similar to: mlm for within subject design

Dear all, is there anyone who can help me extracting p-values from an Anova object from the car library? I can't seem to locate the p-values using str(result) or str(summary(result)) in the example below > A <- factor( rep(1:2,each=3) ) > B <- factor( rep(1:3,times=2) ) > idata <- data.frame(A,B) > fit <- lm( cbind(a1_b1,a1_b2,a1_b3,a2_b1,a2_b2,a2_b3) ? sex,

Hi, it is easiest to explain what I want to do by an example: lets assume there are two factors/variables: A <- c(1,2,3) B <- c(1,3,3) Now I would like to generate a list of strings that should look like ("A1_B1","A1_B2","A2_B1","A2_B2"). So actually the string contains all possible combinations of A and B (separated by _). This should be also

I have been attempting to use cph models to get better calibration of my models for which I had originally used logistic regression. I tried running with 40 repetitions and got an error. I then tried 500 repetitions (thinking that the NaNs in the output below might be caused by that choice) and then let my computer crunch for several hours and got only the same error message and

Hi, I am running the following model: fit1.full <- coxme(Surv(age_sym1, sym1) ~ sex + lifedxm*sex + (1|famid), data=bip.surv) I would like to extract the AIC from that object to calculate the AICC. However, when I look at str(fit1.full) and summary(fit1.full) (pasted below) I don't see anything that would allow me to get pull the AIC out from that object. Is there a way to retrieve the

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

I'd like to fit and explore a collection of hierarchical loglinear models that might range from the independence model, ~ 1 + 2 + 3 + 4 to the saturated model, ~ 1 * 2 * 3 * 4 I can use add1 starting with a baseline model or drop1 starting with the saturated model, but I can't see how to get the model formulas or terms in each model as a *list* that I can work with further. Consider

Dear list: Given > str(b3) 'data.frame': 159 obs. of 6 variables: $ index_pollution : num 8.228 10.513 0.549 0.915 10.416 ... $ position_descrip: chr "2" "2" "2" NA ... $ position_geo : chr "3" "0" "3" "3" ... $ institution : Factor w/ 3 levels "digesa","mem",..: 3 3 3 3 3 3

Dear R-helpers; While using gnls() to fit a function > Gbht0t.gnls <- gnls(h2 ~ Rht(b0, b1, b2, h1,t1, t2), data=gbht10, + params=list(b0 + b1 + b2 ~ Sisp -1), start=c(strssb0,strssb1,strssb2)) I encountered an error: "Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type " Rht is a defined function to be

I have an application where I have a function to calculate results for a 2-way table or matrix, which returns a matrix with one less row and column. To keep this short, the function below captures the structure: fun2way <- function(f){ if (!length(dim(f)) ==2) stop("only for 2-way arrays") R <- dim(f)[1] C <- dim(f)[2] f[1:(R-1), 1:(C-1)] } Now, I want to

Hi, I've a list of list. I want to extract an element by the rownames. I can extract it by: data[[1]][[1]][[4]][1] But I want to exctract it by a command like this: data[[1]][["B0"]][["smac"]][["cont"]][1] It's possible? Thanks, Alfredo > str(data) List of 1 $ :List of 4 ..$ :List of 4 .. ..$ : num [1, 1:3] 0.4 0.458 0.5 .. ..$ : num

Dear All, I'm using apply to do some genetic association analysis along a chromosome, with many thousands markers. For each marker the analysis is the same, so I was planning to use apply(chrom, 2, somefunction) In the specific case I do: my.results = apply(chr, 2, function(x){anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))[1,3]}) This is all good and well in theory, but in

I am using R-2.10.1 binary from CRAN on a WinXP Pro system. I also use SAS v9.2 on the same box. I just started using the SAS ODBC driver that comes with version 9 of SAS. I have been able to set up an ODBC source for SAS datasets using the driver, and then with RODBC I am able to read a sample SAS dataset. > library(RODBC) > ch <- odbcConnect('sasodbc', believeNRows=FALSE)

Dear All, I seem entirely unable to solve what should be a very simple problem. I have imported a SPSS dataset into R using spss.get from Frank Harrell's Hmisc library. The variables are imported classed as 'labelled': missing values are coded as either the SPSS missing value code, 8 or 88. All are imported correctly; 8 and 88 being identified as true numbers in the

All, I have some code that I have been working on that crashes R (1.8.1 on MacOS X installed from source). Here are excerpts of the code and data structures. When the lists that I am using to construct the data.frame are truncated (shortened), R catches the differing rows and warns. However, when the entire lists are used (I haven't looked for an exact breakpoint or for a particular list

Below is a SIMEX object that was generated with the "simex" function from the "simex" package applied to a logistic regression fit. From this mountain of information I would like to extract all of the values summarized in this line: .. ..$ variance.jackknife: num [1:5, 1:4] 1.684 1.144 0.85 0.624 0.519 ... Can someone suggest how to go about doing this? I can extract the

Dear R friends. After having some troubles learning how to create a ffdf object, now I find myself having problems saving it. this is the data i´d like to save: str(DATA) List of 3 $ virtual: 'data.frame': 6 obs. of 7 variables: .. $ VirtualVmode : chr "double" "short" "integer" "integer" ... .. $ AsIs : logi FALSE FALSE FALSE

Hello R helpers, I would like to automate this code for many files of the same type. But I don´t know how to make it. In particular, i don´t know how to read many files each one as an r object with the name of the file. Then a for loop would be sufficient, right? Many thanks and a happy new year. Dominic datos <- read.table('global2001.csv',head=T,sep=';',stringsAsFactors=F)

Full_Name: Henrik Bengtsson Version: R v1.7.1 OS: WinXP Pro, Solaris 9 Submission from: (NULL) (130.235.2.229) A colleague of mine who is new to R had problems setting up his .Rprofile and we tracked it down to the following. On both WinXP and Solaris with Rv1.7.1 we noticed that the *last* line in .Rprofile has to have a *newline* to be evaluated. For instance, starting R with the following

Hello I have a data set that looks like this; > b2 dato chr status PRRSvac PRRSsanVac PRRSsanDk PRRSdk 33 2007-12-03 090432 R?d SPF 34 2007-02-09 090432 R?d SPF+sanDK 35 2002-12-17 090432 R?d SPF+DK 36 2002-11-27 090432 R?d SPF+sanDK 37 2002-07-23

I don't see what's missing in my statements to add rows to a data frame and someone else will probably see what needs to be added to the statements. The data frame has this structure (without any data): $ PHYLUM : chr $ SUBPHYLUM : chr $ SUPERCLASS : chr $ CLASS : chr $ SUBCLASS : chr $ INFRACLASS : chr $ SUPERORDER : chr $ ORDER : chr $ SUBORDER :