similar to: how to check linearity in Cox regression

On examining non-linearity of Cox coefficients with penalized splines - I have not been able to dig up a completely clear description of the test performed in R or S-plus. >From the Therneau and Grambsch book (2000 - page 126) I gather that the test reported for "linear" has as its null hypothesis that the spline coefficient is the same at the center of basis. Thus, in the example

Hello everybody, I am using glmmADMB and when I run some models, I recieve the following message: Erro em glmmadmb(eumencells ~ 1 + (1 | owners), data = pred3, family = "nbinom", : The function maximizer failed (couldn't find STD file) Furthermore: Lost warning messages: Command execution 'C:\Windows\system32\cmd.exe /c

Hi Stephen, Thanks very much for getting back to me. My problem is described below. Any help would be greatly appreciated. Thanks, James Hi, Sorry for bothering you because I know that your time is voluntary, but I would really appreciate some help. I work in a hospital in part of Ireland?s national health service, a service which was struck by a massive cyber attack a couple of years ago. Since

The article on BMA (Bayesian model averaging) presents most valuable tools for model selection, but I find one detail confusing in Example 1. In page 4 of RNews 5/2, second paragraph says that the probability of Time variable not being in the model is 0.445. It seems to me that the figure should be 1 - 0.445 = 0.555, because p!=0.445 is the prob. of Time variable being in the model. The plot in

I have a function that, among other things, runs a linear model and returns r2. But, the number of predictor variables passed to the function changes from 1 to 3. How can I change the formula inside the function depending on the number of variables passed in? An example: get.model.fit <- function(response.dat, pred1.dat, pred2.dat = NULL, pred3.dat = NULL) { res <- lm(response.dat ~

Hi I have two processes which take with a certain probability (p1 and p2) x number of years to complete (age1 and age2). As soon as thge first process is completed, the second one begins. I want to calculate the time it takes for the both processes to be completed. I have the following script which gives me the answer, butI think there must be a more elegant way of doing the calculations

Dear R users, My question is more methodology related rather than specific to R usage. Using time on study as time in a cox model, eg: library(Design) stanf.cph1=cph(Surv(time, status) ~ t5+id+age, data=stanford2, surv=T) #In this case the 1000-day survival probability would be: stanf.surv1=survest(stanf.cph1, times=1000) #Age in this case is a covariate. #I now want to compare the above

Hi, I have a valid SPSS .sav file (which I can open happily in SPSS v11 on Windows XP). Opening it in R2.41 on Linux we get this message :- > HSE3023 <- read.spss("HSE.sav") Error in read.spss("HSE.sav") : error reading system-file header In addition: Warning message: HSE.sav: Variable X234 indicates variable label of invalid length 256 Now variable X234 has indeed a

Hello, Simply put, I'm trying to call a function "testme" with value "age=NA". I wish to use "dotlist<-list(...)" inside the function and have dotlist become: $age [1] NA I'm modifying existing code and need to minimize changing that code so it's easiest to conform how I call the existing function. My sample code fragment, results, and R.version

Dear list I'm using the reshape command and want to reshape a wide data set to a long one e.g. I have the variables y1,y2,y3,age1,age2,age3,sex,ethnic I want my new long data set to consist of the variables y (which has been created from y1,y2,y3), age (which has been created from age1,age2,age3), sex and ethnic I have tried to use the command:

Dear all, I would like to know whether it is possible to unlist elements and keep the original format of the data. To make it more clear, let me give an exemple: I have a list l of dataframes that I created with apply but which looks like this: x1=data.frame(Name=LETTERS[1:2],Age=1:2) x2=data.frame(Name=LETTERS[3:4],Age=3:4) l=list(x1,x2) l [[1]] Name Age 1 A 1 2 B 2 [[2]] Name

Dear R users I have a question related to the interpretation of results based on GAMMs using Simon Woods package gamm4. I have repeated measurements (hours24) of subjects (vpnr) and one factor with three levels (pred). The outcome (dv) is binary. In the first model I'd like to test for differences among factor levels (main effects only): gamm.11<-gamm4(dv ~ pred +s(hours24), random = ~

I'm trying to run an ordered logistic regression model. I've run the following code, but the output does not provide the p-values. Is there some command to include the p-values in the output. reg2 <- polr(trade1 ~ age2 + education2 + personal2 + economy2 + partisan2 + employment2 + union2 + home2 + market2 + race2 + income2) summary(reg2) Re-fitting to get Hessian# Call:

Dear R-Users, I used the box.tidwell () function of the car Package. When I used the following formula: semi.sub.in.mi1.boxtidwell_h<-box.tidwell(RENT_LG ~ I(age+1)+I(age2+1)+X06A + I(X08B+1) + I(X22+1) + I(X24+1) + X31A, ~B_YEAR + C_X01 + C_X14 + C_X19 + C_X29A +C_X21 + C_X23 + D_X12 + D_X17 + D_X18 + D_X25 + D_X27 + D_X30 + D_X32 + D_X35, data = semi.sub.in.mi1) everything is

R-helpers; I used Proc Model in SAS to fit the following model to data: proc model data = dbsmv; a = a1*F**2; b = b1*F + b2*T + b3*F*T; tph2 = tph1 *((1 - exp(-a*age2)) / (1 - exp(-a*age)))**-b; fit tph2; and yielded the following estimated parameters after iterations: a1 = -0.15943, a2 = -1.8177, b1 = -0.01911, b2

Hello everyone, I'm trying to plot the initial and final size of some tadpoles and look at their growth rates (slope of line). They are divided into 6 densities, and so far I have plotted the initial and final sizes (these are means for a pool), and color coded for the 6 densities, but I want a line to connect the initial and final value for each pool (also color coded by density). Any ideas?

Below you will find the output from a failed multi-level model run. I am trying to estimate the following model: Pr(PLFP=1)= logistic regression -> B1_j * bm + B2_j * wm + B3_j bf + B4_j wf + B5 yrsed+ B6 age+ B7 age^2+e_ij B1_j = G01 + G11 bmxd + d1 B2_j = G02 + G12 wmxd + d2 B3_j = G03 + G13 bfxd + d3 B4_j = G04 + G14 wfxd + d4 d1-d4 freely correlated Note that there is no

Greetings to you all, I am performing a semi parametric bootstrap in R on a Gamma Distributed data and a Binomial distributed data. The main challenge am facing is the fact that the residual variance depends on the mean (if I am correct). I strongly feel that the script below may be wrong due to mean-variance relationship #####R code####### fit1s

Hi all, I am hoping someone can help me out with this: If I have dataframe of years and ages and the first column and first row are filled with leading values: Df<- age1 age2 age3 Yr1 1 0.4 0.16 Yr2 1.5 0 0 Yr3 0.9 0 0 Yr4 1 0 0 Yr5 1.2 0 0 Yr6 1.4 0 0 Yr7 0.8 0 0 Yr8 0.6 0 0 Yr9 1.1 0 0 Now the rest of the cells need to be filled according to the previous year and age

Full_Name: Renaud Lancelot Version: Version 2.3.0 (2006-04-24) OS: MS Windows XP Pro SP2 Submission from: (NULL) (82.239.219.108) I think there is a bug in predict.lme, when a polynomial generated by poly() is used as an explanatory variable, and a new data.frame is used for predictions. I guess this is related to * not * using, for predictions, the coefs used in constructing the orthogonal