I encountered the following problem when running the code related to the seven parameter diffusion model using the latest version 2.35 of the cmdstanr package. After repeated modifications, it still persists. I really can’t find the reason. I hope to receive everyone’s help.Thank you.

The code I am running mainly comes from Valentin Pratz - The full diffusion model in Stan - Level 1 And I made corresponding adjustments. The current code does not report any errors, but building a Markov chain was unsuccessful.

##example

I used a new version of the function wiener_lpdf (rt [i] | a, t0, w, v [cnd [i]], sv, sw, st0)

I mainly learned from the following link.

#2822

estimate1.R (1.4 KB)

#code:

library(cmdstanr)

load(“L1dat.RData”)

data ← Level1dat

summary(data)

et_cmdstan_path(path=NULL)

chains = 4

# initial values

init.stan = function(){

L = list()

for (i in 1:chains) {

L[[i]] = list(

sv = 1 + runif(1, -0.1, 0.1),

sw = 0.1 + runif(1, -0.05, 0.05),

st0 = 0.2 + runif(1, -0.05, 0.05)

)

}

return(L)

}

# Compiling model

#mc ← cmdstan_model(“Level1.stan”)

#mc<-cmdstan_model(file)

mc ← cmdstan_model(“D:\seven\level1\level1.stan”)

stan.data = list(

N = nrow(data),

Ncnds = 3,

rt = data$RT,

stim = as.numeric(data$Stim),

resp = as.numeric(data$Resp),

cnd = as.numeric(data$Cond),

a = 1,

t0 = 0.3,

w = 0.45,

v = c(3.5, 2.5, 1.5)

)

outdir = “fits”

dir.create(outdir, recursive = T, showWarnings = FALSE)

m ← mc$sample(data=stan.data,

init = init.stan(),

refresh = 25,

iter_sampling = 250,

iter_warmup = 250,

chains = chains,

parallel_chains = 4,

output_dir = outdir,

output_basename = “fit”,

save_warmup = TRUE

)

##issues

unning MCMC with 4 parallel chains…

Chain 2 Assertion failed: index >= 0 && index < size(), file stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/DenseCoeffsBase.h, line 410Warning: Chain 2 finished unexpectedly!

Chain 1 Assertion failed: index >= 0 && index < size(), file stan/lib/stan_math/lib/eigen_3.4.0/Eigen/src/Core/DenseCoeffsBase.h, line 410Warning: Chain 1 finished unexpectedly!

Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:

Chain 3 Exception: wiener_lpdf: Inter-trial variability in A-priori bias = 0.999729, but must be smaller than 2*(A-priori bias) = 0.9 (in ‘C:/Users/13201/AppData/Local/Temp/RtmpYrSjfs/model-6fc8368c44a1.stan’, line 29, column 8 to column 72)

Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,

Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.

Chain 3 Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:

Chain 4 Exception: wiener_lpdf: Inter-trial variability in A-priori bias = 0.999978, but must be smaller than 2*(A-priori bias) = 0.9 (in ‘C:/Users/13201/AppData/Local/Temp/RtmpYrSjfs/model-6fc8368c44a1.stan’, line 29, column 8 to column 72)

Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,

Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.

##Expected output

I hope to generate Markov chains normally.Hope to receive help.

####Current version:

cmdstanr packages 2.35