search for: fitter

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2007 Feb 05
1
ran out of iteration in coxph
hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here i...
2003 Jul 17
0
glm.nb
...l using few covariates, the model converge. Does it mean that this family is fitted differently from other glm? or the number of zeros in my response variable has a limiting factor? Thanks Bruno fit <- glm.nb(pfde~SEX+...., data=data1) Warning messages: 1: Algorithm did not converge in: glm.fitter(x = X, y = Y, w = w, etastart = eta, offset = offset, 2: Algorithm did not converge in: glm.fitter(x = X, y = Y, w = w, etastart = eta, offset = offset, 3: Algorithm did not converge in: glm.fitter(x = X, y = Y, w = w, etastart = eta, offset = offset, 4: Algorithm did not converge in: glm.fit...
2011 Mar 31
2
fit.mult.impute() in Hmisc
...> kp$kyp <- kp$Kyphosis == "present" > set.seed(7) > imp <- aregImpute( ~ kyp + Age + Start + Number, dat = kp, n.impute = 10, + type = "pmm", match = "closest") Iteration 13 > f <- fit.mult.impute(kyp ~ Age + Start + Number, fitter=glm, xtrans=imp, + family = "binomial", data = kp) Variance Inflation Factors Due to Imputation: (Intercept) Age Start Number 1.06 1.28 1.17 1.12 Rate of Missing Information: (Intercept) Age Start Num...
2009 Dec 02
2
Error when running Conditional Logit Model
...observations in my dataset and try to predict the dependent variable from 14 independent variables. My command is as follows clmtest1 <- clogit(Pin~Income+Bus+Pop+Urbpro+Health+Student+Grad+NE+NW+NCC+SCC+CH+SE+MRD+strata(IDD),data=clmdata) However, it produces the following errors: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning messages: 1: In Surv(rep(1, 4096L), Pinmig) : Invalid status value, converted to NA 2: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out...
2009 Jul 24
1
Making rq and bootcov play nice
...am trying to use the bootcov function to estimate the standard errors for some regression quantiles using a cluster bootstrap. However, it seems that bootcov passes arguments that rq.fit doesn't like, preventing the command from executing. Here is an example: e<-bootcov(rq(y~x),clust,B=10,fitter=rq.fit) (where clust is my clustering variable) results in Error in rq.fit.br(x, y, tau = tau, ...) : unused argument(s) (maxit = 15, penalty.matrix = NULL) In contrast, the lm.fit function seems to just ignore these arguments, resulting in the following warning: 10: In fitter(X[obs, , drop =...
2003 Jul 27
1
multiple imputation with fit.mult.impute in Hmisc
...owing (roughly): f <- aregImpute(~ [list of 32 variables, separated by + signs], n.impute=20, defaultLinear=T, data=t1) # I read that 20 is better than the default of 5. # defaultLinear makes sense for our data. fmp <- fit.mult.impute(Y ~ X1 + X2 ... [for the model of interest], xtrans=f, fitter=lm, data=t1) and all goes well (usually) except that we get the following message at the end of the last step: Warning message: Not using a Design fitting function; summary(fit) will use standard errors, t, P from last imputation only. Use Varcov(fit) to get the correct covariance matrix, sq...
2008 Nov 03
0
NaN causes "error in fitter" with cph.calibrate from pkg Design
...e past (despite having 4 GB in a UNIX OS), I had previously saved it and loaded it back into a clean run of R. The memory overflow did not occur with this approach, but it appears that the NaNs at the "high" end of the survival probability scale are causing fatal errors with the fitter. It appears that for half of the samples, an n of 40 is being used while for the other other half an adaptive sampling size is being used. I hope I have included enough detail below. Any thoughts on a way out of this? Would the full screen output be useful in construction a calibration cur...
2007 Dec 17
2
Capture warning messages from coxph()
...(results)=c("coef","se","p") > > for(i in 1:ncol(x)){ + fit=summary(coxph(TIME~x[,i])) + results[i,1]=fit$coef[1] + results[i,2]=fit$coef[3] + results[i,3]=fit$coef[5] + rm(fit) + } Warning message: Loglik converged before variable 1 ; beta may be infinite. in: fitter(X, Y, strats, offset, init, control, weights = weights, > > results coef se p [1,] -0.5117033 5.647385e-01 0.36 [2,] -10.2256937 1.146168e+04 1.00 > > #To see which model gave the warning message > coxph(TIME~x[,1]) Call: coxph(formula = TIME ~ x[, 1])...
2007 Oct 18
0
upgrade: relations
Dear useRs, a new version of the 'relations' package has appeared on CRAN. New features include: o support for fuzzy relations added o support for sets moved to separate 'sets' package o new SD fitters for the S ("symmetric") and M ("matches") families o fitters for Cook-Seiford method and Euclidean consensus added o fitters can now use a sparse constraint matrix representation o relations are now subsettable o relation_choice() for choosing "winner"...
2007 Oct 18
0
upgrade: relations
Dear useRs, a new version of the 'relations' package has appeared on CRAN. New features include: o support for fuzzy relations added o support for sets moved to separate 'sets' package o new SD fitters for the S ("symmetric") and M ("matches") families o fitters for Cook-Seiford method and Euclidean consensus added o fitters can now use a sparse constraint matrix representation o relations are now subsettable o relation_choice() for choosing "winner"...
2004 May 16
2
Error in using coxph()
Hi, I am getting errors of the following kind. I can't seem to point the source of the error. I would greatly appreciate any advice. Many thanks and good day, -Melinda Error message : ---------------- "Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights,..." Details : --------- E is a vector of survival times (or censored times), 1-F is a vector of '0's, and cov is a matrix of 1 column. There are altogether 75 observations. Tried : ------ P <- try(surv.cox <- coxph(Surv(E,...
2007 Sep 13
2
Multivariate, multilevel regression?
...also strictly ordinal: I have a factor such that lower-order data *must* be on a curve that is offset beneath a higher-order curve. Don't ask where the factors come from...but *given* these factors the assumption, or rather the *constraint*, is that lower orders are better (lower-order rats are fitter rats with better cardiovascular response). Most important is that these curves do not intersect because of these factors (a fitter rat can not have a worse heart-rate response than a less fit rat!). Here's a schematic to show you what I mean. It's very rough, but it gets the point across:...
2006 Feb 28
1
Capturing warning messages within R
Hi, Just wondering, how do you capture "warning messege"s from R? I'm using Rpy (the python plug-in for R). I guess those are not python exception so I couldn't use the "try" block. For example: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, MPR Regards, Kylie-Anne Richards [[alternative HTML version deleted]]
2009 Apr 23
0
Cox regression
...roblem with the data I would also get some sort of warning in Stata? The second problem concerns the estimation of a weighted Cox regression i.e I am using coxph with the weights option (I have calculated the weights in Stata). Basically I am getting the following error message: "Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 10) In addition: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge" Is there anything I can do to tr...
2013 Feb 12
0
NA/NaN/Inf in foreign function call (arg 6) error from coxph
...a multivariate Cox proportional model, I got the following error. I'm not quite what that means. Any help would be much appreciated! # perform multivariate Cox proportional hazards model coxph(sample.data$survobj ~ sample.data$therapy + sample.data$ReceptorA + sample.data$ReceptorB) Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge Best regards, Cindy -- output of sessio...
2007 Dec 14
1
problem with coxph
...yone, I encountered a problem using the coxph function for the conditional logistic regression. I am trying to do some simulations and I really don’t understand a mistake which happened maybe only 1 time among more than 1,000 simulations. What appeared on the screen is the following: Error in fitter(X,Y,strats,offset,init,control,weights=weights,: NA/NaN/Inf in a foreign function (arg 6) Warning message: Ran out of iterations and did not converge in: fiiter(X,Y,strats,offset,init,control,weights=weights, I don’t know if the warning message could have caused the error or vice versa....
2013 Apr 16
1
assistant
...ar Sir/Ma, I Adelabu.A.A, one of the R-users from Nigeria. When am running a coxph command the below error was generated, and have try some idea but not going through. kindly please assist: > cox1 <- coxph(Surv(tmonth,status) ~ sex + age + marital + sumassure, X) Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not converge > summary(cox1, conf.int=0.95, exact = TRUE) Call: coxph(formula = Surv(tmonth, status) ~ sex + age + marital + sumassure, data = X) n= 5958, number of events= 316...
2008 Apr 02
2
Overdispersion in count data
Hi all, I have count data (number of flowering individuals plus total number of individuals) across 24 sites and 3 treatments (time since last burn). Following recommendations in the R Book, I used a glm with the model y~ burn, with y being two columns (flowering, not flowering) and burn the time (category) since burn. However, the residual deviance is roughly 10 times the number of degrees of
2007 Jun 04
0
New package: relations
...* predicate functions for the most common standard characteristics, * operators known from relational algebra theory (such as projection, selection, cartesian product, joins, etc.), * transitive/reflexive reduction and closure of a relation, * relation ensembles for combining relations, * fitters for determining (possibly all) consensus relations of a relation ensemble including the Borda and Condorcet methods, as well as exact solvers for minimizing a criterion function based on the symmetric difference (Kemeny-Snell) metric. * a simple plot method for Hasse-diagrams using RGraphviz. K...
2007 Jun 04
0
New package: relations
...* predicate functions for the most common standard characteristics, * operators known from relational algebra theory (such as projection, selection, cartesian product, joins, etc.), * transitive/reflexive reduction and closure of a relation, * relation ensembles for combining relations, * fitters for determining (possibly all) consensus relations of a relation ensemble including the Borda and Condorcet methods, as well as exact solvers for minimizing a criterion function based on the symmetric difference (Kemeny-Snell) metric. * a simple plot method for Hasse-diagrams using RGraphviz. K...