search for: augpr

All, I have a question RE plotting the prediction lines of a random effects model via augPred. I'll illustrate via the Pixel dataset within the nlme package: library(nlme) attach(Pixel) fm1Pixel = lme(pixel ~ day + I(day^2), data = Pixel, random = list(Dog = ~ 1)) plot(augPred(fm1Pixel)) ### 10 fitted lines since there are 10 dogs fm2Pixel = update(fm1Pixel, . ~ . + Side) plot(a...

All, I'm trying to create an augPred plot in the nlme library, similar to the plot on p.43 of Pinheiro & Bates (Mixed Effects Models in S and S-Plus) for their Pixel data. My data structure is the same as the example but I still get the error msg below. > comp.adj.UKV <- groupedData(adj.UKV ~ Time | Patient_no/Lisino...

Dear all as I did not get any response on my post about abline and plot(augPred)) I try again. I hope I do not break some posting guide rules. I would try to contact package maintainer directly but there is stated to be R-core people, so I feel R-help list shall be OK. I need to draw straight lines through augPred plotted panels (vertical or horizontal) at specified poin...

Dear R-users, I am a newbie to this site and a relative new-comer to S/R, so please tread lightly, for you tread... There have been several posting relating to problems with augPred() from the nlme library. Here is a "fix" for one of these problems which may lie at the root of others. In my case the problem with augPred() lay in gsummary(), which augPred() uses, causing it to fail. [From mucking around &c using getAnywhere("augPred.lme"), and setting...

I read the posts about augPred with lme, but does anyone know if there is a correlate for augPred for lmer? Specifically, I want to be able to use it to plot projections for all groups in an lmer class object using plot(augPred(lmer.object)). Thanks, Kyle *************************************** J. Kyle Roberts, Ph.D. Bayl...

Hello, I want to use lme to fit two (or more) models, and then compare the fits on each individual. I know how to write my own code to do this (for each individual, plot the raw data, followed by lines() to plot each fitted curve) but I would like to use plot(augPred(... as it produces a nice trellis plot. I thought I could do this with par(new=T) but it does not seem to work. trellis.par.set() does not have a component called "new" so I cannot use that to imitate what I would do with par. Does anyone know how to overlay two or more plots produ...

Dea-R community. I'd like to draw your attention to an issue I have recently encountered while doing my current data analysis. I've got an unexpected (to me) result from the command: > augPred(lmList(my.object)), 'my.object' being a grouped data frame of class: > class(my.object) [1] "nfnGroupedData" "nfGroupedData" "groupedData" "data.frame" The problem is more easily explained by showing these two to Trellis plot: > plot(m...

Hello, Is there a way to get augPred to work with lme if a subset statement is used? For example, if I modify the example from ?augPred.lme to include a subset statement, I get the following error: fm1 <- lme(Orthodont, random = ~1, subset=distance>19) augPred(fm1, length.out = 2, level = c(0,1)) Error in tapply(object[[nm]]...

Dear all I am trying nlme together with Pinheiro/Bates book. I constructed grouped data object with suitable plotting layout (according to some common factor, panels from bottom to top are in increasing order). When I do nlme(... some stuff...) I get fitted object which I can plot with plot(augPred(fit.nlme6, level=0:1)) but it results in completely different ordering. Is there any way how I can plot panels in some defined order e.g. ord.f<-order(my.1.fac, my.2.fac) plot(augPred(fit.nlme6, level=0:1), ord.f) The only thing I found out is that if I order grouped.data object gr.dat&lt...

Posted this to r-sig-mixed-models (https://stat.ethz.ch/pipermail/r-sig-mixed-models/2019q1/027620.html) but this might rather need to go to r-devel anyway, so reposting here: I came across a weird problem / bug with augPred() from nlme (nlme_3.1-137). Here is a reproducible example to illustrate the issue (tested on R 3.5.2 and R-devel 2019-03-03 r76192): library(nlme) dat <- data.frame(id = c(1,1,1,2,3,3,4,4,4,4), xi = c(1,2,3,1,1,2,1,2,3,4), yi = c(2,1,4,2,3,2,5,4,6,8),...

Hi using this code example: library(nlme) fm1 <- lme(Orthodont, random = ~1) plot(augPred(fm1)) is there any way to have the plots in each cell labelled and ordered according to Orthodont$Sex? I.e. in addition to the bar with the label for Orthodont$Subject there is another bar labelling the Sex of the subject? thanks a lot christoph --

...r". -- David. > I could check which column is offending but actually it is only minor nuisance, I can live with selection of columns before fitting a model. What seems to me strange is that both full dataset and only selected colums gave me identical fit results but only one works within augPred. > > Cheers > Petr > >> -----Original Message----- >> From: Bert Gunter [mailto:bgunter.4567 at gmail.com] >> Sent: Wednesday, August 23, 2017 4:50 PM >> To: PIKAL Petr <petr.pikal at precheza.cz> >> Cc: r-help mailing list <r-help at r-project...

...awaits moderator approval. I could check which column is offending but actually it is only minor nuisance, I can live with selection of columns before fitting a model. What seems to me strange is that both full dataset and only selected colums gave me identical fit results but only one works within augPred. Cheers Petr > -----Original Message----- > From: Bert Gunter [mailto:bgunter.4567 at gmail.com] > Sent: Wednesday, August 23, 2017 4:50 PM > To: PIKAL Petr <petr.pikal at precheza.cz> > Cc: r-help mailing list <r-help at r-project.org> > Subject: Re: [R] strange n...

Dear Friends, Is there a workaround to this problem or must the object plotted by plot(augPred(object, ...)) be a grouped object? score <- c(108, 103, 96, 84, 118, 110, 129, 90, 84, 96, 105, 113, 96, 117, 107, 85, 125, 107, 128, 84, 104, 100, 114, 117, 110, 127, 106, 92, 125, 96, 123, 101, 100, 103, 105, 132, 122, 133, 107, 99, 116, 91, 128, 113, 88, 105, 112, 130)...

Hi, I'm new at this, I'm very confused, and I think I'm missing something important here. In our pet example we have this: > fm <- lme(Orthodont) > plot(Orthodont) > plot(augPred(fm, level = 0:1)) which gives us a trellis plot with the females above the males, starting with "F03", "F04", "F11", "F06", etc. I thought the point of this was to create an ordering where the females are ordered ("F01", "F02", "F...

Dear r-helpers, When I issue the commands plot(augPred(mcc.lme, primary = ~ mcc$age, length.out = 2, level = c (0, 1))) or plot(comparePred(mcc1.lis, mcc.lme, primary = ~ mcc$age, length.out = 2), layout = c(4, 3))) no lines are drawn. But fm1 <- lme(Orthodont) plot(augPred(fm1, level = 0:1, length.out = 2)) does plot lines. augPred() and com...

Dear all I encountered strange behaviour of augPred with virtually the same data First I made groupedData object. > mar.g<-groupedData(rutilizace~doba|int, data=mar) When I perform nlme on complete dataset I get an error with augPred > fit<-nlsList(rutilizace~SSasymp(doba, Asym, R0, lrc), data=mar.g) Warning message: c("1 error...

...pen mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Aug 23, 2017 at 5:17 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote: > Dear all > > I encountered strange behaviour of augPred with virtually the same data > > First I made groupedData object. >> mar.g<-groupedData(rutilizace~doba|int, data=mar) > > When I perform nlme on complete dataset I get an error with augPred >> fit<-nlsList(rutilizace~SSasymp(doba, Asym, R0, lrc), data=mar.g) > W...

Dear R users; Ive got two questions concerning nlme library 3.1-65 (running on R 2.2.0 / Win XP Pro). The first one is related to augPred function. Ive been working with a nonlinear mixed model with no problems so far. However, when the parameters of the model are specified in terms of some other covariates, say treatment (i.e. phi1~trt1+trt2, etc) the augPred function give me the following error: "Error in predict.nlme(object...

Dear all I try to refine my nlme models and with partial success. The model is refined and fitted (using Pinheiro/Bates book as a tutorial) but when I try to plot plot(augPred(fit4)) I obtain Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop = FALSE], : Levels (0,3.5],(3.5,5],(5,7],(7,Inf] not allowed for vykon.fac > Is it due to the fact that I have unbalanced design with not all levels of vykon.fac present in all levels of other explana...