Re: [R] Lattice device page options-margins
Hi Bock, Michael wrote: -Original Message- From: Deepayan Sarkar [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 09, 2005 5:09 PM To: r-help@stat.math.ethz.ch Cc: Paul Murrell; Bock, Michael; Sundar Dorai-Raj Subject: Re: [R] Lattice device page options-margins On Wednesday 09 March 2005 13:54, Paul Murrell wrote: Hi Sundar Dorai-Raj wrote: Bock, Michael wrote on 3/9/2005 1:19 PM: I am using lattice to make figures as pdfs: trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) I need to specify some blank space on the left-hand margins (the pages will be bound so we need about 0.5 inch)). I have tried a number of solutions but none seems to work (e.g. par.set). Can this be done when initiating the plotting device? Or is the some other way that does not require me to manually move everything over? Michael, I believe you can do this using print.trellis and setting the position argument. E.g. trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) xy - xyplot(...) print(xy, pos = c(0.10, 0, 1, 1)) dev.off() Or if you want exactly 0.5 inches, something like ... # may need # library(grid) trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) xy - xyplot(1:10 ~ 1:10) pushViewport(viewport(x=1, width=unit(1, npc) - unit(0.5, inches), just=right)) # to show region you're plotting in # grid.rect(gp=gpar(col=grey)) print(xy, newpage=FALSE) popViewport() dev.off() Yet another option, especially if you want this for multiple plots without having to handle each one separately, is to say (after loading lattice): lattice.options(layout.widths = list(left.padding = list(x = 0.5, units = inches))) Unlike par settings though, this would stay in effect across devices. Deepayan Thanks for the suggestions. None of these do exactly what I want. I have some multi panel plotts Excepted Commands: BC.PP-bwplot(PP.PAH ~ Area, Crab, horizontal = FALSE, ylab = Priority Pollutant PAHs (mg/kg), scales = list(x=free,rot=90), aspect = 1.5, main = list(label = Blue Crabs,cex=0.8,font=1), fontfamily = HersheySans) RM.PP-bwplot( PP.PAH ~ Area, Mussel, horizontal = FALSE, ylab = , scales = list(x=free,rot=90), aspect = 1.5, main = list(label= Ribbed Mussels,cex =0.8,font=1), fontfamily = HersheySans) print(BC.PP, split = c(1,1,2,1), more = TRUE ) print(RM.PP, split = c(2,1,2,1),more = TRUE ) grid.text(label = Figure 6. Priority Pollutant PAH Tissue Concentrations, x = unit(0.01, npc), y = unit(0.1, npc), just = left, rot = 0, check.overlap = FALSE, default.units = npc, name = NULL, gp = gpar(fontsize = 10, font = 2), draw = TRUE) grid.text(label = Privileged and Confidential \nAttorney Work Product, x = unit(0.01, npc), y = unit(0.95, npc), just = left, rot = 0, check.overlap = FALSE, default.units = npc, name = NULL, gp = gpar(fontsize = 6, font = 3), draw = TRUE) All of the suggestions shrink the individual boxplots so they both now have empty space on the left size. I guess what I really want is to be able define the plotting area as a portion of the page, allowing for a blank region on the left. Basically defining the margin of the print area. BSomething like: trellis.device(device = pdf,file = Figure6.pdf,color = FALSE,left = 0.1, right = 0.9) Assuming the hypothetical left and right commands set the print area for the pdf. Hopefully this better defines my ideal solution. Thanks for the suggestions, if an ideal solution can not be found I at least have enough to develop a work around. It just too bad I hadn't though of this issue before writing so many scripts to make my plots that will now have to be adjusted manually. Do you mean like this ...? # Dummy data # (it would be easier to give an answer if you gave us the real thing) Crab - data.frame(PP.PAH=rnorm(20), Area=factor(sample(20, 1:2, replace=TRUE))) Mussel - data.frame(PP.PAH=rnorm(20), Area=factor(sample(20, 1:2, replace=TRUE))) BC.PP-bwplot(PP.PAH ~ Area, Crab, horizontal = FALSE, ylab = Priority Pollutant PAHs (mg/kg), scales = list(x=free,rot=90), aspect = 1.5, main = list(label = Blue Crabs,cex=0.8,font=1), fontfamily = HersheySans) RM.PP-bwplot( PP.PAH ~ Area, Mussel, horizontal = FALSE, ylab = , scales = list(x=free,rot=90), aspect = 1.5, main = list(label= Ribbed Mussels,cex =0.8,font=1), fontfamily = HersheySans) trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) # push viewport for ALL drawing pushViewport(viewport(x=.1, width=.8, just=left)) # just to show region you're plotting in grid.rect(gp=gpar(col=grey)) print(BC.PP, split = c(1,1,2,1), more = TRUE, newpage=FALSE) print(RM.PP, split = c(2,1,2,1),more = TRUE) grid.text(label = Figure 6. Priority Pollutant PAH Tissue Concentrations,
RE: [R] Lattice device page options-margins
-Original Message- From: Deepayan Sarkar [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 09, 2005 5:09 PM To: r-help@stat.math.ethz.ch Cc: Paul Murrell; Bock, Michael; Sundar Dorai-Raj Subject: Re: [R] Lattice device page options-margins On Wednesday 09 March 2005 13:54, Paul Murrell wrote: Hi Sundar Dorai-Raj wrote: Bock, Michael wrote on 3/9/2005 1:19 PM: I am using lattice to make figures as pdfs: trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) I need to specify some blank space on the left-hand margins (the pages will be bound so we need about 0.5 inch)). I have tried a number of solutions but none seems to work (e.g. par.set). Can this be done when initiating the plotting device? Or is the some other way that does not require me to manually move everything over? Michael, I believe you can do this using print.trellis and setting the position argument. E.g. trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) xy - xyplot(...) print(xy, pos = c(0.10, 0, 1, 1)) dev.off() Or if you want exactly 0.5 inches, something like ... # may need # library(grid) trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) xy - xyplot(1:10 ~ 1:10) pushViewport(viewport(x=1, width=unit(1, npc) - unit(0.5, inches), just=right)) # to show region you're plotting in # grid.rect(gp=gpar(col=grey)) print(xy, newpage=FALSE) popViewport() dev.off() Yet another option, especially if you want this for multiple plots without having to handle each one separately, is to say (after loading lattice): lattice.options(layout.widths = list(left.padding = list(x = 0.5, units = inches))) Unlike par settings though, this would stay in effect across devices. Deepayan Thanks for the suggestions. None of these do exactly what I want. I have some multi panel plotts Excepted Commands: BC.PP-bwplot(PP.PAH ~ Area, Crab, horizontal = FALSE, ylab = Priority Pollutant PAHs (mg/kg), scales = list(x=free,rot=90), aspect = 1.5, main = list(label = Blue Crabs,cex=0.8,font=1), fontfamily = HersheySans) RM.PP-bwplot( PP.PAH ~ Area, Mussel, horizontal = FALSE, ylab = , scales = list(x=free,rot=90), aspect = 1.5, main = list(label= Ribbed Mussels,cex =0.8,font=1), fontfamily = HersheySans) print(BC.PP, split = c(1,1,2,1), more = TRUE ) print(RM.PP, split = c(2,1,2,1),more = TRUE ) grid.text(label = Figure 6. Priority Pollutant PAH Tissue Concentrations, x = unit(0.01, npc), y = unit(0.1, npc), just = left, rot = 0, check.overlap = FALSE, default.units = npc, name = NULL, gp = gpar(fontsize = 10, font = 2), draw = TRUE) grid.text(label = Privileged and Confidential \nAttorney Work Product, x = unit(0.01, npc), y = unit(0.95, npc), just = left, rot = 0, check.overlap = FALSE, default.units = npc, name = NULL, gp = gpar(fontsize = 6, font = 3), draw = TRUE) All of the suggestions shrink the individual boxplots so they both now have empty space on the left size. I guess what I really want is to be able define the plotting area as a portion of the page, allowing for a blank region on the left. Basically defining the margin of the print area. BSomething like: trellis.device(device = pdf,file = Figure6.pdf,color = FALSE,left = 0.1, right = 0.9) Assuming the hypothetical left and right commands set the print area for the pdf. Hopefully this better defines my ideal solution. Thanks for the suggestions, if an ideal solution can not be found I at least have enough to develop a work around. It just too bad I hadn't though of this issue before writing so many scripts to make my plots that will now have to be adjusted manually. Mike __ 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] plotting
On Wed, 2005-03-09 at 14:28 -0400, Owen Buchner wrote: I have two questions for you. Firstly I'm having troubles trying to plot more then 1 graph. I'm attempting to make a plot with 9 panels, but i have no clue what type of code to use. If you are using R's base graphics and you want 9 plots arranged vertically, you can use par(mfrow = 9) before your first plot. The first plot will then be in the top panel (row). Each successive call to a high level plot function [ie. plot(), boxplot (), barplot()] will draw the plot in the next panel (row) down. See ?par for more information and some examples. Another option, for base graphics, is to use the layout() function and yet another, is to use the grid/lattice packages for creating Trellis type plots. Secondly i was wondering if there was some code to generate random numbers between two defined intervals and then have R chose one randomly in a program. If you could answer either of these questions for me I would appreciate it. If you want to generate random numbers from a pre-specified sequence of numbers between some min and max values (each number having an equal probability of being selected) and then return one of them, you can use the sample function: sample(min:max, 1) See ?sample for more information. Note that the sequence need not be all integers: sample(seq(1, 10, 0.5), 1) [1] 2.5 If you want the random numbers to be within some min:max set of limits, such that: min = x = max each 'x' having an equal probability of being selected and then return one of the numbers, use runif(): runif(1, min, max) See ?runif for more information. HTH, Marc Schwartz __ 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] RMySQL installed but not availalable
require(RMySQL)
help('MySQL')
then see the examples shown by the help page
At 9:12 PM -1200 3/9/05, Adriano von Sydow wrote:
Hi
I run Linux SuSE 9.1, with MSQL 4.0.18
I installed R 2.0.1 and it is working fine
I installed RM 0.5-5 package and verified all installed.packages
(see below) but when I tried to use any RMySQL specific comand is
gives me the same error messages
dbConnect
Error: Object dbConnect not found
It looks like the packages is not installed
Any ideas or help would be welcome
Thanks,
Popolito
*** INSTALL *
ginossauro:/home/avonsydow/Download/Stats # R CMD INSTALL RMySQL_0.5-5.tar.gz
* Installing *source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... yes
checking for mysql.h... no
checking for /usr/local/include/mysql/mysql.h... no
checking for /usr/include/mysql/mysql.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include
-I/opt/gnome/
include -fPIC -c RS-DBI.c -o RS-DBI.o
gcc -I/usr/lib/R/include -I/usr/include/mysql -I/usr/local/include
-I/opt/gnome/
include -fPIC -c RS-MySQL.c -o RS-MySQL.o
gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o RMySQL.so RS-DBI.o
RS-MySQL.o -
lmysqlclient -lz -L/usr/lib/R/lib -lR
** R
** inst
** save image
Loading required package: DBI
[1] dbObjectId
[1] format
[1] show
[1] print
[1] MySQLObject
[1] MySQLDriver
[1] dbUnloadDriver
[1] dbGetInfo
[1] dbListConnections
[1] summary
[1] MySQLConnection
[1] dbConnect
[1] dbConnect
[1] dbConnect
[1] dbDisconnect
[1] dbSendQuery
[1] dbGetQuery
[1] dbGetException
[1] dbGetInfo
[1] dbListResults
[1] summary
[1] dbListTables
[1] dbReadTable
[1] dbWriteTable
[1] dbExistsTable
[1] dbRemoveTable
[1] dbListFields
[1] dbCommit
[1] dbRollback
[1] dbCallProc
[1] MySQLResult
[1] dbClearResult
[1] fetch
[1] fetch
[1] dbGetInfo
[1] dbGetStatement
[1] dbListFields
[1] dbColumnInfo
[1] dbGetRowsAffected
[1] dbGetRowCount
[1] dbHasCompleted
[1] dbGetException
[1] summary
[1] dbDataType
[1] make.db.names
[1] SQLKeywords
[1] isSQLKeyword
[1] dbApply
[1] dbApply
** help
Building/Updating help pages for package 'RMySQL'
Formats: text html latex example
MySQL texthtmllatex example
MySQLConnection-class texthtmllatex example
MySQLDriver-class texthtmllatex example
MySQLObject-class texthtmllatex example
MySQLResult-class texthtmllatex example
S4R texthtmllatex
dbApply-methods texthtmllatex example
dbApply texthtmllatex example
dbCallProc-methodstexthtmllatex
dbCommit-methods texthtmllatex example
dbConnect-methods texthtmllatex example
dbDataType-methodstexthtmllatex example
dbDriver-methods texthtmllatex example
dbGetInfo-methods texthtmllatex example
dbListTables-methods texthtmllatex example
dbObjectId-class texthtmllatex example
dbReadTable-methods texthtmllatex example
dbSendQuery-methods texthtmllatex example
dbSetDataMappings-methods texthtmllatex example
fetch-methods texthtmllatex example
isIdCurrent texthtmllatex example
make.db.names-methods texthtmllatex example
mysqlDBApply texthtmllatex example
mysqlSupport texthtmllatex
safe.writetexthtmllatex example
summary-methods texthtmllatex
* DONE (RMySQL)
*INSTALLED.PACKAGES ***
installed.packages()
Package LibPath Version Priority Bundle
base base /usr/lib/R/library 2.0.1 baseNA
boot boot /usr/lib/R/library 1.2-20 recommended NA
class class /usr/lib/R/library 7.2-10 recommended VR
clustercluster/usr/lib/R/library 1.9.6 recommended NA
datasets datasets /usr/lib/R/library 2.0.1 baseNA
DBIDBI/usr/lib/R/library 0.1-8 NANA
foreignforeign/usr/lib/R/library 0.8-0 recommended NA
graphics graphics /usr/lib/R/library 2.0.1 baseNA
grDevices grDevices /usr/lib/R/library 2.0.1 baseNA
grid grid /usr/lib/R/library 2.0.1 baseNA
KernSmooth KernSmooth /usr/lib/R/library 2.22-14 recommended NA
latticelattice/usr/lib/R/library 0.10-14 recommended NA
MASS MASS
Re: [R] two-dimensional integration?
Nils,
For 2D, see package 'adapt' on CRAN. e.g.
adapt(2, c(0,0), c(1,1), functn=function(x) sin(prod(x))*exp(x[1]-x[2]))
Package `adapt' will do larger numbers of dimensions, but numerical
quadrature is often no more effective than Monte-Carlo methods in more
than a few dimensions. For very smooth functions, quasi-random numbers
can help.
A good reference aimed at statisticians is
@Book{Evans.Swartz.00,
author = {Michael Evans and Tim Swartz},
title ={Approximating Integrals via Monte Carlo and
Deterministic Methods},
publisher ={Oxford University Press},
year = 2000,
address = {Oxford},
ISBN = 0-19-850278-8,
}
BTW, we are not good are predicting to 2014, but fairly good at the
present. In this case I could not guess a good search term on
http://search.r-project.org, but it often gets you there. It has a
`complete' list of packages, as does CRAN, and searching those pages for
`integrate' works.
Brian
On Thu, 10 Mar 2005, Nils-at-Duke Lid Hjort wrote:
I find the one-dimensional integrate very helpful,
but often enough I stumble into problems that require
two (or more)-dimensional integrals. I suppose there
are no R functions that can do this for me, directly?
The ideal thing would be to be able to define say
f - function(x)
{
x1 - x[1]
x2 - x[2]
sin(x1*x2)*exp(x1-x2)
}
and then write say
integrate(f, xlim=c(0,1), ylim=c(0,1)) .
(a) No such thing exists, as of today, right?
(b) There *are* general numerical routines out there
for doing such things, right? (Importance sampling
or adaptive important sampling would often do the
job, but it would be difficult to find something that
always works -- at least in higher dimension?
Also, iterated one-dimensional integrations could
be attempted, but I find that messy, also because
things lose the g(many) = many(g) property, and
then R refuses to integrate g.)
(c) Will a thing like the above exist in R before
the Tromsoe Olympics in 2014? For which dimensions?
Nils Lid Hjort
[Professor of statistics at Oslo, but currently at Duke]
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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] two-dimensional integration?
This existed even before the Athens Olympics 2004 :)
look at package adapt which integrates a function from 2 to 20
dimensions, e.g.,
library(adapt)
f - function(x){
x1 - x[1]
x2 - x[2]
sin(x1*x2)*exp(x1-x2)
}
adapt(2, c(0,0), c(1,1), functn=f)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Nils-at-Duke Lid Hjort [EMAIL PROTECTED]
To: R-help@stat.math.ethz.ch; [EMAIL PROTECTED]
Sent: Thursday, March 10, 2005 6:22 AM
Subject: [R] two-dimensional integration?
I find the one-dimensional integrate very helpful,
but often enough I stumble into problems that require
two (or more)-dimensional integrals. I suppose there
are no R functions that can do this for me, directly?
The ideal thing would be to be able to define say
f - function(x)
{
x1 - x[1]
x2 - x[2]
sin(x1*x2)*exp(x1-x2)
}
and then write say
integrate(f, xlim=c(0,1), ylim=c(0,1)) .
(a) No such thing exists, as of today, right?
(b) There *are* general numerical routines out there
for doing such things, right? (Importance sampling
or adaptive important sampling would often do the
job, but it would be difficult to find something that
always works -- at least in higher dimension?
Also, iterated one-dimensional integrations could
be attempted, but I find that messy, also because
things lose the g(many) = many(g) property, and
then R refuses to integrate g.)
(c) Will a thing like the above exist in R before
the Tromsoe Olympics in 2014? For which dimensions?
Nils Lid Hjort
[Professor of statistics at Oslo, but currently at Duke]
__
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-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] two-dimensional integration?
Nils-at-Duke Lid Hjort [EMAIL PROTECTED] writes: I find the one-dimensional integrate very helpful, but often enough I stumble into problems that require two (or more)-dimensional integrals. I suppose there ... (c) Will a thing like the above exist in R before the Tromsoe Olympics in 2014? For which dimensions? Nils Lid Hjort [Professor of statistics at Oslo, but currently at Duke] Did you check the CRAN package adapt? It's been around at least since Nagano 1998, I believe. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Dropping coloumns while redaing dtaa from text file.
Hi I have a huge text file and .dat file from which I want to read data. I do not need all the columns in the files. I want to extract only some columns from the .txt file or the .dat file, because reading the entire file is becoming very difficult due to memory issues. Is it possible to extract a few columns from .txt or .dat file while reading the data in R? Thanks Upasna -- The past is a history, the future is a mystery, and this moment is a gift. That is why this moment is called 'the present'. Anonymous __ 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] R: LIST function and LOOPS
hi all
another simple question.
i've written a dummy program so that you get the concept. (the code
could be simplfied such that there are no loops. but lets leave the
loops in for now.)
z1-function(w)
{
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
list(ss=ss)
}
}
check.1-z1(3)
check.1
the results is:
$ss
[1] -0.01516304
what i want is something that looks like this:
j=1
$ss
[1] -2.213343
j=2
$ss
[1] -2.904235
j=3
$ss
[1] -0.01516304
i know that i could use the print command. (see z2)
z2-function(w)
{
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
print(ss)
}
}
check.2-z2(3)
check.2
check.2-z2(3)
[1] -2.213343
[1] -2.904235
[1] -0.01516304
check.2
[1] -0.01516304
the problem with z2 is that only the last value is saved.
what i could do is use matrices like the following: (but i dont want to
do this AND WOULD PREFER TO USE list.)
z3-function(w)
{
results.-matrix(nrow=w,ncol=1)
colnames(results.)-c(ss)
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
results.[i,1]-ss
}
results.
}
check.3-z3(3)
check.3
check.3
ss
[1,] -2.21334260
[2,] -2.90423463
[3,] -0.01516304
what if i have a new program (something different) and i want the
following:
j=1
$a
1
2
3
$b
1
2
3
4
5
$c
1
###
j=2
$a
11
21
31
$b
11
21
31
41
51
$c
11
###
j=3
$a
21
22
32
$b
21
22
32
42
52
$c
21
MATRICES SEEMS TO BE A GOOD WAY OF DOING THIS (but then you would have
to set up three matrices, one for a,b and c). BUT WHAT IF I WANT TO USE
THE LIST FUNCTION? i.e. there is a list in the first loop that i want to
display!
sorry for the long mail.
***
ALLAN__
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] contrast matrix for aov
On Wed, 9 Mar 2005, Darren Weber wrote: How do we specify a contrast interaction matrix for an ANOVA model? We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) Cue Direction (2) x Brain Hemisphere(2) Each of these has 2 levels, 'left' and 'right', so it's a simple 2x2 design matrix. We have 8 subjects in each cell (a balanced design) and we want to specify the interaction contrast so that: CueLeftCueRght for the Right Hemisphere CueRghtCueLeft for the Left Hemisphere. Here is a copy of the relevant commands for R: lh_cueL - rowMeans( LHroi.cueL[,t1:t2] ) lh_cueR - rowMeans( LHroi.cueR[,t1:t2] ) rh_cueL - rowMeans( RHroi.cueL[,t1:t2] ) rh_cueR - rowMeans( RHroi.cueR[,t1:t2] ) roiValues - c( lh_cueL, lh_cueR, rh_cueL, rh_cueR ) cuelabels - c(CueLeft, CueRight) hemlabels - c(LH, RH) roiDataframe - data.frame( roi=roiValues, Subject=gl(8,1,32,subjectlabels), Hemisphere=gl(2,16,32,hemlabels), Cue=gl(2,8,32,cuelabels) ) roi.aov - aov(roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), data=roiDataframe) I think the error model should be Error(Subject). In what sense are `Cue' and `Cue:Hemisphere' random effects nested inside `Subject'? Let me fake some `data': set.seed(1); roiValues - rnorm(32) subjectlabels - paste(V1:8, sep = ) options(contrasts = c(contr.helmert, contr.poly)) roi.aov - aov(roi ~ Cue*Hemisphere + Error(Subject), data=roiDataframe) roi.aov Call: aov(formula = roi ~ Cue * Hemisphere + Error(Subject), data = roiDataframe) Grand Mean: 0.1165512 Stratum 1: Subject Terms: Residuals Sum of Squares 4.200946 Deg. of Freedom 7 Residual standard error: 0.7746839 Stratum 2: Within Terms: Cue Hemisphere Cue:Hemisphere Residuals Sum of Squares 0.216453 0.019712 0.057860 21.896872 Deg. of Freedom 1 1 121 Residual standard error: 1.021131 Estimated effects are balanced Note that all the action is in one stratum, and the SSQs are the same as aov(roi ~ Subject + Cue * Hemisphere, data = roiDataframe) (and also the same as for your fit). print(summary(roi.aov)) It auto-prints, so you don't need print(). I've tried to create a contrast matrix like this: cm - contrasts(roiDataframe$Cue) which gives the main effect contrasts for the Cue factor. I really want to specify the interaction contrasts, so I tried this: # c( lh_cueL, lh_cueR, rh_cueL, rh_cueR ) # CueRightCueLeft for the Left Hemisphere. # CueLeftCueRight for the Right Hemisphere cm - c(-1, 1, 1, -1) dim(cm) - c(2,2) (That is up to sign what Helmert contrasts give you.) roi.aov - aov( roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), contrasts=cm, data=roiDataframe) print(summary(roi.aov)) but the results of these two aov commands are identical. Is it the case that the 2x2 design matrix is always going to give the same F values for the interaction regardless of the contrast direction? Yes, as however you code the design (via `contrasts') you are fitting the same subspaces. Not sure what you mean by `contrast direction', though. However, you have not specified `contrasts' correctly: contrasts: A list of contrasts to be used for some of the factors in the formula. and cm is not a list, and an interaction is not a factor. OR, is there some way to get a summary output for the contrasts that is not available from the print method? For more than two levels, yes: see `split' under ?summary.aov. Also, see se.contrasts which allows you to find the standard error for any contrast. For the fixed-effects model you can use summary.lm: fit - aov(roi ~ Subject + Cue * Hemisphere, data = roiDataframe) summary(fit) Df Sum Sq Mean Sq F value Pr(F) Subject 7 4.2009 0.6001 0.5756 0.7677 Cue 1 0.2165 0.2165 0.2076 0.6533 Hemisphere 1 0.0197 0.0197 0.0189 0.8920 Cue:Hemisphere 1 0.0579 0.0579 0.0555 0.8161 Residuals 21 21.8969 1.0427 summary.lm(fit) Call: aov(formula = roi ~ Subject + Cue * Hemisphere, data = roiDataframe) Residuals: Min 1Q Median 3Q Max -1.7893 -0.4197 0.1723 0.5868 1.3033 Coefficients: Estimate Std. Error t value Pr(|t|) [...] Cue1 -0.082240.18051 -0.4560.653 Hemisphere1 0.024820.18051 0.1370.892 Cue1:Hemisphere1 -0.042520.18051 -0.2360.816 where the F values are the squares of the t values. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44
Re: [R] Dropping coloumns while redaing dtaa from text file.
Upasna Sharma [EMAIL PROTECTED] writes: Hi I have a huge text file and .dat file from which I want to read data. I do not need all the columns in the files. I want to extract only some columns from the .txt file or the .dat file, because reading the entire file is becoming very difficult due to memory issues. Is it possible to extract a few columns from .txt or .dat file while reading the data in R? You're not sayin what tools you are using to read in the first place, but notice that the colClasses argument to read.table can have NULL elements. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Dropping coloumns while redaing dtaa from text file.
On Thu, 10 Mar 2005, Upasna Sharma wrote: Hi I have a huge text file and .dat file from which I want to read data. I do not need all the columns in the files. I want to extract only some columns from the .txt file or the .dat file, because reading the entire file is becoming very difficult due to memory issues. Is it possible to extract a few columns from .txt or .dat file while reading the data in R? Yes. Look at the use of NULL for 'colClasses' (read.table) or 'what' (scan), and also 'flush'. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] function in order to plot the same graph to postscript and pdf
I guess you would want eval(MYPLOT) there?
But the function above works if you say
plot.both(myplot = expression(plot(x)), filename = foo)
and that is what I said above: set myplot = expression(plot(x)).
Z
My syntax in the example was a little bit messed, sorry for that.
However Gabor Grothendieck's reply has brought me to the solution. The
following function does the job right:
print.both - function(myplot, filename){
pdf(file=paste(filename, .pdf, sep=))
postscript(file=paste(filename, .eps, sep=))
dev.control(displaylist=enable)
myplot
dev.copy(which=dev.next())
graphics.off()
}
The dev.control(displaylist=enable) is necessary here because only then R
does record the plot and dev.copy can be used.
So, thank you all for your help.
Ronny
__
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] Flattening a list of data frames
try this: do.call(rbind, z) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/336899 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/ http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm - Original Message - From: Lorin Hochstein [EMAIL PROTECTED] To: R-help@stat.math.ethz.ch Sent: Wednesday, March 09, 2005 9:07 PM Subject: [R] Flattening a list of data frames Hello all, Simple version of my problem: I've got a list of data frames, where each data frame has the same number of columns and the same column names. I'd like to flatten the list into one large data frame. Is there an easy way to do this? Quick example code: a - data.frame(x=c(1,2,3),y=c(5,7,9) b - data.frame(x=c(2,4,7,9),y=c(2,3,5,4)) z - list(a,b) # Do something to get the equivalent of rbind(z[[1]],z[[2]]) ??? More complex version: My data is in this format because it's the output of a by statment that looks like this: y - by(d,list(d$StudentID,d$Assignment),gapfun) (where gapfun is a function I've defined that takes a data frame and returns another data frame). What I would like is to do is transform y into a data frame that has columns StudentID, Assignment, and the columns in the data frame returned by gapfun. Any ideas? Lorin -- Lorin Hochstein Graduate Research Assistant Experimental Software Engineering Group Computer Science Department University of Maryland, College Park __ 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-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] Flattening a list of data frames
Hello all, Simple version of my problem: I've got a list of data frames, where each data frame has the same number of columns and the same column names. I'd like to flatten the list into one large data frame. Is there an easy way to do this? Quick example code: a - data.frame(x=c(1,2,3),y=c(5,7,9) b - data.frame(x=c(2,4,7,9),y=c(2,3,5,4)) z - list(a,b) # Do something to get the equivalent of rbind(z[[1]],z[[2]]) ??? More complex version: My data is in this format because it's the output of a by statment that looks like this: y - by(d,list(d$StudentID,d$Assignment),gapfun) (where gapfun is a function I've defined that takes a data frame and returns another data frame). What I would like is to do is transform y into a data frame that has columns StudentID, Assignment, and the columns in the data frame returned by gapfun. Any ideas? Lorin -- Lorin Hochstein Graduate Research Assistant Experimental Software Engineering Group Computer Science Department University of Maryland, College Park __ 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 get standard deviation of rows in a matrix
Jagarlamudi, Choudary wrote on 3/9/2005 1:49 PM: Hi all, I am trying to find sd of my rows in a matrix and i get column sd inspite of extracting rows. I tried to do the sqrt(var(x)) but that did'nt work as well, Here is my data genes 15 24 63 40 25 42 46 35 23 53 37 45 30 37 50 55 40 51 30 48 x-sd(genes[1:5,]) y-sqrt(var(genes[1:5,])) I get 4 sds for the 4 columns instead of 5 sds for my 5 rows. Thanks you in advance. This has come up several times in the past and a quick search of the archives would have lead you to: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/34169.html HTH, --sundar __ 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] contrast matrix for aov
Prof Brian Ripley [EMAIL PROTECTED] writes: On Wed, 9 Mar 2005, Darren Weber wrote: How do we specify a contrast interaction matrix for an ANOVA model? We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) Actually, that's not usual in SAS (and not SPSS either, I believe) in things like proc glm; model y1-y4= ; repeated row 2 col 2; [Not that SAS/SPSS is the Gospel, but they do tend to set the terminology in these matters.] There you'd get the analysis split up as analyses of three contrasts corresponding to the main effects and interaction, c(-1,-1,1,1), c(-1,1,-1,1), and c(-1,1,1,-1) in the 2x2 case (up to scale and sign). In the 2x2 case, this corresponds exactly to the 4-stratum model row*col + Error(block/(row*col)). (It is interesting to note that it is still not the optimal analysis for arbitrary covariance patterns because dependence between contrasts is not utilized - it is basically assumed to be absent.) With more than two levels, you get the additional complications of sphericity testing and GG/HF epsilons and all that. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Interval censoring in Survival analysis
Hi, I would like to know if R programme allows doing different kinds of censoring in his last version. What kind of package should I use and is this censoring applicable to parametric and semi-parametric(Cox) models? Thanks, Àlex. __ 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] contrast matrix for aov
Prof Brian Ripley wrote: On Wed, 9 Mar 2005, Darren Weber wrote: We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) roi.aov - aov(roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), data=roiDataframe) I think the error model should be Error(Subject). In what sense are `Cue' and `Cue:Hemisphere' random effects nested inside `Subject'? I do not understand this, and I think I am probably not the only one. That is why I would be grateful if you could give a bit more information. My understanding is that the fixed factors Cue and Hemisphere are crossed with the random factor Subject (in other words, Cue and Hemisphere are within-subjects factors, and this is probably why Darren called it a repeated measure design). In this case, it seems to me from the various textbooks I read on Anova, that the appropriate MS to test the interaction Cue:Hemisphere is Subject:Cue:Hemisphere (with 7 degress of freedom, as there are 8 independent subjects). If you input Error(Subject/(Cue*Hemisphere)) in the aov formula, then the test for the interaction indeed uses the Subject:Cue:Hemisphere source of variation in demoninator. This fits with the ouput of other softwares. If you include only 'Subjet', then the test for the interaction has 21 degrees of Freedom, and I do not understand what this tests. I apologize in if my terminology is not accurate. But I hope you can clarify what is wrong with the Error(Subject/(Cue*Hemisphere)) term, or maybe just point us to the relevant textbooks. Thanks in advance, Christophe Pallier Let me fake some `data': set.seed(1); roiValues - rnorm(32) subjectlabels - paste(V1:8, sep = ) options(contrasts = c(contr.helmert, contr.poly)) roi.aov - aov(roi ~ Cue*Hemisphere + Error(Subject), data=roiDataframe) roi.aov Call: aov(formula = roi ~ Cue * Hemisphere + Error(Subject), data = roiDataframe) Grand Mean: 0.1165512 Stratum 1: Subject Terms: Residuals Sum of Squares 4.200946 Deg. of Freedom 7 Residual standard error: 0.7746839 Stratum 2: Within Terms: Cue Hemisphere Cue:Hemisphere Residuals Sum of Squares 0.216453 0.019712 0.057860 21.896872 Deg. of Freedom 1 1 121 Residual standard error: 1.021131 Estimated effects are balanced Note that all the action is in one stratum, and the SSQs are the same as aov(roi ~ Subject + Cue * Hemisphere, data = roiDataframe) (and also the same as for your fit). print(summary(roi.aov)) It auto-prints, so you don't need print(). I've tried to create a contrast matrix like this: cm - contrasts(roiDataframe$Cue) which gives the main effect contrasts for the Cue factor. I really want to specify the interaction contrasts, so I tried this: # c( lh_cueL, lh_cueR, rh_cueL, rh_cueR ) # CueRightCueLeft for the Left Hemisphere. # CueLeftCueRight for the Right Hemisphere cm - c(-1, 1, 1, -1) dim(cm) - c(2,2) (That is up to sign what Helmert contrasts give you.) roi.aov - aov( roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), contrasts=cm, data=roiDataframe) print(summary(roi.aov)) but the results of these two aov commands are identical. Is it the case that the 2x2 design matrix is always going to give the same F values for the interaction regardless of the contrast direction? Yes, as however you code the design (via `contrasts') you are fitting the same subspaces. Not sure what you mean by `contrast direction', though. However, you have not specified `contrasts' correctly: contrasts: A list of contrasts to be used for some of the factors in the formula. and cm is not a list, and an interaction is not a factor. OR, is there some way to get a summary output for the contrasts that is not available from the print method? For more than two levels, yes: see `split' under ?summary.aov. Also, see se.contrasts which allows you to find the standard error for any contrast. For the fixed-effects model you can use summary.lm: fit - aov(roi ~ Subject + Cue * Hemisphere, data = roiDataframe) summary(fit) Df Sum Sq Mean Sq F value Pr(F) Subject 7 4.2009 0.6001 0.5756 0.7677 Cue 1 0.2165 0.2165 0.2076 0.6533 Hemisphere 1 0.0197 0.0197 0.0189 0.8920 Cue:Hemisphere 1 0.0579 0.0579 0.0555 0.8161 Residuals 21 21.8969 1.0427 summary.lm(fit) Call: aov(formula = roi ~ Subject + Cue * Hemisphere, data = roiDataframe) Residuals: Min 1Q Median 3Q Max -1.7893 -0.4197 0.1723 0.5868 1.3033 Coefficients: Estimate Std. Error t value Pr(|t|) [...] Cue1
Re: [R] from long/lat to UTM
On 10-Mar-05 Sander Oom wrote: Hi Yyan, The proj4R package by Roger Bivand will allow you to project data in many ways and directions. http://spatial.nhh.no/R/Devel/proj4R-pkg.pdf It uses the proj libraries from: http://www.remotesensing.org/proj/ Not sure where you would derive the time zone! Good luck, Sander. While there is a longitude-based nominal time-zone structure (0deg E is the centre of Zone 0 which extends for 7.5deg either side; successive time-zones move round by 15deg), this does not apply cleanly to the time-shifts adopted in different places for local time. A World map of regions with different local-time offsets is a crazy patchwork, with all sorts of contradictory looking regions. For instance, the -0700 region of the USA extends from approx -0830 to approx -0620, covering over 2 hours, and parts of -0800 touch the -0700 line and are more than 0100 East of parts of -0700. Even worse can be found over the Indian/Central Asian and Malaysian parts of the world, where time-shifts of 30 miniutes are also frequent (and, according to my Atlas, one country, Nepal, has 52/3 i.e. +0540!). As Sander says, Not sure where you would derive the time zone!. Unless you can refer a (long,lat) position to a look-up table, you can't predict what the zone will be to less the 1 hour (except of course for the nominal time-zones by 15deg sectors). I've never encountered a digital version of such a table (my Atlas must be based on one, though). Best wishes, Ted. yyan liu wrote: Hi: Is there any function in R which can convert the long/lat to UTM(Universal Transverse Mercator)? There are quite a few converters on Internet. However, the interface is designed as input-output which I can not convert lots of locations at the same time. Another question is whether there is a function in R which can tell the time zone from the location's lat/long? Thank you! liu __ 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 -- Dr. Sander P. Oom Animal, Plant and Environmental Sciences, University of the Witwatersrand Private Bag 3, Wits 2050, South Africa Tel (work) +27 (0)11 717 64 04 Tel (home) +27 (0)18 297 44 51 Fax +27 (0)18 299 24 64 Email [EMAIL PROTECTED] Web www.oomvanlieshout.net/sander __ 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 E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 10-Mar-05 Time: 09:47:25 -- XFMail -- __ 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 get standard deviation of rows in a matrix
On Wed, 9 Mar 2005 13:49:44 -0600 Jagarlamudi, Choudary [EMAIL PROTECTED] wrote: Hi all, I am trying to find sd of my rows in a matrix and i get column sd inspite of extracting rows. I tried to do the sqrt(var(x)) but that did'nt work as well, Here is my data genes 15 24 63 40 25 42 46 35 23 53 37 45 30 37 50 55 40 51 30 48 x-sd(genes[1:5,]) y-sqrt(var(genes[1:5,])) I get 4 sds for the 4 columns instead of 5 sds for my 5 rows. Thanks you in advance. mymat - matrix(rnorm(20), 5) mymat [,1] [,2] [,3] [,4] [1,] -0.1418666 -0.6754704 -0.2525154 -1.4832003 [2,] -0.2254920 1.8705093 -0.9678318 -0.1108883 [3,] 2.2501392 0.1687349 -0.1279790 0.7055311 [4,] 0.9893453 -0.5924199 0.2410576 0.9001638 [5,] -0.4179559 0.9334556 -0.6501605 0.6148958 apply(mymat, 1, sd) [1] 0.6084171 1.2135998 1.0584750 0.7318231 0.7722641 See ?apply HTH, Tobias __ 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] contrast matrix for aov
On Thu, 10 Mar 2005, Christophe Pallier wrote: Prof Brian Ripley wrote: On Wed, 9 Mar 2005, Darren Weber wrote: We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) roi.aov - aov(roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), data=roiDataframe) I think the error model should be Error(Subject). In what sense are `Cue' and `Cue:Hemisphere' random effects nested inside `Subject'? I do not understand this, and I think I am probably not the only one. That is why I would be grateful if you could give a bit more information. My understanding is that the fixed factors Cue and Hemisphere are crossed with the random factor Subject (in other words, Cue and Hemisphere are within-subjects factors, and this is probably why Darren called it a repeated measure design). The issue is whether the variance of the error really depends on the treatment combination, which is what the Error(Subject/(Cue*Hemisphere)) assumes. With that model Error: Subject:Cue Df Sum Sq Mean Sq F value Pr(F) Cue1 0.2165 0.2165 0.1967 0.6708 Residuals 7 7.7041 1.1006 Error: Subject:Hemisphere Df Sum Sq Mean Sq F value Pr(F) Hemisphere 1 0.0197 0.0197 0.0154 0.9047 Residuals 7 8.9561 1.2794 Error: Subject:Cue:Hemisphere Df Sum Sq Mean Sq F value Pr(F) Cue:Hemisphere 1 0.0579 0.0579 0.0773 0.789 Residuals 7 5.2366 0.7481 you are assuming different variances for three contrasts. In this case, it seems to me from the various textbooks I read on Anova, that the appropriate MS to test the interaction Cue:Hemisphere is Subject:Cue:Hemisphere (with 7 degress of freedom, as there are 8 independent subjects). If you input Error(Subject/(Cue*Hemisphere)) in the aov formula, then the test for the interaction indeed uses the Subject:Cue:Hemisphere source of variation in demoninator. This fits with the ouput of other softwares. If you include only 'Subjet', then the test for the interaction has 21 degrees of Freedom, and I do not understand what this tests. It uses a common variance for all treatment combinations. I apologize in if my terminology is not accurate. But I hope you can clarify what is wrong with the Error(Subject/(Cue*Hemisphere)) term, or maybe just point us to the relevant textbooks. Nothing is `wrong' with it, it just seems discordant with the description of the experiment. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] contrast matrix for aov
On Thu, 10 Mar 2005, Peter Dalgaard wrote: Prof Brian Ripley [EMAIL PROTECTED] writes: On Wed, 9 Mar 2005, Darren Weber wrote: How do we specify a contrast interaction matrix for an ANOVA model? We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) Actually, that's not usual in SAS (and not SPSS either, I believe) in things like proc glm; model y1-y4= ; repeated row 2 col 2; [Not that SAS/SPSS is the Gospel, but they do tend to set the terminology in these matters.] That seems to be appropriate only if the four treatments are done in a particular order (`repeated') and one expects correlations in the responses. However, here the measurements seem to have been averages of replications. It may be usual to (mis?)specify experiments in SAS that way: I don't know what end users do, but it is not the only way possible in SAS. There you'd get the analysis split up as analyses of three contrasts corresponding to the main effects and interaction, c(-1,-1,1,1), c(-1,1,-1,1), and c(-1,1,1,-1) in the 2x2 case (up to scale and sign). In the 2x2 case, this corresponds exactly to the 4-stratum model row*col + Error(block/(row*col)). (It is interesting to note that it is still not the optimal analysis for arbitrary covariance patterns because dependence between contrasts is not utilized - it is basically assumed to be absent.) It also assumes that there is a difference between variances of the contrasts, that is there is either correlation between results or a difference in variances under different treatments. Nothing in the description led me to expect either of those, but I was asking why it was specified that way. (If the variance does differ with the mean then there are probably more appropriate analyses.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 get standard deviation of rows in a matrix
You should read ?var and ?sd more carefully. For a data frame or a matrix, var() returns the covariance matrix of the columns, whereas sd() returns the standard deviations of the columns. If you want standard deviations of the rows, you need to transpose the data. Andy From: Jagarlamudi, Choudary Hi all, I am trying to find sd of my rows in a matrix and i get column sd inspite of extracting rows. I tried to do the sqrt(var(x)) but that did'nt work as well, Here is my data genes 15 24 63 40 25 42 46 35 23 53 37 45 30 37 50 55 40 51 30 48 x-sd(genes[1:5,]) y-sqrt(var(genes[1:5,])) I get 4 sds for the 4 columns instead of 5 sds for my 5 rows. Thanks you in advance. Choudary Jagarlamudi Instructor Southwestern Oklahoma State University STF 254 100 campus Drive Weatherford OK 73096 Tel 580-774-7136 __ 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] Interval censoring in Survival analysis
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of AMOROS
NAVARRO, ALEX
I would like to know if R programme allows doing different
kinds of censoring in his last version. What kind of package
should I use
Yes, try the following:
library(survival)
?Surv
Best,
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
__
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] Lattice device page options-margins
You can add some space to the left by setting the left.padding component of the layout.widths trellis setting. For example: library(lattice) trellis.device(new=TRUE) trellis.par.set(layout.widths = list(left.padding = 20)) require(stats) ## Tonga Trench Earthquakes Depth - equal.count(quakes$depth, number=8, overlap=.1) xyplot(lat ~ long | Depth, data = quakes) hope this helps, Chuck Cleland Bock, Michael wrote: I am using lattice to make figures as pdfs: trellis.device(device = pdf,file = Figure6.pdf,color = FALSE) I need to specify some blank space on the left-hand margins (the pages will be bound so we need about 0.5 inch)). I have tried a number of solutions but none seems to work (e.g. par.set). Can this be done when initiating the plotting device? Or is the some other way that does not require me to manually move everything over? Michael J. Bock, PhD. ARCADIS 24 Preble St. Suite 100 Portland, ME 04101 207.828.0046 fax 207.828.0062 [[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 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ 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] Structural equation models with R
Dear John, Thanks very much! I dont know how I didnt see this before. I checked a thousand of times There is one more thing that I can not understand. What are the possible reasons for problems on calculation of confidence interval for RMSEA? For the same model I sent before (after correction of the variable name) the lower CI output was NA: Model Chisquare = 10.824 Df = 13 Pr(Chisq) = 0.62558 Goodness-of-fit index = 0.91656 Adjusted goodness-of-fit index = 0.76895 RMSEA index = 0 90 % CI: (NA, 0.15652) BIC = -60.425 I have other models with the same behavior, even when the estimative of RMSEA is different from zero. Model Chisquare = 15.165 Df = 14 Pr(Chisq) = 0.367 Goodness-of-fit index = 0.89038 Adjusted goodness-of-fit index = 0.71811 RMSEA index = 0.053558 90 % CI: (NA, 0.19141) BIC = -61.564 Thanks and all the best. André --- André Tavares Corrêa Dias Laboratório de Ecologia Vegetal Departamento de Ecologia - IB Universidade Federal do Rio de Janeiro Ilha do Fundão, CCS Rio de Janeiro, RJ. Brasil CEP 21941-590CP 68020 Tel. (21)2562-6377 __ 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] multiple comparisons for lme using multcomp
Dear R-help list, I would like to perform multiple comparisons for lme. Can you report to me if my way to is correct or not? Please, note that I am not nor a statistician nor a mathematician, so, some understandings are sometimes quite hard for me. According to the previous helps on the topic in R-help list May 2003 (please, see Torsten Hothorn advices) and books such as Venables Ripley or Pinheiro Bates. I need multcomp library. I followed the different examples and get these results : In this example, response is the mass of earthworms after one month of exposure to different concentrations of pollutants (treatment). The experimental design was three containers per treatment with five animals in each container (or less if mortality occurred). Containers were referred as box and considered as the random variable. tab-read.delim(example1.txt) tab treatment box response 1control a 1.8 2control a 2.3 3control a 1.3 4control a 0.8 5control a 2.0 6control b 1.1 7control b 2.2 8control b 1.3 9control b 2.0 10 control b 1.3 11 control c 1.5 12 control c 1.4 13 control c 2.1 14 control c 1.7 15 control c 1.3 16 Al100 d 1.6 17 Al100 d 2.1 18 Al100 d 0.7 19 Al100 d 1.8 20 Al100 d 1.2 21 Al100 e 1.5 22 Al100 e 1.5 23 Al100 e 2.0 24 Al100 e 1.0 25 Al100 e 1.6 26 Al100 f 0.9 27 Al100 f 2.0 28 Al100 f 1.9 29 Al100 f 1.7 30 Al100 f 1.7 68 Al800 q 1.0 69 Al800 r 0.8 70 Al800 r 0.9 71 Al800 r 0.9 72 Al800 r 0.6 73 Al800 s 0.9 74 Al800 s 1.0 75 Al800 s 0.8 76 Al800 s 0.8 77 Al800 s 0.7 attach(tab) library(nlme) lm1-lme(response~treatment,random=~1|box) library(multcomp) Loading required package: mvtnorm # first way to do (seem uncorrect) summary(csimtest(coef(lm1),vcov(lm1),cmatrix=contrMat(table(treatment), type=Tukey),df=59)) Error in csimtest(coef(lm1), vcov(lm1), cmatrix = contrMat(table(treatment), : estpar not a vector #indeed coef(lm1) (Intercept) treatmentAl200 treatmentAl400 treatmentAl600 treatmentAl800 a1.546679 -0.1648540 -0.4895219 -0.6383375 -0.7066632 b1.546657 -0.1648540 -0.4895219 -0.6383375 -0.7066632 c1.546664 -0.1648540 -0.4895219 -0.6383375 -0.7066632 d1.546643 -0.1648540 -0.4895219 -0.6383375 -0.7066632 s1.546667 -0.1648540 -0.4895219 -0.6383375 -0.7066632 treatmentcontrol a 0.06 b 0.06 c 0.06 d 0.06 s 0.06 # second way to do could be to get a vector for lm1 coefficient removing intercept(is it correct?) vect-as.numeric(coef(lm1)[1,]) vect [1] 1.5466787 -0.1648540 -0.4895219 -0.6383375 -0.7066632 0.060 summary(csimtest(vect,vcov(lm1),cmatrix=contrMat(table(treatment),type=Tukey),df=59)) Simultaneous tests: user-defined contrasts user-defined contrasts for factor Contrast matrix: Al100 Al200 Al400 Al600 Al800 control Al200-Al100 -1 10 00 0 Al400-Al100 -1 0 1 0 0 0 Al600-Al100 -1 0 01 0 0 Al800-Al100 -1 0 00 1 0 control-Al100-1 0 00 0 1 Al400-Al200 0-1 10 0 0 Al600-Al200 0-1 0 1 0 0 Al800-Al200 0-1 0 01 0 control-Al200 0-1 0 00 1 Al600-Al400 0 0-1 10 0 Al800-Al400 0 0-1 0 1 0 control-Al400 0 0-1 0 0 1 Al800-Al600 0 00-1 1 0 control-Al600 0 00-1 0 1 control-Al800 0 00 0-1 1 Absolute Error Tolerance: 0.001 Coefficients: Estimate t value Std.Err. p raw p Bonf p adj Al800-Al100 -2.253 -10.4670.213 0.000 0.000 0.000 Al600-Al100 -2.185 -10.3890.207 0.000 0.000 0.000 Al400-Al100 -2.036 -9.8500.210 0.000 0.000 0.000 Al200-Al100 -1.712 -8.0510.215 0.000 0.000 0.000 control-Al100 -1.487 -7.2430.205 0.000 0.000 0.000 control-Al8000.767 -5.2820.143 0.000 0.000 0.000 control-Al6000.698 -5.0720.148 0.000 0.000 0.000 control-Al4000.550 -4.1600.155 0.000 0.001 0.001 Al800-Al200 -0.542 -3.4880.141 0.001 0.006 0.006 Al600-Al200 -0.473 -3.1910.140 0.002 0.014 0.012 Al400-Al200 -0.325 -2.2670.147 0.027 0.135 0.110 control-Al2000.225 -1.5930.132 0.116 0.466 0.341 Al800-Al400 -0.217 -1.4750.152
[R] Re: plotting several series on the sames axes
Many thanks to all those who replied to my 'simple' query, all of which have been posted to the list. __ 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] about kpss.test()
On Wed, 9 Mar 2005 14:32:09 -0500 (EST) Weiguang Shi wrote: --- Achim Zeileis [EMAIL PROTECTED] wrote: First of all, could you tell me what the KPSS Level in the output of the test means? Thanks. But I meant to also ask about the number after that, e.g., KPSS Level = 0.0027 If you wouldn't have deleted my reply to that question, you could still see the answer! It was: quote It means that you tested for level stationarity and gives you the test statistic. /quote Note the second half of the sentence. Please check the references of kpss.test or any book on economectric time series analysis for which alternatives the KPSS test was designed. Will soon do. Hint: it's not designed for detecting cyclical variations. OK. I guess there must be some pre-requisite on the data before kpss-ing it. In particular it means: There are infinitely many conceivable ways of deviation from stationarity and the KPSS test is only good at detecting certain kinds of deviation (which do not include cyclical variations). Z __ 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] problem using uniroot with integrate
Thank you very much. Yes, that was the problem, partial matching.
I saw a warning about that in integrate and some discussion from 1999
in the archives and so added the m0 for integrate but somehow
I wasn't bright enough to see that I had the same problem
in uniroot.
Sorry about no working example, but I'm not sure what I could
have added, if I understand what you mean by working example,
because my function wasn't working.
best,
ken
Quoting Sundar Dorai-Raj [EMAIL PROTECTED]:
Ken Knoblauch wrote on 3/9/2005 10:27 AM:
Hi,
I'm trying to calculate the value of the variable, dp, below, in the
argument to the integral of dnorm(x-dp) * pnorm(x)^(m-1). This
corresponds to the estimate of the sensitivity of an observer in an
m-alternative forced choice experiment, given the probability of
a correct response, Pc, a Gaussian assumption for the noise and
no bias. The function that I wrote below gives me an error:
Error in f(x, ...) : recursive default argument reference
The problem seems to be at the statement using uniroot,
because the furntion est.dp works fine outside of the main function.
I've been using R for awhile but there are still many nuances
about the scoping and the use of environments that I'm weak on
and would like to understand better. I would appreciate any
suggestions or solutions that anyone might offer for fixing
my error. Thank you.
dprime.mAFC - function(Pc, m) {
est.dp - function(dp, Pc = Pc, m = m) {
pr - function(x, dpt = dp, m0 = m) {
dnorm(x - dpt) * pnorm(x)^(m0 - 1)
}
Pc - integrate(pr, lower = -Inf, upper = Inf,
dpt = dp, m0 = m)$value
}
dp.res - uniroot(est.dp, interval = c(0,5), Pc = Pc, m = m)
dp.res$root
}
Ken,
Look at the argument list for ?uniroot and think partial matching.
You're m is being interpretted for maxiter. Simply change to
dp.res - uniroot(est.dp, interval = c(0,5), Pc = Pc, m0 = m)
and in other places for consistency and the error goes away. Of course,
since you gave no working example, I'm not sure if other errors are
present that I'm missing.
--sundar
Ken Knoblauch
Inserm U 371
Cerveau et Vision
18 avenue du Doyen Lepine
69675 Bron cedex
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: 06 84 10 64 10
__
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] multiple comparisons for lme using multcomp
Michaël Coeurdassier [EMAIL PROTECTED] writes: summary(csimtest(vect,vcov(lm1),cmatrix=contrMat(table(treatment),type=Tukey),df=59)) Coefficients: Estimate t value Std.Err. p raw p Bonf p adj Al800-Al100 -2.253 -10.4670.213 0.000 0.000 0.000 Al600-Al100 -2.185 -10.3890.207 0.000 0.000 0.000 Al400-Al100 -2.036 -9.8500.210 0.000 0.000 0.000 Al200-Al100 -1.712 -8.0510.215 0.000 0.000 0.000 control-Al100 -1.487 -7.2430.205 0.000 0.000 0.000 control-Al8000.767 -5.2820.143 0.000 0.000 0.000 control-Al6000.698 -5.0720.148 0.000 0.000 0.000 control-Al4000.550 -4.1600.155 0.000 0.001 0.001 Al800-Al200 -0.542 -3.4880.141 0.001 0.006 0.006 Al600-Al200 -0.473 -3.1910.140 0.002 0.014 0.012 Al400-Al200 -0.325 -2.2670.147 0.027 0.135 0.110 control-Al2000.225 -1.5930.132 0.116 0.466 0.341 Al800-Al400 -0.217 -1.4750.152 0.145 0.466 0.341 Al600-Al400 -0.149 -1.0640.138 0.292 0.583 0.466 Al800-Al600 -0.068 -0.4490.145 0.655 0.655 0.655 #a friend told me that it is possible to do multiple comparisons for lme in a simplest way, i.e. : anova(lm1,L=c(treatmentcontrol=1,treatmentAl200=-1)) F-test for linear combination(s) treatmentAl200 treatmentcontrol -11 numDF denDF F-value p-value 1 112 2.538813 0.1371 anova(lm1,L=c(treatmentcontrol=1,treatmentAl400=-1)) F-test for linear combination(s) treatmentAl400 treatmentcontrol -11 numDF denDF F-value p-value 1 112 17.30181 0.0013 anova(lm1,L=c(treatmentcontrol=1,treatmentAl600=-1)) F-test for linear combination(s) treatmentAl600 treatmentcontrol -11 numDF denDF F-value p-value 1 112 25.72466 3e-04 anova(lm1,L=c(treatmentcontrol=1,treatmentAl800=-1)) F-test for linear combination(s) treatmentAl800 treatmentcontrol -11 numDF denDF F-value p-value 1 112 27.9043 2e-04 # however, p values are different that those obtained above. Is this way OK or not? Notice that in all cases, the F-value is exactly the square of the t-value from Csimtest. The main difference is that you have claimed that the vcov matrix has 59 DF, whereas the lme analysis says 12. I'd suspect the latter to be (more) correct. Apart from that, notice that the L approach at best gives you the p raw value, i.e., it is uncorrected for multiple testing. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] R-help:loading data from text file and viewing it in persp
Hi All i would like to get some help on how to use the persp() for 3d surface plotting with the data from txt file. it has format like x1 y1 z1 x2 y2 z2 x3 y3 z3 and so on...sometimes the txt file data may be very large also.. how could i load this txt file and view its 3d view. thanks in advance - [[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] how modify object in parent.env
[I sent this last night but it does not appear to have shown up
so this is second attempt. Apologies if this gets posted twice.]
The search for the left hand side of the - starts in
the parent while search for the right side is in the
current environment so:
x - 1:3
local( for (i in seq(along = x)) { x - 99; x[i] - x } )
Its important not to define the local x prior seq(along = x)
so that that seq(along=x) refers to the x in the parent. If
you do define it first and therefore need to force reference
to the parent x use get or eval in the seq:
seq(along = get(x, parent.frame()))
Actually, it may be less confusing to just use a different,
but related, variable name. If you don't like x0, perhaps
x. would be ok:
x - 1:3
local( { x. - 99; for (i in seq(along = x)) x[i] - x. } )
Vadim Ogranovich vograno at evafunds.com writes:
:
: Thank you to Gabor and Mark Schwartz for the answers. Both of them
: solved the problem I posted, but my actual problem, as I now see, is a
: little bit more involved. Let me try again.
:
: I have a vector 'x'. I want to compute its entries in a loop (yes, I
: know...). Say
:
: x = seq(3)
:
: for (i in seq(length(x)) {
: x0 = someValue
: x[i] = x0
: }
:
: There are two problems with the above code:
: 1. x0 pollutes the global envirnoment (not to mention possible
: over-write of an existing x0). Therefore I thought I'd wrap it with
: local().
: 2. x0 is not a good name from a readability perspective. I'd rather call
: it x to emphasize it's an entry in an outer vector 'x'. (In this small
: example it doesn't really matter, but I have much more involved scripts
: where consistent naming is important)
:
: Gabor's solution solves 1 but not 2. Maybe there is a simple way around
: this restriction?
:
: Thanks,
: Vadim
:
: -Original Message-
: From: r-help-bounces at stat.math.ethz.ch
: [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Gabor
: Grothendieck
: Sent: Tuesday, March 08, 2005 4:06 PM
: To: r-help at stat.math.ethz.ch
: Subject: Re: [R] how modify object in parent.env
:
:
: You can use - like this:
:
: x - 1:3
: local(x[1] - x[1]+1)
:
: Vadim Ogranovich vograno at evafunds.com writes:
:
: :
: : Assign() re-binds the value, not modifies it (the latter is what I
: : needed)
: :
: : -Original Message-
: : From: McGehee, Robert [mailto:Robert.McGehee at
: geodecapital.com]
: : Sent: Tuesday, March 08, 2005 3:48 PM
: : To: Vadim Ogranovich; r-help at stat.math.ethz.ch
: : Subject: RE: [R] how modify object in parent.env
: :
: : This isn't an environment problem. Assigning something to a
: : get call doesn't make any sense. Use assign.
: :
: : a - 5
: : get(a) - 10
: : Error: couldn't find function get-
: :
: : And from the ?assign help page, you can pick what environment
: : you want to make the assignment. Just pick the parent environment.
: :
: :
: : -Original Message-
: : From: Vadim Ogranovich [mailto:vograno at evafunds.com]
: : Sent: Tuesday, March 08, 2005 6:36 PM
: : To: r-help at stat.math.ethz.ch
: : Subject: [R] how modify object in parent.env
: :
: :
: : Hi,
: :
: : Is it possible to modify an object in the parent.env (as
: opposed to
: : re-bind)? Here is what I tried:
: :
: : x = 1:3
: : # try to modify the first element of x from within a new
: environment
: : local(get(x, parent.env(environment()))[1] - NA)
: : Error in eval(expr, envir, enclos) : Target of assignment
: expands to
: : non-language object
: :
: : # On the other hand retrieval works just fine
: : local(get(x, parent.env(environment()))[1])
: : [1] 1
: :
: : Thanks,
: : Vadim
: :
: : __
: : R-help at 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-help at 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-help at 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-help at 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-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] Gap statistic
Dear All, I need to calculate the optimal number of clusters for a classification based on a large number of observations (tens of thousands). Thibshirani et al. proposed the gap statistic for this purpose. I tried the R-code developed by R. Jörnsten but R hangs with such amount of data (). Is it available any other (optimised) code? Any help would be appreciated, including suggestions about other alternatives for the selection of an optimal number of cluster from large datasets. Thanks, Néstor Fernández, PhD. Department of Ecological Modelling UFZ - Centre for Environmental Research PF 500136, DE-04301, Leipzig, Germany. Tel: +49 341-2352034 E-mail: [EMAIL PROTECTED] __ 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] Gregmisc
Dear all, I use R 2.0.1 on Windows XP professional. When I want to load the 'Gregmisc' library I get the following error message: Error in library(pkg, character.only = TRUE) : 'gregmisc' is not a valid package -- installed 2.0.0? Can anybody tell me what's wrong with this package? Cheers, Christian __ 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] Gregmisc
It's a bundle of 4 packages (gtools, gdata, gmodels, and gplots), so you need to load one of those packages. See the following: http://cran.us.r-project.org/src/contrib/Descriptions/gregmisc.html Chuck Cleland Christian Kamenik wrote: Dear all, I use R 2.0.1 on Windows XP professional. When I want to load the 'Gregmisc' library I get the following error message: Error in library(pkg, character.only = TRUE) : 'gregmisc' is not a valid package -- installed 2.0.0? Can anybody tell me what's wrong with this package? Cheers, Christian __ 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 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ 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] Gregmisc
On Thu, 2005-03-10 at 14:44 +0100, Christian Kamenik wrote: Dear all, I use R 2.0.1 on Windows XP professional. When I want to load the 'Gregmisc' library I get the following error message: Error in library(pkg, character.only = TRUE) : 'gregmisc' is not a valid package -- installed 2.0.0? Can anybody tell me what's wrong with this package? gregmisc is a _bundle_, not a package. It is now comprised of four separate packages: 1. gtools 2. gdata 3. gmodels 4. gplots You will need to load the particular package that you wish to use or load all four if you wish. HTH, Marc Schwartz __ 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] from long/lat to UTM
Ted.Harding at nessie.mcc.ac.uk writes: : : yyan liu wrote: : Hi: :Is there any function in R which can convert the : long/lat to UTM(Universal Transverse Mercator)? :There are quite a few converters on Internet. : However, the interface is designed as input-output : which I can not convert lots of locations at the same : time. :Another question is whether there is a function in R : which can tell the time zone from the location's : lat/long? :Thank you! : : liu : : On 10-Mar-05 Sander Oom wrote: : Hi Yyan, : : The proj4R package by Roger Bivand will allow you to project data in : many ways and directions. : : http://spatial.nhh.no/R/Devel/proj4R-pkg.pdf : : It uses the proj libraries from: : : http://www.remotesensing.org/proj/ : : Not sure where you would derive the time zone! : : Good luck, : : Sander. : : While there is a longitude-based nominal time-zone : structure (0deg E is the centre of Zone 0 which extends : for 7.5deg either side; successive time-zones move round : by 15deg), this does not apply cleanly to the time-shifts : adopted in different places for local time. : : A World map of regions with different local-time offsets : is a crazy patchwork, with all sorts of contradictory : looking regions. For instance, the -0700 region of : the USA extends from approx -0830 to approx -0620, : covering over 2 hours, and parts of -0800 touch the : -0700 line and are more than 0100 East of parts of -0700. : Even worse can be found over the Indian/Central Asian : and Malaysian parts of the world, where time-shifts : of 30 miniutes are also frequent (and, according to my : Atlas, one country, Nepal, has 52/3 i.e. +0540!). : : As Sander says, Not sure where you would derive the time zone!. : : Unless you can refer a (long,lat) position to a look-up : table, you can't predict what the zone will be to less : the 1 hour (except of course for the nominal time-zones : by 15deg sectors). I've never encountered a digital : version of such a table (my Atlas must be based on one, : though). : : Best wishes, : Ted. The fBasics package of the rmetrics project uses the Olsen time zone data base which does take some of these things into account. __ 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] Gregmisc
On Thu, 10 Mar 2005, Christian Kamenik wrote: Dear all, I use R 2.0.1 on Windows XP professional. When I want to load the 'Gregmisc' library I get the following error message: Error in library(pkg, character.only = TRUE) : 'gregmisc' is not a valid package -- installed 2.0.0? Can anybody tell me what's wrong with this package? gregmisc is a package bundle these days. Probably you have installed the new package bundle (including packages such as gtools) but did not remove your old package gregmuisc. Try, e.g., library(gtools) Uwe Ligges Cheers, Christian __ 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-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] Structural equation models with R
Dear Andre, -Original Message- From: André TavaresCorrêa Dias [mailto:[EMAIL PROTECTED] Sent: Thursday, March 10, 2005 6:14 AM To: John Fox Cc: r-help@stat.math.ethz.ch Subject: RE: [R] Structural equation models with R Dear John, Thanks very much! I dont know how I didnt see this before. I checked a thousand of times (Recall that there was a typo in Andre's model specification.) There is one more thing that I can not understand. What are the possible reasons for problems on calculation of confidence interval for RMSEA? For the same model I sent before (after correction of the variable name) the lower CI output was NA: Model Chisquare = 10.824 Df = 13 Pr(Chisq) = 0.62558 Goodness-of-fit index = 0.91656 Adjusted goodness-of-fit index = 0.76895 RMSEA index = 0 90 % CI: (NA, 0.15652) BIC = -60.425 I have other models with the same behavior, even when the estimative of RMSEA is different from zero. Model Chisquare = 15.165 Df = 14 Pr(Chisq) = 0.367 Goodness-of-fit index = 0.89038 Adjusted goodness-of-fit index = 0.71811 RMSEA index = 0.053558 90 % CI: (NA, 0.19141) BIC = -61.564 The method used to get the confidence interval (from Browne and Du Toit, Multivariate Behavioral Research, 1992, 27:269-300) can produce a lower bound above the RMSEA estimate or an upper bound below the estimate; when this happens, the bound is set to NA. One of the nice things about R is that you can look at the code for a function -- in this case, summary.sem() -- to see exactly what it does. Take a look at how RMSEA.L and RMSEA.U are computed. Regards, John __ 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] install R redhat rpm as a normal user
On Wed, 2005-03-09 at 16:17 -0800, Eric Hu wrote: Hi, I wonder if anyone has done this before. I have rpm-build installed in my workstation. Thanks. Eric I have not seen any other replies to this, but as far as I know Martyn's RPMS are not relocatable and a test this morning confirms that. If you need to install R as a non-root user, you are likely better off installing from source code. Modify the --prefix argument to ./configure as per the R Administration Manual. For example: ./configure --prefix=TargetDir where TargetDir is a directory that you have write privileges to. Then use make and make install which will then build and install R. R will be installed in TargetDir (ie. /home/UserName/R) with a set of subdirs bin, lib and man. To run R, you would then use: TargetDir/bin/R Or you can create a symlink in /home/UserName/bin to the above file and then just use R to start it. See the R Administration Manual for more information. HTH, Marc Schwartz __ 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] R: LIST function and LOOPS
You will need to capture the value of ss at the end of each 'i' as such
z4 -function(w){
output - numeric(w)
for (i in 1:w){
set.seed(i+6) # this is redundant line
ss-0
for (j in 1:5){
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
output[i] - ss
}
return(output)
}
BTW, I do not think it is a good idea to set.seed() so many times.
To answer you more general question, see if the following is useful.
I am trying to simulate 'n' values from a standard normal distribution
but 'n' is random variable itself.
f -function(w, lambda=3){
tmp - list(NULL)
for (i in 1:w){
n - 1 + rpois(1, lambda=lambda) # number of simulation required
tmp[[ i ]] - rnorm(n)
}
# flatten the list into a ragged matrix
out.lengths - sapply(tmp, length)
out - matrix( nr=w, nc=max( out.lengths ) )
rownames(out) - paste(w =, 1:w)
for(i in 1:w) out[i, 1:out.lengths[i] ] - tmp[[i]]
return(out)
}
f(6, lambda=3)
It is not very elegant but I hope that helps you out somehow.
Regards, Adai
On Thu, 2005-03-10 at 10:16 +0200, Clark Allan wrote:
hi all
another simple question.
i've written a dummy program so that you get the concept. (the code
could be simplfied such that there are no loops. but lets leave the
loops in for now.)
z1-function(w)
{
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
list(ss=ss)
}
}
check.1-z1(3)
check.1
the results is:
$ss
[1] -0.01516304
what i want is something that looks like this:
j=1
$ss
[1] -2.213343
j=2
$ss
[1] -2.904235
j=3
$ss
[1] -0.01516304
i know that i could use the print command. (see z2)
z2-function(w)
{
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
print(ss)
}
}
check.2-z2(3)
check.2
check.2-z2(3)
[1] -2.213343
[1] -2.904235
[1] -0.01516304
check.2
[1] -0.01516304
the problem with z2 is that only the last value is saved.
what i could do is use matrices like the following: (but i dont want to
do this AND WOULD PREFER TO USE list.)
z3-function(w)
{
results.-matrix(nrow=w,ncol=1)
colnames(results.)-c(ss)
for (i in 1:w)
{
set.seed(i+6)
ss-0
for (j in 1:5)
{
set.seed(j+1+(i-1)*6)
r-rnorm(1)
ss-ss+r
}
results.[i,1]-ss
}
results.
}
check.3-z3(3)
check.3
check.3
ss
[1,] -2.21334260
[2,] -2.90423463
[3,] -0.01516304
what if i have a new program (something different) and i want the
following:
j=1
$a
1
2
3
$b
1
2
3
4
5
$c
1
###
j=2
$a
11
21
31
$b
11
21
31
41
51
$c
11
###
j=3
$a
21
22
32
$b
21
22
32
42
52
$c
21
MATRICES SEEMS TO BE A GOOD WAY OF DOING THIS (but then you would have
to set up three matrices, one for a,b and c). BUT WHAT IF I WANT TO USE
THE LIST FUNCTION? i.e. there is a list in the first loop that i want to
display!
sorry for the long mail.
***
ALLAN
__ 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-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] Vogelsang test? RATS? Time series analysis.
Has anybody implemented the Vogelsang test from Vogelsang's 1998 Econometrica paper? Or the tests by Fomby and Vogelsang from their 2002 paper? I have been looking for trends in many time series (1000's) with unknown autocorrelation. In brief, I have fit AR models and classified them as stochastic or deterministic with augmented Dickey-Fuller tests. A colleague has suggested that we use a new and more elegant test that is robust to the nature of serial correlation in the residuals and pointed me the RATS program in general and Fomby and Vogelsang test in particular. Any leads appreciated, Andy ~~ Fomby TB, Vogelsang TJ, The application of size-robust trend statistics to global-warming temperature series. JOURNAL OF CLIMATE 15 (1): 117-123 2002 Vogelsang TJ, Trend function hypothesis testing in the presence of serial correlation. ECONOMETRICA 66 (1): 123-148 1998 __ 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] problem using uniroot with integrate
On Wed, 9 Mar 2005, Ken Knoblauch wrote:
Thank you very much. Yes, that was the problem, partial matching.
I saw a warning about that in integrate and some discussion from 1999
in the archives and so added the m0 for integrate but somehow
I wasn't bright enough to see that I had the same problem
in uniroot.
It is perhaps worth pointing out that in R you usually don't need to pass
these extra arguments down
dprime.mAFC - function(Pc, m) {
est.dp - function(dp) {
pr - function(x) {
dnorm(x - dp) * pnorm(x)^(m - 1)
}
Pc - integrate(pr, lower = -Inf, upper = Inf)$value
}
dp.res - uniroot(est.dp, interval = c(0,5))
dp.res$root
}
Because pr() is defined inside est.dp, which is defined inside
dprime.mAFC, the arguments are already accessible.
In most cases, passing extra arguments through a higher-order function is
not needed in R, as lexical scope allows the function to have access to
the information directly. You also don't have to keep thinking up
different names for 'm'.
Sorry about no working example, but I'm not sure what I could
have added, if I understand what you mean by working example,
because my function wasn't working.
A set of arguments at which you wanted to evaluate the function, so that
a) we could get the same error that you did
b) we could tell when it worked.
-thomas
best,
ken
Quoting Sundar Dorai-Raj [EMAIL PROTECTED]:
Ken Knoblauch wrote on 3/9/2005 10:27 AM:
Hi,
I'm trying to calculate the value of the variable, dp, below, in the
argument to the integral of dnorm(x-dp) * pnorm(x)^(m-1). This
corresponds to the estimate of the sensitivity of an observer in an
m-alternative forced choice experiment, given the probability of
a correct response, Pc, a Gaussian assumption for the noise and
no bias. The function that I wrote below gives me an error:
Error in f(x, ...) : recursive default argument reference
The problem seems to be at the statement using uniroot,
because the furntion est.dp works fine outside of the main function.
I've been using R for awhile but there are still many nuances
about the scoping and the use of environments that I'm weak on
and would like to understand better. I would appreciate any
suggestions or solutions that anyone might offer for fixing
my error. Thank you.
dprime.mAFC - function(Pc, m) {
est.dp - function(dp, Pc = Pc, m = m) {
pr - function(x, dpt = dp, m0 = m) {
dnorm(x - dpt) * pnorm(x)^(m0 - 1)
}
Pc - integrate(pr, lower = -Inf, upper = Inf,
dpt = dp, m0 = m)$value
}
dp.res - uniroot(est.dp, interval = c(0,5), Pc = Pc, m = m)
dp.res$root
}
Ken,
Look at the argument list for ?uniroot and think partial matching.
You're m is being interpretted for maxiter. Simply change to
dp.res - uniroot(est.dp, interval = c(0,5), Pc = Pc, m0 = m)
and in other places for consistency and the error goes away. Of course,
since you gave no working example, I'm not sure if other errors are
present that I'm missing.
--sundar
Ken Knoblauch
Inserm U 371
Cerveau et Vision
18 avenue du Doyen Lepine
69675 Bron cedex
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: 06 84 10 64 10
__
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
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
__
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] Interval censoring in Survival analysis
On Thu, 10 Mar 2005, AMOROS NAVARRO, ALEX wrote: Hi, I would like to know if R programme allows doing different kinds of censoring in his last version. What kind of package should I use and is this censoring applicable to parametric and semi-parametric(Cox) models? To some extent. The survival package allows left censoring and interval censoring, but only for parametric models. The Icens package estimates survival curves for interval censored data (including multivariate times), but does not do regression. I am not aware of any package that allows semiparametric regression modelling of interval censored or doubly censored data. -thomas __ 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] Re: [Rd] dealing with package bundles
Liaw, Andy [EMAIL PROTECTED] writes: Given the confusions that some users have regarding package bundles, I'd like to suggest some changes to how package bundles are handled. I wonder if a guideline of naming packages bundles in a manner that identifies them as bundles would help? An example of what I'm thinking: gregmisc-bundle_x.y.z.tar.gz Then users could (once familiar with the convention) know when they are dealing with a bundle. Such a name scheme fits with my understanding of bundles: they provide a mechanism to download and install multiple packages at once. After installation there is no notion of bundle. One doesn't call library on a bundle (and I think that is a good thing). Best, + seth __ 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] from long/lat to UTM
On 10-Mar-05 Gabor Grothendieck wrote: Ted.Harding at nessie.mcc.ac.uk writes: : [...] : As Sander says, Not sure where you would derive the time zone!. : : Unless you can refer a (long,lat) position to a look-up : table, you can't predict what the zone will be to less : the 1 hour (except of course for the nominal time-zones : by 15deg sectors). I've never encountered a digital : version of such a table (my Atlas must be based on one, : though). : : Best wishes, : Ted. The fBasics package of the rmetrics project uses the Olsen time zone data base which does take some of these things into account. Thanks, Gabor! However, this seems to be just the usual sort of thing -- TimeZone name with corresponding TZ data. You first have to know the TZ name. (Unless I have overlooked sonething in the Olsen database). What I had in mind was a look-up facility whereby a (long,lat) pair could be submitted as a query, returning the TZ region (name) within which that geographical point lay. The only completely general mechanism I can think of would consist of a) a named list of boundary contours b) a function which, for each name in the list, returns the TZ name Then, for instance, given a point P = (long,lat), the list could be searched by verifying, for each contour in the list, whether the point lay in the region circumscribed by the coutour (e.g. by computing the winding number for the contour with respect to the point). This would also work for regions with holes in them, provided the boundary of the hole was presented in the correct order of points (e.g. such that the region of which it was the boundary lies to the left as you go through the sequence). If, for instance, I had the contour data for the TZ map in my Atlas, I could construct such a thing! But, as I say, I have not come across such a dataset. I'd be interested to learn of one, though! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 10-Mar-05 Time: 16:13:01 -- XFMail -- __ 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 could I catch the R data-output stream and presented by other software func
There are quite a few packages which allow R to be accessed from other
software systems. Examples include RDCOM (included with Windows R), RSOAP
(http://rsoap.sf.net), Rpy (Python, http://rpy.sf.net), RSPerl
(http://www.omegahat.org/RSPerl/). Duncan Temple Lang, the developer of
RSPerl, has a whole pile of these tools, see http://www.omegahat.org for a
full list.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Michael shen
Sent: Thursday, March 10, 2005 1:37 AM
To: r-help@stat.math.ethz.ch
Subject: [R] How could I catch the R data-output stream and
presented by
other software func
Dear All R-helper,
I wonder to know that could I do the computation staff in R
environment and
get the R data output stream ,then presented by other
software functions in
their GUI.(for example: get the R data output streamand
present the data
using SPSS function in SPSS output GUI). Is there some R
-packages in CRAN
already do this kind of function? and what kind of document
should I read?
Thanks in advance
Michael
__
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
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
__
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] Online short course: Advanced Resampling Methods
Online short course: Advanced Resampling Methods Phillip Good will offer his online short course Advanced Resampling Methods March 18 April 8. In the bootstrap area, it will cover BCA (bias corrected and accelerated) confidence intervals, bootstrap-t intervals, the parametric bootstrap, and the tilted bootstrap. The use of bootstrapping for estimating power and sample sizes will be covered, as will model validation. Permutation tests will also be discussed, with coverage of 2-sided alternatives, matched pairs, strata, and ordered RxC tables. Dr. Good will also discuss decision trees. (Note: topic coverage may be adjusted slightly to accommodate the needs of participants.) Examples will be provided in R. Participants will interact with Dr. Good via a private discussion board over approximately 4 weeks; the course will require about 10 hours per week and there are no set hours when you must be online. Details and registration: http://www.statistics.com/content/courses/advancedresamp/index.html Peter Bruce [EMAIL PROTECTED] __ 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] from long/lat to UTM
Ted Harding [EMAIL PROTECTED] 03/10/05 09:13AM
On 10-Mar-05 Gabor Grothendieck wrote:
Ted.Harding at nessie.mcc.ac.uk writes:
: [...]
: As Sander says, Not sure where you would derive the time
zone!.
:
[snip]
The only completely general mechanism I can think of would
consist of
a) a named list of boundary contours
I found a shapefile of time zones at:
http://openmap.bbn.com/data/shape/timezone/
A google search on the keywords timezone shapefile finds a
few other possibilities.
b) a function which, for each name in the list, returns
the TZ name
The maptools package can read in the above shapefile and
convert it to a list of polygons and the sgeostat has an
in.polygon function to see if a point is in a given polygon.
The following code worked for me:
library(maptools)
tz - read.shape('c:/maps/WrldTZA')
plot(tz)
plot(tz,xlim=c(-150,-50), ylim=c(20,50))
mappoly - Map2poly(tz)
library(sgeostat)
tmp - sapply(mappoly, function(x){ x - na.exclude(x)
in.polygon( -110, 42, x[,1], x[,2] ) } )
tz$att.data[tmp,]
the -110 and 42 come from me plotting the map and using
locator to approximate where I am at. I was actually
suprized at how quick the sapply was (under a second on
my fairly fast pc (windows 2000)).
It shouldn't be too hard to convert this into a more general
function.
Greg Snow, Ph.D.
Statistical Data Center
[EMAIL PROTECTED]
(801) 408-8111
__
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] from long/lat to UTM
On 10-Mar-05 Greg Snow wrote: [...] I found a shapefile of time zones at: http://openmap.bbn.com/data/shape/timezone/ A google search on the keywords timezone shapefile finds a few other possibilities. b) a function which, for each name in the list, returns the TZ name The maptools package can read in the above shapefile and convert it to a list of polygons and the sgeostat has an in.polygon function to see if a point is in a given polygon. The following code worked for me: [] Many thanks, Greg. That looks just the job, and I'll look into it. All best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 10-Mar-05 Time: 18:10:23 -- XFMail -- __ 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] contrast matrix for aov
Prof Brian Ripley wrote: On Wed, 9 Mar 2005, Darren Weber wrote: How do we specify a contrast interaction matrix for an ANOVA model? We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) Each subject experiences multiple instances of a visual stimulus that cues them to orient their attention to the left or right visual field. For each instance, we acquire brain activity measures from the left and right hemisphere (to put it simply). For each condition in this 2x2 design, we actually have about 400 instances for each cell for each subject. These are averaged in several ways, so we obtain a single scalar value for each subject in the final analysis. So, at this point, it does not appear to be a repeated measures analysis. Perhaps another way to put it - each subject experiences every cell of the design, so we have within-subjects factors rather than between-subjects factors. That is, each subject experiences all experimental conditions, we do not separate and randomly allocate subjects to only one cell or another of the experiment. I hope this clarifies the first question. I will try to digest further points in this thread, if they are not too confounded by this first point of contention already. __ 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] about R CMD check
hello, everybody,
I create a package by myself named var on Linux system. I attach a C code
which uses R_ext/Lapack.h in directory src. But when I carry out R CMD
check var, it shows
wxt0124()
Error in .C(wxt1221, PACKAGE = var) : C function name not in DLL for package
var
Execution halted
Could you tell me what is the problem?
Maggie
[EMAIL PROTECTED] myrpackages]$ R CMD check var
* checking for working latex ... OK
* using log directory '/home/credsim/src/myrpackages/var.Rcheck'
* checking for file 'var/DESCRIPTION' ... OK
* checking if this is a source package ... OK
* Installing *source* package 'var' ...
** libs
gcc -I/usr/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp
-fPIC -O2 -g -march=i386 -mcpu=i686 -c wxt1221.c -o wxt1221.o
wxt1221.c: In function `Matrix_A_12':
wxt1221.c:774: warning: passing arg 3 of `dpotrf_' from incompatible pointer
type
wxt1221.c:775: warning: passing arg 4 of `dpotrs_' from incompatible pointer
type
wxt1221.c: In function `Matrix_A_1':
wxt1221.c:1038: warning: passing arg 3 of `dpotrf_' from incompatible pointer
type
wxt1221.c:1039: warning: passing arg 4 of `dpotrs_' from incompatible pointer
type
wxt1221.c: In function `Matrix_A_2':
wxt1221.c:1290: warning: passing arg 3 of `dpotrf_' from incompatible pointer
type
wxt1221.c:1291: warning: passing arg 4 of `dpotrs_' from incompatible pointer
type
gcc -shared -L/usr/local/lib -o var.so wxt1221.o -L/usr/lib/R/bin -lRlapack
-L/usr/local/lib -L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2
-L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2/../../.. -lfrtbegin -lg2c -lm
-lgcc_s
** R
** help
Warning: \alias{wxt0124} already in wxt0124.Rd -- skipping the one in wxt1221.Rd
Building/Updating help pages for package 'var'
Formats: text html latex example
wxt0124 texthtmllatex example
wxt1221 texthtmllatex example
* DONE (var)
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking for replacement functions with final arg not named 'value' ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
b
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C sources/headers ... OK
* creating var-Ex.R ... OK
* checking examples ... ERROR
Running examples in var-Ex.R failed.
The error most likely occurred in:
### * wxt0124
flush(stderr()); flush(stdout())
### Name: wxt0124
### Title: Estimation of Optimal Variance Components in CCC Model
### Aliases: wxt0124
### Keywords: array
wxt0124()
Error in .C(wxt1221, PACKAGE = var) : C function name not in DLL for package
var
Execution halted
### ** Examples
__
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] contrast matrix for aov
As an R newbie (formerly SPSS), I was pleased to find some helpful notes on ANOVA here: http://personality-project.org/r/r.anova.html In my case, I believe the relevant section is: Example 4. Two-Way Within-Subjects ANOVA This is where I noted and copied the error notation. Sorry for any confusion about terms - I did mean within-subjects factors, rather than repeated measures (although, as noted earlier, we do have both in this experiment). Prof Brian Ripley wrote: On Thu, 10 Mar 2005, Christophe Pallier wrote: Prof Brian Ripley wrote: On Wed, 9 Mar 2005, Darren Weber wrote: We have a two-factor, repeated measures design, with Where does `repeated measures' come into this? You appear to have repeated a 2x2 experiment in each of 8 blocks (subjects). Such a design is usually analysed with fixed effects. (Perhaps you averaged over repeats in the first few lines of your code?) roi.aov - aov(roi ~ (Cue*Hemisphere) + Error(Subject/(Cue*Hemisphere)), data=roiDataframe) I think the error model should be Error(Subject). In what sense are `Cue' and `Cue:Hemisphere' random effects nested inside `Subject'? I do not understand this, and I think I am probably not the only one. That is why I would be grateful if you could give a bit more information. My understanding is that the fixed factors Cue and Hemisphere are crossed with the random factor Subject (in other words, Cue and Hemisphere are within-subjects factors, and this is probably why Darren called it a repeated measure design). The issue is whether the variance of the error really depends on the treatment combination, which is what the Error(Subject/(Cue*Hemisphere)) assumes. With that model Error: Subject:Cue Df Sum Sq Mean Sq F value Pr(F) Cue1 0.2165 0.2165 0.1967 0.6708 Residuals 7 7.7041 1.1006 Error: Subject:Hemisphere Df Sum Sq Mean Sq F value Pr(F) Hemisphere 1 0.0197 0.0197 0.0154 0.9047 Residuals 7 8.9561 1.2794 Error: Subject:Cue:Hemisphere Df Sum Sq Mean Sq F value Pr(F) Cue:Hemisphere 1 0.0579 0.0579 0.0773 0.789 Residuals 7 5.2366 0.7481 you are assuming different variances for three contrasts. In this case, it seems to me from the various textbooks I read on Anova, that the appropriate MS to test the interaction Cue:Hemisphere is Subject:Cue:Hemisphere (with 7 degress of freedom, as there are 8 independent subjects). If you input Error(Subject/(Cue*Hemisphere)) in the aov formula, then the test for the interaction indeed uses the Subject:Cue:Hemisphere source of variation in demoninator. This fits with the ouput of other softwares. If you include only 'Subjet', then the test for the interaction has 21 degrees of Freedom, and I do not understand what this tests. It uses a common variance for all treatment combinations. I apologize in if my terminology is not accurate. But I hope you can clarify what is wrong with the Error(Subject/(Cue*Hemisphere)) term, or maybe just point us to the relevant textbooks. Nothing is `wrong' with it, it just seems discordant with the description of the experiment. __ 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] how to view the syntax of a method which is not a generic method
Hello - I'm trying to modify an option for the lme() or nlme() macros. I want to write my own specification for the variance function and am following homework problem 4, Chapter 5, page 268 of Pinheiro and Bates book on mixed effect. I'm up to point where I've created a new class using an existing variance function class, varExp as a template. Next I need to write an initialize method. The book suggests that I use the inialize method for one of the exisiting variance functions for lme(), eg varExp. What I want is the syntax of the initialize.varExp method so that I can edit it to create an initialize method for my newly constructed class. So - I tried to get the text of this method, called initialize.varExp by using the showMethods command. Here's what happened. showMethods(initialize.varExp) Function initialize.varExp: not a generic function So I assume that inialize.varExp is not a generic method. I also have the following information. findFunction(initialize.varExp) list() and findFunction(varExp) [[1]] environment: package:nlme attr(,name) [1] package:nlme attr(,path) [1] C:/PROGRA~1/R/rw1091/library/nlme So I'm guessing I somehow need to tell the showMethods command that initialize.varExp is part of the nlme package. And now I'm stuck - any suggestions? Thanks so much - Sarah Holte __ 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] RODBC autocommit
How can I turn autocommit off using my RODBC connection to an Informix database? I want to turn autocommit off, insert a thousand or so rows then commit. __ 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] Transparent colors OR two series on one histogram
Hi, I want to be able to plot a single histogram of a measured trait with trait values from two conditions on the same histogram to allow easy comparison. I have previously done this in excel by plotting the two series on a single bargraph having calculated frequencies in bins. You then get one condition plotted immediately to the right of the other. I hope that makes sense? I don't know if this is possible in R? If not, I could plot the second one on top of the first i.e. hist(x) hist(y,add=TRUE) but i would need to set one as having a semi-transparent color so that where the two sets of are plotted on top of each other, you can see the frequency of the first series 'behind' the second. Can anyone help me do this? It would be another step towards never using excel again :) Thanks __ 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 view the syntax of a method which is not a generic method
Hi Sarah, Sarah Holte [EMAIL PROTECTED] writes: The book suggests that I use the inialize method for one of the exisiting variance functions for lme(), eg varExp. What I want is the syntax of the initialize.varExp method so that I can edit it to create an initialize method for my newly constructed class. You might want to download the source package for nlme. You can get it here: http://cran.fhcrc.org/src/contrib/nlme_3.1-56.tar.gz I think the function you are looking for is defined in varFunc.R and it looks like it is Initialize.varExp (initial cap) so you might retry your search techniques with that name. Hope that helps, + seth __ 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] Transparent colors OR two series on one histogram
On Thu, 10 Mar 2005, Nathaniel Street wrote: Hi, I want to be able to plot a single histogram of a measured trait with trait values from two conditions on the same histogram to allow easy comparison. I have previously done this in excel by plotting the two series on a single bargraph having calculated frequencies in bins. You then get one condition plotted immediately to the right of the other. I hope that makes sense? I don't know if this is possible in R? You can do it for bar plots, but not for histograms. Look at barplot(beside=TRUE) If not, I could plot the second one on top of the first i.e. hist(x) hist(y,add=TRUE) but i would need to set one as having a semi-transparent color so that where the two sets of are plotted on top of each other, you can see the frequency of the first series 'behind' the second. Semitransparent colors are available for the pdf() and quartz() devices. They were described by Paul Murrell in R News Vol 4 No 2. -thomas __ 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] Question regarding mosaicplot
I tried this : mosaicplot(stoc ~ q9r + segca,data=tmp2,color=T) : works fine. And now, this : mosaicplot(stoc ~ q9r + segca, data=tmp2, color=T, main=Big title) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type I'm probably stupid and missed something simple in the manual (and wouldn't like to be flamed if insinuating that, may be... a bug ? Oh no !). It can be done with : mosaicplot(table(tmp2$stoc,tmp2$q9r,tmp2$segca),color=T,main=Big title) : works fine. So, no real trouble for me... version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor8.0 year 2003 month10 day 08 language R __ 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] Logistic regression goodness of fit tests
I was unsure of what suitable goodness-of-fit tests existed in R for logistic regression. After searching the R-help archive I found that using the Design models and resid, could be used to calculate this as follows: d - datadist(mydataframe) options(datadist = 'd') fit - lrm(response ~ predictor1 + predictor2..., data=mydataframe, x =T, y=T) resid(fit, 'gof'). I set up a script to first use glm to create models use stepAIC to determine the optimal model. I used this instead of fastbw because I found the AIC values to be completely different and the final models didn't always match. Then my script takes the reduced model formula and recreates it using lrm as above. Now the problem is that for some models I run into an error to which I can find no reference whatsoever on the mailing list or on the web. It is as follows: test.lrm - lrm(cclo ~ elev + aspect + cti_var + planar + feat_div + loamy + sands + sandy + wet + slr_mean, data=datamatrix, x = T, y = T) singular information matrix in lrm.fit (rank= 10 ). Offending variable(s): slr_mean Error in j:(j + params[i] - 1) : NA/NaN argument Now if I add the singularity criterion and make the value smaller than the default of 1E-7 to 1E-9 or 1E-12 which is the default in calibrate, it works. Why is that? Not being a statistician but a biogeographer using regression as a tool, I don't really understand what is happening here. Does changing the tol variable, change how I should interpret goodness-of-fit results or other evaluations of the models created? I've included a summary of the data below (in case it might be helpful) with all variables in the data frame as it was easier than selecting out the ones used in the model. Thanks in advance. T -- Trevor Wiens [EMAIL PROTECTED] The significant problems that we face cannot be solved at the same level of thinking we were at when we created them. (Albert Einstein) summary(datamatrix) siteid block recordyearcclo 564-125: 5 Min. :1.000 Min. :2000 Min. :0. 564-130: 5 1st Qu.:2.000 1st Qu.:2001 1st Qu.:1. 564-135: 5 Median :3.000 Median :2002 Median :1. 564-140: 5 Mean :3.042 Mean :2002 Mean :0.7509 564-145: 5 3rd Qu.:4.000 3rd Qu.:2003 3rd Qu.:1. 564-150: 5 Max. :5.000 Max. :2004 Max. :1. (Other):1098 elevslopeaspect slr_mean Min. :0. Min. :0.1499 Min. :0. Min. :7681 1st Qu.:0. 1st Qu.:0.5876 1st Qu.:0. 1st Qu.:7852 Median :1. Median :0.9195 Median :0. Median :7877 Mean :0.6259 Mean :1.2523 Mean :0.2482 Mean :7871 3rd Qu.:1. 3rd Qu.:1.6694 3rd Qu.:0. 3rd Qu.:7892 Max. :1. Max. :5.3366 Max. :1. Max. :7981 cti cti_var planar feat_div Min. :7.157 Min. :0.4497 Min. :0. Min. :1.000 1st Qu.:7.651 1st Qu.:0.6187 1st Qu.:1. 1st Qu.:2.000 Median :7.720 Median :0.8495 Median :1. Median :3.000 Mean :7.763 Mean :0.9542 Mean :0.8254 Mean :3.379 3rd Qu.:7.822 3rd Qu.:1.1918 3rd Qu.:1. 3rd Qu.:4.000 Max. :8.769 Max. :2.5615 Max. :1. Max. :6.000 chop_san loamysandssandy Min. :0.0 Min. :0. Min. :0. Min. :0. 1st Qu.:0.0 1st Qu.:0. 1st Qu.:0. 1st Qu.:0. Median :0.0 Median :0. Median :0. Median :0. Mean :0.05762 Mean :0.3094 Mean :0.3236 Mean :0.1099 3rd Qu.:0.0 3rd Qu.:1. 3rd Qu.:1. 3rd Qu.:0. Max. :1.0 Max. :1. Max. :1. Max. :1. wet timesinceburn ndvi evi Min. :0.0 Min. : 1.00 Min. :0.1140 Min. :0.1041 1st Qu.:0.0 1st Qu.:100.00 1st Qu.:0.2973 1st Qu.:0.1667 Median :0.0 Median :100.00 Median :0.3342 Median :0.2027 Mean :0.01950 Mean : 87.84 Mean :0.3629 Mean :0.2184 3rd Qu.:0.0 3rd Qu.:100.00 3rd Qu.:0.4463 3rd Qu.:0.2711 Max. :1.0 Max. :100.00 Max. :0.5932 Max. :0.4788 msavi2 fc gddprecip Min. :0.09156 Min. :0.1552 Min. :380.6 Min. : 50.04 1st Qu.:0.14936 1st Qu.:0.3246 1st Qu.:492.8 1st Qu.: 76.17 Median :0.18257 Median :0.4082 Median :500.8 Median : 85.50 Mean :0.19653 Mean :0.4398 Mean :476.4 Mean : 94.35 3rd Qu.:0.24626 3rd Qu.:0.5630 3rd Qu.:501.6 3rd Qu.: 95.16 Max. :0.33258 Max. :0.6996 Max.
Re: [R] Question regarding mosaicplot
Jean: On Tue, 18 Nov 2003 23:32:05 Jean Vidal wrote: I tried this : mosaicplot(stoc ~ q9r + segca,data=tmp2,color=T) : works fine. And now, this : mosaicplot(stoc ~ q9r + segca, data=tmp2, color=T, main=Big title) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type I'm probably stupid and missed something simple in the manual (and wouldn't like to be flamed if insinuating that, may be... a bug ? Oh no !). OK, so you're getting flamed for something else: 1. Your example is not reproducible because you didn't provide the data (or use artificial data or ...)! If I use tmp2 - data.frame(stoc = gl(2, 1, 8), q9r = gl(2, 2, 8), segca = gl(2, 4, 8)) the above works correct. But then again... 2. ...your R version is ancient, please upgrade before posting such requests! 3. Please read the posting guide. Best, Z It can be done with : mosaicplot(table(tmp2$stoc,tmp2$q9r,tmp2$segca),color=T,main=Big title) : works fine. So, no real trouble for me... version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor8.0 year 2003 month10 day 08 language R __ 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-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] Logistic regression goodness of fit tests
On Thu, 10 Mar 2005, Trevor Wiens wrote: I was unsure of what suitable goodness-of-fit tests existed in R for logistic regression. After searching the R-help archive I found that using the Design models and resid, could be used to calculate this as follows: d - datadist(mydataframe) options(datadist = 'd') fit - lrm(response ~ predictor1 + predictor2..., data=mydataframe, x =T, y=T) resid(fit, 'gof'). I set up a script to first use glm to create models use stepAIC to determine the optimal model. I used this instead of fastbw because I found the AIC values to be completely different and the final models didn't always match. Then my script takes the reduced model formula and recreates it using lrm as above. Now the problem is that for some models I run into an error to which I can find no reference whatsoever on the mailing list or on the web. It is as follows: test.lrm - lrm(cclo ~ elev + aspect + cti_var + planar + feat_div + loamy + sands + sandy + wet + slr_mean, data=datamatrix, x = T, y = T) singular information matrix in lrm.fit (rank= 10 ). Offending variable(s): slr_mean Error in j:(j + params[i] - 1) : NA/NaN argument Now if I add the singularity criterion and make the value smaller than the default of 1E-7 to 1E-9 or 1E-12 which is the default in calibrate, it works. Why is that? Not being a statistician but a biogeographer using regression as a tool, I don't really understand what is happening here. From one geographer to another, and being prepared to bow to better-founded explanations, you seem to have included a variable - the offending variable slr_mean - that is very highly correlated with another. Making the tolerance tighter says that you are prepared to take the risk of confounding your results. You've already been fishing for right hand side variables anyway, so your results are somewhat prejudiced, aren't they? I think you may also like to review which of the right hand side variables should be treated as factors rather than numeric (looking at the summary suggests that many are factors), and perhaps the dependent variable too, although lrm() seems to take care of this if you haven't. Does changing the tol variable, change how I should interpret goodness-of-fit results or other evaluations of the models created? I've included a summary of the data below (in case it might be helpful) with all variables in the data frame as it was easier than selecting out the ones used in the model. Thanks in advance. T -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ 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] Logistic regression goodness of fit tests
Trevor Wiens wrote: I was unsure of what suitable goodness-of-fit tests existed in R for logistic regression. After searching the R-help archive I found that using the Design models and resid, could be used to calculate this as follows: d - datadist(mydataframe) options(datadist = 'd') fit - lrm(response ~ predictor1 + predictor2..., data=mydataframe, x =T, y=T) resid(fit, 'gof'). I set up a script to first use glm to create models use stepAIC to determine the optimal model. I used this instead of fastbw because I found the AIC values to be completely different and the final models didn't always match. Then my script takes the reduced model formula and recreates it using lrm as above. Now the problem is that for some models I run into an error to which I can find no reference whatsoever on the mailing list or on the web. It is as follows: test.lrm - lrm(cclo ~ elev + aspect + cti_var + planar + feat_div + loamy + sands + sandy + wet + slr_mean, data=datamatrix, x = T, y = T) singular information matrix in lrm.fit (rank= 10 ). Offending variable(s): slr_mean Error in j:(j + params[i] - 1) : NA/NaN argument Now if I add the singularity criterion and make the value smaller than the default of 1E-7 to 1E-9 or 1E-12 which is the default in calibrate, it works. Why is that? Not being a statistician but a biogeographer using regression as a tool, I don't really understand what is happening here. Does changing the tol variable, change how I should interpret goodness-of-fit results or other evaluations of the models created? I've included a summary of the data below (in case it might be helpful) with all variables in the data frame as it was easier than selecting out the ones used in the model. Thanks in advance. T The goodness of fit test only works on prespecified models. It is not valid when stepwise variable selection is used (unless perhaps you use alpha=0.5). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] install R redhat rpm as a normal user
Thank you all. Best, Eric On Mar 10, 2005, at 7:21 AM, Marc Schwartz wrote: On Wed, 2005-03-09 at 16:17 -0800, Eric Hu wrote: Hi, I wonder if anyone has done this before. I have rpm-build installed in my workstation. Thanks. Eric I have not seen any other replies to this, but as far as I know Martyn's RPMS are not relocatable and a test this morning confirms that. If you need to install R as a non-root user, you are likely better off installing from source code. Modify the --prefix argument to ./configure as per the R Administration Manual. For example: ./configure --prefix=TargetDir where TargetDir is a directory that you have write privileges to. Then use make and make install which will then build and install R. R will be installed in TargetDir (ie. /home/UserName/R) with a set of subdirs bin, lib and man. To run R, you would then use: TargetDir/bin/R Or you can create a symlink in /home/UserName/bin to the above file and then just use R to start it. See the R Administration Manual for more information. HTH, Marc Schwartz __ 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] Logistic regression goodness of fit tests
On Thu, 10 Mar 2005 22:36:09 +0100 (CET) Roger Bivand [EMAIL PROTECTED] wrote: From one geographer to another, and being prepared to bow to better-founded explanations, you seem to have included a variable - the offending variable slr_mean - that is very highly correlated with another. Making the tolerance tighter says that you are prepared to take the risk of confounding your results. You've already been fishing for right hand side variables anyway, so your results are somewhat prejudiced, aren't they? I think you may also like to review which of the right hand side variables should be treated as factors rather than numeric (looking at the summary suggests that many are factors), and perhaps the dependent variable too, although lrm() seems to take care of this if you haven't. Thanks for your informative reply. The nature of the research is habitat selection for 15 species of grassland birds (my masters project). The response here is presence of Chestnut-collared Longsur (cclo). I very carefull reviewed the variables for collinearity and none of them showed any difficulty except in a few cases which I've used to break some cases into two models where one would have otherwise seemed reasonable. Just out of interest however I did run the global model, and this problem didn't occur, which seems to indicate to me, based on your comments, I'm seeing an interaction effect, not a result of two closely correlated variables. I don't think I've been fishing. I selected variables for inclusion in competing models based on ecologically reasonable criteria. I did examine relationships between species occurance and static variables such as dem derived variables, to see if the data supported including all variables that based on ecological criteria should explain the birds distribution. I have included some variables inspite of weak statistical relationships based on a paper by Anderson, Burnham and Thompson in Journal of Wildlife Management which talks about how factors that are ecologically significant, can have interaction effects in a model to provide explanation in your response variable, even though individually they are not statistically significant by themselves. So, I've tried to avoid fishing, but instead simply trying to select the most parsimonious models from the set of selected models for each species. Based on your advice once I've selected my top candidate models, I'll re-run at lower tolerances and only keep models that can pass at that level. Alternatively I could simply reject models that don't pass at lower tolerances. I do find it curious however that they run fine using glm (family = binomial) without complaint. Thanks again. T -- Trevor Wiens [EMAIL PROTECTED] The significant problems that we face cannot be solved at the same level of thinking we were at when we created them. (Albert Einstein) __ 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] Logistic regression goodness of fit tests
On Thu, 10 Mar 2005 16:19:41 -0600 Frank E Harrell Jr [EMAIL PROTECTED] wrote: The goodness of fit test only works on prespecified models. It is not valid when stepwise variable selection is used (unless perhaps you use alpha=0.5). Perhaps I'm blind, but I can't find any reference to an alpha parameter on the help page for stepAIC. It runs fine however when I set the parameter and produces as model with the same right hand variables as without. Can you tell me what it is ? T -- Trevor Wiens [EMAIL PROTECTED] The significant problems that we face cannot be solved at the same level of thinking we were at when we created them. (Albert Einstein) __ 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] Is anyone using the MiniR distribution?
On Fri, 04 Feb 2005 14:45:35 +, Duncan Murdoch [EMAIL PROTECTED] wrote : On Fri, 4 Feb 2005 14:46:03 +0100, Martin Maechler [EMAIL PROTECTED] wrote : Duncan == Duncan Murdoch [EMAIL PROTECTED] on Fri, 04 Feb 2005 09:50:22 + writes: Duncan The miniR files only include a minimal installation Duncan of R, and are rarely tested. Rather than building Duncan something that may not even work, I'd like to stop Duncan building them. Duncan Would this be a problem for anyone? People for which this is a problem will probably not be subscribed to R-help because they'll be living in places / situations with bad / expensive internet connection. (Sorry to be not really constructive here). That's a good point; I'll put a copy of my question in the miniR directory on CRAN. It's not a big problem to build it, but I don't want to test it if it's not being used. Not having heard any complaints on this issue, I have now stopped building the mini distribution. I have taken the 2.0.1 files offline (but still have them available in case this causes hardship for anyone). Duncan Murdoch __ 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] Any upcoming R Advanced Programming in Bay area?
Hi all, I am taking a new job in San Francisco and wonder if there's an upcoming R advanced course in bay area. Best- Paul __ 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] Setting variable main in plot-function
Hi, I am plotting the residuals of z like this plot(resid(z)) and I want the title of the graph to be main=Residuals from regression [name of regression] where in this case z is the name of the regression. Is there a way to automaticall put the name of the regression in the title, e.g if the regressions name changes to y, the title changes accordingly? Regards T Petersen __ 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] Ploting a function of two arguments
Hi,
I've written a function:
myfun - function(x, y) {
// blah blah
}
and I want to graph it. My plan is to use persp(), and my question is:
how do I create the array of values? One possibility is:
x - seq(0, 10, by=.1)
y - seq(0, 10, by=.1)
inputs - somehow create an array of x,y pairs
outputs - apply(A, c(1,2), myfun)
The inputs array would need to be 101x101x2 array, i.e. basically a 2D
array of pairs. I might need to write a little wrapper for myfun.
Am I on the right track, or is there an easier way to do this? It seems
there should be an easier way to graph a 2 argument function like this.
- Martin
__
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] trouble loading R function code
I created an R function offline with a text editor and saved it as fhv.R When I type in load(file=fhv.R) I get the message Error: bad restore file magic number (file may be corrupted)-- no data loaded I've checked the file, and it opens up fine in Notepad and other text editors. I also tried this from another folder and got the same message. What's going on? Thanks in advance. David Reinke Senior Transportation Engineer/Economist Dowling Associates, Inc. 180 Grand Avenue, Suite 250 Oakland, California 94612-3774 510.839.1742 x104 (voice) 510.839.0871 (fax) www.dowlinginc.com __ 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] trouble loading R function code
try: source(fhv.R) David Reinke wrote: I created an R function offline with a text editor and saved it as fhv.R When I type in load(file=fhv.R) I get the message Error: bad restore file magic number (file may be corrupted)-- no data loaded I've checked the file, and it opens up fine in Notepad and other text editors. I also tried this from another folder and got the same message. What's going on? Thanks in advance. David Reinke Senior Transportation Engineer/Economist Dowling Associates, Inc. 180 Grand Avenue, Suite 250 Oakland, California 94612-3774 510.839.1742 x104 (voice) 510.839.0871 (fax) www.dowlinginc.com __ 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-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] Errors reading data file?
Hi all -- I tried loading a data file with the following command: data = read.table(filename.txt, header = TRUE, sep = ,) This appeared to work fine, except it silently skipped 400 records (out of 1200). It turns out, some of the text fields included quotes, and I needed to use 'quote = '. Why wasn't there an error message? Is there some way to enable one? -- Chris __ 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] Bonferroni simultaneous confidence intervals for multiple regression
Hi, I'm having no luck figuring out how to find Bonferroni simultaneous confidence intervals to obtain a family of estimates in R. Does anyone know how to do this? Thank you! __ 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] Setting variable main in plot-function
On Fri, 2005-03-11 at 00:50 +0100, T Petersen wrote: Hi, I am plotting the residuals of z like this plot(resid(z)) and I want the title of the graph to be main=Residuals from regression [name of regression] where in this case z is the name of the regression. Is there a way to automaticall put the name of the regression in the title, e.g if the regressions name changes to y, the title changes accordingly? I am presuming that by the name of the regression, you mean the model formula. Using one of the example models from ?lm, where a model is created called lm.D9: plot(resid(lm.D9), main = paste(Residuals from regression, deparse(lm.D9$call))) In this case, the model function call is: deparse(lm.D9$call) [1] lm(formula = weight ~ group) which gets pasted to your initial text. The initial model function call is stored in the linear model object as ModelName$call. So in your case use: plot(resid(z), main = paste(Residuals from regression, deparse(z$call))) Just replace 'z' with the name of each new model object and the title will change or use the same model object name each time you create a new model, whichever makes sense for your application. One way to figure these things out, if you know that it has been done by some other function, is to review the code for that function. In this case review the code for print.lm or even plot.lm to gain some insight into how R expressions are used in function text or plot title and axis label outputs. HTH, Marc Schwartz __ 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] XML to data frame or list
Dear useRs, I have a simple/RTFM question about XML parsing. Given an XML file, such as (fragment) A100/A B23/B Ctrue/C how do I import it in a data frame or list, so that the values (100, 23, true) can be accessed through the names A, B and C? I installed the XML package and looked over the documentation... however after 20 minutes and a couple of tests I still don't know what I should start with. Can someone provide an example or point me to the appropriate function(s)? Thank you, b. __ 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] How to reply to a posting if I subscribe to the digest version of R-help?
Dear listmembers, Is there a recommended method of responding to a thread if I am getting the mailing list in digest form? Will the mailing list program automatically match threads if I copy the subject from the original posting? Thank you. Keith __ 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] sample function
Hi everyone, I need help. I want to have a uniform kind distribution. When I used sample function I got almost twice many zeros compared to other numbers. What's wrong with my command ? temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) hist(temp) Thanks in advance, Taka, __ 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] sample function
hist is lumping things together. Try: sum(temp == 0) compare to the height of the left most bar. Is this a bug in hist? - Martin mirage sell wrote: Hi everyone, I need help. I want to have a uniform kind distribution. When I used sample function I got almost twice many zeros compared to other numbers. What's wrong with my command ? temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) hist(temp) Thanks in advance, Taka, __ 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-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] sample function
It's not the simulated data, but how hist() handled it. If you use truehist() in the MASS package, you don't see the problem. Nor would you see it like this: table(temp)/length(temp) temp 0 1 2 3 4 5 6 7 8 9 10 11 0.0745 0.0745 0.0830 0.0755 0.0760 0.0750 0.0700 0.0765 0.0775 0.0805 0.0830 0.0765 12 0.0775 Andy From: mirage sell Hi everyone, I need help. I want to have a uniform kind distribution. When I used sample function I got almost twice many zeros compared to other numbers. What's wrong with my command ? temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) hist(temp) Thanks in advance, Taka, __ 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-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] sample function
On Thu, 10 Mar 2005, mirage sell wrote: Hi everyone, I need help. I want to have a uniform kind distribution. When I used sample function I got almost twice many zeros compared to other numbers. What's wrong with my command ? Nothing is wrong with your sampling, it is the display in the histogram. Try temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) table(temp) David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics __ 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] sample function
On Thu, 10 Mar 2005, Martin C. Martin wrote: hist is lumping things together. Try: sum(temp == 0) compare to the height of the left most bar. Is this a bug in hist? No, hist is the wrong thing to use to display this data. Try temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) barplot(table(temp)) David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 AucklandNEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics __ 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] sample function
On Thu, 2005-03-10 at 20:54 -0600, mirage sell wrote: Hi everyone, I need help. I want to have a uniform kind distribution. When I used sample function I got almost twice many zeros compared to other numbers. What's wrong with my command ? temp -sample(0:12, 2000, replace=T,prob=(rep(1/13,13))) hist(temp) Thanks in advance, Hint: take note that there are only 12 cells in the plot, not 13... However, note that the frequency of the 13 elements are appropriate: table(sample(0:12, 2000, replace=T)) 0 1 2 3 4 5 6 7 8 9 10 11 12 158 156 151 163 156 158 146 154 134 158 146 147 173 Review the details of how the breaks are selected in ?hist. BTW, you do not need to specify the 'prob' argument if you want equal probabilities as per my example above. HTH, Marc Schwartz __ 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] Interval censoring in Survival analysis
On Thu, 10 Mar 2005 08:01:57 -0800 (PST), Thomas Lumley [EMAIL PROTECTED] wrote: On Thu, 10 Mar 2005, AMOROS NAVARRO, ALEX wrote: I am not aware of any package that allows semiparametric regression modelling of interval censored or doubly censored data. I'm aware of 2 such packages, but the one that is more accurate won't be published due to licensing restrictions on one of the subcomponents (nonlinear programming with nonlinear constraints optimizer), and the other is less accurate (a profiling approach) and shouldn't be. That being said, I'm sure others have tried. -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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
Apologies --- Re: [R] Question regarding mosaicplot
May I present my apologies to all, on this list, and to you Achim ? It's an old message that was sent by accident yesterday when testing the Thunderbird mail program. So, please, ignore this question. It was answered and solved months ago. At 22:16 10/03/2005, Achim Zeileis wrote: Jean: On Tue, 18 Nov 2003 23:32:05 Jean Vidal wrote: I tried this : mosaicplot(stoc ~ q9r + segca,data=tmp2,color=T) : works fine. And now, this : mosaicplot(stoc ~ q9r + segca, data=tmp2, color=T, main=Big title) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type I'm probably stupid and missed something simple in the manual (and wouldn't like to be flamed if insinuating that, may be... a bug ? Oh no !). OK, so you're getting flamed for something else: 1. Your example is not reproducible because you didn't provide the data (or use artificial data or ...)! If I use tmp2 - data.frame(stoc = gl(2, 1, 8), q9r = gl(2, 2, 8), segca = gl(2, 4, 8)) the above works correct. But then again... 2. ...your R version is ancient, please upgrade before posting such requests! 3. Please read the posting guide. Best, Z It can be done with : mosaicplot(table(tmp2$stoc,tmp2$q9r,tmp2$segca),color=T,main=Big title) : works fine. So, no real trouble for me... version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor8.0 year 2003 month10 day 08 language R __ 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-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] help on warning message when using anova
Hi can someone help me with the following warning message I got when I used two way anova: Warning messages: 1: Models with response NULL removed because response differs from model 1 in: anova.lmlist(object, ...) 2: Models with response NULL removed because response differs from model 1 in: anova.lmlist(object, ...) (I have two rows of separate data sets) Thanks in advance, tao __ 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] howto: plot location, web search
Hi, new to the list, R and rpy. my first post. using rpy, i find this r.X11(height=3, width=6) allows me to preset the size of a subsequent r.plot(x, y) but i've been unable to find documention on related aspects, such as programatic control of the plot window location on the monitor, or programatic resizing of a plot once it is generated. Are these possible? In general I've found it diffcult to use google to search for answers because R is not a very effective keyword. Are there tricks to googling for R info? And If a start a web accessible html page for R, what keywords can I include that would make it easier for search engines to index so that other R-folk could find it? Thanks in advance, mike __ 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] xlab cex bug in Lattice/grid and multipage-output (Windows only?)
The following problem seems to be Windows-specific. Deepayan informed me that it cannot be reproduced on platform i386-pc-linux-gnu. - library(lattice) trellis.device(png, file=sepal%02d.png,color=T, theme=col.whitebg) p=xyplot(Sepal.Length + Sepal.Width ~ Petal.Length + Petal.Width | Species, data = iris, scales = free, layout = c(1, 1) ) print(p) dev.off() Compare the x-label on the first and on all following pages: font size is different. Same for bmp. Does not occur on multipage-devices such as ps. By comparing with the png files from Deepayan/Linux, I believe that only the first xlab has the correct small size, and all others are not correct. My version: (all libraries updated today) platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R __ 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] howto: plot location, web search
If it's specifically R that I am looking for I use the following link http://finzi.psych.upenn.edu/search.html If I were going to use google I would go to the advanced page and insert finzi.psych.upenn.edu into the Domain field so as to restrict the search. As you have found out the letter R is ubiquitous. There are other search engines listed on the CRAN website that you can also use http://cran.r-project.org/search.html However rpy is much less frequent. In fact google comes up with it straight away. From that I discovered that RPy has a mailing list http://rpy.sourceforge.net/maillist.html. Maybe you should try searching their archives http://rpy.sourceforge.net/maillist.html. I hope that helps Tom -Original Message- From: Mike R [mailto:[EMAIL PROTECTED] Sent: Friday, 11 March 2005 2:44 PM To: r-help@stat.math.ethz.ch Subject: [R] howto: plot location, web search Hi, new to the list, R and rpy. my first post. using rpy, i find this r.X11(height=3, width=6) allows me to preset the size of a subsequent r.plot(x, y) but i've been unable to find documention on related aspects, such as programatic control of the plot window location on the monitor, or programatic resizing of a plot once it is generated. Are these possible? In general I've found it diffcult to use google to search for answers because R is not a very effective keyword. Are there tricks to googling for R info? And If a start a web accessible html page for R, what keywords can I include that would make it easier for search engines to index so that other R-folk could find it? Thanks in advance, mike __ 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-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] howto: plot location, web search
Sorry about the wrong link. The archives are at http://sourceforge.net/mailarchive/forum.php?forum=rpy-list -Original Message- From: Mike R [mailto:[EMAIL PROTECTED] Sent: Friday, 11 March 2005 2:44 PM To: r-help@stat.math.ethz.ch Subject: [R] howto: plot location, web search Hi, new to the list, R and rpy. my first post. using rpy, i find this r.X11(height=3, width=6) allows me to preset the size of a subsequent r.plot(x, y) but i've been unable to find documention on related aspects, such as programatic control of the plot window location on the monitor, or programatic resizing of a plot once it is generated. Are these possible? In general I've found it diffcult to use google to search for answers because R is not a very effective keyword. Are there tricks to googling for R info? And If a start a web accessible html page for R, what keywords can I include that would make it easier for search engines to index so that other R-folk could find it? Thanks in advance, mike __ 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-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] about R CMD check
Please show us at least the prototype of the C function(s) being called, and
the .C call in the R code.
Just to make sure: The first argument to .C() should be the name of the C
function, not the name of the C source file.
Andy
From: [EMAIL PROTECTED]
hello, everybody,
I create a package by myself named var on Linux system. I
attach a C code
which uses R_ext/Lapack.h in directory src. But when I
carry out R CMD
check var, it shows
wxt0124()
Error in .C(wxt1221, PACKAGE = var) : C function name not
in DLL for package
var
Execution halted
Could you tell me what is the problem?
Maggie
[EMAIL PROTECTED] myrpackages]$ R CMD check var
* checking for working latex ... OK
* using log directory '/home/credsim/src/myrpackages/var.Rcheck'
* checking for file 'var/DESCRIPTION' ... OK
* checking if this is a source package ... OK
* Installing *source* package 'var' ...
** libs
gcc -I/usr/lib/R/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp
-fPIC -O2 -g -march=i386 -mcpu=i686 -c wxt1221.c -o wxt1221.o
wxt1221.c: In function `Matrix_A_12':
wxt1221.c:774: warning: passing arg 3 of `dpotrf_' from
incompatible pointer
type
wxt1221.c:775: warning: passing arg 4 of `dpotrs_' from
incompatible pointer
type
wxt1221.c: In function `Matrix_A_1':
wxt1221.c:1038: warning: passing arg 3 of `dpotrf_' from
incompatible pointer
type
wxt1221.c:1039: warning: passing arg 4 of `dpotrs_' from
incompatible pointer
type
wxt1221.c: In function `Matrix_A_2':
wxt1221.c:1290: warning: passing arg 3 of `dpotrf_' from
incompatible pointer
type
wxt1221.c:1291: warning: passing arg 4 of `dpotrs_' from
incompatible pointer
type
gcc -shared -L/usr/local/lib -o var.so wxt1221.o
-L/usr/lib/R/bin -lRlapack
-L/usr/local/lib -L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2
-L/usr/lib/gcc-lib/i386-redhat-linux/3.2.2/../../..
-lfrtbegin -lg2c -lm
-lgcc_s
** R
** help
Warning: \alias{wxt0124} already in wxt0124.Rd -- skipping
the one in wxt1221.Rd
Building/Updating help pages for package 'var'
Formats: text html latex example
wxt0124 texthtmllatex example
wxt1221 texthtmllatex example
* DONE (var)
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking for replacement functions with final arg not named
'value' ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
b
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C sources/headers ... OK
* creating var-Ex.R ... OK
* checking examples ... ERROR
Running examples in var-Ex.R failed.
The error most likely occurred in:
### * wxt0124
flush(stderr()); flush(stdout())
### Name: wxt0124
### Title: Estimation of Optimal Variance Components in CCC Model
### Aliases: wxt0124
### Keywords: array
wxt0124()
Error in .C(wxt1221, PACKAGE = var) : C function name not
in DLL for package
var
Execution halted
### ** Examples
__
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-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
