[R] set type of SS in anova()
When you use the 'general linear model' analysis in SPSS, the first result is a table with all terms with F-tests and significance values for all IV's. It uses http://joyx.joensuu.fi/~ek/anova/sstypes.txt SS Type III , which has the advantage that the order in which the variables are added to the model does not matter, and therefore it is relatively objective. I would like to reproduce this output in R. However, when using anova(glm.object, test=F), the F test shows Terms added sequentially (first to last). Because of this, the F values and p values of the terms depend on the sequence in which they were added. Eg: an anova() of glm(a~b+c) will give other results than glm(a~c+b). How can I specify the SS type of an anova in R, so that i can reproduce the exact results as that i got in SPSS? -- View this message in context: http://www.nabble.com/set-type-of-SS-in-anova%28%29-tp18287076p18287076.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] set type of SS in anova()
drop1() in R meets both your objection and that to 'Type III'. If you really want the so-called Type III, look at function Anova() in package car. But also consider library(fortunes); fortune(54); fortune((55); fortune(56) On Fri, 4 Jul 2008, jeroenooms wrote: When you use the 'general linear model' analysis in SPSS, the first result is a table with all terms with F-tests and significance values for all IV's. It uses http://joyx.joensuu.fi/~ek/anova/sstypes.txt SS Type III , which has the advantage that the order in which the variables are added to the model does not matter, and therefore it is relatively objective. No, as the terms may well have a natural hierachy in which case the order does matter. I would like to reproduce this output in R. However, when using anova(glm.object, test=F), the F test shows Terms added sequentially (first to last). Because of this, the F values and p values of the terms depend on the sequence in which they were added. Eg: an anova() of glm(a~b+c) will give other results than glm(a~c+b). Hmm: glm() is used for generalized linear models, and there sums of squares are only appropriate for those models where lm() is more appropriate. How can I specify the SS type of an anova in R, so that i can reproduce the exact results as that i got in SPSS? -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] synthax for R CMD INSTALL
I do not know what 'the R Utils docs' are, but --configure-args is plural! You are not using the correct shell syntax: you need to use quotes when arguments contain spaces. E.g. --configure-args='--args=val1 --arg2=val2' (and note that quotes are used in error info you quote). That said, the error you got suggests that the value of --with-proj-include is incorrect. I think you would be better off asking questions about installing on Mac OS X on r-sig-mac. On Fri, 4 Jul 2008, Naiara Pinto wrote: Dear all, I am trying to install rgdal from source on a Mac OS 10.4.11. I installed GDAL and PROJ as frameworks so the installation does not work unless I explicitly state where the GDAL and PROJ libraries are. I tried: R CMD INSTALL rgdal_0.5-25 --configure-args=--with-proj-include=/Library/Frameworks/PROJ.framework/unix/include --with-proj-lib=/Library/Frameworks/PROJ.framework/unix/lib but I still get error messages saying it was not able to find the PROJ include file: If the PROJ.4 library is installed in a non-standard location, use --configure-args='--with-proj-include=/opt/local/include' for example, replacing /opt/local/* with appropriate values for your installation. If PROJ.4 is not installed, install it. ERROR: configuration failed for package 'rgdal' If I understood the R Utils docs correctly, --configure-args will accept one argument only (so the first statement is always dropped). What should I do if I need to specify the paths to several files? Thank you, Naiara. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] trying to superimpose a line plot onto a histogram
Hello, I'm trying to superimpose a line plot onto a histogram but I'm not having any luck. I've attached the dataset. What I did was: hist(data,freq=F) Now I'm trying to superimpose the following points with a line connecting them onto the histogram: xy 100 0.535665393824959 200 0.212744329736556 300 0.0844933242968584 400 0.0335572838043417 500 0.0133275771274986 600 0.00529316714442912 700 0.0021022289461042 800 0.000834919136549392 900 0.000331595645597124 1000 0.000131696193518099 1100 5.2304327929049e-05 1200 2.07731343406939e-05 Basically, the x values correspond to the break points in the histogram. Next I used the command points(x,y,type=l) But for some reason, the line plot is shifted to the right and doesn't line up with the histogram. Thanks for the help! Edwin Lei data.pdf Description: Adobe PDF document __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lattice smooth
Dear friends - I have a data.frame hh with columns Na ID fit time 135 13 134.7945 60 133 13 132.9084 120 131 13 131.0848 180 129 13 129.3372 240 127 13 127.5546 300 126 13 125.8162 360 124 13 124.1836 420 123 13 122.6077 480 When I use lattice xyplot(Na+fit~time|ID,hh,type=c(smooth,g,p), auto.key=list(lines=TRUE)) the curve for Na after time 240 takes some wild swings, and a warning is issued Warning messages: 1: pseudoinverse used at 482.1 2: neighborhood radius 242.1 3: reciprocal condition number 0 4: at 360 5: radius 14400 6: all data on boundary of neighborhood. make span bigger 7: There are other near singularities as well. 14400 8: pseudoinverse used at 482.1 9: neighborhood radius 242.1 10: reciprocal condition number 0 11: at 360 12: radius 14400 13: all data on boundary of neighborhood. make span bigger 14: There are other near singularities as well. 14400 Otherwise for the whole dataset of 16 pigs it works quite OK - but only this pig number 13 makes troubles. I wonder what occurs. Best wishes Troels -- Troels Ring - - Department of nephrology - - Aalborg Hospital 9100 Aalborg, Denmark - - +45 99326629 - - [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bland-Altman method to measure agreement with repeated measures
Dear all, I want to use the Bland-Altman method to measure agreement with repeated measures collected over period of time (seven periods). How can I do this with R Many thanks _ o.fr [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] update search path for attached data
On Fri, 2008-07-04 at 15:13 +0100, Prof Brian Ripley wrote: On Fri, 4 Jul 2008, Ulrich Leopold wrote: Dear list, is there a way of updating the search path when using attach() for a data set. I am overwriting a variable in a data frame. To update teh search path I do the follwoing: attach(dataset) some data manipulation of dataset detach(dataset) attach(dataset) # to update the search path Is there a way to avoid the numerous detach() and attach() commands? Not if 'dataset' is that data frame (you didn't actually say). From the help page: The database is not actually attached. Rather, a new environment is created on the search path and the elements of a list (including columns of a data frame) or objects in a save file or an environment are _copied_ into the new environment. If you use '-' or 'assign' to assign to an attached database, you only alter the attached copy, not the original object. So you can both change the data frame and assign the column to pos=2 to get the effect of what you appear to want. How can I update directly the search path without using detach() attach() or '-' assign()? Maybe using attach() or assign methods is not so convenient anyway in my case as it creates always a copy of each data set? Is there a good practise in programming in R by using search paths but keep memory as well as updating of the search path to a minimum? Ulrich -- __ Ulrich Leopold Resource Centre for Environmental Technologies, Public Research Centre Henri Tudor, Technoport Schlassgoart, 66 rue de Luxembourg, P.O. BOX 144, L-4002 Esch-sur-Alzette, Luxembourg tel: +352 425991 618 fax: +352 425991 601 mobile: +352 691 304813 http://www.crte.lu Computational Bio- and Physical Geography, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 166, NL-1018WV Amsterdam, The Netherlands http://www.science.uva.nl/ibed __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] p-value for Nonmetric Multidimentional Scaling?
On Fri, 2008-07-04 at 21:14 -0700, Michael Denslow wrote: Dear R-helpers, I am running metaMDS in the vegan package, which uses isoMDS in MASS, to perform Nonmetric Multidimentional Scaling (NMDS). I have seen some authors report a p-value for the NMDS ordination based on randomization of the dataset. As I understand it this is meant to compare the stress in your dataset to multiple runs of randomized data. I do not see a way to perform such a test in vegan or MASS. So my questions are: Is this necessary? and Does R have a function to do this? No, but the following discussion on the r-forge repository for vegan presents some ways that an analysis of this type could be done using metaMDS: http://r-forge.r-project.org/forum/forum.php?thread_id=586forum_id=194 But read Jari's comments carefully. If your data are species, then consider whether permuting row, columns or both is appropriate when they don't preserve the row or column totals. So a question to ask yourself is, is permuting rows, columns or both going to derive the appropriate Null hypothesis for the test you have in mind? Please feel free to follow this up in the forum post I refer to. All the best, G Thanks in advance for your help, Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] set type of SS in anova()
Dear j.c.l.omms, The Anova() function in the car package can compute so-called type-II and type-III tests. When there are terms in the model that are marginal to others (such as main effects marginal to interactions), type-III tests are of questionable interest and have to be formulated carefully to test sensible hypotheses. As well, since glm() with no family argument fits a linear model with normal errors, it would be more usual in R to use lm(). Regards, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of jeroenooms Sent: July-04-08 6:37 PM To: r-help@r-project.org Subject: [R] set type of SS in anova() When you use the 'general linear model' analysis in SPSS, the first result is a table with all terms with F-tests and significance values for all IV's. It uses http://joyx.joensuu.fi/~ek/anova/sstypes.txt SS Type III , which has the advantage that the order in which the variables are added to the model does not matter, and therefore it is relatively objective. I would like to reproduce this output in R. However, when using anova(glm.object, test=F), the F test shows Terms added sequentially (first to last). Because of this, the F values and p values of the terms depend on the sequence in which they were added. Eg: an anova() of glm(a~b+c) will give other results than glm(a~c+b). How can I specify the SS type of an anova in R, so that i can reproduce the exact results as that i got in SPSS? -- View this message in context: http://www.nabble.com/set-type-of-SS-in- anova%28%29-tp18287076p18287076.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Test for multiple comparisons: Nonlinear model, autocorrelation?
Thanks. Here is a similar example from a book by Pinheiro and Bates (2000, chapter 6): library(nlme) data(Soybean) fm1Soy.lis - nlsList( weight ~ SSlogis(Time, Asym, xmid, scal),data = Soybean ) fm1Soy.nlme - nlme( fm1Soy.lis ) If we would like to make comparisons among the years we could just simply involve years as a covariate, and later we could use L argument to ANOVA to could compute contrasts. soyFix - fixef( fm1Soy.nlme ) fm2Soy.nlme - update( fm1Soy.nlme,fixed = Asym + xmid + scal ~ Year,start = c(soyFix[1], 0, 0, soyFix[2], 0, 0, soyFix[3], 0, 0) ) My question is: How can I compare variety of soybeans in a separate month, i.e. if there was a difference in weight of soybeans F and P in first month, in twelve month? The dataset Soybean: Plot Variety Year Timeweight 1 1988F1 F 1988 14 0.106000 2 1988F1 F 1988 21 0.261000 3 1988F1 F 1988 28 0.666000 4 1988F1 F 1988 35 2.11 5 1988F1 F 1988 42 3.56 . 407 1990P8 P 1990 30 1.478330 408 1990P8 P 1990 37 2.601667 409 1990P8 P 1990 43 6.343330 410 1990P8 P 1990 51 6.131670 411 1990P8 P 1990 64 16.411700 412 1990P8 P 1990 79 16.946700 1) Involving months and variety as a covariates will probably create too many parameters for the model? 2) Is it possible to use some test for comparisons, lets say t test? Perhaps not in case the data are dependent (i.e. previous measurement is dependent on the next measurement, i.e. there is temporal correlation (as in my study of Soil temperature)? What is an alternative suggestion? Thanks, Julia Date: Fri, 4 Jul 2008 17:36:29 -0700 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] Test for multiple comparisons: Nonlinear model, autocorrelation? The question seems too general for me to offer specific suggestions. What problem are you trying to solve that you think 'multiple comparisons' will answer? Can you produce a similar problem that is completely self-contained example that eliminates complexity that may not be needed to understand your question (similar to the 'Auxiliary Problem' technique in How to Solve It, http://en.wikipedia.org/wiki/How_to_Solve_It)? If you can, it may lead you to a solution. If you get such an example but still can't see a solution, send that example to this list (following the advice in the posting guide http://www.R-project.org/posting-guide.html). The simpler the example, the more likely someone on this list will reply quickly with a useful suggestion. I know this doesn't solve your problem, but I hope it helps. Spencer J S wrote: Dear R community, I have a nonlinear model describing average daily soil temperature. What test should I use to compare differences in soil temperature of the two studied vegetation types depending upon month?Building linear contrasts for the developed nonlinear model does not help since this model does not include variable Months (only Days). 1) Just a Students test is not probably an option because I would violate an assumption of independency, since the daily soil temperature observations have high autocorrelation. Or maybe I could average the observations for each month and then use this test since I have observations for a few years, and it might overcome the problem of independency?2) Should I develop a second nonlinear model with months instead of days, but it would considerably increase a number of parameters in the model...Or: 3) ?Thanks for your help, Julia _ Its a talkathon but its not just talk. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ The im Talkaton. Can 30-days of conversation change the world? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trying to superimpose a line plot onto a histogram
How about the answer by Demitris? Regards a lot, miltinho From: Dimitris Rizopoulos [EMAIL PROTECTED] Date: Jun 16, 2008 4:05 AM Subject: Re: [R] Superimposing Line over Histogram in Density Plot To: Gundala Viswanath [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] try something like this: x - rnorm(200) hist(x, col = blue, freq = FALSE) lines(density(x), col = red, lwd = 2) On 7/5/08, Edwin Lei [EMAIL PROTECTED] wrote: Hello, I'm trying to superimpose a line plot onto a histogram but I'm not having any luck. I've attached the dataset. What I did was: hist(data,freq=F) Now I'm trying to superimpose the following points with a line connecting them onto the histogram: xy 100 0.535665393824959 200 0.212744329736556 300 0.0844933242968584 400 0.0335572838043417 500 0.0133275771274986 600 0.00529316714442912 700 0.0021022289461042 800 0.000834919136549392 900 0.000331595645597124 1000 0.000131696193518099 1100 5.2304327929049e-05 1200 2.07731343406939e-05 Basically, the x values correspond to the break points in the histogram. Next I used the command points(x,y,type=l) But for some reason, the line plot is shifted to the right and doesn't line up with the histogram. Thanks for the help! Edwin Lei __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help about random generation of a Normal distribution of several variables
Hello. Somebody knows how can I generate a set of n random vectors of a normal distribution of several variables? For example, I want to generate n=100 random vectors of two dimensions for a normal with mean c(0,1) and variance matrix: matrix(c(2,1,1,3),2,2). Thanks in advance, Arnau. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution of several variables
Hi, Arnau, mvrnorm() in MASS library is what you need. ? mvrnorm to see the detail but first you need to load the MASS library, i.e,library(MASS) regards/ On 2008-7-6, at 上午12:21, Arnau Mir wrote: Hello. Somebody knows how can I generate a set of n random vectors of a normal distribution of several variables? For example, I want to generate n=100 random vectors of two dimensions for a normal with mean c(0,1) and variance matrix: matrix(c(2,1,1,3), 2,2). Thanks in advance, Arnau. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Peng Jiang 江鹏 ,Ph.D. Candidate Antai College of Economics Management 安泰经济管理学院 Department of Mathematics 数学系 Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution of several variables
On Sat, 2008-07-05 at 18:21 +0200, Arnau Mir wrote: Hello. Somebody knows how can I generate a set of n random vectors of a normal distribution of several variables? For example, I want to generate n=100 random vectors of two dimensions for a normal with mean c(0,1) and variance matrix: matrix(c(2,1,1,3),2,2). One is mvrnorm() in the MASS package, part of the VR bundle that comes with R. require(MASS) mu - c(0,1) Sigma - matrix(c(2,1,1,3),2,2) res - mvrnorm(100, mu = mu, Sigma = Sigma) head(res) [,1][,2] [1,] 2.7582876 1.04208798 [2,] 0.6364184 -0.08043244 [3,] -1.8897731 0.04051395 [4,] 2.6699881 0.83163661 [5,] -1.1942385 -1.17503716 [6,] -0.4303459 -0.80880649 HTH G __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bland-Altman method to measure agreement with repeated measures
on 07/05/2008 03:17 AM kende jan wrote: Dear all, I want to use the Bland-Altman method to measure agreement with repeated measures collected over period of time (seven periods). How can I do this with R Many thanks The following links should be helpful from a design/methodology perspective: Comparing within-subject variances in a study to compare two methods of measurement http://www-users.york.ac.uk/~mb55/meas/compsd.htm Agreement between methods of measurement with multiple observations per individual http://www-users.york.ac.uk/~mb55/meas/ba2007.htm and perhaps more generally: http://www-users.york.ac.uk/~mb55/meas/comfaq.htm You will need to provide more detail on your experimental design and data for any R specific guidance, which could feasibly include the use of mixed effects models where subject is a random effect. In the latter case, there is a R e-mail list focused on that approach: https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution of
There is no need to load the MASS library, since the code for
mvrnorm therein is compact and self-contained:
mvrnorm - function (n=1, mu, Sigma, tol=1e-06, empirical=FALSE)
{
p - length(mu)
if(!all(dim(Sigma) == c(p, p)))
stop(incompatible arguments)
eS - eigen(Sigma, symmetric = TRUE, EISPACK = TRUE)
ev - eS$values
if(!all(ev = -tol * abs(ev[1])))
stop('Sigma' is not positive definite)
X - matrix(rnorm(p * n), n)
if(empirical) {
X - scale(X, TRUE, FALSE)
X - X %*% svd(X, nu = 0)$v
X - scale(X, FALSE, TRUE)
}
X - drop(mu) +
eS$vectors %*% diag(sqrt(pmax(ev, 0)), p) %*% t(X)
nm - names(mu)
if(is.null(nm) !is.null(dn - dimnames(Sigma)))
nm - dn[[1]]
dimnames(X) - list(nm, NULL)
if(n == 1)
drop(X)
else t(X)
}
Define that function as above, then proceed along the lines suggested
by Gavin Simpson below.
Ted.
On 05-Jul-08 16:43:46, Gavin Simpson wrote:
On Sat, 2008-07-05 at 18:21 +0200, Arnau Mir wrote:
Hello.
Somebody knows how can I generate a set of n random vectors of a
normal distribution of several variables?
For example, I want to generate n=100 random vectors of two
dimensions for a normal with mean c(0,1) and variance matrix:
matrix(c(2,1,1,3),2,2).
One is mvrnorm() in the MASS package, part of the VR bundle that comes
with R.
require(MASS)
mu - c(0,1)
Sigma - matrix(c(2,1,1,3),2,2)
res - mvrnorm(100, mu = mu, Sigma = Sigma)
head(res)
[,1][,2]
[1,] 2.7582876 1.04208798
[2,] 0.6364184 -0.08043244
[3,] -1.8897731 0.04051395
[4,] 2.6699881 0.83163661
[5,] -1.1942385 -1.17503716
[6,] -0.4303459 -0.80880649
HTH
G
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jul-08 Time: 18:09:23
-- XFMail --
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[R] SciViews GUI
HI: After following all the instructions on how to install the SciViews package from CRAN I still can't make the GUI show. Can someone give me a hint on how to do this? I have tried library(svGUI), library(svDialogs) and so on with the rest of the packages. I have also placed all the 'sv' packages in my Rprofile but nothing works. Any help would be appreciated. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SciViews GUI
Hello, We need a little more information (which platform? which R version?). Also, the GUI is NOT provided with the SciViews package. The version on CRAN is quite outdated and is designed to communicate with the old SciViews R Console GUI for Windows only. We are currently working on a new version that uses a new platform-independent GUI based on Komodo Edit. It will be uploaded to CRAN as soon as it will be finished, but for the moment, you can install alpha version from R-Forge. See detailed instructions on http://www.sciviews.org/SciViews-K. Note that alpha version is unsupported. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Felipe Carrillo wrote: HI: After following all the instructions on how to install the SciViews package from CRAN I still can't make the GUI show. Can someone give me a hint on how to do this? I have tried library(svGUI), library(svDialogs) and so on with the rest of the packages. I have also placed all the 'sv' packages in my Rprofile but nothing works. Any help would be appreciated. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using texmacs as front for R on windows xp sp2...
Hi ho: Has anybody made use of this 'editor' as a front for R v2.7.0? I'm running xp sp2. The texmacs website mentions the possibility of it but seems a little short on instruction or direction to explain the how of it. -- Brian Lunergan Nepean, Ontario Canada --- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] extracting values from a by function
Hello, I am trying to extract t and pvalues from a 1000 ttests using the by-function but everythinhg I tried did not work. Unfortunately googling by is not very helpful. Any help will be very appreciated. Cheers, Danile Stall *creating a data set library(MASS) dataset - mvrnorm(160, mu, Sigma) dataset - as.data.frame(dataset) dataset$GROUP - rep(1:10, each=16) data.uni - reshape(df, varying = list(c(V1,V2)), v.names=Y,direction=long) *the actual tests: test-by(data.uni, data.uni$GROUP, function(x)t.test(Y ~ time, data = x, paired = TRUE)) *in case this will help you: summary(test) str(test) summary(test) Length Class Mode 1 9 htest list 2 9 htest list 3 9 htest list 4 9 htest list 5 9 htest list 6 9 htest list 7 9 htest list 8 9 htest list 9 9 htest list 10 9 htest list str(test) List of 10 $ 1 :List of 9 ..$ statistic : Named num -4.26 .. ..- attr(*, names)= chr t ..$ parameter : Named num 15 .. ..- attr(*, names)= chr df ..$ p.value: num 0.000682 ..$ conf.int : atomic [1:2] -3.13 -1.04 .. ..- attr(*, conf.level)= num 0.95 ..$ estimate : Named num -2.09 .. ..- attr(*, names)= chr mean of the differences ..$ null.value : Named num 0 .. ..- attr(*, names)= chr difference in means ..$ alternative: chr two.sided ..$ method : chr Paired t-test ..$ data.name : chr Y by time ..- attr(*, class)= chr htest $ 2 :List of 9 -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem solved: extracting values from a by function
Hi I just discovered the answer thanks to a previous thread from Peter Daalgart The command is: sapply(test, [[, statistic) Cheers, Daniel - Original Message - To: r-help@r-project.org Subject: extracting values from a by function Date: Sun, 6 Jul 2008 05:59:04 +0800 Hello, I am trying to extract t and pvalues from a 1000 ttests using the by-function but everythinhg I tried did not work. Unfortunately googling by is not very helpful. Any help will be very appreciated. Cheers, Danile Stall *creating a data set library(MASS) dataset - mvrnorm(160, mu, Sigma) dataset - as.data.frame(dataset) dataset$GROUP - rep(1:10, each=16) data.uni - reshape(df, varying = list(c(V1,V2)), v.names=Y,direction=long) *the actual tests: test-by(data.uni, data.uni$GROUP, function(x)t.test(Y ~ time, data = x, paired = TRUE)) *in case this will help you: summary(test) str(test) summary(test) Length Class Mode 1 9 htest list 2 9 htest list 3 9 htest list 4 9 htest list 5 9 htest list 6 9 htest list 7 9 htest list 8 9 htest list 9 9 htest list 10 9 htest list str(test) List of 10 $ 1 :List of 9 ..$ statistic : Named num -4.26 .. ..- attr(*, names)= chr t ..$ parameter : Named num 15 .. ..- attr(*, names)= chr df ..$ p.value: num 0.000682 ..$ conf.int : atomic [1:2] -3.13 -1.04 .. ..- attr(*, conf.level)= num 0.95 ..$ estimate : Named num -2.09 .. ..- attr(*, names)= chr mean of the differences ..$ null.value : Named num 0 .. ..- attr(*, names)= chr difference in means ..$ alternative: chr two.sided ..$ method : chr Paired t-test ..$ data.name : chr Y by time ..- attr(*, class)= chr htest $ 2 :List of 9 -- ___ -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error: cannot use PQL when using lmer
library(MASS) attach(bacteria) table(y) y n y 43 177 y-1*(y==y) table(y,trt) trt y placebo drug drug+ 0 12 1813 1 84 4449 library(lme4) model1-lmer(y~trt+(week|ID),family=binomial,method=PQL) Error in match.arg(method, c(Laplace, AGQ)) : 'arg' should be one of “Laplace”, “AGQ” __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: cannot use PQL when using lmer
hpdutra at yahoo.com writes: library(MASS) attach(bacteria) table(y) y n y 43 177 y-1*(y==y) table(y,trt) trt y placebo drug drug+ 0 12 1813 1 84 4449 library(lme4) model1-lmer(y~trt+(week|ID),family=binomial,method=PQL) Error in match.arg(method, c(Laplace, AGQ)) : 'arg' should be one of “Laplace”, “AGQ” What is your question? Doug Bates warned a few weeks ago that the newer version of lmer would no longer use PQL for GLMMs (he found that it was unreliable, even as a starting method for Laplace fits). I think you can still get the older version if you want it, or you can use glmmPQL from the MASS package (glmmPQL has some advantages anyway). It might be better to forward further discussion to r-sig-mixed. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error: cannot use PQL when using lmer
I am trying to do an exercise on Crawley's book and I get this error message. I ran the same analysis in the past but now that I upgraded my R in my Macbook I get this message. Is this a bug or what is going on. It doesn't make any sense library(MASS) attach(bacteria) table(y) y n y 43 177 y-1*(y==y) table(y,trt) trt y placebo drug drug+ 0 12 1813 1 84 4449 library(lme4) model1-lmer(y~trt+(week|ID),family=binomial,method=PQL) Error in match.arg(method, c(Laplace, AGQ)) : 'arg' should be one of “Laplace”, “AGQ” Humberto Dutra __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] interpreting mixed model anova results
Hi, I am trying to do a repeated measures ANOVA to determine if there is a significant difference between two sets of timecourse data. Each individual was given a single treatment and then measured for one variable for 10 days. Here is made-up example of what my data would look like: data-data.frame(subject=rep(c(A1,A2,A3,B1,B2,B3),10),treatment=rep(c(A,B),each=3), day=rep(c(1:10),each=6),response=rnorm(60)) This is the code I run to test for a difference between treatments A and B over the course of the 10 days: aov(response~day*treatment+Error(subject), data=data) I believe this is the correct model to use, though I could definitely be wrong. Here is the output I get from my actual data (using summary(aov)): Error: subject Df Sum Sq Mean Sq F value Pr(F) treatment 1 4258.1 4258.1 12.588 0.001344 ** Residuals 29 9810.2 338.3 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Error: Within Df Sum Sq Mean Sq F valuePr(F) day 9 98345 10927 150.313 2.2e-16 *** day:treatment 9 6844 760 10.461 8.374e-14 *** Residuals 261 18974 73 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 The p-value for treatment is the same as what I would get if I lumped the data from all 10 days together, so I assume this is not what I want here. However, am I correct in interpreting the p-value for day:treatment as what I want? Does this tell me that there is a difference between the two groups over the course of the 10 days (regardless of which days actually are different) with respect to the fact that I am measuring the same subjects each day? Thanks for any help! -- Brooke LaFlamme [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help about random generation of a Normal distribution of several variables
Hello. Somebody knows how can I generate a set of n random vectors of a normal distribution of several variables? For example, I want to generate n=100 random vectors of two dimensions for a normal with mean c(0,1) and variance matrix: matrix(c(2,1,1,3),2,2). Thanks in advance, Arnau. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Random Forest %var(y)
The verbose option gives a display like: rf.500 - + randomForest(new.x,trn.y,do.trace=20,ntree=100,nodesize=500, +importance=T) | Out-of-bag | Tree | MSE %Var(y) | 20 | 0.9279 100.84 | What is the meaning of %var(y)100%? I expected that to correspond to a model that was worse than random, but the predictions seem much better than that on the o-o-bag estimates from predict(rf.500). -- View this message in context: http://www.nabble.com/Random-Forest--var%28y%29-tp18295412p18295412.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trying to superimpose a line plot onto a histogram
Thanks for the quick response. But the points I'm trying to superimpose isn't exactly the density of the data. Is there any other way to do it? From: milton ruser [mailto:[EMAIL PROTECTED] Sent: July 5, 2008 6:56 AM To: Edwin Lei Cc: r-help@r-project.org Subject: Re: [R] trying to superimpose a line plot onto a histogram How about the answer by Demitris? Regards a lot, miltinho From: Dimitris Rizopoulos [EMAIL PROTECTED] Date: Jun 16, 2008 4:05 AM Subject: Re: [R] Superimposing Line over Histogram in Density Plot To: Gundala Viswanath [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] try something like this: x - rnorm(200) hist(x, col = blue, freq = FALSE) lines(density(x), col = red, lwd = 2) On 7/5/08, Edwin Lei [EMAIL PROTECTED] wrote: Hello, I'm trying to superimpose a line plot onto a histogram but I'm not having any luck. I've attached the dataset. What I did was: hist(data,freq=F) Now I'm trying to superimpose the following points with a line connecting them onto the histogram: xy 100 0.535665393824959 200 0.212744329736556 300 0.0844933242968584 400 0.0335572838043417 500 0.0133275771274986 600 0.00529316714442912 700 0.0021022289461042 800 0.000834919136549392 900 0.000331595645597124 1000 0.000131696193518099 1100 5.2304327929049e-05 1200 2.07731343406939e-05 Basically, the x values correspond to the break points in the histogram. Next I used the command points(x,y,type=l) But for some reason, the line plot is shifted to the right and doesn't line up with the histogram. Thanks for the help! Edwin Lei __ R-help@r-project.org mailing list PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution of several variables
Hi , Arnau
Did you ever check your mailbox? your question was answered last
night Beijing time. :)
Just read the following .
-
There is no need to load the MASS library, since the code for
mvrnorm therein is compact and self-contained:
mvrnorm - function (n=1, mu, Sigma, tol=1e-06, empirical=FALSE)
{
p - length(mu)
if(!all(dim(Sigma) == c(p, p)))
stop(incompatible arguments)
eS - eigen(Sigma, symmetric = TRUE, EISPACK = TRUE)
ev - eS$values
if(!all(ev = -tol * abs(ev[1])))
stop('Sigma' is not positive definite)
X - matrix(rnorm(p * n), n)
if(empirical) {
X - scale(X, TRUE, FALSE)
X - X %*% svd(X, nu = 0)$v
X - scale(X, FALSE, TRUE)
}
X - drop(mu) +
eS$vectors %*% diag(sqrt(pmax(ev, 0)), p) %*% t(X)
nm - names(mu)
if(is.null(nm) !is.null(dn - dimnames(Sigma)))
nm - dn[[1]]
dimnames(X) - list(nm, NULL)
if(n == 1)
drop(X)
else t(X)
}
Define that function as above, then proceed along the lines suggested
by Gavin Simpson below.
Ted.
On 05-Jul-08 16:43:46, Gavin Simpson wrote:
On Sat, 2008-07-05 at 18:21 +0200, Arnau Mir wrote:
Hello.
Somebody knows how can I generate a set of n random vectors of a
normal distribution of several variables?
For example, I want to generate n=100 random vectors of two
dimensions for a normal with mean c(0,1) and variance matrix:
matrix(c(2,1,1,3),2,2).
One is mvrnorm() in the MASS package, part of the VR bundle that comes
with R.
require(MASS)
mu - c(0,1)
Sigma - matrix(c(2,1,1,3),2,2)
res - mvrnorm(100, mu = mu, Sigma = Sigma)
head(res)
[,1][,2]
[1,] 2.7582876 1.04208798
[2,] 0.6364184 -0.08043244
[3,] -1.8897731 0.04051395
[4,] 2.6699881 0.83163661
[5,] -1.1942385 -1.17503716
[6,] -0.4303459 -0.80880649
HTH
G
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jul-08 Time: 18:09:23
-- XFMail --
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
On 2008-7-6, at ä¸å12:13, Arnau Mir Torres wrote:
Hello.
Somebody knows how can I generate a set of n random vectors of a
normal distribution of several variables?
For example, I want to generate n=100 random vectors of two
dimensions for a normal with mean c(0,1) and variance matrix:
matrix(c(2,1,1,3),2,2).
Thanks in advance,
Arnau.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution ofseveral variables
library(MASS) set.seed(22134) Y - mvrnorm(100, mu = c(0,1), Sigma = matrix(c(2,1,1,3),2,2)) colMeans(Y) [1] 0.06461359 1.08436419 var(Y) [,1] [,2] [1,] 1.683963 1.300363 [2,] 1.300363 3.280612 Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Arnau Mir Torres Sent: Sunday, 6 July 2008 2:14 AM To: r-help@r-project.org Subject: [R] help about random generation of a Normal distribution ofseveral variables Hello. Somebody knows how can I generate a set of n random vectors of a normal distribution of several variables? For example, I want to generate n=100 random vectors of two dimensions for a normal with mean c(0,1) and variance matrix: matrix(c(2,1,1,3),2,2). Thanks in advance, Arnau. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help about random generation of a Normal distribution ofseveral variables
What's the problem with loading the MASS library???
The MASS library is one of the recommended packages, so should be universally
available.
Pinching code like this and freezing it inside your personal scripts means that
if ever we find bug fixes or improvements you miss out on them.
Bill Venables
CSIRO Laboratories
AUSTRALIA
http://www.cmis.csiro.au/bill.venables/
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peng Jiang
Sent: Sunday, 6 July 2008 1:47 PM
To: Arnau Mir Torres
Cc: r-help@r-project.org
Subject: Re: [R] help about random generation of a Normal distribution
ofseveral variables
Hi , Arnau
Did you ever check your mailbox? your question was answered last
night Beijing time. :)
Just read the following .
-
There is no need to load the MASS library, since the code for
mvrnorm therein is compact and self-contained:
mvrnorm - function (n=1, mu, Sigma, tol=1e-06, empirical=FALSE)
{
p - length(mu)
if(!all(dim(Sigma) == c(p, p)))
stop(incompatible arguments)
eS - eigen(Sigma, symmetric = TRUE, EISPACK = TRUE)
ev - eS$values
if(!all(ev = -tol * abs(ev[1])))
stop('Sigma' is not positive definite)
X - matrix(rnorm(p * n), n)
if(empirical) {
X - scale(X, TRUE, FALSE)
X - X %*% svd(X, nu = 0)$v
X - scale(X, FALSE, TRUE)
}
X - drop(mu) +
eS$vectors %*% diag(sqrt(pmax(ev, 0)), p) %*% t(X)
nm - names(mu)
if(is.null(nm) !is.null(dn - dimnames(Sigma)))
nm - dn[[1]]
dimnames(X) - list(nm, NULL)
if(n == 1)
drop(X)
else t(X)
}
Define that function as above, then proceed along the lines suggested
by Gavin Simpson below.
Ted.
On 05-Jul-08 16:43:46, Gavin Simpson wrote:
On Sat, 2008-07-05 at 18:21 +0200, Arnau Mir wrote:
Hello.
Somebody knows how can I generate a set of n random vectors of a
normal distribution of several variables?
For example, I want to generate n=100 random vectors of two
dimensions for a normal with mean c(0,1) and variance matrix:
matrix(c(2,1,1,3),2,2).
One is mvrnorm() in the MASS package, part of the VR bundle that comes
with R.
require(MASS)
mu - c(0,1)
Sigma - matrix(c(2,1,1,3),2,2)
res - mvrnorm(100, mu = mu, Sigma = Sigma)
head(res)
[,1][,2]
[1,] 2.7582876 1.04208798
[2,] 0.6364184 -0.08043244
[3,] -1.8897731 0.04051395
[4,] 2.6699881 0.83163661
[5,] -1.1942385 -1.17503716
[6,] -0.4303459 -0.80880649
HTH
G
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jul-08 Time: 18:09:23
-- XFMail --
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
On 2008-7-6, at 上åˆ12:13, Arnau Mir Torres wrote:
Hello.
Somebody knows how can I generate a set of n random vectors of a
normal distribution of several variables?
For example, I want to generate n=100 random vectors of two
dimensions for a normal with mean c(0,1) and variance matrix:
matrix(c(2,1,1,3),2,2).
Thanks in advance,
Arnau.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
