non parameter estimator cause error

[ZSRNOG]

I run the example provided by bru() function in inlabru document `# An important addition to the INLA methodology is bru's ability to use

non-linear predictors. Such a predictor can be formulated via like()'s

\code{formula} parameter. For instance

if (require("INLA", quietly = TRUE)) { input.df <- data.frame(x=cos(1:10)) z = 2 input.df <- within(input.df, y <- 5 + exp(z)x + rnorm(10, mean=0, sd=0.1)) lik = like(family = "gaussian", data = input.df, formula = y ~ exp(z)x + Intercept, E = 10000) fit <- bru( ~ z + Intercept, lik)

Check the result (z posterior should be around 2)

fit$summary.fixed } ` the result is

the posterior of $z$ is 0.999, which is far from 2

[finnlindgren]

Thanks for noticing this issue! The notation in the example was unsafe; Model components like +z are interpreted as covariate fixed effects, and it found the z in the global environment, preventing it from treating it as the intended individual latent variable, beta_z that saw intended. The predictor expression was interpreted as exp(z * beta_z) * x instead of the intended exp(beta_z) * x. The safe notation is ~z(1)+Intercept(1) that makes the intended behaviour explicit. Many old examples still use the unsafe notation for "intercept-like" components without including the explicit (1) part; We'll go through and get these corrected, but they're unfortunately scattered to many places so it will take some time to find and fix them all.

[finnlindgren]

The corrected example:

z = 2
input.df <- within(input.df, y <- 5 + exp(z)*x + rnorm(10, mean=0, sd=0.1))
lik = like(family = "gaussian", data = input.df,
            formula = y ~ exp(z)*x + Intercept)
fit <- bru( ~ z(1) + Intercept(1), lik)

# Check the result (z posterior should be around 2)
fit$summary.fixed
#               mean          sd 0.025quant 0.5quant 0.975quant     mode          kld
# z         1.997771 0.003796729   1.990273 1.997771   2.005264 1.997771 4.350033e-05
# Intercept 5.035406 0.015194441   5.005034 5.035406   5.065733 5.035407 1.237536e-04

[ZSRNOG]

Dear finnlindgen: I still have an error when I run your code on Win10 with R 4.03

[ZSRNOG]

Dear finnlindgen:

I correct this error with following code

But, when I use expression z(1) + Interpect(1), same error occurs

[finnlindgren]

What's the sessionInfo() output?

[ZSRNOG]

the sessionInfo is

[finnlindgren]

I need the sessionInfo when inlabru and INLA are loaded.

[ZSRNOG]

OK, finnlindgren , is it this?

[finnlindgren]

OK, thanks! From what I recall, the current CRAN release that you have of inlabru, 2.1.13, didn't fully support the safer syntax z(1), which is why the safe syntax fail on your system. The only workaround is then to make sure that any "automatic intercept" parameter components use unique names that aren't present in the workspace. The development version, currently 2.1.14.901, supports the safe syntax, and, and also gives a warning if it detects a problem (but since z was in the workspace it wouldn't be able to detect the problem in the example case). The development version is under heavy development at the moment, and the tutorial materials haven't yet been updated to match, so if you can make it work with the current CRAN version you don't need to upgrade yet.