similar to: the function lme in package nlme

Dear R-users Coming from a proc mixed (SAS) background I am trying to get into the use of (n)lme. In this connection, I have some (presumably stupid) questions which I am sure someone out there can answer: 1) With proc mixed it is easy to get a hold on the estimated variance parameters as they can be put out into a SAS data set. How do I do the same with lme-objects? For example, I can see the

I know this has been dealt with before on this list, but the previous messages lacked detail, and I haven't figured it out yet. The model is: \x_{ij} = \mu + \alpha_i + \beta_j \alpha is a random effect (subjects), and \beta is a fixed effect (condition). I have a link function: p_{ij} = .5 + .5( 1 / (1 + exp{ -x_{ij} } ) ) Which is simply a logistic transformed to be between .5 and 1.

I have constructed the function mml2 (below) based on the likelihood function described in the minimal latex I have pasted below for anyone who wants to look at it. This function finds parameter estimates for a basic Rasch (IRT) model. Using the function without the gradient, using either nlminb or optim returns the correct parameter estimates and, in the case of optim, the correct standard

Dear all, I am trying to repeat an example from Sokal and Rohlfs "Biometry" -- Box 11.4, example of a randomized-complete-blocks experiment. The data is fairly simple: series genotype weight 1 pp 0.958 1 pb 0.985 1 bb 0.925 2 pp 0.971 2 pb 1.051 2 bb 0.952 3 pp 0.927 3 pb 0.891 3 bb 0.892 4

G'day, All. I have been trying to trackdown a problem in my R analysis script. I perform a scale() operation on a matrix then do further work. Is there any way of inverting the scale() such that sX <- scale(X) Xprime <- inv.scale(x); # does inv.scale exist? resulting in Xprime_{ij} == X_{ij} where Xprime_{ij} \in R There must be some way of doing it but I'm such a newb

Hi all, I have some difficulties with the lme function and so this is my problem. Supoose i have the following model y_(ijk)=beta_j + e_i + epsilon_(ijk) where beta_j are fixed effects, e_i is a random effect and epsilon_(ijk) is the error. If i want to estimate a such model, i execute >lme(y~vec.J , random~1 |vec .I ) where y is the vector of my data, vec.J is a factor object

Dear helpers in this forum, I have the following question: Suppose I have the following data set: id x y 023 1 2 023 2 5 023 4 6 023 5 7 412 2 5 412 3 4 412 4 6 412 7 9 220 5 7 220 4 8 220 9 8 ...... and i want to calculate sum_{i=1}^k sum_{j=1}^{n_i}x_{ij}*y_{ij} is there a simple way to do this within and between subject summation in R?

Hello, I'm trying to fit a special kind of proportional odds model from: Whitehead et al. (2001). Meta-analysis of ordinal outcome using individual patient data. Statistics in medicine 20: 2243-2260. (model 2) The data are as follows: library(nlme) library(geepack) library(Design) library(MASS) options(contrasts=c("contr.SAS","contr.poly")) counts <-

Dear helpers in this forum, This is a clarified version of my previous questions in this forum. I really need your generous help on this issue. > Suppose I have the following data set: > > id x y > 023 1 2 > 023 2 5 > 023 4 6 > 023 5 7 > 412 2 5 > 412 3 4 > 412 4 6 > 412 7 9 > 220 5 7 > 220 4 8 > 220 9 8 > ...... > Now I want to compute the

Dear all, I am trying to define my own corStruct which is different from the classical one available in nlme. The structure of this correlation is given below. I am wondering to know how to continue with this structure by using specific functions (corMatrix, getCovariate, Initialize,...) in order to get a structure like corAR1, corSymm which will be working for my data. Thanks in advance.

Hi all, I am trying to get a handle on gls (package nlme). I have a toy problem: 3 fixed factors (A, B, C), two levels each, 5 replicates per treatment. The response variable is continuous, normal. I have a correlation matrix of the form: > mat A B C A 1.00 0.75 0 B 0.75 1.00 0 C 0.00 0.00 1 which is common to all observations. How do I construct the call to gls? I think I need to

Dear R-helpers, I am struggling with an optimization problem at the moment and decided to write the list looking for some help. I will use a very small example to explain what I would like to. Thanks in advance for your help. We would like to distribute resources from 4 warehouses to 3 destinations. The costs associated are as follows: Destination >From 1 2 3 Total

Dear List: My question is more statistical than R oriented (although it originates from my work with nlme). I know statistical questions are occasionally posted, so I hope my question is relevant to the list as I cannot turn up a solution anywhere else. I will frame it in the context of an R related issue. To illustrate the problem, consider student achievement test score data with multiple

> DATA [,1] [1,] -2.0314185 [2,] -0.3594015 [3,] -1.3225832 [4,] 1.5050892 [5,] -0.4535558 [6,] 3.6335036 [7,] 5.1965750 [8,] 4.2923129 [9,] 6.0913187 [10,] 4.9131070 > RESA [,1] [,2] [,3] [,4] [,5] [1,] -2.0314185 1.5050892 -1.3225832 -1.3225832 -2.0314185 [2,] -0.3594015 -0.3594015 4.2923129 -0.3594015

I need help on calling the svydesign function in the survey package (although this error appears not to be specific to svydesign). I am passing parameters incorrectly but am not sure how to correct the problem. ## Call the main function PS.sim (one of mine). The dots are parameters I omitted to simplify the question. ## y.col, str.col, clus.id, and PS.col are names of columns in the object pop.

Dear R-users I am relatively new to R, i hope my many novice questions are welcome. I have problems accessing some objects (specifically the random effects, correlation structure and variance function) from an object of class gls and lme. I used the following models: yah <- gls (outcome~ -1 + as.factor(Trial):as.factor(endpoint)+

Hi, I'm fitting a relatively simple growth model to some forest plot data. Two species of trees were planted in different mixtures in 10 (nearly-adjacent) plots and measured on four occasions over 10 years. The model is constructed in terms of the diameter increments (per year; DI) in the 3 intervals, in which DI is modelled as a function of mid-interval D and DSQ. The details of the

Dear R-Users I have a problem accessing some values in the output from the summary of an lme fit. I fit the model below: ggg <- lme (ST~ -1 + as.factor(endp):Z.sas + as.factor(endp), data=dat4a, random=~-1 + as.factor(endp) + as.factor(endp):Z.sas|as.factor(trials), correlation = corSymm(form=~1|as.factor(trials)/as.factor(id)), weights=varIdent(form=~1|endp)) hh

Good day R-Users, I have a problem accessing some values in the output from the summary of an lme fit. The structure of my data is as shown below (I have attached a copy of the full data). id trials endp Z.sas ST 1 1 -1 -1 42.42884 1 1 1 -1 48.12007 2 1 -1 -1 43.42878 2 1 1 -1

Dear WizaRds, I am trying to compute the (adjusted) Rand Index in order to comprehend the variable selection heuristic (VS-KM) according to Brusco/ Cradit 2001 (Psychometrika 66 No.2 p.249-270, 2001). Unfortunately, I am unable to correctly use cl_ensemble and cl_agreement (package: clue). Here is what I am trying to do: library(clue) ## Let p1..p4 be four partitions of the kind