(qr)) stop(argument is not a QR decomposition)
Browse[1]
debug: if (is.complex(qr$qr)) {
y - as.matrix(y)
if (!is.complex(y))
y[] - as.complex(y)
return(.Call(qr_qy_cmplx, qr, y, 1, PACKAGE = base))
}
Browse[1]
debug: a - attr(qr, useLAPACK)
Browse[1]
debug: if (!is.null(a) is.logical(a) a) return(.Call(qr_qy_real,
qr, as.matrix(y), 1, PACKAGE = base))
Browse[1]
debug: n - nrow(qr$qr)
Browse[1]
debug: k - as.integer(qr$rank)
Browse[1]
debug: ny - NCOL(y)
Browse[1]
debug: if (NROW(y) != n) stop(qr and y must have the same number of
rows) Browse[1] ny [1] 1 Browse[1] NCOL(y) [1] 1 Browse[1]
nrow(qr$qr) [1] 192 Browse[1] print(n) [1] 192 Browse[1] dim(qr$qr)
[1] 192 24 Browse[1] NROW(y) [1] 192 Browse[1] NROW(y)==n [1] TRUE
Browse[1] Q
So, if NROW(y)==n, why do I get the message qr and y must have the same
number of rows
Any help gratefully appreciated
Duncan
**
R, me bucko
*
Dr. Duncan Mackay
School of Biological Sciences
Flinders University
GPO Box 2100
Adelaide
S.A.5001
AUSTRALIA
Ph (08) 8201 2627FAX (08) 8201 3015
http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html
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[R] se.contrast ???????????
Hi all, Just to follow up Don Driscoll's earlier post, can anyone please explain why se.contrast fails here?? shp-factor(rep(c(reserve,strip),each=96)) site-factor(rep(c(1g,1p,1t,2g,2p,2t,3g,3p,3t,4g,4p ,4t),each=16)) pit-factor(rep(1:16,12)) reptsp-c(4,5,6,4,6,6,6,7,3,5,2,2,4,8,5,4,2,4,2,2,4,5,2,4,4,4,3,2,3,2,5, 3,5,3,4,4,4,3,4, + 3,4,4,4,3,4,3,6,3,3,5,4,6,4,4,2,4,2,6,5,5,5,7,4,4,5,1,4,5,6,5,5,2,6,3,5, 6,4,5, + 4,8,2,4,2,4,2,4,3,3,4,4,3,2,1,3,4,4,2,2,3,2,4,1,2,2,3,4,5,5,3,5,5,4,1,1, 2,1,3, + 1,4,1,6,1,2,3,2,2,2,1,1,2,2,6,5,3,2,3,5,3,2,3,2,1,3,2,4,4,3,3,3,1,2,4,3, 4,5,6, + 5,2,3,2,2,5,5,5,2,2,5,2,4,4,3,2,2,3,2,2,2,2,5,4,3,3,5,2,5,4,3,2,2,2,1,2) ddata-data.frame(shp,pit,site,reptsp) repmod2-aov(reptsp~shp/site+ Error(shp/site)) summary(repmod2) Error: shp Df Sum Sq Mean Sq shp 1 53.13 53.13 Error: shp:site Df Sum Sq Mean Sq shp:site 10 61.885 6.189 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 180 318.561.77 table(ddata$shp) reserve strip 96 96 se.contrast(repmod2, list(shp==strip, shp==reserve),data=ddata) Error in qr.qty(strata$qr, scontrast) : qr and y must have the same number of rows ? Thanks, Duncan ** R, me bucko * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ [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] plot mean + S.E. over time
check out plotCI and plotmeans in the gregmisc library. Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Jan Wantia Sent: Wednesday, 26 November 2003 12:34 AM To: [EMAIL PROTECTED] Subject: [R] plot mean + S.E. over time Hi, there! I finally became a disciple of 'R', after having lost years of my life handling data with a popular, rather wide-spread spreadsheet-software. Now I want to plot the results of many runs of my simulation over time, so that the means +/- Standard error are on the y-axis, and time on the x-axis. I have tried 'boxplot', with timesteps as the grouping variable, but did not manage to replace quartils by S.E. Then, with 'plot' I do not know how to handle the data of 100 runs for a given time to produce the mean and S.E. Are there any suggestions? Any help would be appreciated! Cheers, Jan -- __ Jan Wantia Dept. of Information Technology, University of Zürich Andreasstr. 15 CH 8050 Zürich Switzerland Tel.: +41 (0) 1 635 4315 Fax: +41 (0) 1 635 45 07 email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Calculating great circle distances
Have you seen Online calculations Downloadable spreadsheets to perform Geodetic Calculations. at http://www.ga.gov.au/nmd/geodesy/datums/calcs.jsp ? Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Wednesday, 26 November 2003 2:55 PM To: [EMAIL PROTECTED] Subject: [R] Calculating great circle distances Hi, Has anyone got any R code (or are there any packages) that calculates the great circle distance between two geographical (lat, lon) positions? Cheers Toby Patterson Pelagic Ecosystems Research Group CSIRO Marine Research Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] kruskal wallis for manova?
Hi,
you may also be interested in Marti Anderson's NPMANOVA program, described
at http://www.stat.auckland.ac.nz/~mja/Programs.htm
Cheers, Duncan
*
Dr. Duncan Mackay
School of Biological Sciences
Flinders University
GPO Box 2100
Adelaide
S.A.5001
AUSTRALIA
Ph (08) 8201 2627FAX (08) 8201 3015
http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Torsten Hothorn
Sent: Monday, 24 November 2003 6:54 PM
To: Nicolaas Busscher
Cc: [EMAIL PROTECTED]
Subject: Re: [R] kruskal wallis for manova?
Hello,
Is there like the kruskal wallis test in relation to ANOVA (no
restrictions on normallity and variance homogenity) something (in R)
for MANOVA?
You may know Fortunato Pesarin's book
@book{multivaria:2001,
key = {386},
author= {Fortunato Pesarin},
title = {Multivariate Permutation Tests:
With Applications to Biostatistics},
year = {2001},
publisher = {John Wiley \ Sons},
address = {Chichester}
}
which addresses those problems. There is some S-Code on the authors
web-page which may be point to start.
Best,
Torsten
thanks
--
Dr.Nicolaas Busscher Universität GH Kassel
Nordbahnhofstrasse: 1a, D-37213 Witzenhausen
Phone: 0049-(0)5542-98-1715, Fax: 0049-(0)5542-98-1713
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[R] Hidden Rhistory files
Hi all, I've ecountered a problem in the last few days with my .Rhistory file not being able to be updated when I quit an R session because its file attributes under Windows have been set as Hidden. Recently, I put the following line in my global Rprofile file:- history(max.show=Inf) so that I automatically open the entire history file for a project when I begin a session, but I don't see why that would cause a problem. This problem has arisen several times in the last few days while working on different Rdata files in different folders. When I manually uncheck the hidden attribute of my Rhistory file, the problem goes away. But why did the files get that attribute in the first place? Is this something that R itself may have done? I'm running R Version 1.8.0 (2003-10-08) under WinXP. Cheers, Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] covariate data errors
Hello, I'm not qualified to judge about definitiveness, but you may find the discussion of Time Series Regression and Generalized Least Squares in Chapter 14 of Applied Regression Analysis, Linear Models, and Related Models by John Fox (1997, Sage Publications) helpful. He also has an accompanying package car on the CRAN R site. Duncan * Dr. Duncan Mackay School of Biological Sciences Flinders University GPO Box 2100 Adelaide S.A.5001 AUSTRALIA Ph (08) 8201 2627FAX (08) 8201 3015 http://www.scieng.flinders.edu.au/biology/people/mackay_d/index.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Andy Jacobson Sent: Friday, 13 June 2003 1:10 PM To: [EMAIL PROTECTED] Subject: [R] covariate data errors Greetings, I would like to fit a multiple linear regression model in which the residuals are expected to follow a multivariate normal distribution, using weighted least squares. I know that the data in question have biases that would result in correlated residuals, and I have a means for quantifying those biases as a covariance matrix. I cannot, unfortunately, correct the data for these biases. It seems that this should be a straightforward task, but so much of the literature is concerned with the probability model in which the residuals are uncorrelated that I can't find a good reference. So in order of importance, please, can someone point me to a definitive reference for least squares with correlated residuals, and is there a standard R package to handle this case? Many thanks in advance, Anthony __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
FW: [R] update.packages through proxy failing
Hi all, I have tried the helpful suggestion below from Andrew Ward, but I now get the following error:- update.packages() trying URL `http://cran.r-project.org/bin/windows/contrib/PACKAGES' Error in download.file(url = paste(contriburl, PACKAGES, sep = /), : cannot open: HTTP status was `407 Proxy Authentication Required' From previous correspondence on this help server, i believe that this problem may arise from my site's requirement for a password to be entered when outside sites are accessed. ?? Duncan -Original Message- From: Andrew C. Ward [mailto:[EMAIL PROTECTED]] Sent: Wednesday, 8 January 2003 12:29 PM To: Duncan Mackay Subject: Re: [R] update.packages through proxy failing Duncan, My organisation also uses a proxy/firewall. I specify --internet2 on the Target line of my R shortcut. This then uses the proxy configuration within your web browser, and I have no problems. Regards, Andrew C. Ward CAPE Centre Department of Chemical Engineering The University of Queensland Brisbane Qld 4072 Australia [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
