Re: [R] How to do Clustered Standard Errors for Regression in R?

Hi Bo, I can't seem to find the right set of commands to enable me to do perform a regression with cluster-adjusted standard-errors. Frank Harrell's Design package has ?bootcov and ?robcov, which will both do it. Regards, Mark. Bo Cowgill wrote: I can't seem to find the right set of

Re: [R] Help please! How to code a mixed-model with 2 within-subject factors using lme or lmer?

Hi Roberto, The other thing you can do --- if you don't wish to step across to lmer(), where you will be able to exactly replicate the crossed-factor error structure --- is stay with aov(... + Error()), but fit the factor you are interested in last. Assume it is Sex. Then fit your model as

Re: [R] Ward's Clustering Doubts

Hi Rodrigo, [apropos of Ward's method] ... we saw something like You must use it with Euclidean Distance... Strictly speaking this is probably correct, as Ward's method does an analysis of variance type of decomposition and so doesn't really make much sense (I think) unless Euclidean

Re: [R] Looking for function tree.matrix

Hi Meir, It's part of Prof. Ripley's package tree, but is not exported. library(tree) ls(asNamespace(tree)) RSiteSearch(tree.matrix) Regards, Mark. Meir Preiszler wrote: Hi, Does anyone know where such a function can be found? Thanks Meir

Re: [R] Help please! How to code a mixed-model with 2 within-subject factors using lme or lmer?

Hi Roberto, but I can't figure out the /(Lobe*Tissue) part... This type of nesting is easier to do using lmer(). To do it using lme() you have to generate the crossed factor yourself. Do something like this: ## tfac - with(vslt, interaction(Lobe, Tissue, drop=T)) str(tfac); head(tfac)

Re: [R] Help please! How to code a mixed-model with 2 within-subject factors using lme or lmer?

Hi Roberto, It's difficult to comment further on specifics without access to your data set. A general point is that the output from summary(aov.object) is not directly comparable with summary(lme.object). The latter gives you a summary of a fitted linear regression model, not an analysis of

Re: [R] Symbols on a capscale object plot

Hi Rodrigo, I would like to use something like squares, triangles and circles (filled and empty). You would normally add this using points(): ?points ## plot(1:10, type=n) points(1:5, pch=21:25, bg=1:5) points(6:10, pch=21:25, bg=c(1,darkgrey,cyan, bisque)) points(6:10, y=rep(6,5), pch=1:5)

Re: [R] Symbols on a capscale object plot

. -- From: Mark Difford [EMAIL PROTECTED] Sent: Saturday, September 13, 2008 9:21 AM To: r-help@r-project.org Subject: Re: [R] Symbols on a capscale object plot Hi Rodrigo, I would like to use something like squares, triangles and circles (filled and empty). You

Re: [R] Symbols on a capscale object plot

Hi Rogrido, Sorry: The first points() call was missing a vital comma. It should have been. points(ord.obj$scores[mydf$Site==MarkerA, ], pch=21, bg=red) See ?[ Mark Difford wrote: Hi Rodrigo, Maybe if I can define a factor that specifies these groups and use this factor to assign

Re: [R] Greyed text in the background of a plot

Hi Agustin, Is there any way of having a greyed (ghosted) text... Yes! ## plot(1, type=n) text(1, Old Grey Whistle Test, col=slategray4, cex=2) text(1, y=1.2, OH!, col=grey95, cex=4) Then plot what you want on top. If you export or plot to a PDF/ps device the last-plotted items will overlie

Re: [R] Greyed text in the background of a plot

Hi Yihui, That's good, I like it! Very nice site. Regards, Mark. Yihui Xie wrote: Well, his talk seems to have attracted a lot of people... You may simply use gray text in your plot. Here is an example: ## x = runif(10) y = runif(10) z

Re: [R] Modality Test

Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Difford Sent: Tuesday, September 09, 2008 1:23 PM To: r-help@r-project.org Subject: Re: [R] Modality Test Hi Amin, And I have just remembered that there is a function called curveRep

Re: [R] Modality Test

Hi Amin, First, does R have a package that can implement the multimodality test, e.g., the Silverman test, DIP test, MAP test or Runt test. Jeremy Tantrum (a Ph.D. student of Werner Steutzle's, c. 2003/04) did some work on this. There is some useful code on Steutzle's website:

Re: [R] Modality Test

Whoops! I think that should be Stuetzle --- though I very much doubt that he reads the list. Mark Difford wrote: Hi Amin, First, does R have a package that can implement the multimodality test, e.g., the Silverman test, DIP test, MAP test or Runt test. Jeremy Tantrum (a Ph.D. student

Re: [R] Modality Test

Hi Amin, And I have just remembered that there is a function called curveRep in Frank Harrell's Hmisc package that might be useful, even if not quite in the channel of your enquiry. curveRep was added to the package after my struggles, so I never used it and so don't know how well it performs

Re: [R] ANCOVA/glm missing/ignored interaction combinations

Hi Lara, And I cant for the life of me work out why category one (semio1) is being ignored, missing etc. Nothing is being ignored Lara --- but you are ignoring the fact that your factors have been coded using the default contrasts in R, viz so-called treatment or Dunnett contrasts. That is,

Re: [R] ANCOVA/glm missing/ignored interaction combinations

And perhaps I should also have added: fit your model without an intercept and look at your coefficients. You should be able to work it out from there quite easily. Anyway, you now have the main pieces. Regards, Mark. Mark Difford wrote: Hi Lara, And I cant for the life of me work out why

Re: [R] model II regression - how do I do it?

Hi Danilo, I need to do a model II linear regression, but I could not find out how!! The smatr package does so-called model II (major axis) regression. Regards, Mark. Danilo Muniz wrote: I need to do a model II linear regression, but I could not find out how!! I tryed to use the lm

Re: [R] model II regression - how do I do it?

Hi Danilo, I need to do a model II linear regression, but I could not find out how!! The smatr package does so-called model II (major axis) regression. Regards, Mark. Danilo Muniz wrote: I need to do a model II linear regression, but I could not find out how!! I tryed to use the lm

Re: [R] Density estimates in modelling framework

Hi Hadley, There is also locfit, which is very highly regarded by some authorities (e.g. Hastie, Tibs, and Friedman). Cheers, Mark. hadley wrote: Hi all, Do any packages implement density estimation in a modelling framework? I want to be able to do something like: dmodel -

Re: [R] model II regression - how do I do it?

often I have seen analysts put the (usually) inaccurately determined analyte on x and the spec reading on y. HTH, Mark. Dylan Beaudette-2 wrote: On Friday 29 August 2008, Mark Difford wrote: Hi Danilo, I need to do a model II linear regression, but I could not find out how!! The smatr

Re: [R] non-parametric Anova and tukeyHSD

Hi Stephen, See packages: coin nparcomp npmc There is also kruskalmc() in package pgirmess Regards, Mark. stephen sefick wrote: I have insect data from twelve sites and like most environmental data it is non-normal mostly. I would like to preform an anova and a means seperation like

Re: [R] convert princomp output to equation for plane?

Hi Bill, Since x, y,and z all have measurement errors attached, the proper way to do the fit is with principal components analysis, and to use the first component (called loadings in princomp output). The easiest way for you to do this is to use the pcr [principal component regression]

Re: [R] random error with lme for repeated measures anova

Hi Jean-Pierre, A general comment is that I think you need to think more carefully about what you are trying to get out of your analysis. The random effects structure you are aiming for could be stretching your data a little thin. It might be a good idea to read through the archives of the

Re: [R] Two envelopes problem

... To pick up on what Mark has said: it strikes me that this is related to the simplex, where the bounded nature of the vector space means that normal arithmetical operations (i.e. Euclidean) don't work---that is, they can be used, but the results are wrong. Covariances and correlations for

Re: [R] aov, lme, multcomp

Hi Richard, The tests give different Fs and ps. I know this comes up every once in a while on R-help so I did my homework. I see from these two threads: This is not so, or it is not necessarily so. The error structure of your two models is quite different, and this is (one reason) why the F-

Re: [R] Test of Homogeneity of Variances

Have you read the documentation to either of the functions you are using? ?bartlett.test Performs Bartlett's test of the null that the variances in each of the groups (samples) are the same. This explicitly tells you what is being tested, i.e. the null tested is that var1 = var2. ?rnorm

Re: [R] How to solve this problem ?

Hi Daren, Small progress, ... m4 - list(m1=m1, m2=m2, m3=m3) boxplot(m4) It's always a good idea to have a look at your data first (assuming you haven't). This shows that the reliable instrument is m2. HTH, Mark. Daren Tan wrote: Small progress, I am relying on levene test to check

Re: [R] before-after control-impact analysis with R

Hi Nikolaos, My question again is: Why can't I reproduce the results? When I try a simple anova without any random factors: Lack of a right result probably has to do with the type of analysis of variance that is being done. The default in R is to use so-called Type I tests, for good reason.

Re: [R] before-after control-impact analysis with R

Hi ... Sorry, an e was erroneously elided from Ripley... Mark Difford wrote: Hi Nikolaos, My question again is: Why can't I reproduce the results? When I try a simple anova without any random factors: Lack of a right result probably has to do with the type of analysis of variance

Re: [R] Re lational Operators in Legend

Hi Lorenzo, ...but I would like to write that 5=k=15. This is one way to do what you want plot(1,1) legend(topright, expression(paste(R[g]~k^{1/d[f]^{small}}~5=k, {}=15))) HTH, Mark. Lorenzo Isella wrote: Dear All, I am sure that what I am asking can be solved by less than a

Re: [R] Re lational Operators in Legend

Hi Lorenzo, I may (?) have left something out. It isn't clear what ~ is supposed to mean; perhaps it is just a spacer, or perhaps you meant the following: plot(1,1) legend(topright, expression(paste(R[g] %~~% k^{1/d[f]^{small}},~5=k, {}=15))) HTH, Mark. Mark Difford wrote: Hi Lorenzo

Re: [R] ylab with an exponent

what is the problem? A solution is: plot(1,2, ylab=expression(paste(insects , m^2))) The problem is very much more difficult to determine. stephen sefick wrote: plot(1,2, ylab= paste(insects, expression(m^2), sep= )) I get insects m^2 I would like m to the 2 what is the problem?

Re: [R] Simple lme/lmer random effects questions

Hi Brandon, ...is it sufficient to leave the values as they are or should I generate unique names for all combinations of sleeve number and temperature, using something like data$sleeve.in.temp - factor(with(data, temp:sleeve)[drop=TRUE]) You might be luckier posting this on

Re: [R] [lme4]Coef output with binomial lmer

Hi Tom, 1|ass%in%pop%in%fam This is non-standard, but as you have found, it works. The correct translation is in fact 1|fam/pop/ass and not 1|ass/pop/fam as suggested by Harold Doran. Dropping %, ass%in%pop%in%fam reads [means] as: nest ass in pop [= pop/ass], and then nest this in fam ==

Re: [R] Tick marks that correspond with bars on barplot

Hi Megan, I would like to have an X-axis where the labels for the years line up after every two bars in the plot (there is one bar for hardwood, and another for softwood). It isn't clear to me from your description what you really want (I found no attachment)? What you seem to be trying to

Re: [R] Problems using hetcor (polycor)

Hi Birgitle, You need to get this right if someone is going to spend their time helping you. Your code doesn't work: You have specified more columns in colClasses than you have in the provided data set. TestPart-read.table(TestPart.txt, header=TRUE,row.names=1, na.strings=NA ,colClasses =

Re: [R] Problems using hetcor (polycor)

Hi Birgitle, It seems to be failing on those columns that have just a single entry (i.e = 1, with the rest as 0; having just 1, an NA, and then 0s gets you through). And there are other reasons for failure (in the call to get a positive definite matrix). The main problem lies in the calculation

Re: [R] Problems using hetcor (polycor)

missing values. But I will try which variables I can finally use. Many thanks again. B. Mark Difford wrote: Hi Birgitle, It seems to be failing on those columns that have just a single entry (i.e = 1, with the rest as 0; having just 1, an NA, and then 0s gets you through

Re: [R] Where is the archive? Calling a function within a function.

Hi Kevin, Where is the archive? Start with this: ?RSiteSearch HTH, Mark. rkevinburton wrote: I seem to remember this topic coming up before so I decided to look at the archive and realized that I didn't know where it was. Is there a searchable archive for this list? Thank you. My

Re: [R] Correlation dichotomous factor, continous (numerical) and ordered factor

Hi Birgitle, ... my variables are dichotomous factors, continuous (numerical) and ordered factors. ... Now I am confused what I should use to calculate the correlation using all my variables and how I could do that in R. Professor Fox's package polycor will do this for you in a very nice

Re: [R] defining the distance between axis label and axis

Hi Jörg, I haven't found anything in par()... No? Well don't bet your bottom $ on it (almost never in R). ?par (sub mgp). Mark. Jörg Groß wrote: Hi, How can I make the distance between an axis-label and the axis bigger? I haven't found anything in par()...

Re: [R] re quest for fine panel axis controls in lattice

Hi David, Specifically, within each panel, I want to set the limits for x and y equal to each other since it is paired data (using the max value of the two). In addition to the code Chuck Cleland sent you, you may want to square things up by adding the argument: aspect = iso before the

Re: [R] subset inside a lattice plot using panel.lines

Hi Michael, Pulling my hair out here trying to get something very simple to work. ... I can't quite see what you are trying to do [and I am not sure that you clearly state it], but you could make things easier and simpler by (1) creating a factor to identify your groups of rows more cleanly

Re: [R] Is there any way to make pretty tables in R to pdf?

Hi Arthur, I was wondering if there was a package that can make pretty R tables to pdf. You got through TeX/LateX, but PDF could be your terminus. Package Hmisc: ? summary.formula and its various arguments and options. You can't get much better.

Re: [R] Is there any way to make pretty tables in R to pdf?

Hi Arthur, Sorry, sent you down the wrong track: this will help you to get there: http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatReport/summary.pdf Regards, Mark. Arthur Roberts wrote: Hi, all, All your comments have been very useful. I was wondering if there was a package

Re: [R] How do I get an inset graph (i.e. graph within a graph)?

Hi Arthur, This can be done quite easily using the appropriate arguments listed under ?par; and there are other approaches. Ready-made functions exist in several packages. I tend to use ?add.scatter from package ade4. It's a short function, so it's easy to customize it, but it works well

Re: [R] How to get the p-value from lmer on a longitudinal analysis

Hi Ronaldo, ... lmer p-values There are two packages that may help you with this and that might work with the current implementation of lmer(). They are languageR and RLRsim. HTH, Mark. Bugzilla from [EMAIL PROTECTED] wrote: Hi, I have a modelo like this: Yvar - c(0, 0, 0, 0, 1, 0,

Re: [R] Re peated Measure ANOVA-Old question

Hi Chunhao, I google the website and I found that there are three ways to perform repeated measure ANOVA: aov, lme and lmer. It's also a good idea to search through the archives. I use the example that is provided in the above link and I try

Re: [R] Re peated Measure ANOVA-Old question

Hi Chunhao, If you carefully read the posting that was referred to you will see that lme() and not lmer() was used as an example (for using with the multcomp package). lmer() was only mentioned as an aside... lmer() is S4 and doesn't work with multcomp, which is S3. Apropos of specifying random

Re: [R] Mixed effects model where nested factor is not the repeated across treatments lme???

Hi Miki and Chunhao, Rusers (Anna, and Mark {thank you guys}) provide me a vary valuable information. Also see Gavin Simpson's posting earlier today: apparently multcomp does now work with lmer objects (it's gone through phases of not working, then working: it's still being developed).

Re: [R] Help interpreting density().

Hi Kevin, The documentation indicates that the bw is essentially the sd. d - density(rnorm(1000)) Not so. The documentation states that the following about bw: The kernels are scaled such that this is the standard deviation of the smoothing kernel..., which is a very different thing. The

Re: [R] Help interpreting density().

to the negative one-fifth power (= Silverman's ‘rule of thumb’ But how does that relate to say a Poisson distribution or a two-parameter distribution like a normal, beta, or binomial distribution? Thank you. Kevin Mark Difford [EMAIL PROTECTED] wrote: Hi Kevin

Re: [R] Help interpreting density().

, and then... HTH, Mark. rkevinburton wrote: Sorry I tried WikiPedia and only found: Wikipedia does not have an article with this exact name. I will try to find some other sources of information. Kevin Mark Difford [EMAIL PROTECTED] wrote: Hi Kevin, I still have my original

Re: [R] graphing regression coefficients and standard errors

Hi Murali, I am interested in plotting my regression analysis results(regression coefficients and standard errors obtained through OLS and Tobit models) in the form of graphs. plot(obj$lm) will give you a set of diagnostic plots. What you seem to be after is ?termplot. Also look at John

Re: [R] multiv

Hi Ileana, See this thread: http://www.nabble.com/R-package-install-td18636993.html HTH, Mark. Somesan, Ileana wrote: Hello, I want to install the package multiv which is not maintained any more (found in the archive: multiv_1.1-6.tar.gz from 16 July 2003). I have installed an older

Re: [R] A easy way to write formula

Hi Jinsong and Thierry, (x1 + x2 + x3) ^2 will give you the main effects and the interactions. Although it wasn't specifically requested it is perhaps important to note that (...)^2 doesn't expand to give _all_ interaction terms, only interactions to the second order, so the interaction term

Re: [R] Beginning lm

Hi Kevin, Can anyone give me a short tutorial on the formula syntax? ... I am sorry but I could not glean this information from the help page on lm. You can give yourself a very good tutorial by reading ?formula and Chapter 12 of

Re: [R] Just 2 more questions - for now!

Hi Robin, I ... can't get lm to work despite reading the help. I can get it to work with a single explanatory variable, EG model - lm(data$admissions~data$maxitemp) I'll answer just the second of your questions. Advice: don't just read the help file, look at the examples and run them; look

Re: [R] factor question

Hi Edna, Because I am always subsetting, I keep the following function handy mydata[] - lapply(mydata, function(x) if(is.factor(x)) x[,drop=T] else x) This will strip out all factor levels that have been dropped by a previous subsetting operation. For novice users of R (though I am not

Re: [R] Accessing individual variables from summary of lm

Hi Ben, Sorry (still a little out-of-tune), perhaps what you really need to know about is ?[ HTH, Mark. Mark Difford wrote: Hi Ben, If you wouldn't mind, how do I access the individual components inside coefficients matrix? What you want to know about is ?attributes

Re: [R] Accessing individual variables from summary of lm

Hi Ben, If you wouldn't mind, how do I access the individual components inside coefficients matrix? What you want to know about is ?attributes ## attributes(model) model$coefficients model$coefficients[1] model$coefficients[2:4] model$coefficients[c(1,5)] HTH, Mark. ascentnet wrote:

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

Hi All, It really comes down to a question of attitude: you either want to learn something fundamental or core and so bootstrap yourself to a better place (at least away from where you are), or you don't. As Marc said, Michal seems to have erected a wall around his thinking. I don't think it's

Re: [R] Histogram

Hi Angelo, Look carefully at package vcd; and at log-linear models (+ glm(..., family=poisson)). For overdispersion there are more advanced methods. HTH, Mark. Angelo Scozzarella wrote: Hi, how can I treat data organised in classes and frequencies? Ex. class frequency

Re: [R] R version 2.7.1 (warnings)

Hi Jaap, Great stuff! As the old adage went, Go well, go Bye, Mark. Van Wyk, Jaap wrote: Thanks, Mark, for the response. The problem is vith SciViews. It is not stable under the latest version of R. I found a solution by downloading the latest version of Tinn-R, which communicates

Re: [R] R version 2.7.1 (warnings)

Hi Jaap, With all those packages loading it could take some time, unless it's a known problem (?). Why don't you do a vanilla start (add switch --vanilla to startup) and do some simple core-related stuff. Then add packages one-by-one... Or: search through the source code of the packages for

Re: [R] help with bivariate density plot question

Hi Daniela, Spencer (? Graves) is not at home. Seriously, this is a list that many people read and use. If you wish to elicit a response, then you would be wise to give a better statement of what your difficulty is. The function you enquire about is well documented with an example, see ##

Re: [R] calculate differences - strange outcome

Hi Andreas, It's because you are dealing with binary or floating point calculations, not just a few apples and oranges, or an abacus (which, by the way, is an excellent calculating device, and still widely used in some [sophisticated] parts of the world).

Re: [R] Newbie's question about lm

Hi Ptit, I would like to fit data with the following formula : y=V*(1+alpha*(x-25)) where y and x are my data, V is a constant and alpha is the slope I'm looking for. Priorities first: lm() or ordinary least-square regression is a basically a method for finding the best-fitting straight

Re: [R] Font quality in base graphics

Hi willemf, Glad to hear that it helped. Years ago (late-90s) I Linuxed, but have since been forced into the Windows environment (where, however, I have the great pleasure of being able to use MiKTeX and LyX, i.e. TeX/LaTeX). I therefore can't help you further, except to say that I have never

Re: [R] Font quality in base graphics

, it's not possible to help further. Of course, you could send me the data and a script showing how you want it plotted, and I would send you a PDF in return, showing you what R can do ;). HTH, Mark. Mark Difford wrote: Hi willemf, Glad to hear that it helped. Years ago (late-90s) I Linuxed

Re: [R] meaning of tests presented in anova(ols(...)) {Design package}

Hi Dylan, I am curious about how to interpret the table produced by anova(ols(...)), from the Design package. Frank will perhaps come in with more detail, but if he doesn't then you can get an understanding of what's being tested by doing the following on the saved object from your OLS call

Re: [R] Font quality in base graphics

Hi wf I just cannot believe that R does not have a good command of this. Curious. I find R's graphical output matchless. Almost without exception I use postscript and find the controls available under base graphics (?par) or lattice adequate (to understate). Very occassionally I fiddle with

Re: [R] Strptime/ date time classes

Hi Caroline, is.na(strptime(19810329012000,format=%Y%m%d%H%M%S)) [1] TRUE The problem was to do with daylight saving time. I need to specify a time zone as this time doesn't exist in my operating system's current time zone. I still think this is odd behaviour though! When you look at

Re: [R] cex.axis for the x axis

Hi Pavel, First, annonations should have the same cex-size on each axis. That said, the way that this is implemented is not too cexy (ouch!). You need to plot without axes, e.g. plot(obj, axes=F), then you add your axes afterwards using your own specifications. ?axes Also see ?par (sub ann)

Re: [R] cex.axis for the x axis

Hi Pavel, And perhaps read the entry for cex.axis a little more carefully. And bear in mind that labels, main, and sub are distinct, having their own cex.- settings. HTH, Mark. Mark Difford wrote: Hi Pavel, First, annonations should have the same cex-size on each axis. That said

Re: [R] Strptime/ date time classes

Hi Caroline, Because POSIXlt is a complicated structure: you are dealing with a list, not with what you think you are. Maybe this will help you to see more clearly. strptime(19800604062759, format=%Y%m%d%H%M%S) [1] 1980-06-04 06:27:59 str(strptime(19800604062759, format=%Y%m%d%H%M%S))

Re: [R] Can R do this ?

Hi Daren, Can R (out)do Emacs? I think you just need to ?Sweave a little. Mark. Daren Tan wrote: I have a folder full of pngs and jpgs, and would like to consolidate them into a pdf with appropriate title and labels. Can this be done via R ?

Re: [R] spineplot (graphics package): how to control font size?

Hi Paul, Duncan has shown you how to do it. There is often a simpler route that is worth knowing about. Whether it works depends on how the function was coded. In this case it works: ## Example par(cex.main = 3) spineplot (table (tbl$DAY, tbl$SEX), main='TIPS') par(cex.main = 1.2) spineplot

Re: [R] Measuring Goodness of a Matrix

Hi Gundala, Suppose I have 2 matrices A and B. And I want to measure how good each of this matrix is. You really want to be using Robert Escoufier's RV-coefficient (A unifying tool for linear multivariate statistical methods: The $RV$-coefficient Appl. Statist., 1976, 25, 257-265). Several

Re: [R] handling the output of strsplit

Hi Denis, h = c(3h30, 6h30, 9h40, 11h25, 14h00, 15h55, 23h) I could not figure out how to use chron to import this into times, so I tried to extract the hours and minutes on my own. Look at ?strptime for this: ## strptime(6h30, format=%Ih%M) [1] 2008-06-21

Re: [R] How to combine to PCAs

Hi Stefan, Is it possible to combine both PCAs in order to get only one set of eigenvectors? Yes there is: statis() in the ade4 package is probably what you want. In short, it does a k-table analysis that will give you a common ordination/position. It also shows how each time-set deviates

Re: [R] Tukey HSD (or other post hoc tests) following repeated measures ANOVA

Hi Ullrich, The model is RT.aov - aov(RT~Cond + Error(Subj/Cond), WMU3C) I understand that TukeyHSD only works with an aov object, but that RT.aov is an aovlist object. You want to use lme() in package nlme, then glht() in the multcomp package. This will give you multiplicity adjusted

Re: [R] Tukey HSD (or other post hoc tests) following repeated measures ANOVA

Hi Ullrich, # what does '~1 | Subj/Cond' mean? It is equivalent to your aov() error structure [ ... +Error(Subj/Cond) ]. It gives you a set of random intercepts, one for each level of your nesting structure. ## To get some idea of what's being done it helps to have a continuous covariate in

Re: [R] Installing Packages in Windows Vista -- YES I tried Run as Administrator

Hi Scotty, Can't give an answer from what you've provided, but one temp. work-around that might work is to get onto CRAN -- packages and download the packages you need from your web browser as zip files, then do an Install package(s) from local zip files... from the Packages menu. HTH, Mark.

Re: [R] Hmisc xYplot won't do conditioning on factors?

Hi Ivan, It appears that xYplot, unlike standard xyplot (or coplot to that matter) does not accept factors as x variable in formula. To add to what you have said. It may not be too well documented in ?xYplot, but xYplot() is really designed to do a number of very useful things with two sets

Re: [R] model R^2 and partial R^2 values

Hi Mirela, Are the relative R^2 values the CP values? No. CP is your complexity parameter. I’ve read that the R^2 = 1-rel error, so I am assuming that in my case this would be 1-0.64949. Is this correct? Yes. See ?rsq.rpart, and run the example, which I've copied below. ## par(ask=T)

Re: [R] [OT] Make plots with GNUplot. Have anyone tried that?

Hi Everyone, Please don't denigrate the capabilities of GNUplot (Louise excluded). It can, in fact, do some truly awesome stuff. http://linuxgazette.net/133/luana.html The PDF is worth a shot. Cheers, Mark. Louise Hoffman-3 wrote: If you still want to then read ?write.table, that can

Re: [R] mixed model nested ANOVA (part two)

Hi Stephen, Also i have read in Quinn and Keough 2002, design and analysis of experiments for biologists, that a variance component analysis should only be conducted after a rejection of the null hypothesis of no variance at that level. Once again the caveat: there are experts on this list

Re: [R] mixed model nested ANOVA (part two)

Hi Stephen, Slip of the dactylus: lm() does not, of course, take a fixed=arg. So you need To recap: mod.rand - lme(fixed=y ~ x, random=~x|Site, data=...) mod,fix - lm(y ~ x, data=...) ## or ##mod,fix - lm(formula=y ~ x, data=...) Bye. Mark Difford wrote: Hi Stephen, Also i have

Re: [R] Mixed model Nested ANOVA

Hi Stephen, Hopefully you will get an answer from one of the experts on mixed models who subscribe to this list. However, you should know that both lme() and lmer() currently have anova() methods. The first will give you p-values (but no SS), and the second will give you SS (but no p-values).

Re: [R] Why does plot() ignore the data type for axis labels?

, make perfect sense. HTH, Mark. Duncan Murdoch-2 wrote: On 19/02/2008 5:40 PM, Stiffler wrote: Mark Difford wrote: I was wondering why the plot() command ignores the datatype when displaying axis labels... plot() doesn't ignore the datatype: [...] plot(x,y) calls xy.coords(), which

Re: [R] Getting started help

Hi Rthoughts, I am currently discouraged by the use of r. I cannot figure out how to use it despite extensive searches. Can anyone help me with getting started? How can import a txt file with series... There are piles of documents that you could (and should) read. I am surprised that you

Re: [R] Getting started help

platforms. I will look further into them. As for everyone else who sent e-mails, thank you. I have printed them out and will look into them. Mark Difford wrote: Hi Rthoughts, I am currently discouraged by the use of r. I cannot figure out how to use it despite extensive searches. Can

Re: [R] Getting started help

of computers but command lines for many programs is something that cna throw me sometimes! Regrads, Seb. Mark Difford wrote: Hi Rthoughts, It isn't clear what you mean. When you install R, the installation program usually puts an icon on your desktop that you can click on to run

Re: [R] Why does plot() ignore the data type for axis labels?

Hi Stiffler, I was wondering why the plot() command ignores the datatype when displaying axis labels... plot() doesn't ignore the datatype: x - as.integer(c(1,2,3)) y -x typeof(x) [1] integer mode(x) [1] numeric plot(x,y) calls xy.coords(), which recasts x as: x = as.double(x), which is

Re: [R] fitted values are different from manually calculating

Hi Yianni, This just proves that you should be using R as your calculator, and not the other one! Regards, Mark. gatemaze wrote: Hello, on a simple linear model the values produced from the fitted(model) function are difference from manually calculating on calc. Will anyone have a

Re: [R] plotDensity

Hi Conny, It still isn't clear what your question is, but a density plot simply shows you the distribution of your data, say a set of measurements of something. Think of it as a modern replacement for the histogram. See http://en.wikipedia.org/wiki/Density_estimation for greater insight.

Re: [R] Help - linear regression

Hi All, Thanjuvar wrote: model2-lm(lavi~age+sex+age*race+diabetes+hypertension, data=tb1) David wrote: in the second equation you are only including the interaction of age*race, the main effect of age, but not the main effect of race which is what came out significant in your first

Re: [R] plotting other axes for PCA

Hi Silvia, What I need is exactly what I get using biplot (pca.object) but for other axes. You need to look at ?biplot.prcomp (argument: choices=) ## Try biplot(prcomp(USArrests), choices=c(1,2)) ## plots ax1 and ax2 biplot(prcomp(USArrests), choices=c(1,3)) ## plots ax1 and ax3

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