similar to: GAM Penalised Splines - Intercept

Dear community, I encountered a very disturbing phenomenon today: When I try to fit any gam() with mgcv R aborts. I could not find any post regarding this in google, which mades in even more strange. I am using the latest Ubuntu, latest R and latest mgcv everything up to date. The crash occured too with the last mgcv 1.7-11. This is the output from the R shell: <pre> R version 2.14.0

Hi, I have been trying to fit an un-penalised gam in mgcv (in order to get more reliable p-values for hypothesis testing), but I am struggling to get the model to fit sucessfully when I add in a te() interaction. The model I am trying to fit is: gam(count~ s(x1, bs = "ts", k = 4, fx = TRUE) + s(x2, bs = "ts", k = 4, fx = TRUE) + te(x2, x3, bs =

Hi R-users I am trying to use the GAM function of the mgcv package. But I am having problem trying to specify the k parameter. Although I managed to run some models by giving to the parameter some (random) value, and it is explained by Wood (2006) that it does not seem to "really" affect the final result, I would like to grasp better its meaning. I understand that is the

Dear users, I am trying to show the equation (including coefficients from the model estimates) for a gam model but do not understand how to. Slide 7 from one of the authors presentations (gam-theory.pdf URL: http://people.bath.ac.uk/sw283/mgcv/) shows a general equation log{E(yi )} = ?+ ?xi + f (zi ) . What I would like to do is put my model coefficients and present the equation used. I am an

Hi, I wonder if predict.gam is supposed to work with family=negbin() definition? It seems to me that the values returned by type="response" are far off the observed values. Here is an example output from the negbin examples: > set.seed(3) > n<-400 > dat<-gamSim(1,n=n) > g<-exp(dat$f/5) > dat$y<-rnbinom(g,size=3,mu=g) >

Hi, all I want to choose same knots in GAM for 10 different studies so that they has the same basis function. Even though I choose same knots and same dimensions of basis smoothing, the basis representations are still not same. My command is as follows: data.gam<-gam(y~s(age,bs='cr',k=10)+male,family=binomial,knots=list(age=seq(45,64,length=10))) What is my mistake for choice of

Good Afternoon Everyone, I am looking for advice fitting a linear mixed model where the random components do not seem to fit within the model formulae for lmer. The columns of Z are not stratified and have the notional random formula (z1 | 1) + ... + (zk | 1). Context I am fitting a penalised thin plate spline with knots k1 to kn. The basis functions Zk are |x-ki|^3 and the penalty matrix has

Hi everyone, I can't figure out how to extract by-factor random effect adjustments from a gam model (mgcv package). Example (from ?gam.vcomp): library(mgcv) set.seed(3) dat <- gamSim(1,n=400,dist="normal",scale=2) a <- factor(sample(1:10,400,replace=TRUE)) b <- factor(sample(1:7,400,replace=TRUE)) Xa <- model.matrix(~a-1) ## random main effects Xb <-

Does anybody have any suggestions on how I might simulate from fitted GAM model? I am using the gam function in the mgcv package to fit a variable coefficient model like the following from the examples. I would like simulate based on the fitted model like the simulate function in the stats package does for lm models. library(mgcv) set.seed(10) ## simulate date from y = f(x2)*x1 + error dat

Hi all, I try to interpolate a data set in the form: time Erg 0.000000 48.650000 1.500000 56.080000 3.000000 38.330000 4.500000 49.650000 6.000000 61.390000 7.500000 51.250000 9.000000 50.450000 10.500000 55.110000 12.000000 61.120000 18.000000 61.260000 24.000000 62.670000 36.000000 63.670000 48.000000 74.880000 I want to get smoothed splines by using the class gam The first way I tried , was

hi I'm puzzled as to the relation between the REML score computed by gam and the formula (4) on p.4 here: http://opus.bath.ac.uk/22707/1/Wood_JRSSB_2011_73_1_3.pdf I'm ok with this for poisson, or for quasipoisson when phi=1. However, when phi differs from 1, I'm stuck. #simulate some data library(mgcv) set.seed(1) x1<-runif(500) x2<-rnorm(500)

I've got a small problem. I have some observational data (environmental samples: abiotic explanatory variable and biological response) to which I've fitted both a multiple linear regression model and also a gam (mgcv) using smooths for each term. The gam clearly fits far better than the lm model based on AIC (difference in AIC ~ 8), in addition the adjusted R squared for the gam is

Dear List, I've just tried to specify a GAM without an intercept -- I've got one of the (rare) cases where it is appropriate for E(y) -> 0 as X ->0. Naively running a GAM with the "-1" appended to the formula and the calling "predict.gam", I see that the model isn't behaving as expected. I don't understand why this would be. Google turns up this old

Dear list, does anybody know whether there is a way to easily retrieve the so called "partial residuals" of a gam fit with package mgcv? The partial residuals are the residuals you would get if you would "leave out" a particular predictor and are the dots in the plots created by plot(gam.object,residuals=TRUE) residuals.gam() gives me whole model residuals and

Hello, I'm a student at the University of Klagenfurt / Austria and I need some help ! I have to predict 24 daily load-values. Therefor I got a dataset with following colums: 24 past daily load-values 6 past daily temperature-values My goal is to find a model (GAM with thin plate splines) in R. I found the function "gam" in the R-library "mgcv", but it just fits

Hello, in the paper "Avoiding the effects of concurvity in GAM's .." of Figueiras et al. (2003) it is mentioned that in GLM collinearity is taken into account in the calc of se but not in GAM (-> results in confidence interval too narrow, p-value understated, GAM S-Plus version). I haven't found any references to GAM and concurvity or collinearity on the R page. And I

Dear all, I'm using the mgcv library by Simon Wood to fit gam models with interactions and I have been reading (and running) the "factor 'by' variable example" given on the gam.models help page (see below, output from the two first models b, and b1). The example explains that both b and b1 fits are similar: "note that the preceding fit (here b) is the same as

dear all, i have a little question, but it make me torment long time hope you can help me and give some advices , thanks i use smoothing spline in package gam the model > m1=gam(y~ost+wst+park10+sch50+comm+build+suite+y05+y06+y07+y99+y98+s(builarea)+s(age)+s(fl)+s(totfl)+s(cbd)+s(redl)) and summary(m1) can show the "s"(smoothing) variables' Signif. codes.

Hi, there, I have 5 datasets. I would like to choose a basis spline with same knots in GAM function in order to obtain same basis function for 5 datasets. Moreover, the basis spline is used to for an interaction of two covarites. I used "cr" in one covariate, but it can only smooth w.r.t 1 covariate. Can anyone give me some suggestion about how to choose a proper smoothing spline

I've been doing a simple time-series analysis looking at the relationship between daily pneumonia hospitalizations and daily temperature. To mimic some of the literature, I've been including a time-trend to try to account for normal cyclical trends in hospitalization. So I've been using a function that looks something like this: gam(pneucount ~ temp_f +