similar to: Error in family$family : $ operator is invalid for atomic vectors

dear community, I am a beginer in R , and can't predict with logistic model in package logistf, could anyone help me ? thanks ! the following is my command and result : >library(logistf) >data(sex2) >fit<-logistf(case ~ age+oc+vic+vicl+vis+dia, data=sex2) >predict(fit,newdata=sex2) Error in predict(fit, newdata = sex2) : no applicable method for "predict"

Dear List, today I turn to you with a next problem. I'm trying to compare species richness between various datasets (locations) using species accumulation curves (Chapter 4, page 54 in Tree diversity analysis<http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp>by Kindt & Coe). To accomplish this I'm using package BiodiversityR. My data is comprised of

Hi im trying to add error bars to my barplots, there very basic, i have a few grapghs where the y variable is different but on all the X variable is Age (Adult and Juvenile) however this is split into two levels so i have males and females, so my graph basically has four bars on it. I know how to add eror bars for instance when there is only one level eg lookng at the diffrence between male and

Hi all, The last e-mails about beginners gave me the courage to post a question; from a beginner's perspective, there are a lot of questions that I'm tempted to ask. But I'm trying to find the answers either in the documentation, either in the about 15 free books I have, either in the help archives (I often found many similar questions posted in the past). Being an (still actual)

Hi All, I am currently conducting some survival analyses. I would like to extract coefficients at each level of the IVs. I read on a previous posting that dummy regression using coxph was not possible. Therefore I though, hey why not categorize the variables (I realize some folks object to categorization but the paper I am replicating appears to have done so ...) and turn the variables

Hi List, I'm having problems installing certain packages. When I try to install fields, I get the output below. I have highlighted the what I perceive as the first error (spam seems to be a dependency of fields). Can I assume this is causing dependency problems for fields, which fails to install at the end, or is there a deeper problem? I run Ubuntu Karmic Koala on R 2.9.2. 2>

Dear R-Help subsribers, upon running into a wonderful ggplot2 package by accident, I abruptly encountered another problem. Almost every command run with ggplot2 results in some sort of error. The one below is far the most common one. Kind people from ggplot2 mailing list couldn't manage to solve the problem, so I'm re-posting it here to try my luck. I will recommend myself for any tips

Hi, I have imported some data to R from stata and my factor variables have an Indeterminate level which I don't really want. For example the variable sex has the levels Male, Female and Indeterminate. There are no 'Indeterminate' values in the data. Can somebody tell me how to get rid of this level as it restricting my cox ph model. Thanks Neil

Dear all, while preparing some exercises I came across some highly surprising behaviour of file.exists(). The specific value "prn.us.txt" always returns TRUE, even though that file is nowhere to be found on my system. In a fresh R session 3.4.4 installed on Windows 10: > grep("prn.us.txt", dir(recursive = TRUE)) integer(0) > file.exists("prn.us.txt") [1] TRUE

Thank you. I was just replying my own message with the same information. Sorry for not doing the research properly before filing. Cheers Joris On Sat, Mar 24, 2018 at 11:36 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > On 24/03/2018 6:16 AM, Joris Meys wrote: > >> Dear all, >> >> while preparing some exercises I came across some highly surprising

Dear All, I got a warning message "X matrix deemed to be singular" in Cox model with a time dependent coefficient. In my analysis, the variable "SEX" is a categorical variable which violate the PH assumption in Cox. I first used the survSplit() function to break the data set into different time intervals, and then fit the model. The procedures can be described as follows:

I apologize in advance if this is the wrong forum for this report/request, and for the fact that I have not read the code for ftable.formula in any detail. >From reading the documentation for ftable.formula, I expected that the following two calls to ftable would produce the same results: data(UCBAdmissions) ftable(UCBAdmissions, row.vars = "Dept", col.vars = c("Gender",

I posted a similar message on the freeradius list a few months ago and it was suggested I come here. Now that this effort is once again underway I am looking for some assistance. We are trying to replace our existing AAA solution with FreeRadius. The user base is contained in an Active Directory single forest-multi domain model. The only feature of samba that we need to leverage is the

I'm looking for an R method to produce latex versions of tables for table/array objects of 3 or more dimensions, which, of necessity is flattened to a 2D display, for example with ftable(), or vcd::structable, as shown below. I'd be happy to settle for a flexible solution for the 3D case. > UCB <- aperm(UCBAdmissions, c(2, 1, 3)) > ftable(UCB) Dept A B

Just a general question concerning the woolf test (package vcd), when we have stratified data (2x2 tables) and when the p.value of the woolf-test is below 0.05 then we assume that there is a heterogeneity and a common odds ratio cannot be computed? Does this mean that we have to try to add more stratification variables (stratify more) to make the woolf-test p.value insignificant? Also in the

Suppose I have a table constructed from structable or simply just an object of class table. How can I convert it to a latex object? I looked in RSiteSearch, but only found info about matrices or data frames. Steve For example, here is a table t2 > str(t2) table [1:2, 1:2, 1:2] 6 8 594 592 57 ... - attr(*, "dimnames")=List of 3 ..$ Hospital : chr [1:2] "A"

> addmargins(UCBAdmissions, FUN = list(Total=sum)) works with no problems, but consider: > myFUN <- list(Total=sum) > addmargins(UCBAdmissions, FUN = myFUN) Error in "names<-.default"(`*tmp*`, value = "") : names() applied to a non-vector Is this a bug? > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system

Hello, I was using the mantelhaen.test function (2x2 J tables for conditional independence testing). I noticed that the option for the continuity correction (correction=T or correction=F) sometimes made a difference while sometimes it did give the same results regardless of correction=T or correction=F. Does the continuity correction apply only in certain cases or in certain strata with some

I'm trying to visualise relationships between a number of categorical variables with values 0 and 1. Plot(table(x,y)) ..works well for one relationship, so I want to use this to examine all relationships using pairs function. pairs(data_array, upper.panel=panel.tab) where panel.tab <- function (x,y) { plot(tables(x,y)) } ..produces the error.. Error in pairs.default(a,

aperm() was designed for multidimensional arrays, but is also useful for table objects, particularly with the lattice, vcd and vcdExtra packages. But aperm() was designed and implemented before other related object classes were conceived, and I propose a small tune-up to make it more generally useful. The problem is that aperm() always returns an object of class 'array', which