similar to: LME prediction - object not subsettable?

I am writing a program in which I would like to take in a formula, change the response (Y) variable into something else, and then pass the formula, with the new Y variable to another function. That is, I am starting with formula <- Y~X1+X2+X3 and I'd like to do something like Y <- formula$Y newY <- f(Y) lm(newY~X1+X2+X3) So far, it seems that my

When I use a model fit with LME, I get an error if I try to use "predict" with a dataset consisting of a single line. For example, using this data: > simpledata Y t D ID 1 -1.464740870 1 0 1 2 1.222911373 2 0 1 3 -0.605996798 3 0 1 4 0.155692707 4 0 1 5 3.849619772 1 0 2 6 4.289213902 2 0 2 7 2.369407737 3 0 2 8 2.249052533 4 0 2 9 0.920044316 1

I am trying to estimate models with subsets using the NLME package. However, I am getting an error in the case below (among others): > subset <- c(rep(TRUE, 107), FALSE) > fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1, subset=subset) Error in xj[i] : invalid subscript type 'closure' > fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1,

I am in the process of submitting a package to CRAN. R CMD check ran successfully on the package on my local computer, using R version 2.1.1. However, on the computers for CRAN (with version 2.10.0), the following errors occurred: Warning in parse_Rd("./man/predict.Rd", encoding = "unknown") : ./man/predict.Rd:28: unknown macro '\dquote' *** error on file

I am creating an R package. I ran R CMD check on the package, and everything passed until it tried to run the examples. Then, the result was: * checking examples ... ERROR Running examples in REEMtree-Ex.R failed. The error most likely occurred in: > ### * AutoCorrelationLRtest > > flush(stderr()); flush(stdout()) > > ### Name: AutoCorrelationLRtest > ### Title: Test for

Dear All, I've come across a problem in predict.lme. Assigning a model formula to a variable and then using this variable in lme (instead of typing the formula into the formula part of lme) works as expect. However, when performing a predict on the fitted model I gan an error messag - predict.lme (but not predictlm) seems to expect a 'properly' typed in formula and a cannot extract

I am trying to optimize a likelihood function using NLMINB. After running without a problem for quite a few iterations (enough that my intermediate output extends further than I can scroll back), it tries a vector of parameter values NaN. This has happened with multiple Monte Carlo datasets, and a few different (but very similar) likelihood functions. (They are complicated, but I can send them

Hi everyone, Would somebody please explain (or point me to a reference that explains) the following error: "Error: object of type 'closure' is not subsettable" I was trying to use rep() to replicate a function: > example_function <- function() { return(TRUE) } > rep(example_function, 3) Error: object of type 'closure' is not subsettable But I just cannot

Dear all, for a cross-validation I have to use predict.glmmPQL() , where the formula of the corresponding glmmPQL call is not given explicitly, but constructed using as.formula. However, this does not work as expected: x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2) mydata<-data.frame(x1,x2,y) library(MASS) # works as expected model1<-glmmPQL(y~x1, ~1 | factor(x2),

Hi All, I am trying to start R Server to run some Java Script in my local machine using the library, 'Rook'. I use Windows 7. And my codes are following, > library(Rook) > myD3dir <- 'D:\\STUDIES\\Java script\\d3-master' > s <- Rhttpd$new > s$start(quiet=TRUE) and i get the following error for the above line, Error in s$start : object of type

I tried to use LME (on a fairly large dataset, so I am not including it), and I got this error message: Error in lme.formula(formula(paste(c(toString(TargetName), "as.factor(nodeInd)"), : nlminb problem, convergence error code = 1 message = false convergence (8) Is there any way to get more information or to get the potentially wrong estimates from LME? (Also, the page in the

Hi all, when i run this script: >read.table("Angelika.txt",header=T,sep="\t") >mytable=read.table("Angelika.txt",header=T,sep="\t") >for ( dye in c("A","B","C","F","G","K","L","M")) + { + for (cond in 1:8) + { + measurement =

I'm attempting to write a general function to implement Faraway's bootstrapping algorithm for mixed models with lmer, but have run into a curious problem. I'm comparing two models model.1<-lmer(Response ~ Treatment + (1|Trial), data=exp.data, method="ML") model.2<-lmer(Response ~ 1 + (1|Trial), data=exp.data, method="ML") When I attempt to update

Hello folks: I have a data frame which includes two numeric vectors: "Pa1" and "Ingr" (which represents income).  I run the following code on the R console: ingreso <- factor(ifelse(Ingr<=3000,"bajo","alto")) tapply(Pa1,ingreso,summary) boxplot(Pa1~ingreso) and it works fine.  However, when I "Sweave" through an rnw file containing that

hey there! The object 'cit' contains: > cit ##################################################### # Johansen-Procedure Unit Root / Cointegration Test # ##################################################### The value of the test statistic is: 5.3484 9.0681 10.6433 --------------- I want R to save the value 5.3484 in a new object. I am used to use the command x=cit[a] where a

I am having the same problem as one Rebecca Sela(see bellow). On 21/12/2007 12:07 AM, Rebecca Sela wrote: >* I am trying to optimize a likelihood function using NLMINB. After running without a problem for quite a few iterations (enough that my intermediate output extends further than I can scroll back), it tries a vector of parameter values NaN. This has happened with multiple Monte Carlo

Hello All, I have written three functions. First: To input user specified SAS dataset and plot the boxplots of relevant variables. Second: Extract the number of hours, minutes etc. from a variable describing a time-point using regular expressions. E.g. 'Per1, Day 2, 24 Hour' would be separated into three columns, Per (value 1), Day (value 2) and Hour (value 24) Third:

Hi everyone I am using the wavelet and waveslim package in R to find the wave variance.Here is the code return.modwt<-modwt(X, filter="la8", n.levels=5, boundary="periodic", fast=TRUE) return.modwt.var<- wave.variance(return.modwt, type="nongaussian") Where X is a uni-variate time series. I am expecting a matrix with 5 rows(no. of levels) and 3

Hi all, How can I overcome the error "object of type 'closure' not subsettable" I ran the following script seq <- paste(seq(1914, 1916, by=1), "*.y", sep=".") # make sequence c <- 3 # total number of files d2 <- file # creates dummy file # Input sequence in loop for (i in 1:3){ list <- list.files("~/ukcp09/txt/x.djf", seq[[i]]) file

Dear colleagues, I've just come across a problem with the following command which is a part of the "metaOverview.R" code file provided as an monography- accompanying file at http://www.bioconductor.org/docs/mogr/metadata: ################################## R> hasChr <- eapply(GOTERM, function(x) + x[grep("chromosome", Term(x))]) Error in