Initialization problems using brms with weibull distribution and identity link

Hi all,

I have reaction time data, and comparing models with different distributions suggests that the weibull (with the identity link) is the best fit for my data. The data has a multi-level structure (different participants and different conditions), but I can only get relatively simple models to fit. The reason being is that the sampler has trouble finding initial values for the scale parameter and throws the following error multiple times:

Chain 1: Rejecting initial value:
Chain 1: Error evaluating the log probability at the initial value.
Chain 1: Exception: weibull_lpdf: Scale parameter[1] is -1.16905, but must be > 0! (in ‘model2124403820f7_fedaec10e52be962e84af56da16ca07c’ at line 40)

For simple models it manages to initialise eventually, but as the number of parameters increase it becomes more problematic.

The following is the stan code from brms::make_stancode for a very simple y ~ x model.

functions {
data {
  int<lower=1> N;  // number of observations
  vector[N] Y;  // response variable
  int<lower=1> K;  // number of population-level effects
  matrix[N, K] X;  // population-level design matrix
  int prior_only;  // should the likelihood be ignored?
transformed data {
  int Kc = K - 1;
  matrix[N, Kc] Xc;  // centered version of X
  vector[Kc] means_X;  // column means of X before centering
  for (i in 2:K) {
    means_X[i - 1] = mean(X[, i]);
    Xc[, i - 1] = X[, i] - means_X[i - 1];
parameters {
  vector[Kc] b;  // population-level effects
  real temp_Intercept;  // temporary intercept
  real<lower=0> shape;  // shape parameter
transformed parameters {
model {
  vector[N] mu = temp_Intercept + Xc * b;
  for (n in 1:N) {
    mu[n] = (mu[n]) / tgamma(1 + 1 / shape);
  // priors including all constants
  target += student_t_lpdf(temp_Intercept | 3, 3, 10);
  target += gamma_lpdf(shape | 0.01, 0.01);
  // likelihood including all constants
  if (!prior_only) {
    target += weibull_lpdf(Y | shape, mu);
generated quantities {
  // actual population-level intercept
  real b_Intercept = temp_Intercept - dot_product(means_X, b);

I can see that the issue is in the line mu[n] = (mu[n]) / tgamma(1 + 1 / shape);, which then gets used for the scale parameter when calculating the log likelihood. Without exp(mu[n]) (which is present when I use a log link) the scale parameter can be negative, hence the error. Which makes me wonder whether it is sensible to use the identity link with the weibull at all?

I’m relatively new to stan so I’m not sure what the best way to solve this is. I’ve tried setting priors that constrain the intercept and coefficient to be positive, and also to set initial values on my parameters (as per the advice for similar issues to mine), but this doesn’t appear to solve the issue. Perhaps I also need to turn centering off (as well as sensible priors and initial values), but when I try to do that it either runs super slow or doesn’t converge.

Any advice appreciated.

Hi, it does not make sense to use the identity link function for an outcome that follows a weibull distribution, exactly because of the thing you point out yourself: the expectation (mu) should always be positive. Use the log link instead

Thanks. In my case the expectation of mu should always be positive (Reaction Times), and the weibull comes out best when comparing different distributions. However, the mean RTs have a linear relationship with the main predictor, hence the identity link.