First bug found:
library(survival)
library(rstan)
library(rstanarm)
data("kidney")
ms <- stan_surv(Surv(time, status) ~ age + sex + disease + (1|id), data = kidney, basehaz = 'ms')
bs <- update(ms, basehaz = 'bs')
This immediately spits out pages of error messages. They look like this
`Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4: Rejecting initial value:
Chain 4: Error evaluating the log probability at the initial value.
Chain 4: Exception: lb_constrain: lb is -inf, but must be finite! (in ‘surv’, line 476, column 4 to column 14)
Chain 4:
Chain 4: Initialization between (-2, 2) failed after 100 attempts.
Chain 4: 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
here are whatever error messages were returned
[[1]]
Stan model ‘surv’ does not contain samples.
[[2]]
Stan model ‘surv’ does not contain samples.
[[3]]
Stan model ‘surv’ does not contain samples.
[[4]]
Stan model ‘surv’ does not contain samples.
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
In addition: Warning messages:
1: In for (v in val) { : closing unused connection 6 (<-localhost:11173)
2: In for (v in val) { : closing unused connection 5 (<-localhost:11173)
3: In for (v in val) { : closing unused connection 4 (<-localhost:11173)
4: In for (v in val) { : closing unused connection 3 (<-localhost:11173)
5: In .local(object, …) :
some chains had errors; consider specifying chains = 1 to debug