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Hi list, can I extract the cov.unscaled ("the unscaled covariance matrix") from a gls fit (package nlme), like with summary.lm? Background: In a fixed effect meta analysis regression the standard errors of the coefficients can be computed as sqrt(diag(cov.unscaled)) where cov.unscaled is (X'WX). I try do do this with a gl...

...4 d=.04 t=180; model Y = b/(1+exp(-d*(X-t))); output out=b p=yhat r=yresid ; run; proc print data=a; run; A summary of the outputs: - Same coefficients (this is a good thing) - Same standard errors of the coefficients (also good) - Different covariance matrices (WHY?) I convert the cov.unscaled from R's NLS to a correlation and compare it to SAS's correlation. They are identical; e.g., cov2cor(summary.nls.L$cov.unscaled) I have even written a function to convert an NLS object into a "cov.scaled" element that is equivalent to SAS: scaledCOV = function (nlsObject) {...

...me number of >> bytes. > > "scalable" instead of "scalable x." Yep, missed that in the conversion from the old <n x m x ty> format. > >> For derived types, a function (getSizeExpressionInBits) to return a pair of >> integers (one to indicate unscaled bits, the other for bits that need to be >> scaled by the runtime multiple) will be added. For backends that do not need to >> deal with scalable types, another function (getFixedSizeExpressionInBits) that >> only returns unscaled bits will be provided, with a debug assert that...

...low: ## START PROGRAM trial <- function(input) { pmvnorm(lower = c(0,0), upper = c(2, 2), mean = input, sigma = matrix(c(.1, 0, 0, .1), nrow = 2, ncol = 2, byrow = FALSE)) } require(mvtnorm) require(adapt) bottomB <- -5*sqrt(.1) topB <- 2 + 5*sqrt(.1) areaB <- (topB - bottomB)^2 unscaled.Po.in.a <- adapt(2, lo = c(bottomB, bottomB), up = c(topB, topB), minpts = 1000, eps = 1e-4, functn = trial) (1/areaB)*unscaled.Po.in.a$value ## FINISH PROGRAM I tried to run the program again changing a.) sigma in the trial function, b.) upper in the trial function, and c.) the bounds of...

Hi, I am running a simple linear model with (say) 5 independent variables. Is there a simple way of getting the variance-covariance matrix of the coeffcient estimates? None of the values of the lm() seem to provide this. Thanks in advance, Ritwik Sinha rsinha@darwin.cwru.edu Grad Student Case Western Reserve University [[alternative HTML version deleted]]

Hi, does anyone know which of the scaled or unscaled version of the variance-covariance matrix of regression coefficients (as produced by ls.diag) is the correct one, or when one is better than the other? I am interested in univariate linear regression (lm). Thank you very much. Dipl.-Psych. Johannes Ullrich Philipps-Univer...

Hello, I''m inexperienced with linux, X11 and R. A font problem have surfaced. When I use pairs in John Fox''s car library e.g.: > pairs(cbind(prestige, income, education, women)) Error in text.default(x, y, txt, cex = cex, font = font) : X11 font at size 16 could not be loaded In addition: Warning message: freeing previous text buffer in GText > Evidently

In summary.glm I'm trying to get a better feel for the z output. The following lines can be found in the function 1 if (p > 0) { 2 p1 <- 1:p 3 Qr <- object$qr 4 coef.p <- object$coefficients[Qr$pivot[p1]] 5 covmat.unscaled <- chol2inv(Qr$qr[p1, p1, drop = FALSE]) 6 dimnames(covmat.unscaled) <- list(names(coef.p), names(coef.p)) 7 covmat <- dispersion * covmat.unscaled 8 var.cf <- diag(covmat) 9 s.err <- sqrt(var.cf) 10 tvalue <- coef.p/s.err 11 dn <-...

...this from R). I have re-installed x11-common via the Synaptic package manager (so I suppose X11 is well installed) without improvement. I have checked /etc/X11/ xorg.conf Section "Files" FontPath "/usr/share/X11/fonts/misc" FontPath "/usr/share/X11/fonts/100dpi/:unscaled" FontPath "/usr/share/X11/fonts/75dpi/:unscaled" FontPath "/usr/share/X11/fonts/Type1" FontPath "/usr/share/X11/fonts/100dpi" FontPath "/usr/share/X11/fonts/75dpi" FontPath "/usr/share/fonts/X11/misc" FontPath "/v...

Some plots fail due to a problem with the X11 fonts. I get a message that "X11 font at size 22 could not be loaded." The demo() graphics routine for instance dies during the third chart. The graphics demo calls "font.main=1" and that seems to be where the error is. I believe this is due to a configuration problem on my system, however I can't find where in the

In postscript graphs (pointsize = 10, different sizes in graph adjusted via cex) I would like to use different font sizes but get the following warning message: Warning messages: 1: X11 used font size 8 when 9 was requested 2: X11 used font size 8 when 7 was requested 3: X11 used font size 8 when 5 was requested This is probably not a R but a X11 problem, nevertheless I would be most

...the effects are orthogonal, so order is not an issue, but as I move onto the tougher cases, I need model.matrix to preserve order, and it doesn't. Q 4) What are the $effects in lm.objects? For the moment I've stuck in the coefficients. Q 5) Any objection to passing cov.unscaled from aov to summary.aov? (Since I'm not using qr and can't pass R) Feedback needed, comments are welcome. Jim Robison-Cox ____________ Department of Math Sciences | | phone: (406)994-5340 2-214 Wilson Hall \ BZN, M...

...g64428.html Still, I am not sure how to pre-process the data and to post-process the results. Since write.svm() writes .scale and .ysale files as well as an svm file, I figure that the scaling data is included in the svm object. Does that mean that I do not have to worry about scaling my data and unscaling the results provided by the predict function on a model reloaded using save/load ? I am asking this because I previously succeeded in loading the svm model from libsvm in Java, but the results using unscaled data were obviously wrong. Thanks in advance, Thomas

Full_Name: M. Mu?oz M?rquez Version: 2.3.1 OS: Ubuntu Submission from: (NULL) (150.214.231.66) Here is the reply to the edit command using gnome > edit(data.frame()) Erro en dataentry(datalist, modes) : invalid device Adem?s: Warning message: unable to create fontset -*-fixed-medium-r-normal--13-*-*-*-*-*-*-* > Sys.getlocale() [1]

...ufffice? We could add a ConstantVScale or something to make it work. >> >> I agree the name is not ideal and I'm open to suggestions -- I was thinking of the two >> integers representing the known-at-compile-time terms in an expression: >> '(scaled_bits * vscale) + unscaled_bits'. >> >> Assuming the pair is of the form (unscaled, scaled), then for a type with a size known at >> compile time like <4 x i32> the size would be (128, 0). >> >> For a scalable type like <scalable 4 x i32> the size would be (0, 128). >>...

In ubuntu 6,06 the R normally run, but latter to install the a vesion 6,10 plot this not appearing. computer with problem: /usr/share/X11/fonts$ ls misc Type1 X11R7 In computer OK: /usr/share/X11/fonts$ls 100dpi(*) 75dpi encodings fonts.cache-1 misc Type1 ----- Mensagem original ---- De: Peter Dalgaard <p.dalgaard@biostat.ku.dk> Para: Ricardo Arias Brito

...names(x) [1] "call" "terms" "residuals" [4] "coefficients" "aliased" "sigma" [7] "df" "r.squared" "adj.r.squared" [10] "fstatistic" "cov.unscaled" x$fstatistic value numdf dendf 72.04064 1.00000 31.00000 But can not find the p value of F statistics. Thanks Ted -- View this message in context: http://www.nabble.com/extract-the-p-value-of-F-statistics-from-the-lm-class-tp22891475p22891475.html Sent from the R help m...

Core dumped when plot() is used with pch="c" & cex > 2, e.g., plot(1,1, pch="+", cex=2.2) Thank you and best wishes for 2000! Rashid Nassar --please do not edit the information below-- Version: platform = i586-unknown-linux arch = i586 os = linux system = i586, linux status = major = 0 minor = 90.1 year = 1999 month = December day = 15 language = R

...d problems because they had failed to install fonts: my Knoppix/tracking Debian unstable distribution claims that the most recent versions of xfonts-100dpi and xfonts-75dpi are both installed. (version 1:1.0.0-2) I'm using the Xorg version of X11. xset -q says: /usr/X11R6/lib/X11/fonts/misc:unscaled,/usr/X11R6/lib/X11/fonts/misc,/usr/X11R6/lib/X11/fonts/75dpi:unscaled, /usr/X11R6/lib/X11/fonts/75dpi,/usr/X11R6/lib/X11/fonts/100dpi:unscaled,/usr/X11R6/lib/X11/fonts/100dpi, /usr/X11R6/lib/X11/fonts/Speedo,/usr/X11R6/lib/X11/fonts/Type1,/usr/share/fonts/ttf/western, /usr/share/fonts/ttf/decorat...

...this message: > x11() Error in x11() : could not find any X11 fonts Check that the Font Path is correct. I can't think of what could have happened to have changed anything. So I tried this: $ /usr/sbin/chkfontpath -l Current directories in font path: 1: /usr/X11R6/lib/X11/fonts/misc:unscaled 2: /usr/X11R6/lib/X11/fonts/75dpi:unscaled 3: /usr/X11R6/lib/X11/fonts/100dpi:unscaled 4: /usr/X11R6/lib/X11/fonts/misc 5: /usr/X11R6/lib/X11/fonts/Type1 6: /usr/X11R6/lib/X11/fonts/Speedo 7: /usr/X11R6/lib/X11/fonts/cyrillic 8: /usr/X11R6/lib/X11/fonts/TTF 9: /usr/share/fonts/default/Type1 10:...