similar to: GAM (mgcv) warning: matrix not positive definite

Displaying 20 results from an estimated 1000 matches similar to: "GAM (mgcv) warning: matrix not positive definite"

2009 Mar 27
1
deleting/removing previous warning message in loop
Hello R Users, I am having difficulty deleting the last warning message in a loop so that the only warning that is produced is that from the most recent line of code. I have tried options(warn=1), rm(last.warning), and resetting the last.warning using something like: > warning("Resetting warning message") This problem has been addressed in a previous listserve string,
2012 Aug 14
1
Random effects in gam (mgcv 1.7-19)
Hi, I am using the gam function in the mgcv package, I have random effects in my model (bs="re") this has worked fine, but after I updated the mgcv package to version 1.7-19 I recive an error message when I run the model. > fit1<-gam(IV~s(RUTE,bs="re")+s(T13)+s(H40)+factor(AAR)+s(V3)+s(G1)+s(H1)+s(V1)+factor(LEDD),data=data5,method="ML") > summary.gam(fit1)
2012 Oct 21
1
suppress *specific* warnings?
Not desperately important, but nice to have and possibly of use to others, is the ability to suppress specific warnings rather than suppressing warnings indiscriminately. I often know of a specific warning that I want to ignore (because I know that's it's a false positive/ignorable), but the current design of suppressWarnings() forces me to ignore *any* warnings coming from the
2019 Feb 24
1
stopifnot
>From https://github.com/HenrikBengtsson/Wishlist-for-R/issues/70 : ... and follow up note from 2018-03-15: Ouch... in R-devel, stopifnot() has become yet 4-5 times slower; ... which is due to a complete rewrite using tryCatch() and withCallingHandlers(). >From https://stat.ethz.ch/pipermail/r-devel/2017-May/074256.html , it seems that 'tryCatch' was used to avoid the following
2019 Feb 27
1
stopifnot
My points: - The 'withCallingHandlers' construct that is used in current 'stopifnot' code has no effect. Without it, the warning message is the same. The overridden warning is not raised. The original warning stays. - Overriding call in error and warning to 'cl.i' doesn't always give better outcome. The original call may be "narrower" than 'cl.i'. I
2010 Dec 05
1
How to catch both warnings and errors?
Dear expeRts, I am struggling with warning/error handling. I would like to call a function which can produce either a) normal output b) a warning c) an error Since the function is called several (thousand) times in a loop, I would like to proceed "quietly" and collect the warnings and errors [to deal with them at a later point]. I have seen constructs with tryCatch (which can
2019 May 03
1
Strange error messages from parallel::mcparallel family under 3.6.0
Dear All, Since upgrading to 3.6.0, I've been getting a strange error messages from the child process when using mcparallel/mccollect. Before filing a report in the Bugzilla, I want to figure out whether I had been doing something wrong all this time and R 3.6.0 has exposed it, or whether something else is going on. # Background # Ultimately, what I want to do is to be able to set a time
2018 Mar 06
0
Capturing warning within user-defined function
You can capture warnings by using withCallingHandlers. Here is an example, its help file has more information. dataList <- list( A = data.frame(y=c(TRUE,TRUE,TRUE,FALSE,FALSE), x=1:5), B = data.frame(y=c(TRUE,TRUE,FALSE,TRUE,FALSE), x=1:5), C = data.frame(y=c(FALSE,FALSE,TRUE,TRUE,TRUE), x=1:5)) withWarnings <- function(expr) { .warnings <- NULL # warning handler will
2012 Feb 03
1
Resume processing after warning handler.
Dear list! I have a script that processes a large number of data files. When one file fails to process correctly, I want the script to write a message and to continue with the next file. I achieved this with tryCatch: for (f in files) tryCatch({heavy.lifting(f)}, error=function(e) log.error.to.file(e)) I also want to log warning messages and tried something like this: for (f in
2013 Apr 18
1
Suppress specific warnings
Hello, is there a convenient way to suppress only *specific* warnings? (I know about ?suppressWarnings) I depend on another package, from which I want to suppress only some warnings, but not others. Felix
2011 Feb 18
2
How to flag those iterations which yield a warning?
Hi, I am running a simulation study with the survival::coxph. Some of the simulations result in problematic fits due to flat partial likelihood. So, you get the warning message: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, ... : Loglik converged before variable 2 ; beta may be infinite. How can I keep track of the simulations which yield any kind of
2003 Aug 04
4
bootstrapping vinum root
Well, colleagues, I'm stuck a bit. I tried many different ways to setup system with vinum root (the only reference I found yet besides old "bootstrapping vinum" article is Joerg's commit message: http://freebsd.rambler.ru/bsdmail/cvs-all_2003/msg01225.html I failed. I have 4-stable system set up at ad0, and tried to set up pair of drives for new system at ad2 and ad3 (actually,
2012 Feb 07
1
lme, lmer, convergence
Hello, all, I am running some simulations to estimate power for a complicated epidemiological study, and am using lme and lmer to get these estimates. I have to run a few thousand iterations, and once in a great while, an iteration will create fake data such that the model won't converge. I see from Google searches that this is not an uncommon situation. My question: is there a way to
2010 Jan 11
2
warning inside loop
Hi, I'm running some data simulations using (mixed effects)* regression models that show difficulty to converge. Therefore, I seek a way of capturing warnings (of false convergence) inside a loop. Inside that loop, I modify data and estimate a model. I do so many times with slightly different modifications of the data. Next, I extract some of the model parameters and store these in a matrix.
2006 Feb 19
2
Problems with gain
Hello. CE wrote: > Hails! The reason this occurs is the default adjust value for > mp3gain is stupid. I always do an mp3gain -g 6 to mine after other > adjustments. Also with a player like XMMS that uses the FLAC plugin > you can control the volume the flac play back at. So what exact dB value does flac use? mp3gain + 6 dB are 95 dB IIRC. I tried to apply mp3gain -m 6 to my mp3s,
2004 Mar 11
2
No traceback available when using try(...)
Hello, 1. The Situation : ------------------------ The stack traceback is not available when error ouccured in a try(....) -- test.R -------------------------------- f<-function(a){ return ( log(a) ) } try(f("A")) traceback() ------------------------------------------- I get the following message : > try(f("A")) Error in log(x) : Non-numeric argument to mathematical
2018 Mar 06
4
Capturing warning within user-defined function
Hi, I am trying to automate the creation of tables for some simply analyses. There are lots and lots of tables, thus the creation of a user-defined function to make and output them to excel. My problem is that some of the analyses have convergence issues, which I want captured and included in the output so the folks looking at them know how to view those estimates. I am successfully able to do
2011 Mar 07
0
Conflict between gam::gam and mgcv::gam
I am trying to compare and contrast the smoothing in the {mgcv} version of gam vs. the {gam} version of gam but I get a strange side effects when I try to alternate calls to these routines, even though I detach and unload namespaces. Specifically when I start up R the following code runs successfully until the last line i.e. plot(g4,se=TRUE) when I get "Error in dim(data) <- dim :
2008 Jun 11
1
mgcv::gam error message for predict.gam
Sometimes, for specific models, I get this error from predict.gam in library mgcv: Error in complete.cases(object) : negative length vectors are not allowed Here's an example: model.calibrate <- gam(meansalesw ~ s(tscore,bs="cs",k=4), data=toplot, weights=weight, gam.method="perf.magic") > test <- predict(model.calibrate,newdata) Error in
2008 Aug 19
0
gam.check in gam (mgcv)
Hallo I need some help with the output provided by gam.check after a gam fit (using the package mgcv). To give a brief description of my data, I have claims: a vector of values, which include NA's and one large negative value - otherwise all positive (55 values in total that are not NA). origin: a factor with 10 levels j : taking the values 1, 2, ...., 10 I have fitted a gam, with: >