search for: logistf

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"

Hi everyone, I'm wondering how to select the "best" model when using logistf? AIC does not work neither does anova. I tried fitting a glm model but got the separation warning message so I tried using the logistf package but as I stepwise simplify the model I don't know if the simplification is motivated or not... Can anyone explain to me how I should approach this probl...

...however I was having 2 warnings concerning glm.fit () : # 1: glm.fit: algorithm did not converge # 2: glm.fit: fitted probabilities numerically 0 or 1 occurred After some investigation I found out that the problem was most probably quasi complete separation and therefor decide to use brglm and/or logistf. * logistf : analysis does not run When running logistf() I get a error message saying : # error in chol.default(x) : # leading minor 39 is not positive definite I looked into logistf package manual, on Internet, in the theoretical and technical paper of Heinze and Ploner and cannot find where th...

...rst, is the penalized maximum likelihood estimation(Firth Type Estimation) only fit for binary response (0,1 or TRUE, FALSE)? Can it be applied to multinomial logistic regression? If yes, what's the formula for LL and U(beta_i)? Can someone point me to the right reference? Second, when I used *logistf *on a dataset with binary response, I got the following error msg: "Error in if (mx > 1) delta <- delta/mx : missing value where TRUE/FALSE needed" What does this msg mean? does it mean the dataset includes missing response? I checked my dataset several times and didn't find...

I am new to using R. Currently, I am using the logistf package to run logistic regression analysis. When I run the following line of code: attach(snpriskdata) logisticpaper<-logistf(sascasecon~saspackyrs+newsbmi+EDUCATION+sasagedx+sasflung+condobst+sasadultasprev) I get the following error message: Error in sum(y) : invalid 'type' (ch...

...the function glm. But we notice that this function don't give the same results as the SAS proc catmod (differents estimate given). We try to change the contrast on R system with: > options(contrasts=c(unordered="contr.SAS",ordered="contr.poly")) We also try with brlr and logistf functions. Unfortunately, the estimate aren't still the same. Please could someone help us. Thank you -------------------------------------------------- This mail sent through Polytech'Lille WebMail (IMP)

Hi, all, Anyone has experience on Logistf package? I am using logistftest in Logistf package to selelct diagnosis genes. The result seems not the same as I expected. I have 10 gene expression data for 27 tumor 1 and 11 tumor 0. I want to select the best one using Maximum likelihood ratio test in logistic regression model. This is the...

...w/ 3 levels "0","1","2": 2 2 2 2 2 2 2 2 2 2 ... With the regular glm() function, I get a warning about "perfect or quasi-perfect separation"[1]. I looked for a method to deal with this and a penalized GLM is an accepted method[2]. This is implemented in logistf(). I used the default settings for the function. Just before I run the model, memory.size() for my session is ~4500 (MB). memory.limit() is ~25500. When I start the model, R immediately becomes non-responsive. This is in a Windows environment and in Task Manager, the instance of R is, and has b...

...G. and Schemper, M. (2002), but I'm unsure of how to implement the analogue for log-linear models. A procedure using IWLS is described by Firth (1992) in Dodge and Whittaker (1992), but this book isn't in the local library, and its $141+ on Amazon. I've tried looking at the code in the logistf and brlr libraries, but I haven't had any (successful) ideas. Can anyone help me in describing how to implement this in R? Thanks! Simon

The major changes for R 2.0.0 are now in place, and we have provided a set of notes for package maintainers at http://developer.r-project.org/200update.txt on both changes needed and new opportunities. The main thing which needs to be done is to revise the DESCRIPTION file, in particular to ensure the Depends: field is accurate. We do run daily checks over all the CRAN packages. See

...2 2 2 2 2 2 >> ... >> >> >> With the regular glm() function, I get a warning about "perfect or >> quasi-perfect separation"[1]. I looked for a method to deal with this >> and a penalized GLM is an accepted method[2]. This is implemented in >> logistf(). I used the default settings for the function. >> >> Just before I run the model, memory.size() for my session is ~4500 >> (MB). memory.limit() is ~25500. When I start the model, R immediately >> becomes non-responsive. This is in a Windows environment and in Task >&...

...t;1","2": 2 2 2 2 2 2 2 2 2 2 ... > > > With the regular glm() function, I get a warning about "perfect or > quasi-perfect separation"[1]. I looked for a method to deal with this > and a penalized GLM is an accepted method[2]. This is implemented in > logistf(). I used the default settings for the function. > > Just before I run the model, memory.size() for my session is ~4500 (MB). > memory.limit() is ~25500. When I start the model, R immediately becomes > non-responsive. This is in a Windows environment and in Task Manager, > the in...

...ot;,"2": 2 2 2 2 2 2 2 2 2 2 ... >>> >>> >>> With the regular glm() function, I get a warning about "perfect or quasi-perfect separation"[1]. I looked for a method to deal with this and a penalized GLM is an accepted method[2]. This is implemented in logistf(). I used the default settings for the function. >>> >>> Just before I run the model, memory.size() for my session is ~4500 (MB). memory.limit() is ~25500. When I start the model, R immediately becomes non-responsive. This is in a Windows environment and in Task Manager, the inst...

...2": 2 2 2 2 2 2 2 2 2 2 ... >>>> >>>> >>>> With the regular glm() function, I get a warning about "perfect or quasi-perfect separation"[1]. I looked for a method to deal with this and a penalized GLM is an accepted method[2]. This is implemented in logistf(). I used the default settings for the function. >>>> >>>> Just before I run the model, memory.size() for my session is ~4500 (MB). memory.limit() is ~25500. When I start the model, R immediately becomes non-responsive. This is in a Windows environment and in Task Manager, t...

can anyone tell me how can i control the method of estimation (i.e. scoring method or Newton raphson method) in glm and compute deviance function ? -- View this message in context: http://r.789695.n4.nabble.com/changing-method-of-estimation-in-GLM-tp3170836p3170836.html Sent from the R help mailing list archive at Nabble.com.

Hello R users I ran more than 100 logistic regression analyses. Some of the analyses gave me this kind warning below. ########################################################### Warning messages: 1: algorithm did not converge in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, ... 2: fitted probabilities numerically 0 or 1 occurred in: glm.fit(x = X, y = Y,

...of neutral-mood participants did so (0/20). Thus, if drawing a 2x2 (mood x response, in the non-fair game) table, there was an empty cell. I've learned that I can use Firth's penalized likelihood method for bias reduction, which could be achieved using R packages "brglm" or "logistf". However, I found the packages only deal with non-clustered data, which is not the case for my data. I included game type as a within-subject variable and mood as a between-subject variable, and I am interested in their interaction. So, when involving the interaction term as a predictor, I al...

...","leaps","lgtdl","limma","linprog","lme4","lmeSplines","LMGene","lmm","lmomco","Lmoments","lmtest","locfdr","locfit","lodplot","LogicReg","logistf","logspline","lokern","longitudinal","longmemo","LoopAnalyst","LowRankQP","lpridge","lpSolve","lsa","lspls","ltm","maanova","magic","mapLD","mapproj&...

Hi All, When I tried to do logistic regression (with high maximum number of iterations) I got the following warning message Warning message: fitted probabilities numerically 0 or 1 occurred in: (if (is.empty.model(mt)) glm.fit.null else glm.fit)(x = X, y = Y, As I checked from the Archive R-Help mails, it seems that this happens when the dataset exhibits complete separation. However, p-values

...aning of data set variables To: r-help@r-project.org Message-ID:     <699bb6720908300725l6162ce2dg59b7c2fa78f72d6a@mail.gmail..com> Content-Type: text/plain Hi all, Does anybody know the meaning of the values 0 - 1, for each variable from data "sex2" avaible from the package "logistf"? Thanks in advance. Best, Caio     [[alternative HTML version deleted]] ------------------------------ Message: 8 Date: Sun, 30 Aug 2009 16:30:41 +0200 From: Uwe Ligges <ligges@statistik.tu-dortmund.de> Subject: Re: [R] Meaning of data set variables To: Caio Azevedo <cnaberdl...