similar to: Error from termplot() with make.panel.svysmooth() for complex survey data

Hi all- So sorry to bother you all with something pretty basic. I am trying to add the lines method output from svysmooth to a svyplot with style="grayhex". However, the line either appears in the wrong place or if I am running in R Studio it causes the system to crash. I know this is something to do with Lattice graphics, but for the life of me I can not figure out how. Dr. Lumley

On Thu, 18 Mar 2004 k.hansen@biostat.ku.dk wrote: > The bug exists on R-1.9.0-alpha compiled the 10/3. > > Termplot has a problem if either the model only contains a single term > or if asked to plot a single term. In addition there are problems with > the option se = TRUE. I can't reproduce this in either R-devel or 1.8.1, and termplot hasn't changed since January. I do

I am fitting a cox PH model w/ 2 predictors, x1 = 0/1 treatment variable and x2=continuous variable. I am using natural splines (ns) to model the effect of x2. I would like to examine the estimated effect of x2 on the hazard. I have tried various approaches (below; let model.fit= fitted model using coxph in survival library): 1. The simplest method appears to be using termplot(model.fit).

Hi, Is this a bug in termplot, or (once again) do I just not understand what R is really doing? I am using termplot to contruct partial residual plots, 1. For all terms at once 2. One term at a time but I get different results from these two methods. To give a concrete example, I would have thought the top and bottom rows of the plot constructed with the following code would be identical.

At 11:57 25/10/00 +0100, Brian Ripley wrote: >> Date: mer., 25 oct. 2000 12:38:55 +0200 >> From: Emmanuel Paradis <paradis@isem.univ-montp2.fr> > >> I think it would be nice to have par(ask=T) set by default in termplot(), >> like it is in plot.lm(). > >Well, it isn't really the default in plot.lm, the default for `ask' being > >interactive()

termplot() does not carry subsetting over to carriers that are in the environment but not in the data frame. This generates a "subscript out of bounds" error. > data(ToothGrowth) > logdose <- log(ToothGrowth$dose) > tooth.lm <- lm(len ~ logdose, data=ToothGrowth) > termplot(tooth.lm) ## Works fine > toothVC2.lm <- lm(len ~ poly(dose,2),

I have a suggested addition to termplot. We have a local mod that is used whenever none of the termplot options is quite right. It is used here almost daily for Cox models in order to put the y axis on a risk scale: ---- fit <- coxph(Surv(time, status) ~ ph.ecog + pspline(age), data=lung) zz <- termplot(fit, se=TRUE, plot=FALSE) yy <- zz$age$y + outer(zz$age$se, c(0, -2, 2),

Brian, I used termplot(..., plot=FALSE) recently in R-devel: works like a charm. Thanks much for the update. Our in-house "gamterms" function, which this obviates, would also return the "constant" attribute from the underlying predict(..., type="terms") call. I have occasionally found this useful, and so it would be a worthwhile addition to termplot.

From ?termplot: col.se, lty.se, lwd.se: color, line type and line width for the ?twice-standard-error curve? when ?se = TRUE?. ...which is findable, but might usefully also be made explicit in the definition of the se= argument. -pd > On 10 Jan 2018, at 23:27 , Eric Goodwin <Eric.Goodwin at cawthron.org.nz> wrote: > > Thanks for your prompt reply Duncan. > >

I'm making some functions to illustrate regressions and I have been staring at termplot and predict.lm and residuals.lm to see how this is done. I've wondered who wrote predict.lm originally, because I think it is very clever. I got interested because termplot doesn't work with interactive models: > m1 <- lm(y ~ x1*x2) > termplot(m1) Error in `[.data.frame`(mf, , i) :

I have used glm and stepAIC to choose a best model. I can use termplot to assess the contribution of each explanatory variable in the glm. However the final model after running stepAIC includes interaction terms, and when I do termplot I get "Error in `[.data.frame`(mf, , i) : undefined columns selected". I also see the termplot detail saying "Nothing sensible happens for

Hi all, I noticed some very odd behaviour in the termplot function of the stats package due to the following lines : 18. if (is.null(data)) 19. data <- eval(model$call$data, envir) This one will look in the global environment, and renders the two lines after this 20. if (is.null(data)) 21. data <- mf completely obsolete. If nothing is found, an error is returned. If

I'd like to make the following change to termplot(): Add panel=points as an extra parameter. Replace if (partial.resid) points(xx, pres[, i], cex = cex, pch = pch, col = col.res, ...) by if (partial.resid) panel(xx, pres[, i], cex = cex, pch = pch, col = col.res, ...) Also, I think, add col.smooth, span and iter as named parameters; see below.

# r-bugs@r-project.org `termplot' bombs if the original dataset contains NAs in the predictors, even if these were ignored during fitting: test> bug.data_ data.frame( x=c(1:3, NA), y=runif( 4)) test> lm.tpbug_ lm( y~x, data=bug.data) test> termplot( lm.tpbug) Error in xy.coords(x, y, xlabel, ylabel, log) : subscript out of bounds A simple fix seems to be add the

On Sat, 24 Jan 2004 13:29:02 +1100, John Maindonald <john.maindonald@anu.edu.au> wrote: >Hi Duncan - >Are you a good person to check with re the inclusion of my fix, >or some equivalent, for Problem # 6327? I'm as good as any. You can view the bug repository at <http://bugs.r-project.org/>. There's an entry there that says Thomas Lumley has fixed things. I tried

Thanks for your prompt reply Duncan. I had indeed assumed they were what the help file says until observation raised doubts, which is why I queried it. >From reading the code for termplot(), it seems that either the predict() function doesn't return the 1x standard error, or the curves plotted by the termplot() function are not 1x standard errors. If they're not 1x standard errors,

Hi together, I always get an error message with using ylim in termplot(), like this: > x<-(1:10) > y<-(10:1) > l<-lm(y~x) > termplot(l,ylim=c(1,2)) Is this a bug, or is there another possibility to do that? Especially, I would like to use term.plot() for gamlss objects. Thanks for your help! Andreas -- Echte DSL-Flatrate dauerhaft f?r 0,- Euro*!

Hi all I was playing with termplot(), and came across what appears to be an inconsistency. It would appreciate if someone could enlighten me: > # First, generate some data: > y <- rnorm(100) > x <- runif(length(y),1,2) > # Now find the log of x: > logx <- log(x) > > # Now fit two models that are exactly the same, but specified differently: > m1 <-

While termplot is under discussion, here's another proposal. I'd like to change the default for partial.resid to TRUE, and for smooth to panel.smooth. I'd be surprised if those changes were to break existing code. John Maindonald email: john.maindonald at anu.edu.au phone : +61 2 (6125)3473 fax : +61 2(6125)5549 Centre for Mathematics & Its Applications, Room

I am running R 1.2.1 under Windows 98SE. termplot() currently fails when there are composite terms, thus: > library(mass) > data(hills) > hills.lm <- lm(time ~ climb + poly(dist, 2), data = hills) > termplot(hills.lm) Hit <Return> to see next plot: Error in eval(expr, envir, enclos) : Object "dist" not found The call >