I was working through problem 15.5 of Regression and Other Stories, which asks to fit a probit regression to a previous example with a logistic regression. I used a model I had built on the National Election Survey dataset (on rstanarm 2.21.1):

fit_nes_probit <- 
 rstanarm::stan_glm(rvote ~ income_int_std + gender + race + 
                           region + religion + education_cts +
                           advanced_degree + party + ideology3 +
                           gender : party,

When I got this error about the chains not converging:

Chain 1: Rejecting initial value:
Chain 1:   Log probability evaluates to log(0), i.e. negative infinity.
Chain 1:   Stan can't start sampling from this initial value.
Chain 1: 
Chain 1: Initialization between (-2, 2) failed after 100 attempts. 
Chain 1:  Try specifying initial values, reducing ranges of constrained values, or reparameterizing the model.
[1] "Error in sampler$call_sampler(args_list[[i]]) : Initialization failed."
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug

Even worse it crashed my Jupyter IRkernel, and the only way I could get it running again was to restart the whole process! I continued to debug it in an R console which wouldn't crash after a fail.

This surprised me because I found it worked fine with link="logit", that is logistic regression. The solution was to set a lower scale value in the prior (the default is 4):

fit_nes_probit <- 
 rstanarm::stan_glm(rvote ~ income_int_std + gender + race + 
                           region + religion + education_cts +
                           advanced_degree + party + ideology3 +
                           gender : party,
        prior=rstanarm::normal(scale=0.5, autoscale=TRUE),

Why this works

To work out what was going on I started trying to simulate similar data that led to the same error. After some experimentation I found a simple reproducable failing example with a few noise predictors:

N <- 1000
fake_data <- data.frame(a=rbinom(N,1,0.5),

fit <- rstanarm::stan_glm(y ~ a + b + c + d + e

This seems to have a better than 25% chance of failing because one of the chains fails most times I run it. If I remove just one of the predictors it succeeds.

I got suspicious about the priors, in Regression and Other Stories they state (at least for logistic regression) the priors on the coefficients are 2.5/sd(x). Here the standard deviation of all our predictors is just 0.5 (since they're binomial with probaibility 0.5). I tried to check this on a model that fit:

fit <- rstanarm::stan_glm(y ~ a + b + c + d,

Which resulted in:

Priors for model 'fit' 
Intercept (after predictors centered)
 ~ normal(location = 0, scale = 4)

  Specified prior:
    ~ normal(location = [0,0,0,...], scale = [4,4,4,...])
  Adjusted prior:
    ~ normal(location = [0,0,0,...], scale = [7.98,8.00,7.97,...])

So it looks like the default scale was 4, and they've been increased by the inverse standard deviation, that is a factor of 2.

The next thing I tried was a flat prior on the coefficients, which converged (to my surprise):

fit_flat <- rstanarm::stan_glm(y ~ a + b + c + d + e,

The next idea I had was to make the priors slightly tighter, to try to make the coefficients closer to 0. Some experimentation found it would start to converse consistently around a scale of 1:

fit_weak <- rstanarm::stan_glm(y ~ a + b + c + d + e,
                          prior=rstanarm::normal(scale=1, autoscale=TRUE),

I found for the NES model I was fitting I had to further reduce the scale to 0.5 for it to converge, or alternatively set a flat prior.

I don’t understand how Stan works, but I’m guessing as we add more predictors there’s a greater chance of getting one that is far from it’s actual value (in this case 0). I suspect because the probabilities in the normal distribution go to zero much faster than in the logistic distribution, this leads to numerical errors in link="probit" that don’t occur in link="logit". I've asked in the Stan Discourse to see if anyone can give more insight.

Getting the data

For reproducability, here's how the nes92 dataset above was generated, with a bit of feature engineering.


nes <- foreign::read.dta('https://raw.githubusercontent.com/avehtari/ROS-Examples/master/NES/data/nes5200_processed_voters_realideo.dta')

nes92 <- 
nes %>%
filter(year == 1992) %>%
# Only people who actually voted republican or democrat
filter(!is.na(presvote_2party)) %>%
    age= age,
    party = partyid3_b,
    rvote = presvote_2party == '2. republican',
    ideology = ideo7, # ideo is just a summary
) %>%
select(-father_party, -mother_party) %>%
filter_all(~!is.na(.))  %>%
mutate(income_int = as.integer(income) - 1,
       income_int_std = (income_int - mean(income_int))/(2*sd(income_int)),
       advanced_degree = education == '7. advanced degrees incl. llb',
       education_cts = (as.integer(education) - 5)/6,
       ideology_int = (as.numeric(ideology) - 5)/6,
       ideology3 = if_else(ideology_int < 0, "liberal", if_else(ideology_int > 0, "conservative", "moderate")))