Well, as long as its written before
# Adaptation terminated
# Step size = 0.822884
you are fine. And I guess this also finishes before adaptation (yes?). The following example returns the correct value if I do:
a<- read_stan_csv(“~/Desktop/cmdstan/src/test/test-models/gq_model_output.csv”)
a@sim$iter
[1] 1112
# stan_version_major = 2
# stan_version_minor = 18
# stan_version_patch = 1
# model = bernoulli_model
# method = sample (Default)
# sample
# num_samples = 1000 (Default)
# save_warmup = 0 (Default)
# thin = 1 (Default)
# adapt
# engaged = 1 (Default)
# gamma = 0.050000000000000003 (Default)
# delta = 0.80000000000000004 (Default)
# kappa = 0.75 (Default)
# t0 = 10 (Default)
# init_buffer = 75 (Default)
# term_buffer = 50 (Default)
# window = 25 (Default)
# algorithm = hmc (Default)
# hmc
# engine = nuts (Default)
# nuts
# max_depth = 10 (Default)
# metric = diag_e (Default)
# metric_file = (Default)
# stepsize = 1 (Default)
# stepsize_jitter = 0 (Default)
# id = 0 (Default)
# data
# file = examples/bernoulli/bernoulli.data.json
# init = 2 (Default)
# random
# seed = 2057108222
# output
# file = output.csv (Default)
# diagnostic_file = (Default)
# refresh = 100 (Default)
lp__,accept_stat__,stepsize__,treedepth__,n_leapfrog__,divergent__,energy__,theta
# num_warmup = 112
# Adaptation terminated
# Step size = 0.822884
# Diagonal elements of inverse mass matrix:
# 0.417943
-7.1053,0.953597,0.822884,2,3,0,7.96837,0.364082
-7.27881,0.989561,0.822884,3,7,0,7.30662,0.390752
-7.11597,1,0.822884,1,1,0,7.27771,0.365875
-6.98136,1,0.822884,3,7,0,7.08989,0.341094
-6.84576,1,0.822884,1,1,0,6.95638,0.307776
-6.79428,0.903813,0.822884,3,7,0,7.65851,0.289241
-6.88147,0.944843,0.822884,1,3,0,7.24226,0.189408
-6.80644,0.967211,0.822884,3,7,0,7.28921,0.294255
-6.78961,1,0.822884,1,1,0,6.80642,0.287149
-6.75497,1,0.822884,3,7,0,6.78592,0.26492
-6.74848,0.999216,0.822884,2,7,0,6.76339,0.246229
-6.89863,0.946399,0.822884,2,3,0,7.28267,0.322389
-6.91067,0.997765,0.822884,1,1,0,6.93378,0.325363
-7.00688,0.982414,0.822884,2,7,0,7.13223,0.167972
-6.94034,1,0.822884,2,3,0,7.00674,0.178291
-6.88987,1,0.822884,1,1,0,6.94007,0.187666
-7.09596,0.979745,0.822884,2,3,0,7.1828,0.156488
-6.9546,1,0.822884,1,1,0,7.07972,0.175914
-6.82338,0.97417,0.822884,2,3,0,7.29343,0.203688
-6.85475,0.99835,0.822884,3,7,0,6.85771,0.195414