diff --git a/DESCRIPTION b/DESCRIPTION index b28e1cf..c98664b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: bayesdfa Type: Package Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan' -Version: 1.3.1 +Version: 1.3.2 Authors@R: c( person(c("Eric", "J."), "Ward", role = c("aut", "cre"), email = "eric.ward@noaa.gov"), diff --git a/NEWS.md b/NEWS.md index 0c42a10..b7f4ffb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -47,3 +47,8 @@ Change to new Stan syntax # bayesdfa 1.3.1 Versioning + +# bayesdfa 1.3.2 + +- Add compatibility with new rstan +- Changed weights argument to 'inv_var_weights' and 'likelihood_weights' for the glmmTMB/sdmTMB/brms style diff --git a/docs/404.html b/docs/404.html index 017467a..1e290c8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -33,7 +33,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/articles/a1_bayesdfa.html b/docs/articles/a1_bayesdfa.html index e218d08..9e3866c 100644 --- a/docs/articles/a1_bayesdfa.html +++ b/docs/articles/a1_bayesdfa.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -102,7 +102,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a1_bayesdfa.Rmd @@ -294,7 +294,7 @@

DFA model with no extreme eventsloo1$estimates 
##               Estimate           SE
 ## elpd_loo -2.973137e+04 6.859515e+03
-## p_loo    -2.220446e-16 2.107833e-15
+## p_loo    -1.554312e-15 1.057242e-15
 ## looic     5.946275e+04 1.371903e+04

where 5.9462745^{4} is the estimate and 1.371903^{4} is the standard error.

@@ -603,10 +603,9 @@

Applying Hidde

DFA model with weights

-

Just as the weights argument can be ueed with -glm, lmer or glmmTMB, we allow -weights to be used in DFA models. Weights are currently only used for -Gaussian reponses and when data is in long format. Specifically, the +

We allow weights to be used in DFA models in two ways. In the first +form, inverse variance weighting is used to adjust observations based on +some standard error associated with each observation. Specifically, the weights are included by modifying each variance to be \[\sigma^2 / w_i\]. As a concrete example, we’ll simulate a dataset, add some examples of standard errors on the survey indices, and then perform the DFA.

@@ -639,13 +638,13 @@

DFA model with weightsf2 <- fit_dfa( y = df, num_trends = 2, scale="zscore", iter = 500, chains = 1, thin = 1, - weights = "weights", data_shape = "long" + inv_var_weights = "weights", data_shape = "long" )

## 
 ## SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1).
 ## Chain 1: 
-## Chain 1: Gradient evaluation took 5e-05 seconds
-## Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
+## Chain 1: Gradient evaluation took 4.8e-05 seconds
+## Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
 ## Chain 1: Adjust your expectations accordingly!
 ## Chain 1: 
 ## Chain 1: 
@@ -662,9 +661,9 @@ 
DFA model with weights## Chain 1: Iteration: 450 / 500 [ 90%]  (Sampling)
 ## Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
 ## Chain 1: 
-## Chain 1:  Elapsed Time: 120.552 seconds (Warm-up)
-## Chain 1:                22.6953 seconds (Sampling)
-## Chain 1:                143.247 seconds (Total)
+## Chain 1:  Elapsed Time: 19.781 seconds (Warm-up)
+## Chain 1:                6.379 seconds (Sampling)
+## Chain 1:                26.16 seconds (Total)
 ## Chain 1:
## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
 ## Running the chains for more iterations may help. See
@@ -674,144 +673,157 @@ 
DFA model with weights## https://mc-stan.org/misc/warnings.html#tail-ess
## Inference for the input samples (1 chains: each with iter = 250; warmup = 125):
 ## 
-##               Q5  Q50  Q95 Mean  SD  Rhat Bulk_ESS Tail_ESS
-## x[1,1]      -1.1 -0.4  0.2 -0.4 0.4  1.02       95       47
-## x[2,1]      -2.5 -2.0 -1.3 -1.9 0.3  1.05       21       45
-## x[1,2]      -1.7 -1.2 -0.8 -1.2 0.3  1.00      103       85
-## x[2,2]      -2.9 -2.2 -1.3 -2.2 0.5  1.05       24       80
-## x[1,3]       0.2  0.6  0.9  0.6 0.2  1.00      226      145
-## x[2,3]      -1.6 -1.1 -0.8 -1.1 0.3  1.05       22       67
-## x[1,4]       1.1  1.6  2.4  1.7 0.4  1.00       81      117
-## x[2,4]      -2.1 -1.3 -0.6 -1.3 0.5  1.00       25       25
-## x[1,5]       0.0  0.4  0.9  0.4 0.3  1.00      103      103
-## x[2,5]      -1.1 -0.8 -0.5 -0.8 0.2  1.01       27       39
-## x[1,6]       0.9  1.4  1.9  1.4 0.3  1.00      100      143
-## x[2,6]      -1.6 -1.0 -0.3 -1.0 0.4  1.00       24       38
-## x[1,7]       0.2  0.7  1.1  0.7 0.3  1.00      186       39
-## x[2,7]       0.1  0.6  0.8  0.5 0.2  1.01       36      119
-## x[1,8]      -0.1  0.4  0.9  0.4 0.3  1.00      157       81
-## x[2,8]       0.8  1.3  1.6  1.2 0.2  1.06       23       36
-## x[1,9]      -1.2 -0.8 -0.2 -0.7 0.3  0.99      178      131
-## x[2,9]       1.2  1.6  2.3  1.7 0.4  1.06       19       81
-## x[1,10]     -1.6 -0.9 -0.4 -1.0 0.4  1.00       74      108
-## x[2,10]      1.6  2.3  3.1  2.3 0.5  1.03       22       50
-## x[1,11]     -1.7 -1.1 -0.7 -1.2 0.3  1.00      137      106
-## x[2,11]      1.8  2.6  3.5  2.6 0.5  1.05       20       40
-## x[1,12]     -0.7 -0.2  0.3 -0.2 0.3  1.00      171      136
-## x[2,12]      0.8  1.2  1.6  1.2 0.2  1.04       28       37
-## x[1,13]      0.6  1.0  1.6  1.1 0.3  1.00      141      106
-## x[2,13]      0.1  0.6  1.0  0.5 0.3  1.00       27      104
-## x[1,14]      0.9  1.4  2.0  1.4 0.4  1.01       67       94
-## x[2,14]      0.0  0.7  1.3  0.7 0.4  1.00       26       53
-## x[1,15]      0.6  1.1  1.5  1.1 0.3  1.02       56       57
-## x[2,15]      1.1  1.8  2.3  1.7 0.4  1.03       23       32
-## x[1,16]     -1.1 -0.7 -0.3 -0.7 0.3  1.01       95      108
-## x[2,16]      0.4  0.7  1.2  0.8 0.3  1.01       21       39
-## x[1,17]     -1.1 -0.7 -0.2 -0.7 0.3  1.00      174       84
-## x[2,17]     -0.3  0.0  0.4  0.1 0.2  0.99       32       59
-## x[1,18]     -1.2 -0.8 -0.3 -0.8 0.3  1.00      127       96
-## x[2,18]     -1.4 -1.0 -0.5 -1.0 0.3  1.02       26       63
-## x[1,19]     -1.2 -0.7 -0.4 -0.8 0.3  1.02      110       78
-## x[2,19]     -2.1 -1.6 -1.0 -1.6 0.4  1.02       26       69
-## x[1,20]     -1.8 -1.2 -0.7 -1.2 0.4  1.00       83      131
-## x[2,20]     -3.1 -2.3 -1.5 -2.3 0.5  1.03       24       69
-## Z[1,1]       0.6  0.9  1.2  0.9 0.2  1.00       48       80
-## Z[2,1]      -0.4 -0.1  0.1 -0.1 0.2  1.00       25       36
-## Z[3,1]       0.1  0.3  0.6  0.3 0.2  1.00       51       85
-## Z[4,1]      -1.1 -0.8 -0.6 -0.8 0.2  1.03       75       94
-## Z[1,2]       0.0  0.0  0.0  0.0 0.0  1.00      125      125
-## Z[2,2]      -0.9 -0.6 -0.5 -0.7 0.1  1.06       20       36
-## Z[3,2]      -0.8 -0.6 -0.4 -0.6 0.1  1.02       29       52
-## Z[4,2]       0.2  0.3  0.6  0.3 0.1  1.02       47       50
-## log_lik[1]  -1.1 -0.2  0.0 -0.3 0.4  1.00       80      106
-## log_lik[2]   0.5  2.3  2.7  2.0 0.7  1.01       78      106
-## log_lik[3]  -0.6 -0.3 -0.1 -0.3 0.2  1.00      107      138
-## log_lik[4]  -1.3 -0.2  0.1 -0.3 0.5  0.99       90      132
-## log_lik[5]  -0.9  0.2  0.4  0.0 0.4  0.99      108      104
-## log_lik[6]   0.2  2.2  2.7  1.9 1.0  0.99       80       82
-## log_lik[7]  -0.5  0.0  0.3  0.0 0.3  1.00      116      108
-## log_lik[8]  -0.8  0.1  0.4  0.0 0.4  1.01       77       96
-## log_lik[9]  -3.1 -0.7  0.2 -1.0 1.1  1.00      149      108
-## log_lik[10]  0.9  2.3  2.7  2.1 0.6  1.00       64       74
-## log_lik[11] -0.3  0.0  0.2  0.0 0.2  1.02       94       85
-## log_lik[12] -2.7 -0.8  0.1 -1.0 1.0  1.00      146       60
-## log_lik[13] -1.4 -0.2  0.1 -0.4 0.6  1.00      134      108
-## log_lik[14]  0.5  2.3  2.7  2.0 0.8  1.00      106       62
-## log_lik[15] -0.8 -0.3 -0.1 -0.4 0.2  1.00      100       85
-## log_lik[16] -3.0 -0.9 -0.1 -1.2 1.1  0.99      101      108
-## log_lik[17] -3.0 -0.9  0.1 -1.1 0.9  1.00       95      127
-## log_lik[18]  0.6  2.2  2.7  2.0 0.7  1.02       88       85
-## log_lik[19] -1.5 -0.4  0.2 -0.5 0.5  0.99       88      144
-## log_lik[20] -0.6 -0.3 -0.1 -0.3 0.2  1.00      104      101
-## log_lik[21] -2.9 -0.6  0.1 -0.8 0.9  1.02      103       47
-## log_lik[22]  0.0  2.3  2.6  2.0 0.8  1.00      101       83
-## log_lik[23] -0.8 -0.3  0.0 -0.3 0.3  1.00      126      108
-## log_lik[24] -0.7 -0.3  0.0 -0.3 0.3  1.00       82      106
-## log_lik[25] -1.0 -0.2  0.1 -0.3 0.4  1.00      149       83
-## log_lik[26]  1.0  2.4  2.6  2.1 0.7  1.00       67      108
-## log_lik[27] -0.5 -0.2 -0.1 -0.3 0.1  0.99      103       71
-## log_lik[28] -0.7 -0.2  0.0 -0.3 0.3  1.00      110       99
-## log_lik[29] -1.1 -0.1  0.2 -0.2 0.6  1.00      126       85
-## log_lik[30]  1.0  2.3  2.6  2.0 0.6  1.00       77       64
-## log_lik[31] -1.1 -0.1  0.4 -0.2 0.5  0.99      111       83
-## log_lik[32] -0.9 -0.3  0.0 -0.3 0.3  1.00       79       78
-## log_lik[33] -2.4 -0.8 -0.2 -1.1 0.8  0.99      230      127
-## log_lik[34]  0.8  2.3  2.6  2.1 0.6  1.00      192      119
-## log_lik[35] -0.3  0.2  0.4  0.1 0.2  1.04       98      106
-## log_lik[36] -1.4 -0.1  0.2 -0.3 0.6  1.02      188      106
-## log_lik[37] -2.1 -0.3  0.0 -0.6 0.7  1.01      165      101
-## log_lik[38]  1.3  2.4  2.6  2.2 0.5  1.00      108       70
-## log_lik[39] -0.5 -0.1  0.1 -0.2 0.2  1.02      107      101
-## log_lik[40] -1.8 -0.1  0.3 -0.4 0.7  0.99       81       86
-## log_lik[41] -1.3 -0.2  0.1 -0.4 0.4  1.00       89      131
-## log_lik[42]  0.6  2.3  2.7  2.1 0.6  1.00      116      131
-## log_lik[43] -0.6 -0.3  0.0 -0.3 0.2  0.99       83      104
-## log_lik[44] -2.4 -0.4  0.3 -0.7 0.9  1.00      114       98
-## log_lik[45] -2.2 -0.5  0.1 -0.7 0.9  1.00      204      134
-## log_lik[46]  1.0  2.3  2.6  2.1 0.7  1.01       89      106
-## log_lik[47] -3.2 -1.6 -0.2 -1.6 0.9  1.00      133      108
-## log_lik[48] -0.7 -0.2  0.0 -0.3 0.2  0.99      114      108
-## log_lik[49] -1.4 -0.3  0.1 -0.4 0.5  1.00      119       96
-## log_lik[50] -0.2  2.3  2.6  1.9 1.0  0.99      107       70
-## log_lik[51] -1.3 -0.1  0.1 -0.3 0.5  1.00      112      105
-## log_lik[52] -0.9 -0.3  0.0 -0.4 0.3  1.00      169      106
-## log_lik[53] -1.9 -0.7 -0.1 -0.8 0.7  1.00       80       96
-## log_lik[54]  0.6  2.3  2.6  2.0 0.7  1.00       81       98
-## log_lik[55] -0.6 -0.3 -0.1 -0.3 0.2  1.00      125      102
-## log_lik[56] -1.1 -0.2  0.1 -0.3 0.4  1.01       89      119
-## log_lik[57] -0.6  0.2  0.4  0.1 0.4  1.01      132      101
-## log_lik[58]  0.8  2.3  2.7  2.0 0.7  1.00       76       51
-## log_lik[59] -0.6 -0.1  0.2 -0.1 0.2  1.01       89      106
-## log_lik[60] -0.6  0.2  0.4  0.1 0.3  1.01       82      127
-## log_lik[61] -6.5 -3.2 -0.9 -3.5 1.8  1.00      117      136
-## log_lik[62]  0.8  2.3  2.6  2.1 0.7  1.00      109      142
-## log_lik[63] -1.6 -0.7 -0.3 -0.8 0.5  1.02       96      112
-## log_lik[64] -2.5 -0.8 -0.1 -1.0 0.9  1.06       99      130
-## log_lik[65] -0.5  0.1  0.3  0.0 0.3  1.00       93       84
-## log_lik[66]  0.8  2.3  2.6  2.1 0.6  1.02       98       85
-## log_lik[67] -0.3 -0.1  0.1 -0.1 0.1  1.01      107       86
-## log_lik[68] -0.6 -0.2  0.0 -0.2 0.2  0.99       94       85
-## log_lik[69] -1.5 -0.3  0.0 -0.4 0.5  0.99      110      139
-## log_lik[70]  1.3  2.3  2.6  2.2 0.5  1.01       94      106
-## log_lik[71] -0.6 -0.1  0.1 -0.2 0.2  1.00      129      108
-## log_lik[72] -0.9  0.0  0.2 -0.2 0.4  0.99       89      102
-## log_lik[73] -0.6 -0.1  0.2 -0.1 0.3  1.01      107      106
-## log_lik[74]  0.9  2.3  2.6  2.1 0.6  0.99       59       81
-## log_lik[75] -0.5 -0.2 -0.1 -0.2 0.1  1.00       88      134
-## log_lik[76] -0.6  0.2  0.4  0.0 0.4  0.99      102      108
-## log_lik[77] -0.9 -0.2  0.0 -0.3 0.4  1.00      115      101
-## log_lik[78]  1.1  2.3  2.7  2.1 0.5  1.00       64       95
-## log_lik[79] -0.5 -0.3 -0.1 -0.3 0.2  0.99      122      102
-## log_lik[80] -1.1 -0.1  0.2 -0.2 0.5  1.02      122      101
-## xstar[1,1]  -2.7 -1.3  0.5 -1.3 1.0  1.02      117       69
-## xstar[2,1]  -3.9 -2.1 -0.4 -2.1 1.1  0.99       88      108
-## sigma[1]     0.7  0.8  0.9  0.8 0.1  0.99      107      108
-## lp__        11.6 23.8 33.2 22.8 6.7  1.01       26       29
+##                Q5  Q50  Q95 Mean  SD  Rhat Bulk_ESS Tail_ESS
+## x[1,1]       -0.8 -0.4  0.1 -0.4 0.3  1.01       88       71
+## x[2,1]        1.4  2.0  2.5  2.0 0.4  1.00       45       86
+## x[1,2]       -1.7 -1.1 -0.6 -1.2 0.3  1.01       57       50
+## x[2,2]        1.5  2.2  2.9  2.2 0.4  1.00       39       47
+## x[1,3]        0.1  0.5  1.0  0.5 0.3  0.99      164      100
+## x[2,3]        0.7  1.1  1.6  1.1 0.3  1.12       11       28
+## x[1,4]        1.1  1.5  2.2  1.6 0.4  1.00       41       68
+## x[2,4]        0.6  1.3  2.0  1.3 0.4  1.20        4       39
+## x[1,5]       -0.1  0.4  0.8  0.4 0.3  1.00      105      101
+## x[2,5]        0.4  0.8  1.4  0.8 0.3  1.09       10       50
+## x[1,6]        0.8  1.3  1.9  1.3 0.4  1.00       45       78
+## x[2,6]        0.4  0.9  1.6  0.9 0.4  1.19        5       55
+## x[1,7]        0.1  0.6  1.1  0.6 0.3  0.99      185      143
+## x[2,7]       -0.9 -0.5 -0.2 -0.5 0.2  1.00       62       64
+## x[1,8]        0.0  0.3  0.8  0.3 0.2  1.00      131       85
+## x[2,8]       -1.6 -1.2 -0.8 -1.2 0.2  0.99       49      104
+## x[1,9]       -1.2 -0.7 -0.3 -0.7 0.3  0.99       90      108
+## x[2,9]       -2.3 -1.6 -1.1 -1.7 0.4  1.13        8       66
+## x[1,10]      -1.5 -0.9 -0.4 -0.9 0.3  0.99       93      108
+## x[2,10]      -3.5 -2.3 -1.6 -2.3 0.5  1.14        7       50
+## x[1,11]      -1.8 -1.2 -0.7 -1.2 0.4  0.99       73      108
+## x[2,11]      -3.6 -2.5 -1.8 -2.6 0.6  1.15        8       50
+## x[1,12]      -0.6 -0.1  0.3 -0.1 0.3  1.00      118       49
+## x[2,12]      -1.8 -1.3 -0.8 -1.3 0.3  1.07       40       74
+## x[1,13]       0.5  1.1  1.6  1.1 0.3  1.01      110      104
+## x[2,13]      -1.1 -0.6 -0.1 -0.6 0.3  1.04       40       51
+## x[1,14]       0.9  1.5  2.0  1.4 0.3  0.99       58      101
+## x[2,14]      -1.3 -0.7 -0.1 -0.7 0.4  1.05       25      106
+## x[1,15]       0.5  1.0  1.3  1.0 0.3  1.06       81       73
+## x[2,15]      -2.4 -1.7 -1.2 -1.7 0.4  1.00       48       71
+## x[1,16]      -1.1 -0.8 -0.3 -0.7 0.3  1.00       64      108
+## x[2,16]      -1.2 -0.7 -0.3 -0.7 0.3  1.11        7       28
+## x[1,17]      -1.0 -0.6 -0.2 -0.6 0.3  1.00      126      101
+## x[2,17]      -0.4  0.0  0.3  0.0 0.2  1.01       77       94
+## x[1,18]      -1.4 -0.7 -0.3 -0.7 0.3  1.02       84      134
+## x[2,18]       0.6  0.9  1.5  1.0 0.3  1.02       51       55
+## x[1,19]      -1.3 -0.7 -0.3 -0.7 0.3  1.03       45      136
+## x[2,19]       1.1  1.6  2.3  1.6 0.4  1.00       49       71
+## x[1,20]      -1.8 -1.2 -0.6 -1.2 0.4  1.00       59       78
+## x[2,20]       1.6  2.3  3.2  2.3 0.5  0.99       41       53
+## Z[1,1]        0.7  0.9  1.3  0.9 0.2  1.00       44       68
+## Z[2,1]       -0.4 -0.1  0.1 -0.1 0.2  1.12        8       59
+## Z[3,1]        0.1  0.4  0.6  0.3 0.2  1.08       17      124
+## Z[4,1]       -1.2 -0.8 -0.6 -0.8 0.2  1.04       38      106
+## Z[1,2]        0.0  0.0  0.0  0.0 0.0  1.00      125      125
+## Z[2,2]        0.5  0.6  0.9  0.7 0.1  1.04       35       83
+## Z[3,2]        0.5  0.6  0.8  0.6 0.1  1.03       44      136
+## Z[4,2]       -0.5 -0.3 -0.2 -0.3 0.1  1.01       79       85
+## log_lik[1]   -0.9 -0.1  0.2 -0.2 0.4  1.03      103       83
+## log_lik[2]    0.1  1.2  1.5  1.0 0.5  1.00      106      106
+## log_lik[3]   -0.4 -0.1  0.1 -0.1 0.2  1.02       84       69
+## log_lik[4]   -0.6 -0.1  0.2 -0.1 0.3  1.02       95       96
+## log_lik[5]   -0.8  0.0  0.4 -0.1 0.5  0.99       72       99
+## log_lik[6]   -0.7  1.0  1.5  0.8 0.9  1.00       62       83
+## log_lik[7]   -0.7  0.0  0.3 -0.1 0.3  1.06       76       85
+## log_lik[8]   -1.0  0.0  0.3 -0.1 0.4  1.00       98       85
+## log_lik[9]   -3.6 -0.7  0.2 -1.1 1.2  0.99      157       71
+## log_lik[10]  -0.4  1.2  1.5  0.9 0.7  1.04       61       83
+## log_lik[11]  -0.6  0.0  0.3 -0.1 0.3  0.99      132      108
+## log_lik[12]  -2.8 -0.6  0.2 -0.9 1.0  0.99      143      134
+## log_lik[13]  -1.0 -0.1  0.2 -0.2 0.4  0.99      158       81
+## log_lik[14]  -0.4  1.1  1.5  0.9 0.7  1.00      113      144
+## log_lik[15]  -0.9 -0.2  0.1 -0.3 0.4  1.00      155      100
+## log_lik[16]  -3.2 -1.3  0.0 -1.4 1.0  1.00      148      108
+## log_lik[17]  -3.1 -1.0  0.1 -1.2 1.0  1.02      110      134
+## log_lik[18]  -0.5  1.1  1.5  0.8 0.8  1.02       72       83
+## log_lik[19]  -1.4 -0.3  0.2 -0.4 0.5  1.00      170      142
+## log_lik[20]  -0.8 -0.1  0.1 -0.2 0.3  1.00      104      101
+## log_lik[21]  -2.9 -0.6  0.2 -0.9 1.0  1.00      130       63
+## log_lik[22]  -0.9  1.1  1.5  0.7 0.9  1.09       14       74
+## log_lik[23]  -0.8 -0.1  0.1 -0.2 0.3  1.00      114      146
+## log_lik[24]  -0.9 -0.1  0.2 -0.2 0.4  1.01       47       81
+## log_lik[25]  -0.9 -0.1  0.2 -0.2 0.4  0.99       81       69
+## log_lik[26]  -0.5  1.1  1.5  0.9 0.6  0.99       82       83
+## log_lik[27]  -0.5 -0.1  0.1 -0.1 0.2  1.00       75       51
+## log_lik[28]  -0.8 -0.1  0.2 -0.1 0.3  1.00       74      108
+## log_lik[29]  -0.7  0.0  0.3 -0.1 0.4  1.00      126       80
+## log_lik[30]  -0.7  1.1  1.5  0.8 0.8  1.01      113       98
+## log_lik[31]  -0.8 -0.1  0.3 -0.2 0.3  0.99       91       92
+## log_lik[32]  -0.6 -0.1  0.2 -0.2 0.3  1.00      109      108
+## log_lik[33]  -3.1 -0.9  0.0 -1.2 1.0  0.99      115      136
+## log_lik[34]  -0.1  1.1  1.5  0.9 0.5  0.99      111       83
+## log_lik[35]  -0.3  0.1  0.4  0.1 0.2  1.00       91       36
+## log_lik[36]  -1.3 -0.1  0.3 -0.2 0.5  1.00      140       66
+## log_lik[37]  -2.1 -0.4  0.1 -0.6 0.7  1.01      131       96
+## log_lik[38]  -0.2  1.1  1.5  0.9 0.6  1.00      106      105
+## log_lik[39]  -0.5 -0.1  0.2 -0.1 0.3  1.01       80       82
+## log_lik[40]  -1.8 -0.2  0.3 -0.4 0.7  1.00       92      106
+## log_lik[41]  -1.1 -0.1  0.2 -0.3 0.5  0.99      152      104
+## log_lik[42]  -0.2  1.0  1.5  0.9 0.6  1.00       85      106
+## log_lik[43]  -0.4 -0.1  0.1 -0.1 0.2  1.02       52       28
+## log_lik[44]  -2.5 -0.4  0.3 -0.6 0.9  1.00      163       85
+## log_lik[45]  -2.2 -0.4  0.1 -0.6 0.7  1.01       96       69
+## log_lik[46]  -0.8  1.0  1.5  0.7 0.9  1.00       46      108
+## log_lik[47]  -2.7 -1.2 -0.1 -1.3 0.8  1.02       88      106
+## log_lik[48]  -0.5 -0.1  0.2 -0.2 0.3  1.00      111       76
+## log_lik[49]  -1.3 -0.2  0.2 -0.3 0.5  1.00      134      103
+## log_lik[50]  -0.4  1.1  1.5  0.9 0.6  1.00      149      106
+## log_lik[51]  -1.0 -0.1  0.2 -0.3 0.5  1.04      122       60
+## log_lik[52]  -0.9 -0.2  0.2 -0.2 0.3  1.00      117      106
+## log_lik[53]  -1.8 -0.4  0.1 -0.6 0.6  0.99      134      105
+## log_lik[54]  -0.7  1.0  1.5  0.8 0.7  1.00       86      131
+## log_lik[55]  -0.7 -0.1  0.1 -0.2 0.2  0.99       69       88
+## log_lik[56]  -0.9 -0.1  0.2 -0.2 0.4  1.00      108      138
+## log_lik[57]  -0.9  0.1  0.4  0.0 0.4  1.00       75       44
+## log_lik[58]  -0.6  1.0  1.5  0.8 0.7  1.00      102       85
+## log_lik[59]  -0.8 -0.1  0.2 -0.1 0.3  0.99      115      144
+## log_lik[60]  -0.8  0.1  0.4  0.0 0.4  1.00       63       81
+## log_lik[61]  -7.0 -3.3 -0.8 -3.6 2.0  0.99      212      132
+## log_lik[62]  -0.6  1.1  1.5  0.8 0.7  1.00      128      108
+## log_lik[63]  -1.9 -0.7 -0.1 -0.8 0.5  0.99       97      108
+## log_lik[64]  -2.9 -0.9  0.0 -1.1 0.9  0.99      126       85
+## log_lik[65]  -0.7  0.1  0.3  0.0 0.3  1.00       68       31
+## log_lik[66]   0.1  1.1  1.5  1.0 0.5  1.02       67       81
+## log_lik[67]  -0.3  0.0  0.2  0.0 0.2  1.00       84      102
+## log_lik[68]  -0.5 -0.1  0.2 -0.1 0.2  1.00       84       83
+## log_lik[69]  -1.6 -0.1  0.2 -0.4 0.7  1.03      120      103
+## log_lik[70]  -0.4  1.1  1.5  0.9 0.6  1.00       67       82
+## log_lik[71]  -0.8 -0.1  0.2 -0.2 0.3  1.02      123      108
+## log_lik[72]  -1.0 -0.1  0.2 -0.2 0.4  1.02       83      102
+## log_lik[73]  -0.7  0.0  0.3 -0.1 0.3  1.00      103      143
+## log_lik[74]  -0.8  1.1  1.5  0.9 0.7  1.00       81       85
+## log_lik[75]  -0.5 -0.1  0.2 -0.1 0.2  1.02       68       83
+## log_lik[76]  -0.6  0.1  0.3  0.0 0.3  1.05       92      104
+## log_lik[77]  -1.4 -0.2  0.2 -0.3 0.5  1.00       99       78
+## log_lik[78]  -0.1  1.1  1.5  0.9 0.8  1.00       67       95
+## log_lik[79]  -0.5 -0.1  0.1 -0.2 0.2  0.99       89      106
+## log_lik[80]  -1.1 -0.1  0.3 -0.2 0.5  1.01      112       82
+## xstar[1,1]   -3.1 -0.9  0.4 -1.1 1.1  1.00       99      138
+## xstar[2,1]    0.6  2.4  4.4  2.5 1.2  0.99      101      104
+## sigma[1]      0.4  0.5  0.6  0.5 0.1  1.00       74       39
+## lp__        -11.9  2.0 16.2  2.3 8.5  1.00       28       47
 ## 
 ## For each parameter, Bulk_ESS and Tail_ESS are crude measures of 
 ## effective sample size for bulk and tail quantities respectively (an ESS > 100 
 ## per chain is considered good), and Rhat is the potential scale reduction 
 ## factor on rank normalized split chains (at convergence, Rhat <= 1.05).
+

As a second type of weighting, we also have implemented weights in +the same form used in other widely used packages (glmmTMB, sdmTMB, brms, +etc). In this case, weights are used as multipliers on the +log-likelihood of each observation. To specify these kinds of weights, +we use the likelihood_weights argument instead, where +observations with higher weights contribute more to the total log +likelihood.

+
+f2 <- fit_dfa(
+  y = df, num_trends = 2, scale="zscore",
+  iter = 500, chains = 1, thin = 1,
+  likelihood_weights = "weights", data_shape = "long"
+)
diff --git a/docs/articles/a2_combining_data.html b/docs/articles/a2_combining_data.html index 041b08f..52836c2 100644 --- a/docs/articles/a2_combining_data.html +++ b/docs/articles/a2_combining_data.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -102,7 +102,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a2_combining_data.Rmd diff --git a/docs/articles/a3_covariates.html b/docs/articles/a3_covariates.html index 64f2af4..1fe0e5e 100644 --- a/docs/articles/a3_covariates.html +++ b/docs/articles/a3_covariates.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -103,7 +103,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a3_covariates.Rmd diff --git a/docs/articles/a4_smooth.html b/docs/articles/a4_smooth.html index 1563c96..88b757b 100644 --- a/docs/articles/a4_smooth.html +++ b/docs/articles/a4_smooth.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -102,7 +102,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a4_smooth.Rmd diff --git a/docs/articles/a5_estimate_process_sigma.html b/docs/articles/a5_estimate_process_sigma.html index 22bf4fc..79b5d5c 100644 --- a/docs/articles/a5_estimate_process_sigma.html +++ b/docs/articles/a5_estimate_process_sigma.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -103,7 +103,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a5_estimate_process_sigma.Rmd diff --git a/docs/articles/a6_compositional.html b/docs/articles/a6_compositional.html index 4809baa..613703f 100644 --- a/docs/articles/a6_compositional.html +++ b/docs/articles/a6_compositional.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -103,7 +103,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a6_compositional.Rmd diff --git a/docs/articles/a7_bigdata.html b/docs/articles/a7_bigdata.html index 6b82501..6490e79 100644 --- a/docs/articles/a7_bigdata.html +++ b/docs/articles/a7_bigdata.html @@ -34,7 +34,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -103,7 +103,7 @@

Eric J. Ward, Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano, Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

-

2023-06-15

+

2024-01-12

Source: vignettes/a7_bigdata.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 9ed5f51..4a0c8ad 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/authors.html b/docs/authors.html index 1a4ea6e..6b1bbf2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -125,15 +125,15 @@

Citation

-

Ward EJ, Anderson SC, Damiano LA, Malick MJ (2023). +

Ward EJ, Anderson SC, Damiano LA, Malick MJ (2024). bayesdfa: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'. -R package version 1.3.0, https://fate-ewi.github.io/bayesdfa/. +R package version 1.3.2, https://fate-ewi.github.io/bayesdfa/. 

@Manual{,
   title = {bayesdfa: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'},
   author = {Eric J. Ward and Sean C. Anderson and Luis A. Damiano and Michael J. Malick},
-  year = {2023},
-  note = {R package version 1.3.0},
+  year = {2024},
+  note = {R package version 1.3.2},
   url = {https://fate-ewi.github.io/bayesdfa/},
 }
diff --git a/docs/index.html b/docs/index.html index 93e1228..fb1b437 100644 --- a/docs/index.html +++ b/docs/index.html @@ -41,7 +41,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -130,36 +130,36 @@

VignettesCiting

For DFA models in general, we recommend citing the MARSS package or user guide.

-
@article{marss_package,
-    title = {{MARSS}: multivariate autoregressive state-space models for analyzing time-series data},
-    volume = {4},
-    url = {https://pdfs.semanticscholar.org/5d41/b86dff5f977a0eac426a924cf7917220fc9a.pdf},
-    number = {1},
-    journal = {R Journal},
-    author = {Holmes, E.E. and Ward, Eric J. and Wills, K.},
-    year = {2012},
-    pages = {11--19}
-}
-
-@article{marss_user_guide,
-    title = {{MARSS}: Analysis of multivariate timeseries using the MARSS package},
-    url = {https://cran.r-project.org/web/packages/MARSS/vignettes/UserGuide.pdf},
-    author = {Holmes, E.E. and Scheurell, M.D. and Ward, Eric J.},
-    year = {2020},
-}
+
@article{marss_package,
+    title = {{MARSS}: multivariate autoregressive state-space models for analyzing time-series data},
+    volume = {4},
+    url = {https://pdfs.semanticscholar.org/5d41/b86dff5f977a0eac426a924cf7917220fc9a.pdf},
+    number = {1},
+    journal = {R Journal},
+    author = {Holmes, E.E. and Ward, Eric J. and Wills, K.},
+    year = {2012},
+    pages = {11--19}
+}
+
+@article{marss_user_guide,
+    title = {{MARSS}: Analysis of multivariate timeseries using the MARSS package},
+    url = {https://cran.r-project.org/web/packages/MARSS/vignettes/UserGuide.pdf},
+    author = {Holmes, E.E. and Scheurell, M.D. and Ward, Eric J.},
+    year = {2020},
+}

For citing the bayesdfa package using Bayesian estimation, or models with extra features (such as extremes), cite

https://journal.r-project.org/archive/2019/RJ-2019-007/index.html

-
@article{ward_etal_2019,
-  author = {Eric J. Ward and Sean C. Anderson and Luis A. Damiano and
-          Mary E. Hunsicker and Michael A. Litzow},
-  title = {{Modeling regimes with extremes: the bayesdfa package for
-          identifying and forecasting common trends and anomalies in
-          multivariate time-series data}},
-  year = {2019},
-  journal = {{The R Journal}},
-  doi = {10.32614/RJ-2019-007},
-  url = {https://journal.r-project.org/archive/2019/RJ-2019-007/index.html}
-}
+
@article{ward_etal_2019,
+  author = {Eric J. Ward and Sean C. Anderson and Luis A. Damiano and
+          Mary E. Hunsicker and Michael A. Litzow},
+  title = {{Modeling regimes with extremes: the bayesdfa package for
+          identifying and forecasting common trends and anomalies in
+          multivariate time-series data}},
+  year = {2019},
+  journal = {{The R Journal}},
+  doi = {10.32614/RJ-2019-007},
+  url = {https://journal.r-project.org/archive/2019/RJ-2019-007/index.html}
+}

Applications

diff --git a/docs/news/index.html b/docs/news/index.html index c30c5dd..760d844 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2
@@ -115,6 +115,19 @@

bayesdfa 1.1.0bayesdfa 1.2.02021-09-28

Add penalized spline models, so that the ‘trend_model’ argument may take on “rw” for conventional random walks, “bs” for B-splines, “ps” for “P-splines”, or “gp” for Gaussian processes

+
+

bayesdfa 1.3.0

+

Change to new Stan syntax

+
+
+

bayesdfa 1.3.12023-10-11

+

Versioning

+
+
+

bayesdfa 1.3.2

+
diff --git a/docs/reference/dfa_cv.html b/docs/reference/dfa_cv.html index 23439d3..798e65e 100644 --- a/docs/reference/dfa_cv.html +++ b/docs/reference/dfa_cv.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/dfa_fitted.html b/docs/reference/dfa_fitted.html index 03c1578..163258c 100644 --- a/docs/reference/dfa_fitted.html +++ b/docs/reference/dfa_fitted.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -117,8 +117,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000126 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds. +#> Chain 1: Gradient evaluation took 0.000116 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.16 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -143,9 +143,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.011398 seconds (Warm-up) -#> Chain 1: 0.042844 seconds (Sampling) -#> Chain 1: 0.054242 seconds (Total) +#> Chain 1: Elapsed Time: 0.006 seconds (Warm-up) +#> Chain 1: 0.013 seconds (Sampling) +#> Chain 1: 0.019 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low @@ -161,139 +161,139 @@

Examples

#> https://mc-stan.org/misc/warnings.html#tail-ess #> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> -#> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -0.8 -0.8 -0.7 -0.8 0.0 2.06 4 13 -#> x[2,1] -0.6 -0.6 -0.6 -0.6 0.0 2.06 4 13 -#> x[1,2] -1.4 -1.4 -1.4 -1.4 0.0 2.06 3 13 -#> x[2,2] -0.7 -0.6 -0.5 -0.6 0.0 2.06 4 13 -#> x[1,3] -0.2 -0.2 -0.1 -0.2 0.0 2.06 3 13 -#> x[2,3] 0.0 0.1 0.1 0.1 0.1 2.06 4 13 -#> x[1,4] -0.3 -0.2 -0.2 -0.2 0.0 2.06 4 13 -#> x[2,4] -0.8 -0.7 -0.6 -0.7 0.1 2.06 4 13 -#> x[1,5] 1.6 1.6 1.6 1.6 0.0 2.06 4 13 -#> x[2,5] -1.1 -0.9 -0.8 -1.0 0.1 2.06 4 13 -#> x[1,6] 1.5 1.5 1.5 1.5 0.0 2.06 4 13 -#> x[2,6] 0.2 0.4 0.4 0.3 0.1 2.06 4 13 -#> x[1,7] -0.3 -0.2 -0.2 -0.2 0.0 2.06 4 13 -#> x[2,7] -1.7 -1.4 -1.3 -1.5 0.1 2.06 3 13 -#> x[1,8] -1.2 -1.1 -1.1 -1.1 0.1 2.06 3 13 -#> x[2,8] -0.3 0.0 0.0 -0.1 0.1 2.06 4 13 -#> x[1,9] -1.1 -1.0 -1.0 -1.0 0.1 2.06 3 13 -#> x[2,9] -1.7 -1.4 -1.4 -1.5 0.1 2.06 4 13 -#> x[1,10] -0.4 -0.3 -0.3 -0.3 0.0 2.06 4 13 -#> x[2,10] -1.9 -1.7 -1.6 -1.7 0.1 2.06 4 13 -#> x[1,11] -0.4 -0.4 -0.3 -0.4 0.0 2.06 4 13 -#> x[2,11] -0.8 -0.7 -0.6 -0.7 0.1 2.06 4 13 -#> x[1,12] -0.5 -0.4 -0.4 -0.4 0.0 2.06 4 13 -#> x[2,12] 0.5 0.5 0.6 0.5 0.0 2.06 4 13 -#> x[1,13] 0.8 0.8 0.8 0.8 0.0 2.06 4 13 -#> x[2,13] 0.4 0.5 0.5 0.5 0.0 1.48 4 13 -#> x[1,14] -0.9 -0.9 -0.9 -0.9 0.0 2.06 4 13 -#> x[2,14] 0.3 0.4 0.4 0.4 0.0 1.24 5 13 -#> x[1,15] -0.6 -0.6 -0.6 -0.6 0.0 1.87 7 13 -#> x[2,15] 0.7 0.8 0.9 0.8 0.1 2.06 3 13 -#> x[1,16] 0.4 0.4 0.5 0.4 0.0 1.18 7 13 -#> x[2,16] 0.4 0.5 0.6 0.5 0.1 2.06 3 13 -#> x[1,17] 1.7 1.7 1.8 1.7 0.0 1.07 6 13 -#> x[2,17] 1.3 1.5 1.6 1.4 0.1 2.06 3 13 -#> x[1,18] 1.1 1.1 1.2 1.1 0.0 1.39 4 13 -#> x[2,18] -0.4 -0.3 -0.2 -0.3 0.1 2.06 3 13 -#> x[1,19] -0.4 -0.4 -0.4 -0.4 0.0 1.71 4 13 -#> x[2,19] 0.6 0.7 0.8 0.7 0.1 2.06 3 13 -#> x[1,20] -1.0 -1.0 -1.0 -1.0 0.0 1.58 8 13 -#> x[2,20] 0.0 0.2 0.3 0.2 0.1 2.06 3 13 -#> Z[1,1] -99.8 -99.8 -99.8 -99.8 0.0 1.71 4 13 -#> Z[2,1] -26.6 -20.0 -15.7 -21.4 4.1 2.06 3 13 -#> Z[3,1] 27.5 34.0 41.9 35.3 5.4 2.06 3 13 -#> Z[4,1] -31.5 -24.5 -19.8 -25.7 4.5 2.06 3 13 -#> Z[1,2] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> Z[2,2] -98.9 -98.9 -98.9 -98.9 0.0 2.06 4 13 -#> Z[3,2] -41.9 -33.9 -27.8 -35.3 5.1 2.06 3 13 -#> Z[4,2] -11.6 -7.9 -5.7 -8.6 2.4 2.06 3 13 -#> log_lik[1] -47.2 -22.0 -16.5 -28.4 11.5 2.06 3 13 -#> log_lik[2] -49.3 -18.5 -13.8 -26.8 13.5 2.06 3 13 -#> log_lik[3] -3.7 -3.6 -3.4 -3.6 0.1 2.06 4 13 -#> log_lik[4] -10.6 -5.3 -4.4 -6.7 2.4 2.06 3 13 -#> log_lik[5] -145.9 -63.1 -45.9 -84.1 37.1 2.06 3 13 -#> log_lik[6] -72.8 -23.3 -15.6 -36.5 21.5 2.06 3 13 -#> log_lik[7] -10.6 -6.0 -4.8 -7.2 2.2 2.06 3 13 -#> log_lik[8] -22.7 -8.1 -5.8 -11.9 6.4 2.06 3 13 -#> log_lik[9] -6.5 -4.6 -4.2 -5.0 0.9 2.06 3 13 -#> log_lik[10] -4.0 -3.6 -3.3 -3.6 0.3 2.06 4 13 -#> log_lik[11] -3.8 -3.7 -3.5 -3.7 0.1 2.06 4 13 -#> log_lik[12] -3.6 -3.5 -3.5 -3.5 0.1 2.06 3 13 -#> log_lik[13] -7.5 -4.8 -4.5 -5.6 1.2 2.06 3 13 -#> log_lik[14] -57.3 -18.1 -12.8 -28.8 16.8 2.06 3 13 -#> log_lik[15] -7.2 -4.2 -3.9 -5.0 1.2 2.06 3 13 -#> log_lik[16] -5.4 -3.8 -3.8 -4.3 0.6 2.06 4 13 -#> log_lik[17] -166.1 -76.8 -59.6 -100.2 39.6 2.06 3 13 -#> log_lik[18] -34.0 -12.9 -11.0 -18.8 8.8 2.06 4 13 -#> log_lik[19] -87.5 -24.3 -13.5 -40.8 27.7 2.06 3 13 -#> log_lik[20] -11.9 -6.4 -5.2 -7.8 2.5 2.06 3 13 -#> log_lik[21] -151.0 -70.0 -54.1 -91.0 35.7 2.06 3 13 -#> log_lik[22] -24.2 -16.7 -13.5 -18.2 3.8 2.06 3 13 -#> log_lik[23] -23.6 -7.9 -5.5 -12.0 6.8 2.06 3 13 -#> log_lik[24] -19.3 -8.2 -6.0 -11.0 5.0 2.06 3 13 -#> log_lik[25] -7.5 -4.9 -4.4 -5.6 1.2 2.06 3 13 -#> log_lik[26] -201.0 -65.1 -45.2 -103.0 59.6 2.06 3 13 -#> log_lik[27] -26.3 -8.3 -5.9 -13.1 7.7 2.06 3 13 -#> log_lik[28] -7.9 -4.2 -3.9 -5.3 1.6 2.06 3 13 -#> log_lik[29] -100.3 -40.5 -29.7 -56.7 26.9 2.06 3 13 -#> log_lik[30] -28.2 -5.6 -4.1 -12.3 9.5 2.06 3 13 -#> log_lik[31] -13.0 -7.5 -5.7 -8.8 2.7 2.06 3 13 -#> log_lik[32] -14.4 -5.7 -4.6 -8.1 3.8 2.06 3 13 -#> log_lik[33] -82.4 -32.2 -23.9 -46.3 22.4 2.06 3 13 -#> log_lik[34] -264.1 -82.8 -55.4 -134.0 80.2 2.06 3 13 -#> log_lik[35] -7.3 -4.2 -3.9 -5.0 1.3 2.06 3 13 -#> log_lik[36] -22.3 -7.2 -5.2 -11.4 6.6 2.06 3 13 -#> log_lik[37] -11.7 -5.9 -5.2 -7.9 2.6 2.06 3 13 -#> log_lik[38] -262.0 -90.7 -66.2 -139.9 75.3 2.06 3 13 -#> log_lik[39] -29.6 -9.8 -6.7 -15.0 8.6 2.06 3 13 -#> log_lik[40] -9.9 -4.6 -4.0 -6.1 2.3 2.06 3 13 -#> log_lik[41] -14.5 -7.1 -5.8 -9.4 3.4 2.06 3 13 -#> log_lik[42] -59.9 -18.9 -14.1 -31.3 17.9 2.06 3 13 -#> log_lik[43] -4.7 -3.8 -3.7 -4.0 0.4 2.06 3 13 -#> log_lik[44] -6.0 -3.9 -3.8 -4.5 0.9 2.06 3 13 -#> log_lik[45] -17.7 -8.5 -6.8 -11.3 4.2 2.06 3 13 -#> log_lik[46] -11.0 -9.3 -8.8 -9.7 0.8 0.94 8 13 -#> log_lik[47] -14.6 -7.0 -5.3 -9.0 3.4 2.06 3 13 -#> log_lik[48] -3.6 -3.5 -3.4 -3.5 0.1 2.06 3 13 -#> log_lik[49] -46.7 -24.6 -19.6 -29.3 10.0 2.06 3 13 -#> log_lik[50] -32.5 -15.6 -11.5 -19.1 7.4 2.06 3 13 -#> log_lik[51] -4.4 -3.9 -3.8 -4.1 0.3 2.06 3 13 -#> log_lik[52] -9.8 -5.4 -4.5 -6.4 1.9 2.06 3 13 -#> log_lik[53] -59.1 -25.9 -20.6 -36.0 14.8 2.06 3 13 -#> log_lik[54] -5.4 -4.6 -4.3 -4.7 0.4 1.00 8 13 -#> log_lik[55] -24.9 -9.1 -6.2 -13.2 6.9 2.06 3 13 -#> log_lik[56] -6.7 -4.4 -4.1 -5.1 1.0 2.06 3 13 -#> log_lik[57] -24.0 -12.4 -10.8 -16.3 5.3 2.06 3 13 -#> log_lik[58] -36.8 -16.4 -11.7 -20.7 8.9 2.06 3 13 -#> log_lik[59] -27.7 -9.6 -6.4 -14.4 7.9 2.06 3 13 -#> log_lik[60] -3.7 -3.6 -3.4 -3.6 0.1 2.06 3 13 -#> log_lik[61] -18.7 -10.2 -8.2 -11.8 3.7 2.06 3 13 -#> log_lik[62] -36.8 -13.3 -8.3 -18.2 10.0 2.06 3 13 -#> log_lik[63] -3.6 -3.5 -3.2 -3.4 0.2 2.06 3 13 -#> log_lik[64] -6.2 -4.2 -3.9 -4.6 0.9 2.06 3 13 -#> log_lik[65] -219.8 -96.5 -70.4 -126.3 54.6 2.06 3 13 -#> log_lik[66] -276.2 -97.6 -60.2 -140.8 78.6 2.06 3 13 -#> log_lik[67] -4.1 -4.0 -3.9 -4.0 0.1 1.71 4 13 -#> log_lik[68] -38.8 -11.9 -7.2 -18.6 11.8 2.06 3 13 -#> log_lik[69] -100.2 -43.9 -32.9 -57.7 24.7 2.06 3 13 -#> log_lik[70] -4.8 -3.6 -3.3 -3.9 0.6 1.03 6 13 -#> log_lik[71] -26.1 -11.1 -8.0 -15.1 6.9 2.06 3 13 -#> log_lik[72] -10.9 -5.3 -4.4 -6.6 2.4 2.06 3 13 -#> log_lik[73] -11.2 -7.6 -7.0 -8.8 1.7 2.06 3 13 -#> log_lik[74] -34.4 -13.8 -9.3 -18.1 8.9 2.06 3 13 -#> log_lik[75] -17.9 -7.1 -5.1 -9.7 4.7 2.06 3 13 -#> log_lik[76] -3.7 -3.6 -3.1 -3.5 0.2 2.06 3 13 -#> log_lik[77] -68.3 -33.2 -26.6 -43.4 16.0 2.06 3 13 -#> log_lik[78] -4.0 -3.6 -3.1 -3.6 0.3 2.06 3 13 -#> log_lik[79] -21.2 -7.8 -5.4 -11.3 5.9 2.06 3 13 -#> log_lik[80] -8.7 -5.2 -4.6 -6.2 1.6 2.06 3 13 -#> xstar[1,1] -2.6 -1.4 0.5 -1.2 1.1 0.92 13 13 -#> xstar[2,1] -0.6 -0.1 1.5 0.2 0.8 1.38 9 13 -#> sigma[1] 8.6 12.9 14.9 11.9 2.4 2.06 3 13 -#> lp__ -15937.4 -12945.7 -12007.7 -13680.6 1464.3 2.06 3 13 +#> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS +#> x[1,1] 0.1 0.2 0.2 0.2 0.0 2.06 3 13 +#> x[2,1] 0.4 0.5 0.5 0.4 0.0 1.48 4 13 +#> x[1,2] 0.2 0.4 0.4 0.3 0.1 2.06 3 13 +#> x[2,2] 1.3 1.5 1.5 1.4 0.1 1.87 4 13 +#> x[1,3] -0.1 0.1 0.1 0.1 0.1 2.06 3 13 +#> x[2,3] 1.1 1.3 1.3 1.2 0.1 2.06 4 13 +#> x[1,4] 1.0 1.2 1.2 1.1 0.1 2.06 3 13 +#> x[2,4] 1.5 1.7 1.7 1.6 0.1 2.06 4 13 +#> x[1,5] 2.5 2.8 2.9 2.8 0.1 2.06 3 13 +#> x[2,5] 1.0 1.2 1.3 1.2 0.1 2.06 4 13 +#> x[1,6] 1.2 1.5 1.5 1.4 0.1 2.06 3 13 +#> x[2,6] 0.0 0.3 0.3 0.2 0.1 2.06 4 13 +#> x[1,7] 2.8 3.1 3.1 3.0 0.1 2.06 3 13 +#> x[2,7] -0.2 0.0 0.1 0.0 0.1 2.06 4 13 +#> x[1,8] 1.0 1.3 1.3 1.2 0.1 2.06 3 13 +#> x[2,8] 0.3 0.5 0.5 0.4 0.1 2.06 4 13 +#> x[1,9] 0.0 0.3 0.3 0.2 0.1 2.06 3 13 +#> x[2,9] -1.7 -1.5 -1.5 -1.6 0.1 2.06 4 13 +#> x[1,10] 1.4 1.5 1.5 1.5 0.1 2.06 3 13 +#> x[2,10] -1.6 -1.3 -1.3 -1.4 0.1 2.06 4 13 +#> x[1,11] 0.8 0.9 0.9 0.9 0.0 2.06 3 13 +#> x[2,11] -1.6 -1.3 -1.3 -1.4 0.1 2.06 4 13 +#> x[1,12] -0.5 -0.5 -0.4 -0.5 0.0 1.19 11 13 +#> x[2,12] -2.0 -1.7 -1.6 -1.7 0.2 2.06 4 13 +#> x[1,13] -1.3 -1.3 -1.2 -1.3 0.0 2.06 4 13 +#> x[2,13] -0.9 -0.5 -0.5 -0.6 0.2 2.06 4 13 +#> x[1,14] -1.3 -1.3 -1.2 -1.3 0.1 2.06 3 13 +#> x[2,14] -0.7 -0.3 -0.3 -0.4 0.2 2.06 4 13 +#> x[1,15] 0.4 0.4 0.6 0.4 0.1 2.06 3 13 +#> x[2,15] -0.1 0.3 0.4 0.2 0.2 2.06 4 13 +#> x[1,16] 0.0 0.0 0.3 0.1 0.1 2.06 3 13 +#> x[2,16] 1.1 1.7 1.7 1.5 0.3 2.06 4 13 +#> x[1,17] -1.2 -1.2 -0.9 -1.1 0.1 2.06 3 13 +#> x[2,17] 2.2 2.8 2.8 2.6 0.3 2.06 3 13 +#> x[1,18] -1.9 -1.9 -1.6 -1.8 0.2 2.06 3 13 +#> x[2,18] 0.9 1.5 1.5 1.3 0.3 2.06 3 13 +#> x[1,19] -1.1 -1.1 -0.7 -1.0 0.2 2.06 3 13 +#> x[2,19] 0.9 1.5 1.5 1.3 0.3 2.06 3 13 +#> x[1,20] -1.2 -1.1 -0.8 -1.0 0.2 2.06 3 13 +#> x[2,20] -0.1 0.5 0.6 0.3 0.3 2.06 3 13 +#> Z[1,1] -98.5 -98.5 -98.5 -98.5 0.0 1.87 4 13 +#> Z[2,1] -39.9 -39.6 -34.8 -38.4 2.1 1.87 4 13 +#> Z[3,1] 13.2 15.8 15.9 15.1 1.1 1.87 4 13 +#> Z[4,1] 53.5 57.1 57.3 56.1 1.6 2.06 3 13 +#> Z[1,2] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> Z[2,2] -93.5 -93.5 -93.3 -93.5 0.1 2.06 4 13 +#> Z[3,2] -40.4 -40.2 -36.3 -39.2 1.7 2.06 4 13 +#> Z[4,2] -40.9 -40.7 -36.9 -39.7 1.7 2.06 4 13 +#> log_lik[1] -12.9 -11.3 -4.0 -9.6 3.8 2.06 3 13 +#> log_lik[2] -72.7 -63.6 -12.9 -51.2 26.0 2.06 3 13 +#> log_lik[3] -10.7 -9.7 -4.4 -8.4 2.8 2.06 3 13 +#> log_lik[4] -5.3 -5.1 -3.8 -4.8 0.7 2.06 4 13 +#> log_lik[5] -45.3 -39.0 -6.7 -31.3 16.6 2.06 3 13 +#> log_lik[6] -661.6 -581.0 -109.2 -465.2 239.5 2.06 3 13 +#> log_lik[7] -86.6 -76.2 -16.2 -61.6 30.5 2.06 3 13 +#> log_lik[8] -47.7 -42.8 -12.1 -35.1 15.5 2.06 3 13 +#> log_lik[9] -8.2 -6.6 -3.1 -6.1 2.1 2.06 4 13 +#> log_lik[10] -453.0 -393.0 -64.3 -313.2 168.5 2.06 3 13 +#> log_lik[11] -75.9 -66.5 -13.8 -53.7 26.9 2.06 3 13 +#> log_lik[12] -59.8 -53.9 -15.2 -44.2 19.5 2.06 3 13 +#> log_lik[13] -407.5 -353.7 -57.4 -282.0 151.4 2.06 3 13 +#> log_lik[14] -1171.1 -1018.3 -173.9 -813.3 432.3 2.06 3 13 +#> log_lik[15] -69.9 -60.9 -13.3 -49.4 24.6 2.06 3 13 +#> log_lik[16] -3.2 -2.4 -2.4 -2.6 0.3 2.06 4 13 +#> log_lik[17] -2212.5 -1947.9 -379.0 -1562.9 794.7 2.06 3 13 +#> log_lik[18] -1511.6 -1311.1 -208.2 -1043.8 564.4 2.06 3 13 +#> log_lik[19] -3.6 -3.4 -3.1 -3.4 0.2 2.06 4 13 +#> log_lik[20] -352.2 -310.7 -60.8 -249.4 126.2 2.06 3 13 +#> log_lik[21] -601.4 -521.2 -80.8 -414.7 225.2 2.06 3 13 +#> log_lik[22] -218.1 -180.3 -15.5 -142.4 87.4 2.06 3 13 +#> log_lik[23] -5.6 -5.5 -4.1 -5.2 0.6 1.58 4 13 +#> log_lik[24] -153.2 -134.8 -25.2 -108.0 55.3 2.06 3 13 +#> log_lik[25] -2598.8 -2292.8 -454.9 -1840.8 930.0 2.06 3 13 +#> log_lik[26] -465.7 -391.7 -40.3 -309.0 183.7 2.06 3 13 +#> log_lik[27] -61.5 -56.1 -14.2 -45.6 20.4 2.06 3 13 +#> log_lik[28] -847.7 -750.8 -147.9 -602.0 303.4 2.06 3 13 +#> log_lik[29] -448.9 -389.3 -62.0 -310.3 167.1 2.06 3 13 +#> log_lik[30] -271.0 -224.7 -23.9 -178.6 106.5 2.06 3 13 +#> log_lik[31] -3.2 -2.4 -2.4 -2.7 0.4 2.06 4 13 +#> log_lik[32] -76.7 -68.4 -14.2 -55.0 27.0 2.06 3 13 +#> log_lik[33] -21.9 -17.8 -3.2 -14.6 8.0 2.06 3 13 +#> log_lik[34] -454.7 -430.2 -156.8 -358.1 130.1 2.06 3 13 +#> log_lik[35] -115.9 -105.8 -27.1 -85.8 38.5 2.06 3 13 +#> log_lik[36] -163.8 -146.4 -29.5 -117.3 58.0 2.06 3 13 +#> log_lik[37] -638.5 -563.2 -112.4 -452.8 227.3 2.06 3 13 +#> log_lik[38] -104.8 -103.5 -60.5 -92.0 19.0 1.71 6 13 +#> log_lik[39] -167.5 -152.6 -36.7 -123.4 56.6 2.06 3 13 +#> log_lik[40] -561.7 -503.0 -107.0 -404.4 196.8 2.06 3 13 +#> log_lik[41] -208.5 -183.6 -38.7 -148.5 73.0 2.06 3 13 +#> log_lik[42] -204.4 -199.3 -89.9 -169.9 50.0 2.06 3 13 +#> log_lik[43] -124.7 -114.7 -31.0 -93.5 40.5 2.06 3 13 +#> log_lik[44] -299.5 -270.8 -64.2 -219.2 101.6 2.06 3 13 +#> log_lik[45] -59.7 -54.3 -16.0 -44.4 19.4 2.06 3 13 +#> log_lik[46] -789.5 -737.5 -236.4 -607.9 240.4 2.06 3 13 +#> log_lik[47] -96.5 -90.1 -28.4 -74.3 29.5 2.06 3 13 +#> log_lik[48] -47.5 -45.2 -16.6 -37.8 13.1 2.06 4 13 +#> log_lik[49] -455.3 -405.0 -90.7 -326.5 159.2 2.06 3 13 +#> log_lik[50] -259.0 -250.1 -92.7 -208.0 72.2 2.06 3 13 +#> log_lik[51] -4.9 -2.5 -2.4 -3.2 1.1 2.06 4 13 +#> log_lik[52] -80.3 -66.3 -9.4 -53.3 30.7 2.06 3 13 +#> log_lik[53] -492.5 -435.5 -86.7 -348.7 177.0 2.06 3 13 +#> log_lik[54] -171.6 -168.8 -71.1 -142.2 43.6 2.06 3 13 +#> log_lik[55] -4.9 -3.9 -3.8 -4.1 0.5 2.06 4 13 +#> log_lik[56] -117.7 -97.2 -11.1 -77.4 46.1 2.06 3 13 +#> log_lik[57] -35.3 -33.5 -20.6 -30.5 6.0 2.06 4 13 +#> log_lik[58] -66.0 -48.5 -3.3 -40.1 26.4 2.06 4 13 +#> log_lik[59] -4.5 -3.9 -3.1 -3.8 0.6 1.32 10 13 +#> log_lik[60] -12.8 -5.0 -3.9 -6.8 3.7 2.06 4 13 +#> log_lik[61] -7.6 -2.6 -2.4 -4.1 2.4 2.06 4 13 +#> log_lik[62] -714.6 -602.2 -84.4 -480.7 273.1 2.06 3 13 +#> log_lik[63] -128.8 -105.7 -11.2 -84.3 50.8 2.06 3 13 +#> log_lik[64] -130.3 -105.0 -7.2 -83.0 53.0 2.06 3 13 +#> log_lik[65] -384.3 -333.2 -47.0 -263.0 147.1 2.06 3 13 +#> log_lik[66] -1252.1 -1071.4 -176.1 -857.8 467.0 2.06 3 13 +#> log_lik[67] -476.0 -403.2 -50.3 -319.8 184.2 2.06 3 13 +#> log_lik[68] -931.7 -793.9 -99.4 -627.6 361.0 2.06 3 13 +#> log_lik[69] -998.0 -873.1 -147.7 -694.6 370.6 2.06 3 13 +#> log_lik[70] -115.9 -90.0 -6.3 -72.3 46.9 2.06 4 13 +#> log_lik[71] -231.4 -192.1 -18.6 -151.9 92.0 2.06 3 13 +#> log_lik[72] -831.3 -705.2 -84.5 -557.2 324.1 2.06 3 13 +#> log_lik[73] -325.0 -279.0 -33.1 -219.3 127.2 2.06 3 13 +#> log_lik[74] -279.1 -226.2 -21.1 -180.0 111.4 2.06 3 13 +#> log_lik[75] -173.7 -142.4 -12.6 -112.8 69.6 2.06 3 13 +#> log_lik[76] -435.9 -362.5 -32.1 -285.3 174.9 2.06 3 13 +#> log_lik[77] -373.8 -321.1 -39.8 -252.8 145.5 2.06 3 13 +#> log_lik[78] -14.8 -3.3 -2.5 -6.2 5.3 2.06 10 13 +#> log_lik[79] -48.7 -37.5 -3.3 -30.5 19.4 2.06 3 13 +#> log_lik[80] -228.0 -184.8 -11.5 -145.5 93.4 2.06 3 13 +#> xstar[1,1] -3.1 -0.9 0.8 -1.0 1.3 1.02 13 13 +#> xstar[2,1] -0.1 0.8 1.8 0.9 0.7 1.09 13 13 +#> sigma[1] 4.3 4.5 9.2 5.7 2.1 2.06 3 13 +#> lp__ -40283.6 -36850.0 -17092.2 -32041.0 10029.9 2.06 3 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 diff --git a/docs/reference/dfa_loadings.html b/docs/reference/dfa_loadings.html index 79afe9f..95b3af6 100644 --- a/docs/reference/dfa_loadings.html +++ b/docs/reference/dfa_loadings.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -129,8 +129,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. +#> Chain 1: Gradient evaluation took 3.7e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -155,9 +155,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.042954 seconds (Warm-up) -#> Chain 1: 0.392739 seconds (Sampling) -#> Chain 1: 0.435693 seconds (Total) +#> Chain 1: Elapsed Time: 0.034 seconds (Warm-up) +#> Chain 1: 0.411 seconds (Sampling) +#> Chain 1: 0.445 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low @@ -174,78 +174,78 @@

Examples

#> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> #> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -1.5 -0.7 0.8 -0.6 0.8 1.37 6 13 +#> x[1,1] -1.5 -0.7 0.9 -0.5 0.8 1.37 6 13 #> x[2,1] -1.0 -0.2 0.6 -0.2 0.6 1.58 9 13 -#> x[1,2] -1.7 0.2 0.9 -0.3 1.1 2.06 4 13 -#> x[2,2] 0.2 0.5 1.2 0.6 0.4 1.16 12 13 -#> x[1,3] -1.6 0.0 0.8 -0.4 1.0 2.06 4 13 +#> x[1,2] -1.7 0.2 1.2 -0.3 1.2 2.06 4 13 +#> x[2,2] 0.2 0.5 1.2 0.6 0.4 1.03 12 13 +#> x[1,3] -1.6 0.0 1.0 -0.3 1.0 2.06 4 13 #> x[2,3] -1.4 -0.2 0.3 -0.4 0.6 2.06 4 13 #> x[1,4] -1.5 -0.4 0.7 -0.4 0.9 2.06 4 13 -#> x[2,4] -0.1 0.6 1.3 0.6 0.5 1.06 11 13 +#> x[2,4] -0.1 0.5 1.3 0.5 0.5 0.97 10 13 #> x[1,5] -0.7 -0.2 0.7 -0.1 0.5 0.95 11 13 #> x[2,5] -1.4 -0.6 1.5 -0.3 1.2 1.87 6 13 -#> x[1,6] -0.9 -0.3 0.3 -0.3 0.5 1.16 6 13 -#> x[2,6] -0.2 0.1 0.6 0.1 0.3 1.45 10 13 -#> x[1,7] -2.2 -1.2 0.3 -1.1 0.9 1.71 4 13 -#> x[2,7] -1.1 -0.1 0.9 -0.1 0.6 1.47 13 13 -#> x[1,8] -1.7 -0.8 0.5 -0.7 0.8 1.32 5 13 +#> x[1,6] -1.0 -0.3 0.3 -0.3 0.5 1.16 6 13 +#> x[2,6] -0.2 0.1 0.6 0.1 0.3 1.45 9 13 +#> x[1,7] -2.2 -1.2 0.1 -1.1 0.9 1.71 4 13 +#> x[2,7] -1.1 -0.1 0.9 -0.1 0.6 1.58 13 13 +#> x[1,8] -1.8 -0.8 0.5 -0.7 0.9 1.07 7 13 #> x[2,8] -1.1 0.2 1.4 0.2 0.8 1.71 13 13 -#> x[1,9] -1.3 -0.2 0.7 -0.2 0.6 1.15 8 13 -#> x[2,9] -1.2 0.5 1.2 0.2 0.9 2.06 9 13 -#> x[1,10] -1.4 -0.7 0.2 -0.7 0.6 1.48 5 13 -#> x[2,10] -1.0 -0.4 0.3 -0.4 0.4 0.99 13 13 -#> Z[1,1] -3.6 0.3 3.6 0.2 2.4 2.06 13 13 -#> Z[2,1] -0.5 0.5 1.4 0.3 0.7 0.95 13 13 -#> Z[3,1] -1.5 -0.5 1.0 -0.4 0.9 1.87 4 13 +#> x[1,9] -1.6 -0.2 0.7 -0.3 0.7 1.15 8 13 +#> x[2,9] -1.2 0.5 1.2 0.2 0.8 1.71 9 13 +#> x[1,10] -1.4 -0.8 0.2 -0.7 0.6 1.48 4 13 +#> x[2,10] -1.0 -0.3 0.3 -0.4 0.4 1.03 13 13 +#> Z[1,1] -3.6 0.6 3.6 0.2 2.4 2.06 13 13 +#> Z[2,1] -0.5 0.5 1.4 0.3 0.6 0.94 13 13 +#> Z[3,1] -1.5 -0.5 0.8 -0.4 0.9 1.87 4 13 #> Z[4,1] -0.8 0.1 1.9 0.4 0.9 1.20 6 13 #> Z[1,2] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 #> Z[2,2] -4.2 1.0 6.2 0.6 3.9 1.18 13 13 -#> Z[3,2] -1.7 -0.7 0.5 -0.6 0.8 1.06 8 13 -#> Z[4,2] -1.2 0.9 1.8 0.6 1.1 0.97 13 13 -#> log_lik[1] -4.3 -1.5 -0.6 -2.0 1.5 1.87 4 13 -#> log_lik[2] -4.3 -1.3 -0.6 -1.9 1.4 1.87 4 13 +#> Z[3,2] -1.3 -0.7 0.5 -0.6 0.7 1.03 10 13 +#> Z[4,2] -1.2 0.8 1.9 0.6 1.1 0.92 13 13 +#> log_lik[1] -4.3 -1.5 -0.7 -2.0 1.4 1.87 4 13 +#> log_lik[2] -4.3 -1.3 -0.6 -1.9 1.4 1.71 4 13 #> log_lik[3] -4.3 -1.2 -0.6 -1.9 1.5 2.06 4 13 -#> log_lik[4] -4.3 -1.1 -0.5 -2.0 1.5 2.06 4 13 -#> log_lik[5] -4.3 -1.2 -0.8 -2.0 1.4 2.06 4 13 -#> log_lik[6] -4.3 -1.3 -0.6 -2.0 1.4 1.71 4 13 -#> log_lik[7] -4.3 -1.3 -0.6 -2.0 1.4 1.87 4 13 -#> log_lik[8] -4.7 -1.4 -0.5 -2.3 1.8 1.87 4 13 -#> log_lik[9] -5.7 -3.5 -2.2 -3.6 1.3 0.98 13 13 +#> log_lik[4] -4.3 -1.1 -0.6 -2.0 1.5 2.06 4 13 +#> log_lik[5] -4.3 -1.2 -0.7 -2.0 1.4 2.06 3 13 +#> log_lik[6] -4.3 -1.3 -0.5 -2.0 1.5 1.71 4 13 +#> log_lik[7] -4.3 -1.6 -0.6 -2.0 1.4 1.71 4 13 +#> log_lik[8] -4.7 -1.4 -0.6 -2.3 1.7 1.87 4 13 +#> log_lik[9] -4.8 -3.6 -2.2 -3.6 1.0 0.96 13 13 #> log_lik[10] -4.3 -2.2 -0.5 -2.5 1.5 1.24 5 13 -#> log_lik[11] -4.3 -2.1 -0.6 -2.5 1.4 1.32 4 13 -#> log_lik[12] -4.3 -1.6 -0.6 -2.1 1.4 1.47 4 13 +#> log_lik[11] -4.3 -2.1 -0.8 -2.5 1.3 1.32 4 13 +#> log_lik[12] -4.3 -1.6 -0.5 -2.2 1.4 1.38 4 13 #> log_lik[13] -4.3 -1.4 -0.6 -2.1 1.5 1.87 4 13 #> log_lik[14] -4.3 -1.5 -0.5 -2.0 1.5 1.87 4 13 #> log_lik[15] -4.3 -1.5 -0.6 -2.0 1.4 2.06 3 13 #> log_lik[16] -4.3 -1.5 -0.6 -2.2 1.5 1.87 4 13 #> log_lik[17] -4.3 -1.3 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[18] -4.4 -2.0 -0.5 -2.1 1.5 2.06 3 13 -#> log_lik[19] -4.3 -1.9 -0.6 -2.1 1.4 2.06 4 13 +#> log_lik[18] -4.4 -2.0 -0.4 -2.1 1.5 2.06 3 13 +#> log_lik[19] -4.3 -1.9 -0.5 -2.1 1.4 2.06 4 13 #> log_lik[20] -4.3 -1.7 -0.5 -2.0 1.4 2.06 4 13 -#> log_lik[21] -4.3 -1.1 -0.5 -1.9 1.5 2.06 3 13 -#> log_lik[22] -4.3 -1.2 -0.6 -1.9 1.4 2.06 4 13 -#> log_lik[23] -4.3 -1.3 -0.7 -1.9 1.4 1.87 4 13 +#> log_lik[21] -4.3 -1.1 -0.4 -1.9 1.5 2.06 3 13 +#> log_lik[22] -4.3 -1.2 -0.6 -1.9 1.5 2.06 4 13 +#> log_lik[23] -4.3 -1.0 -0.5 -1.8 1.5 2.06 4 13 #> log_lik[24] -4.3 -1.3 -0.7 -1.9 1.4 2.06 4 13 -#> log_lik[25] -4.4 -2.2 -0.6 -2.3 1.6 1.87 4 13 +#> log_lik[25] -4.4 -1.2 -0.5 -2.2 1.6 2.06 4 13 #> log_lik[26] -4.3 -1.5 -0.7 -2.1 1.4 1.58 4 13 -#> log_lik[27] -4.3 -1.6 -0.6 -2.1 1.4 2.06 4 13 -#> log_lik[28] -4.3 -1.5 -0.9 -2.1 1.4 2.06 4 13 -#> log_lik[29] -4.3 -1.5 -0.9 -2.3 1.3 1.47 4 13 -#> log_lik[30] -4.3 -1.3 -0.7 -2.0 1.4 1.71 4 13 +#> log_lik[27] -4.3 -1.6 -0.5 -2.0 1.5 2.06 4 13 +#> log_lik[28] -4.3 -1.5 -0.7 -2.0 1.4 2.06 4 13 +#> log_lik[29] -4.3 -1.5 -0.5 -2.2 1.4 1.45 4 13 +#> log_lik[30] -4.3 -1.3 -0.5 -2.0 1.4 1.71 4 13 #> log_lik[31] -4.3 -1.1 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[32] -4.3 -1.4 -0.6 -1.9 1.4 1.87 4 13 -#> log_lik[33] -4.3 -1.7 -1.0 -2.2 1.2 1.58 4 13 +#> log_lik[32] -4.3 -1.4 -0.5 -1.9 1.4 1.87 4 13 +#> log_lik[33] -4.3 -1.6 -0.5 -2.1 1.3 1.71 4 13 #> log_lik[34] -4.3 -1.6 -0.7 -2.1 1.4 2.06 4 13 -#> log_lik[35] -4.3 -1.0 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[36] -4.3 -1.0 -0.6 -1.9 1.5 2.06 4 13 -#> log_lik[37] -4.3 -2.0 -0.7 -2.1 1.4 2.06 4 13 -#> log_lik[38] -4.3 -1.2 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[39] -4.3 -1.7 -0.6 -2.0 1.3 1.87 4 13 -#> log_lik[40] -4.3 -1.3 -0.6 -2.0 1.4 2.06 4 13 -#> xstar[1,1] -2.1 -0.5 1.3 -0.6 1.2 1.00 9 13 -#> xstar[2,1] -2.0 -0.4 1.2 -0.3 1.2 1.12 8 13 +#> log_lik[35] -4.3 -1.0 -0.4 -1.8 1.5 2.06 3 13 +#> log_lik[36] -4.3 -1.6 -0.6 -1.9 1.4 1.71 4 13 +#> log_lik[37] -4.3 -2.0 -0.7 -2.2 1.4 1.87 4 13 +#> log_lik[38] -4.3 -1.2 -0.4 -1.8 1.5 2.06 3 13 +#> log_lik[39] -4.3 -1.4 -0.5 -2.0 1.4 1.87 4 13 +#> log_lik[40] -4.3 -1.2 -0.7 -2.0 1.4 2.06 4 13 +#> xstar[1,1] -2.1 -0.8 1.3 -0.6 1.2 0.96 10 13 +#> xstar[2,1] -1.7 -0.4 1.2 -0.3 1.1 1.25 6 13 #> sigma[1] 0.6 1.0 29.7 7.5 11.8 2.06 3 13 -#> lp__ -203.1 -43.1 -19.4 -78.8 72.9 2.06 3 13 +#> lp__ -203.1 -43.1 -17.1 -78.4 73.2 2.06 3 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 diff --git a/docs/reference/dfa_trends.html b/docs/reference/dfa_trends.html index fee2c6c..4e31c19 100644 --- a/docs/reference/dfa_trends.html +++ b/docs/reference/dfa_trends.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -113,8 +113,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds. +#> Chain 1: Gradient evaluation took 3.6e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -139,9 +139,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004706 seconds (Warm-up) -#> Chain 1: 0.005915 seconds (Sampling) -#> Chain 1: 0.010621 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.005 seconds (Sampling) +#> Chain 1: 0.009 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low diff --git a/docs/reference/find_dfa_trends.html b/docs/reference/find_dfa_trends.html index 3227cf2..300f575 100644 --- a/docs/reference/find_dfa_trends.html +++ b/docs/reference/find_dfa_trends.html @@ -18,7 +18,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -153,8 +153,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6.8e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds. +#> Chain 1: Gradient evaluation took 5.2e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.52 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -179,9 +179,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003748 seconds (Warm-up) -#> Chain 1: 0.242068 seconds (Sampling) -#> Chain 1: 0.245816 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.247 seconds (Sampling) +#> Chain 1: 0.25 seconds (Total) #> Chain 1: #> Warning: There were 5 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup @@ -297,8 +297,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.8e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds. +#> Chain 1: Gradient evaluation took 4.5e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -323,9 +323,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.018711 seconds (Warm-up) -#> Chain 1: 0.020826 seconds (Sampling) -#> Chain 1: 0.039537 seconds (Total) +#> Chain 1: Elapsed Time: 0.018 seconds (Warm-up) +#> Chain 1: 0.021 seconds (Sampling) +#> Chain 1: 0.039 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low diff --git a/docs/reference/find_inverted_chains.html b/docs/reference/find_inverted_chains.html index 072bf55..00eaef4 100644 --- a/docs/reference/find_inverted_chains.html +++ b/docs/reference/find_inverted_chains.html @@ -18,7 +18,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -115,8 +115,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds. +#> Chain 1: Gradient evaluation took 4e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -136,15 +136,15 @@

Examples

#> Chain 1: Iteration: 27 / 30 [ 90%] (Sampling) #> Chain 1: Iteration: 30 / 30 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002599 seconds (Warm-up) -#> Chain 1: 0.007209 seconds (Sampling) -#> Chain 1: 0.009808 seconds (Total) +#> Chain 1: Elapsed Time: 0.002 seconds (Warm-up) +#> Chain 1: 0.007 seconds (Sampling) +#> Chain 1: 0.009 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 4.6e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds. +#> Chain 2: Gradient evaluation took 0.000729 seconds +#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 7.29 seconds. #> Chain 2: Adjust your expectations accordingly! #> Chain 2: #> Chain 2: @@ -164,9 +164,9 @@

Examples

#> Chain 2: Iteration: 27 / 30 [ 90%] (Sampling) #> Chain 2: Iteration: 30 / 30 [100%] (Sampling) #> Chain 2: -#> Chain 2: Elapsed Time: 0.002685 seconds (Warm-up) -#> Chain 2: 0.004633 seconds (Sampling) -#> Chain 2: 0.007318 seconds (Total) +#> Chain 2: Elapsed Time: 0.002 seconds (Warm-up) +#> Chain 2: 0.004 seconds (Sampling) +#> Chain 2: 0.006 seconds (Total) #> Chain 2: #> Warning: There were 2 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low diff --git a/docs/reference/find_regimes.html b/docs/reference/find_regimes.html index ba00d80..9c312bc 100644 --- a/docs/reference/find_regimes.html +++ b/docs/reference/find_regimes.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -138,8 +138,8 @@

Examples

#> #> SAMPLING FOR MODEL 'regime_1' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.5e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.15 seconds. +#> Chain 1: Gradient evaluation took 1.2e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -164,9 +164,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.001218 seconds (Warm-up) -#> Chain 1: 0.000924 seconds (Sampling) -#> Chain 1: 0.002142 seconds (Total) +#> Chain 1: Elapsed Time: 0.001 seconds (Warm-up) +#> Chain 1: 0 seconds (Sampling) +#> Chain 1: 0.001 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is 1.43, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -182,8 +182,8 @@

Examples

#> #> SAMPLING FOR MODEL 'hmm_gaussian' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000122 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.22 seconds. +#> Chain 1: Gradient evaluation took 0.000112 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -208,9 +208,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.33669 seconds (Warm-up) -#> Chain 1: 0.321606 seconds (Sampling) -#> Chain 1: 0.658296 seconds (Total) +#> Chain 1: Elapsed Time: 0.403 seconds (Warm-up) +#> Chain 1: 0.266 seconds (Sampling) +#> Chain 1: 0.669 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is NA, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -226,7 +226,7 @@

Examples

#> $table #> regimes looic #> 1 1 -49.71780 -#> 2 2 19.44365 +#> 2 2 17.57427 #> #> $best_model #> $best_model$model @@ -439,7 +439,7 @@

Examples

#> log_lik[100] 0.17 0.02 0.09 -0.05 0.13 0.19 0.24 0.28 25 0.96 #> lp__ 114.02 0.15 0.74 112.57 113.57 114.22 114.57 114.94 25 1.09 #> -#> Samples were drawn using NUTS(diag_e) at Thu Jun 15 20:34:28 2023. +#> Samples were drawn using NUTS(diag_e) at Fri Jan 12 07:11:15 2024. #> For each parameter, n_eff is a crude measure of effective sample size, #> and Rhat is the potential scale reduction factor on split chains (at #> convergence, Rhat=1). diff --git a/docs/reference/find_swans-2.png b/docs/reference/find_swans-2.png index ba0275e..31b9d94 100644 Binary files a/docs/reference/find_swans-2.png and b/docs/reference/find_swans-2.png differ diff --git a/docs/reference/find_swans-3.png b/docs/reference/find_swans-3.png index ef6f6a9..bc3c9ee 100644 Binary files a/docs/reference/find_swans-3.png and b/docs/reference/find_swans-3.png differ diff --git a/docs/reference/find_swans.html b/docs/reference/find_swans.html index feacef6..318d30c 100644 --- a/docs/reference/find_swans.html +++ b/docs/reference/find_swans.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -127,8 +127,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds. +#> Chain 1: Gradient evaluation took 4.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -153,9 +153,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.240815 seconds (Warm-up) -#> Chain 1: 0.002819 seconds (Sampling) -#> Chain 1: 0.243634 seconds (Total) +#> Chain 1: Elapsed Time: 0.264 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.266 seconds (Total) #> Chain 1: #> Warning: There were 25 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup @@ -173,132 +173,132 @@

Examples

#> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> #> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -1.3 -1.3 -1.3 -1.3 0.0 1.00 13 13 +#> x[1,1] -1.2 -1.2 -1.2 -1.2 0.0 1.00 13 13 #> x[1,2] -1.9 -1.9 -1.9 -1.9 0.0 1.00 13 13 -#> x[1,3] -2.2 -2.2 -2.2 -2.2 0.0 1.00 13 13 +#> x[1,3] -1.9 -1.9 -1.9 -1.9 0.0 1.00 13 13 #> x[1,4] -2.4 -2.4 -2.4 -2.4 0.0 1.00 13 13 -#> x[1,5] -2.7 -2.7 -2.7 -2.7 0.0 1.00 13 13 -#> x[1,6] -2.1 -2.1 -2.1 -2.1 0.0 1.00 13 13 -#> x[1,7] -2.1 -2.1 -2.1 -2.1 0.0 1.00 13 13 -#> x[1,8] -2.3 -2.3 -2.3 -2.3 0.0 1.00 13 13 -#> x[1,9] -2.1 -2.1 -2.1 -2.1 0.0 1.00 13 13 -#> x[1,10] -1.8 -1.8 -1.8 -1.8 0.0 1.00 13 13 -#> x[1,11] -1.8 -1.8 -1.8 -1.8 0.0 1.00 13 13 -#> x[1,12] -1.4 -1.4 -1.4 -1.4 0.0 1.00 13 13 -#> x[1,13] -1.1 -1.1 -1.1 -1.1 0.0 1.00 13 13 -#> x[1,14] -0.8 -0.8 -0.8 -0.8 0.0 1.00 13 13 -#> x[1,15] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> x[1,16] -0.7 -0.7 -0.7 -0.7 0.0 1.00 13 13 -#> x[1,17] -1.0 -1.0 -1.0 -1.0 0.0 1.00 13 13 +#> x[1,5] -2.2 -2.2 -2.2 -2.2 0.0 1.00 13 13 +#> x[1,6] -1.8 -1.8 -1.8 -1.8 0.0 1.00 13 13 +#> x[1,7] -1.5 -1.5 -1.5 -1.5 0.0 1.00 13 13 +#> x[1,8] -1.7 -1.7 -1.7 -1.7 0.0 1.00 13 13 +#> x[1,9] -1.4 -1.4 -1.4 -1.4 0.0 1.00 13 13 +#> x[1,10] -1.7 -1.7 -1.7 -1.7 0.0 1.00 13 13 +#> x[1,11] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 +#> x[1,12] -1.5 -1.5 -1.5 -1.5 0.0 1.00 13 13 +#> x[1,13] -1.3 -1.3 -1.3 -1.3 0.0 1.00 13 13 +#> x[1,14] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 +#> x[1,15] 0.3 0.3 0.3 0.3 0.0 1.00 13 13 +#> x[1,16] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 +#> x[1,17] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 #> x[1,18] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 -#> x[1,19] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> x[1,20] 0.2 0.2 0.2 0.2 0.0 1.00 13 13 -#> x[1,21] 1.3 1.3 1.3 1.3 0.0 1.00 13 13 -#> x[1,22] 1.1 1.1 1.1 1.1 0.0 1.00 13 13 -#> x[1,23] 0.8 0.8 0.8 0.8 0.0 1.00 13 13 -#> x[1,24] 1.8 1.8 1.8 1.8 0.0 1.00 13 13 -#> x[1,25] 1.9 1.9 1.9 1.9 0.0 1.00 13 13 -#> x[1,26] 3.1 3.1 3.1 3.1 0.0 1.00 13 13 -#> x[1,27] 4.1 4.1 4.1 4.1 0.0 1.00 13 13 -#> x[1,28] 4.9 4.9 4.9 4.9 0.0 1.00 13 13 -#> x[1,29] 5.5 5.5 5.5 5.5 0.0 1.00 13 13 -#> x[1,30] 5.5 5.5 5.5 5.5 0.0 1.00 13 13 -#> Z[1,1] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> Z[2,1] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> Z[3,1] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[1] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> log_lik[2] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[3] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[4] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 -#> log_lik[5] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[6] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[7] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[8] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[9] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[10] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> log_lik[11] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[12] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[13] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[14] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[15] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[16] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 +#> x[1,19] 0.5 0.5 0.5 0.5 0.0 1.00 13 13 +#> x[1,20] 0.4 0.4 0.4 0.4 0.0 1.00 13 13 +#> x[1,21] 0.6 0.6 0.6 0.6 0.0 1.00 13 13 +#> x[1,22] 0.2 0.2 0.2 0.2 0.0 1.00 13 13 +#> x[1,23] 0.4 0.4 0.4 0.4 0.0 1.00 13 13 +#> x[1,24] 1.4 1.4 1.4 1.4 0.0 1.00 13 13 +#> x[1,25] 1.7 1.7 1.7 1.7 0.0 1.00 13 13 +#> x[1,26] 2.0 2.0 2.0 2.0 0.0 1.00 13 13 +#> x[1,27] 2.8 2.8 2.8 2.8 0.0 1.00 13 13 +#> x[1,28] 3.1 3.1 3.1 3.1 0.0 1.00 13 13 +#> x[1,29] 4.2 4.2 4.2 4.2 0.0 1.00 13 13 +#> x[1,30] 4.5 4.5 4.5 4.5 0.0 1.00 13 13 +#> Z[1,1] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 +#> Z[2,1] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 +#> Z[3,1] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 +#> log_lik[1] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[2] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[3] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[4] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[5] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[6] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[7] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[8] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[9] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[10] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[11] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[12] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[13] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 +#> log_lik[14] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 +#> log_lik[15] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[16] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 #> log_lik[17] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 #> log_lik[18] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[19] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[20] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[21] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[22] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[23] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[24] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[25] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[26] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[27] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[19] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[20] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[21] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[22] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[23] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[24] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[25] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[26] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[27] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 #> log_lik[28] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 #> log_lik[29] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[30] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[31] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[32] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[33] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[34] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[35] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[36] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[37] -0.7 -0.7 -0.7 -0.7 0.0 1.00 13 13 -#> log_lik[38] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[39] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 -#> log_lik[40] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 -#> log_lik[41] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[30] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[31] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 +#> log_lik[32] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 +#> log_lik[33] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 +#> log_lik[34] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[35] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[36] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[37] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[38] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[39] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[40] -0.7 -0.7 -0.7 -0.7 0.0 1.00 13 13 +#> log_lik[41] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 #> log_lik[42] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[43] -22.6 -22.6 -22.6 -22.6 0.0 1.00 13 13 -#> log_lik[44] -0.5 -0.5 -0.5 -0.5 0.0 1.00 13 13 -#> log_lik[45] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> log_lik[46] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[47] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[48] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[49] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[50] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[51] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[52] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[53] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[54] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[55] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[56] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[57] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[58] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[59] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> log_lik[60] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[61] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[62] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[63] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[64] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 +#> log_lik[43] -24.8 -24.8 -24.8 -24.8 0.0 1.00 13 13 +#> log_lik[44] -1.8 -1.8 -1.8 -1.8 0.0 1.00 13 13 +#> log_lik[45] -1.4 -1.4 -1.4 -1.4 0.0 1.00 13 13 +#> log_lik[46] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[47] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[48] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[49] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[50] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[51] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[52] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[53] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[54] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[55] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 +#> log_lik[56] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[57] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[58] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[59] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[60] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[61] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[62] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[63] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 +#> log_lik[64] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 #> log_lik[65] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[66] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[67] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[66] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[67] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 #> log_lik[68] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 #> log_lik[69] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[70] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[71] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[72] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[73] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[74] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[75] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[76] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[77] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[78] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[79] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[80] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[81] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[82] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 -#> log_lik[83] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[84] -0.4 -0.4 -0.4 -0.4 0.0 1.00 13 13 -#> log_lik[85] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> log_lik[86] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[87] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 -#> log_lik[88] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[89] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 -#> log_lik[90] -0.2 -0.2 -0.2 -0.2 0.0 1.00 13 13 -#> xstar[1,1] 4.1 5.8 7.8 5.9 1.3 1.07 13 13 -#> sigma[1] 0.4 0.4 0.4 0.4 0.0 1.00 13 13 -#> lp__ -29.7 -29.7 -29.7 -29.7 0.0 1.00 13 13 +#> log_lik[70] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[71] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[72] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[73] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[74] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[75] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[76] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[77] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[78] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 +#> log_lik[79] -0.3 -0.3 -0.3 -0.3 0.0 1.00 13 13 +#> log_lik[80] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[81] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[82] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[83] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[84] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 +#> log_lik[85] -0.6 -0.6 -0.6 -0.6 0.0 1.00 13 13 +#> log_lik[86] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[87] 0.1 0.1 0.1 0.1 0.0 1.00 13 13 +#> log_lik[88] -2.2 -2.2 -2.2 -2.2 0.0 1.00 13 13 +#> log_lik[89] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> log_lik[90] -0.1 -0.1 -0.1 -0.1 0.0 1.00 13 13 +#> xstar[1,1] 2.8 4.3 5.0 4.1 0.8 0.95 13 13 +#> sigma[1] 0.3 0.3 0.3 0.3 0.0 1.00 13 13 +#> lp__ -26.5 -26.5 -26.5 -26.5 0.0 1.00 13 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 diff --git a/docs/reference/fit_dfa.html b/docs/reference/fit_dfa.html index b8207a1..58c67f6 100644 --- a/docs/reference/fit_dfa.html +++ b/docs/reference/fit_dfa.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -110,7 +110,8 @@

Fit a Bayesian DFA

par_list = NULL, family = "gaussian", verbose = FALSE, - weights = NULL, + inv_var_weights = NULL, + likelihood_weights = NULL, gp_theta_prior = c(3, 1), expansion_prior = FALSE, ... @@ -278,10 +279,20 @@

Arguments

Whether to print iterations and information from Stan, defaults to FALSE.

-
weights
-

Optional name of "weights" argument in data frame. This is only implemented when data -are in long format. If not entered, defaults to weights = 1 for all observations. The implementation of weights -varies slightly by family: Gaussian family models use -log(w_i) in the dispersion formula

+
inv_var_weights
+

Optional name of inverse variance weights argument in data frame. This is only implemented when data +are in long format. If not entered, defaults to inv_var_weights = 1 for all observations. The implementation of inv_var_weights +relies on inverse variance weightings, so that if you have standard errors associated with each observation, +the inverse variance weights are calculated as inv_var_weights <- 1 / (standard_errors^2) . The observation error sigma +in the likelihood then becomes sigma / sqrt(inv_var_weights)

+ + +
likelihood_weights
+

Optional name of likelihood weights argument in data frame. These +are used in the same way weights are implemented in packages glmmTMB, brms, sdmTMB, etc. +Weights are used as multipliers on the log-likelihood, with higher weights allowing observations +to contribute more. Currently only implemented with univariate distributions, when data is in long +format

gp_theta_prior
@@ -319,8 +330,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. +#> Chain 1: Gradient evaluation took 3.5e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -345,9 +356,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006447 seconds (Warm-up) -#> Chain 1: 0.107739 seconds (Sampling) -#> Chain 1: 0.114186 seconds (Total) +#> Chain 1: Elapsed Time: 0.006 seconds (Warm-up) +#> Chain 1: 0.109 seconds (Sampling) +#> Chain 1: 0.115 seconds (Total) #> Chain 1: #> Warning: There were 16 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup diff --git a/docs/reference/fit_regimes.html b/docs/reference/fit_regimes.html index 226f6c1..5541bd2 100644 --- a/docs/reference/fit_regimes.html +++ b/docs/reference/fit_regimes.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -133,8 +133,8 @@

Examples

#> #> SAMPLING FOR MODEL 'regime_1' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 7e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -159,9 +159,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.001149 seconds (Warm-up) -#> Chain 1: 0.001079 seconds (Sampling) -#> Chain 1: 0.002228 seconds (Total) +#> Chain 1: Elapsed Time: 0.001 seconds (Warm-up) +#> Chain 1: 0.001 seconds (Sampling) +#> Chain 1: 0.002 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is 1.52, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -383,7 +383,7 @@

Examples

#> log_lik[100] 0.16 0.03 0.13 -0.05 0.06 0.15 0.27 0.38 17 0.97 #> lp__ 113.34 0.44 1.19 111.43 112.13 113.48 114.37 114.92 7 1.50 #> -#> Samples were drawn using NUTS(diag_e) at Thu Jun 15 20:34:33 2023. +#> Samples were drawn using NUTS(diag_e) at Fri Jan 12 07:11:21 2024. #> For each parameter, n_eff is a crude measure of effective sample size, #> and Rhat is the potential scale reduction factor on split chains (at #> convergence, Rhat=1). diff --git a/docs/reference/hmm_init.html b/docs/reference/hmm_init.html index 985b313..9cf2a80 100644 --- a/docs/reference/hmm_init.html +++ b/docs/reference/hmm_init.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/index.html b/docs/reference/index.html index bbc6b81..5cf72c7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/invert_chains.html b/docs/reference/invert_chains.html index b20bff6..96157ee 100644 --- a/docs/reference/invert_chains.html +++ b/docs/reference/invert_chains.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/is_converged.html b/docs/reference/is_converged.html index 8e57bc9..c6c9948 100644 --- a/docs/reference/is_converged.html +++ b/docs/reference/is_converged.html @@ -18,7 +18,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/loo.html b/docs/reference/loo.html index cccf1a6..16731d2 100644 --- a/docs/reference/loo.html +++ b/docs/reference/loo.html @@ -27,7 +27,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -125,8 +125,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. +#> Chain 1: Gradient evaluation took 3.8e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -151,11 +151,11 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006716 seconds (Warm-up) -#> Chain 1: 0.328732 seconds (Sampling) -#> Chain 1: 0.335448 seconds (Total) +#> Chain 1: Elapsed Time: 0.006 seconds (Warm-up) +#> Chain 1: 0.252 seconds (Sampling) +#> Chain 1: 0.258 seconds (Total) #> Chain 1: -#> Warning: There were 2 divergent transitions after warmup. See +#> Warning: There were 4 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them. #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See @@ -173,92 +173,92 @@

Examples

#> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> #> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -2.1 -1.6 -0.5 -1.4 0.6 1.71 9 13 -#> x[1,2] -1.8 -1.2 -0.8 -1.2 0.4 0.94 13 13 -#> x[1,3] -1.6 -1.3 -0.6 -1.2 0.4 0.95 13 13 -#> x[1,4] -1.5 -0.5 0.0 -0.6 0.5 0.91 13 13 -#> x[1,5] -0.5 0.3 0.7 0.2 0.5 1.58 5 13 -#> x[1,6] 0.6 0.8 1.3 0.9 0.3 0.98 13 13 -#> x[1,7] 0.8 1.5 2.3 1.5 0.5 1.01 13 13 -#> x[1,8] 0.8 1.7 2.4 1.6 0.6 1.10 13 13 -#> x[1,9] 0.3 0.9 1.6 0.9 0.5 1.00 13 13 -#> x[1,10] 0.2 0.9 1.3 0.8 0.4 0.94 13 13 -#> x[1,11] -0.3 0.5 0.7 0.4 0.4 1.25 7 13 -#> x[1,12] -0.4 1.1 1.8 0.9 0.7 1.12 8 13 -#> x[1,13] -0.2 0.5 1.0 0.4 0.4 1.24 13 13 -#> x[1,14] 0.1 0.5 1.2 0.6 0.4 1.00 13 13 -#> x[1,15] -1.7 -0.9 -0.3 -1.0 0.5 1.06 13 13 -#> x[1,16] -1.5 -0.6 -0.2 -0.6 0.4 1.19 11 13 -#> x[1,17] -1.6 -0.5 0.0 -0.7 0.6 1.00 13 13 -#> x[1,18] -1.1 -0.3 0.6 -0.3 0.6 0.93 13 13 -#> x[1,19] -0.9 -0.1 0.8 0.0 0.6 1.15 10 13 -#> x[1,20] -0.1 0.6 1.5 0.7 0.6 1.01 13 13 -#> Z[1,1] -1.1 -0.8 -0.5 -0.8 0.2 1.01 13 13 -#> Z[2,1] -0.1 0.1 0.5 0.2 0.2 0.96 13 13 -#> Z[3,1] -1.0 -0.9 -0.5 -0.8 0.2 1.21 12 13 -#> log_lik[1] -3.1 -1.8 -0.7 -1.8 0.8 1.71 4 13 -#> log_lik[2] -2.1 -1.5 -0.7 -1.4 0.5 0.96 13 13 -#> log_lik[3] -2.4 -1.2 -0.6 -1.4 0.7 1.58 4 13 -#> log_lik[4] -1.3 -0.7 -0.6 -0.8 0.2 0.96 13 13 -#> log_lik[5] -3.0 -2.2 -1.7 -2.2 0.5 1.18 13 13 -#> log_lik[6] -1.2 -0.8 -0.5 -0.8 0.2 1.12 13 13 -#> log_lik[7] -1.1 -0.8 -0.5 -0.8 0.2 0.96 13 13 -#> log_lik[8] -1.0 -0.8 -0.5 -0.8 0.2 1.19 13 13 -#> log_lik[9] -1.1 -0.8 -0.6 -0.8 0.2 0.93 9 13 -#> log_lik[10] -1.3 -1.0 -0.6 -1.0 0.3 0.94 13 13 -#> log_lik[11] -0.8 -0.7 -0.5 -0.7 0.1 0.97 13 13 -#> log_lik[12] -1.2 -0.8 -0.5 -0.9 0.2 0.97 13 13 -#> log_lik[13] -1.1 -0.8 -0.6 -0.8 0.2 1.48 5 13 -#> log_lik[14] -1.4 -1.2 -1.0 -1.2 0.2 1.07 13 13 -#> log_lik[15] -0.9 -0.8 -0.6 -0.8 0.1 0.95 13 13 -#> log_lik[16] -1.1 -0.8 -0.5 -0.8 0.2 1.16 9 13 -#> log_lik[17] -2.5 -1.9 -1.4 -2.0 0.4 1.25 13 13 -#> log_lik[18] -0.9 -0.8 -0.6 -0.7 0.1 1.58 4 13 -#> log_lik[19] -2.1 -1.1 -0.5 -1.2 0.6 0.97 13 13 -#> log_lik[20] -0.9 -0.7 -0.5 -0.7 0.1 0.97 13 13 -#> log_lik[21] -1.5 -0.7 -0.5 -0.8 0.5 0.95 13 13 -#> log_lik[22] -1.5 -0.8 -0.5 -0.9 0.3 1.04 12 13 -#> log_lik[23] -1.5 -1.0 -0.6 -1.0 0.3 0.91 13 13 -#> log_lik[24] -1.7 -0.9 -0.6 -1.1 0.4 1.39 5 13 -#> log_lik[25] -1.8 -0.8 -0.6 -0.9 0.4 0.99 13 13 -#> log_lik[26] -2.2 -1.4 -1.1 -1.5 0.4 0.98 13 13 -#> log_lik[27] -1.2 -0.7 -0.5 -0.8 0.3 1.37 8 13 -#> log_lik[28] -1.1 -0.8 -0.5 -0.8 0.2 1.08 10 13 -#> log_lik[29] -1.9 -1.2 -1.0 -1.3 0.3 0.98 13 13 -#> log_lik[30] -1.0 -0.7 -0.5 -0.7 0.2 1.13 12 13 -#> log_lik[31] -0.9 -0.8 -0.6 -0.8 0.1 0.93 13 13 -#> log_lik[32] -0.8 -0.7 -0.5 -0.7 0.1 0.99 13 13 -#> log_lik[33] -0.9 -0.7 -0.5 -0.7 0.1 1.09 12 13 -#> log_lik[34] -1.6 -0.8 -0.5 -0.9 0.4 1.16 13 13 -#> log_lik[35] -2.0 -1.5 -1.1 -1.5 0.3 0.91 13 13 -#> log_lik[36] -2.0 -0.8 -0.5 -1.0 0.6 0.97 13 13 -#> log_lik[37] -1.0 -0.7 -0.6 -0.7 0.1 1.37 6 13 -#> log_lik[38] -1.0 -0.8 -0.6 -0.8 0.1 0.94 13 13 -#> log_lik[39] -1.2 -0.8 -0.5 -0.8 0.2 1.30 5 13 -#> log_lik[40] -1.1 -0.7 -0.5 -0.7 0.2 1.87 13 13 -#> log_lik[41] -2.2 -1.8 -1.3 -1.8 0.3 1.05 13 13 -#> log_lik[42] -1.0 -0.7 -0.6 -0.7 0.2 0.96 11 13 -#> log_lik[43] -2.4 -1.1 -0.9 -1.4 0.7 1.10 13 13 -#> log_lik[44] -5.3 -3.7 -2.6 -3.8 1.0 0.97 13 13 -#> log_lik[45] -2.6 -1.4 -0.9 -1.5 0.7 0.96 11 13 -#> log_lik[46] -2.2 -0.9 -0.6 -1.0 0.5 1.05 13 13 -#> log_lik[47] -1.3 -1.1 -0.7 -1.1 0.2 0.95 13 13 -#> log_lik[48] -1.3 -0.7 -0.6 -0.8 0.4 1.18 11 13 -#> log_lik[49] -1.6 -1.3 -0.6 -1.2 0.4 1.21 8 13 -#> log_lik[50] -0.9 -0.8 -0.6 -0.8 0.1 0.92 13 13 -#> log_lik[51] -1.6 -1.0 -0.7 -1.0 0.3 1.58 13 13 -#> log_lik[52] -1.3 -0.7 -0.5 -0.8 0.3 0.92 13 13 -#> log_lik[53] -6.0 -5.0 -3.6 -4.8 0.9 1.01 13 13 -#> log_lik[54] -2.2 -0.8 -0.7 -1.1 0.5 0.95 13 13 -#> log_lik[55] -1.7 -0.8 -0.6 -1.0 0.4 1.07 13 13 -#> log_lik[56] -1.1 -0.9 -0.6 -0.9 0.2 0.92 13 13 -#> log_lik[57] -1.2 -0.8 -0.6 -0.8 0.2 1.06 13 13 -#> log_lik[58] -1.4 -0.9 -0.6 -0.9 0.3 1.01 13 13 -#> log_lik[59] -1.1 -0.8 -0.6 -0.8 0.2 1.00 13 13 -#> log_lik[60] -2.0 -0.9 -0.7 -1.1 0.5 1.05 13 13 -#> xstar[1,1] -0.6 1.0 2.0 0.7 1.0 0.98 13 13 -#> sigma[1] 0.7 0.8 0.9 0.8 0.1 0.99 13 13 -#> lp__ -68.0 -64.4 -60.4 -64.5 2.6 2.06 4 13 +#> x[1,1] -2.1 -1.8 -1.5 -1.8 0.2 1.05 13 13 +#> x[1,2] -2.1 -1.3 -1.2 -1.6 0.3 1.18 6 13 +#> x[1,3] -1.6 -1.1 -0.7 -1.2 0.4 1.71 8 13 +#> x[1,4] -1.3 -0.8 -0.3 -0.8 0.4 1.21 13 13 +#> x[1,5] -0.3 -0.1 0.8 0.2 0.5 1.71 5 13 +#> x[1,6] 0.7 1.2 1.7 1.3 0.4 1.15 8 13 +#> x[1,7] 0.4 1.6 2.2 1.5 0.6 1.27 6 13 +#> x[1,8] 1.3 1.9 2.3 1.8 0.4 1.07 10 13 +#> x[1,9] 0.6 0.9 1.4 0.9 0.3 1.02 13 13 +#> x[1,10] 0.2 0.6 1.1 0.6 0.3 1.05 9 13 +#> x[1,11] -0.2 0.1 0.6 0.2 0.3 1.30 6 13 +#> x[1,12] -0.6 0.4 1.1 0.3 0.7 1.01 10 13 +#> x[1,13] 0.0 0.3 1.0 0.4 0.4 1.47 5 13 +#> x[1,14] -0.3 0.5 1.3 0.5 0.6 1.58 5 13 +#> x[1,15] -1.1 -0.8 -0.4 -0.8 0.2 1.01 13 13 +#> x[1,16] -0.9 -0.6 -0.1 -0.5 0.3 1.10 7 13 +#> x[1,17] -1.8 -1.3 0.0 -1.1 0.7 1.58 4 13 +#> x[1,18] -0.6 0.0 0.5 -0.1 0.4 0.93 13 13 +#> x[1,19] -1.1 -0.2 1.5 0.1 1.0 1.45 4 13 +#> x[1,20] -0.4 1.0 1.6 0.8 0.7 1.13 7 13 +#> Z[1,1] -1.0 -0.7 -0.4 -0.7 0.2 1.19 13 13 +#> Z[2,1] 0.0 0.3 0.4 0.2 0.1 2.06 9 13 +#> Z[3,1] -0.9 -0.7 -0.6 -0.7 0.1 1.87 4 13 +#> log_lik[1] -3.0 -1.4 -0.8 -1.6 0.8 0.93 13 13 +#> log_lik[2] -2.2 -1.1 -0.7 -1.2 0.5 2.06 8 13 +#> log_lik[3] -1.4 -1.0 -0.6 -1.0 0.3 1.87 4 13 +#> log_lik[4] -1.3 -0.7 -0.5 -0.8 0.3 1.47 5 13 +#> log_lik[5] -3.6 -1.7 -1.4 -2.1 0.8 1.47 4 13 +#> log_lik[6] -1.2 -0.6 -0.4 -0.7 0.3 1.18 6 13 +#> log_lik[7] -0.9 -0.7 -0.5 -0.7 0.1 1.00 7 13 +#> log_lik[8] -1.0 -0.7 -0.4 -0.7 0.2 1.20 7 13 +#> log_lik[9] -0.8 -0.6 -0.5 -0.7 0.1 2.06 4 13 +#> log_lik[10] -1.3 -0.7 -0.6 -0.8 0.3 1.21 7 13 +#> log_lik[11] -0.8 -0.6 -0.5 -0.6 0.1 1.71 4 13 +#> log_lik[12] -1.1 -0.7 -0.5 -0.7 0.2 1.47 5 13 +#> log_lik[13] -1.1 -0.6 -0.5 -0.7 0.2 2.06 4 13 +#> log_lik[14] -1.5 -1.2 -1.0 -1.2 0.2 1.33 6 13 +#> log_lik[15] -0.9 -0.7 -0.6 -0.7 0.1 1.16 13 13 +#> log_lik[16] -1.0 -0.7 -0.5 -0.7 0.2 1.33 5 13 +#> log_lik[17] -2.9 -1.6 -1.3 -1.8 0.6 1.71 4 13 +#> log_lik[18] -0.9 -0.6 -0.4 -0.6 0.2 1.71 4 13 +#> log_lik[19] -3.1 -0.8 -0.5 -1.4 1.1 1.27 6 13 +#> log_lik[20] -0.9 -0.7 -0.5 -0.7 0.2 1.37 8 13 +#> log_lik[21] -1.2 -0.8 -0.5 -0.8 0.3 1.12 13 13 +#> log_lik[22] -1.8 -0.9 -0.4 -1.0 0.5 1.45 4 13 +#> log_lik[23] -1.3 -0.9 -0.5 -0.8 0.3 1.21 9 13 +#> log_lik[24] -1.5 -0.7 -0.4 -0.8 0.4 1.87 4 13 +#> log_lik[25] -1.8 -0.7 -0.5 -0.9 0.5 1.71 6 13 +#> log_lik[26] -2.1 -1.6 -1.3 -1.7 0.3 1.09 8 13 +#> log_lik[27] -0.9 -0.6 -0.4 -0.6 0.2 1.58 4 13 +#> log_lik[28] -1.0 -0.7 -0.5 -0.7 0.2 1.39 5 13 +#> log_lik[29] -2.0 -1.3 -1.1 -1.4 0.4 1.10 11 13 +#> log_lik[30] -1.1 -0.7 -0.6 -0.8 0.2 1.87 6 13 +#> log_lik[31] -0.9 -0.6 -0.4 -0.6 0.2 1.58 4 13 +#> log_lik[32] -0.8 -0.6 -0.4 -0.6 0.1 1.87 4 13 +#> log_lik[33] -0.9 -0.6 -0.5 -0.6 0.2 1.71 4 13 +#> log_lik[34] -1.4 -0.7 -0.4 -0.8 0.4 1.18 6 13 +#> log_lik[35] -2.2 -1.4 -1.1 -1.5 0.4 1.09 8 13 +#> log_lik[36] -2.1 -0.9 -0.4 -1.0 0.6 1.18 6 13 +#> log_lik[37] -1.0 -0.6 -0.5 -0.7 0.2 1.71 4 13 +#> log_lik[38] -1.1 -0.8 -0.6 -0.8 0.2 1.71 4 13 +#> log_lik[39] -1.0 -0.6 -0.4 -0.7 0.2 2.06 4 13 +#> log_lik[40] -1.0 -0.8 -0.5 -0.8 0.2 1.19 8 13 +#> log_lik[41] -2.4 -1.8 -1.3 -1.9 0.4 0.96 13 13 +#> log_lik[42] -1.3 -0.7 -0.5 -0.8 0.3 1.87 4 13 +#> log_lik[43] -2.2 -1.6 -0.9 -1.5 0.5 0.92 13 13 +#> log_lik[44] -5.6 -4.4 -3.0 -4.3 0.9 1.47 5 13 +#> log_lik[45] -2.3 -1.7 -1.1 -1.7 0.4 0.99 12 13 +#> log_lik[46] -1.2 -0.8 -0.5 -0.8 0.2 1.01 13 13 +#> log_lik[47] -1.2 -1.1 -0.9 -1.1 0.1 0.98 10 13 +#> log_lik[48] -0.9 -0.6 -0.5 -0.7 0.1 1.19 6 13 +#> log_lik[49] -1.9 -0.9 -0.7 -1.1 0.5 1.87 6 13 +#> log_lik[50] -0.9 -0.8 -0.5 -0.7 0.1 1.09 13 13 +#> log_lik[51] -1.9 -0.8 -0.5 -1.0 0.5 1.39 5 13 +#> log_lik[52] -1.0 -0.6 -0.5 -0.7 0.2 1.33 6 13 +#> log_lik[53] -6.6 -5.1 -3.7 -5.3 1.1 1.71 4 13 +#> log_lik[54] -1.9 -1.0 -0.5 -1.1 0.5 0.96 10 13 +#> log_lik[55] -2.0 -0.7 -0.5 -1.0 0.6 2.06 4 13 +#> log_lik[56] -1.1 -0.8 -0.5 -0.8 0.2 0.94 13 13 +#> log_lik[57] -2.0 -1.0 -0.5 -1.1 0.5 1.19 6 13 +#> log_lik[58] -2.1 -0.7 -0.4 -0.9 0.8 1.45 5 13 +#> log_lik[59] -1.2 -0.7 -0.5 -0.8 0.3 1.00 8 13 +#> log_lik[60] -2.4 -0.9 -0.5 -1.1 0.8 1.47 5 13 +#> xstar[1,1] -1.2 0.5 2.8 0.5 1.4 1.19 8 13 +#> sigma[1] 0.6 0.7 0.9 0.7 0.1 1.87 4 13 +#> lp__ -68.1 -64.4 -60.4 -64.2 2.8 1.87 4 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 @@ -270,9 +270,9 @@

Examples

#> Computed from 25 by 60 log-likelihood matrix #> #> Estimate SE -#> elpd_loo -260.5 12.8 -#> p_loo 175.8 13.3 -#> looic 521.1 25.6 +#> elpd_loo -261.0 12.8 +#> p_loo 178.6 13.3 +#> looic 522.1 25.6 #> ------ #> Monte Carlo SE of elpd_loo is NA. #> @@ -280,8 +280,8 @@

Examples

#> Count Pct. Min. n_eff #> (-Inf, 0.5] (good) 42 70.0% 1 #> (0.5, 0.7] (ok) 3 5.0% 1 -#> (0.7, 1] (bad) 6 10.0% 1 -#> (1, Inf) (very bad) 9 15.0% 0 +#> (0.7, 1] (bad) 5 8.3% 1 +#> (1, Inf) (very bad) 10 16.7% 0 #> See help('pareto-k-diagnostic') for details. # } diff --git a/docs/reference/plot_fitted.html b/docs/reference/plot_fitted.html index 898440e..d28f840 100644 --- a/docs/reference/plot_fitted.html +++ b/docs/reference/plot_fitted.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -125,8 +125,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds. +#> Chain 1: Gradient evaluation took 4e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -151,9 +151,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007462 seconds (Warm-up) -#> Chain 1: 0.029935 seconds (Sampling) -#> Chain 1: 0.037397 seconds (Total) +#> Chain 1: Elapsed Time: 0.006 seconds (Warm-up) +#> Chain 1: 0.031 seconds (Sampling) +#> Chain 1: 0.037 seconds (Total) #> Chain 1: #> Warning: There were 19 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup diff --git a/docs/reference/plot_loadings-1.png b/docs/reference/plot_loadings-1.png index aa86113..b1f7c44 100644 Binary files a/docs/reference/plot_loadings-1.png and b/docs/reference/plot_loadings-1.png differ diff --git a/docs/reference/plot_loadings-2.png b/docs/reference/plot_loadings-2.png index 755e8c3..c451a80 100644 Binary files a/docs/reference/plot_loadings-2.png and b/docs/reference/plot_loadings-2.png differ diff --git a/docs/reference/plot_loadings-3.png b/docs/reference/plot_loadings-3.png index e8c9005..2367d93 100644 Binary files a/docs/reference/plot_loadings-3.png and b/docs/reference/plot_loadings-3.png differ diff --git a/docs/reference/plot_loadings-4.png b/docs/reference/plot_loadings-4.png index 758c746..3bca3f6 100644 Binary files a/docs/reference/plot_loadings-4.png and b/docs/reference/plot_loadings-4.png differ diff --git a/docs/reference/plot_loadings.html b/docs/reference/plot_loadings.html index 65d96fd..3e2caac 100644 --- a/docs/reference/plot_loadings.html +++ b/docs/reference/plot_loadings.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -136,8 +136,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds. +#> Chain 1: Gradient evaluation took 3.8e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -162,9 +162,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.031472 seconds (Warm-up) -#> Chain 1: 0.383423 seconds (Sampling) -#> Chain 1: 0.414895 seconds (Total) +#> Chain 1: Elapsed Time: 0.033 seconds (Warm-up) +#> Chain 1: 0.398 seconds (Sampling) +#> Chain 1: 0.431 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low @@ -181,78 +181,78 @@

Examples

#> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> #> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -1.5 -0.7 0.8 -0.6 0.8 1.37 6 13 +#> x[1,1] -1.5 -0.7 0.9 -0.5 0.8 1.37 6 13 #> x[2,1] -1.0 -0.2 0.6 -0.2 0.6 1.58 9 13 -#> x[1,2] -1.7 0.2 0.9 -0.3 1.1 2.06 4 13 -#> x[2,2] 0.2 0.5 1.2 0.6 0.4 1.16 12 13 -#> x[1,3] -1.6 0.0 0.8 -0.4 1.0 2.06 4 13 +#> x[1,2] -1.7 0.2 1.2 -0.3 1.2 2.06 4 13 +#> x[2,2] 0.2 0.5 1.2 0.6 0.4 1.03 12 13 +#> x[1,3] -1.6 0.0 1.0 -0.3 1.0 2.06 4 13 #> x[2,3] -1.4 -0.2 0.3 -0.4 0.6 2.06 4 13 #> x[1,4] -1.5 -0.4 0.7 -0.4 0.9 2.06 4 13 -#> x[2,4] -0.1 0.6 1.3 0.6 0.5 1.06 11 13 +#> x[2,4] -0.1 0.5 1.3 0.5 0.5 0.97 10 13 #> x[1,5] -0.7 -0.2 0.7 -0.1 0.5 0.95 11 13 #> x[2,5] -1.4 -0.6 1.5 -0.3 1.2 1.87 6 13 -#> x[1,6] -0.9 -0.3 0.3 -0.3 0.5 1.16 6 13 -#> x[2,6] -0.2 0.1 0.6 0.1 0.3 1.45 10 13 -#> x[1,7] -2.2 -1.2 0.3 -1.1 0.9 1.71 4 13 -#> x[2,7] -1.1 -0.1 0.9 -0.1 0.6 1.47 13 13 -#> x[1,8] -1.7 -0.8 0.5 -0.7 0.8 1.32 5 13 +#> x[1,6] -1.0 -0.3 0.3 -0.3 0.5 1.16 6 13 +#> x[2,6] -0.2 0.1 0.6 0.1 0.3 1.45 9 13 +#> x[1,7] -2.2 -1.2 0.1 -1.1 0.9 1.71 4 13 +#> x[2,7] -1.1 -0.1 0.9 -0.1 0.6 1.58 13 13 +#> x[1,8] -1.8 -0.8 0.5 -0.7 0.9 1.07 7 13 #> x[2,8] -1.1 0.2 1.4 0.2 0.8 1.71 13 13 -#> x[1,9] -1.3 -0.2 0.7 -0.2 0.6 1.15 8 13 -#> x[2,9] -1.2 0.5 1.2 0.2 0.9 2.06 9 13 -#> x[1,10] -1.4 -0.7 0.2 -0.7 0.6 1.48 5 13 -#> x[2,10] -1.0 -0.4 0.3 -0.4 0.4 0.99 13 13 -#> Z[1,1] -3.6 0.3 3.6 0.2 2.4 2.06 13 13 -#> Z[2,1] -0.5 0.5 1.4 0.3 0.7 0.95 13 13 -#> Z[3,1] -1.5 -0.5 1.0 -0.4 0.9 1.87 4 13 +#> x[1,9] -1.6 -0.2 0.7 -0.3 0.7 1.15 8 13 +#> x[2,9] -1.2 0.5 1.2 0.2 0.8 1.71 9 13 +#> x[1,10] -1.4 -0.8 0.2 -0.7 0.6 1.48 4 13 +#> x[2,10] -1.0 -0.3 0.3 -0.4 0.4 1.03 13 13 +#> Z[1,1] -3.6 0.6 3.6 0.2 2.4 2.06 13 13 +#> Z[2,1] -0.5 0.5 1.4 0.3 0.6 0.94 13 13 +#> Z[3,1] -1.5 -0.5 0.8 -0.4 0.9 1.87 4 13 #> Z[4,1] -0.8 0.1 1.9 0.4 0.9 1.20 6 13 #> Z[1,2] 0.0 0.0 0.0 0.0 0.0 1.00 13 13 #> Z[2,2] -4.2 1.0 6.2 0.6 3.9 1.18 13 13 -#> Z[3,2] -1.7 -0.7 0.5 -0.6 0.8 1.06 8 13 -#> Z[4,2] -1.2 0.9 1.8 0.6 1.1 0.97 13 13 -#> log_lik[1] -4.3 -1.5 -0.6 -2.0 1.5 1.87 4 13 -#> log_lik[2] -4.3 -1.3 -0.6 -1.9 1.4 1.87 4 13 +#> Z[3,2] -1.3 -0.7 0.5 -0.6 0.7 1.03 10 13 +#> Z[4,2] -1.2 0.8 1.9 0.6 1.1 0.92 13 13 +#> log_lik[1] -4.3 -1.5 -0.7 -2.0 1.4 1.87 4 13 +#> log_lik[2] -4.3 -1.3 -0.6 -1.9 1.4 1.71 4 13 #> log_lik[3] -4.3 -1.2 -0.6 -1.9 1.5 2.06 4 13 -#> log_lik[4] -4.3 -1.1 -0.5 -2.0 1.5 2.06 4 13 -#> log_lik[5] -4.3 -1.2 -0.8 -2.0 1.4 2.06 4 13 -#> log_lik[6] -4.3 -1.3 -0.6 -2.0 1.4 1.71 4 13 -#> log_lik[7] -4.3 -1.3 -0.6 -2.0 1.4 1.87 4 13 -#> log_lik[8] -4.7 -1.4 -0.5 -2.3 1.8 1.87 4 13 -#> log_lik[9] -5.7 -3.5 -2.2 -3.6 1.3 0.98 13 13 +#> log_lik[4] -4.3 -1.1 -0.6 -2.0 1.5 2.06 4 13 +#> log_lik[5] -4.3 -1.2 -0.7 -2.0 1.4 2.06 3 13 +#> log_lik[6] -4.3 -1.3 -0.5 -2.0 1.5 1.71 4 13 +#> log_lik[7] -4.3 -1.6 -0.6 -2.0 1.4 1.71 4 13 +#> log_lik[8] -4.7 -1.4 -0.6 -2.3 1.7 1.87 4 13 +#> log_lik[9] -4.8 -3.6 -2.2 -3.6 1.0 0.96 13 13 #> log_lik[10] -4.3 -2.2 -0.5 -2.5 1.5 1.24 5 13 -#> log_lik[11] -4.3 -2.1 -0.6 -2.5 1.4 1.32 4 13 -#> log_lik[12] -4.3 -1.6 -0.6 -2.1 1.4 1.47 4 13 +#> log_lik[11] -4.3 -2.1 -0.8 -2.5 1.3 1.32 4 13 +#> log_lik[12] -4.3 -1.6 -0.5 -2.2 1.4 1.38 4 13 #> log_lik[13] -4.3 -1.4 -0.6 -2.1 1.5 1.87 4 13 #> log_lik[14] -4.3 -1.5 -0.5 -2.0 1.5 1.87 4 13 #> log_lik[15] -4.3 -1.5 -0.6 -2.0 1.4 2.06 3 13 #> log_lik[16] -4.3 -1.5 -0.6 -2.2 1.5 1.87 4 13 #> log_lik[17] -4.3 -1.3 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[18] -4.4 -2.0 -0.5 -2.1 1.5 2.06 3 13 -#> log_lik[19] -4.3 -1.9 -0.6 -2.1 1.4 2.06 4 13 +#> log_lik[18] -4.4 -2.0 -0.4 -2.1 1.5 2.06 3 13 +#> log_lik[19] -4.3 -1.9 -0.5 -2.1 1.4 2.06 4 13 #> log_lik[20] -4.3 -1.7 -0.5 -2.0 1.4 2.06 4 13 -#> log_lik[21] -4.3 -1.1 -0.5 -1.9 1.5 2.06 3 13 -#> log_lik[22] -4.3 -1.2 -0.6 -1.9 1.4 2.06 4 13 -#> log_lik[23] -4.3 -1.3 -0.7 -1.9 1.4 1.87 4 13 +#> log_lik[21] -4.3 -1.1 -0.4 -1.9 1.5 2.06 3 13 +#> log_lik[22] -4.3 -1.2 -0.6 -1.9 1.5 2.06 4 13 +#> log_lik[23] -4.3 -1.0 -0.5 -1.8 1.5 2.06 4 13 #> log_lik[24] -4.3 -1.3 -0.7 -1.9 1.4 2.06 4 13 -#> log_lik[25] -4.4 -2.2 -0.6 -2.3 1.6 1.87 4 13 +#> log_lik[25] -4.4 -1.2 -0.5 -2.2 1.6 2.06 4 13 #> log_lik[26] -4.3 -1.5 -0.7 -2.1 1.4 1.58 4 13 -#> log_lik[27] -4.3 -1.6 -0.6 -2.1 1.4 2.06 4 13 -#> log_lik[28] -4.3 -1.5 -0.9 -2.1 1.4 2.06 4 13 -#> log_lik[29] -4.3 -1.5 -0.9 -2.3 1.3 1.47 4 13 -#> log_lik[30] -4.3 -1.3 -0.7 -2.0 1.4 1.71 4 13 +#> log_lik[27] -4.3 -1.6 -0.5 -2.0 1.5 2.06 4 13 +#> log_lik[28] -4.3 -1.5 -0.7 -2.0 1.4 2.06 4 13 +#> log_lik[29] -4.3 -1.5 -0.5 -2.2 1.4 1.45 4 13 +#> log_lik[30] -4.3 -1.3 -0.5 -2.0 1.4 1.71 4 13 #> log_lik[31] -4.3 -1.1 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[32] -4.3 -1.4 -0.6 -1.9 1.4 1.87 4 13 -#> log_lik[33] -4.3 -1.7 -1.0 -2.2 1.2 1.58 4 13 +#> log_lik[32] -4.3 -1.4 -0.5 -1.9 1.4 1.87 4 13 +#> log_lik[33] -4.3 -1.6 -0.5 -2.1 1.3 1.71 4 13 #> log_lik[34] -4.3 -1.6 -0.7 -2.1 1.4 2.06 4 13 -#> log_lik[35] -4.3 -1.0 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[36] -4.3 -1.0 -0.6 -1.9 1.5 2.06 4 13 -#> log_lik[37] -4.3 -2.0 -0.7 -2.1 1.4 2.06 4 13 -#> log_lik[38] -4.3 -1.2 -0.5 -1.8 1.5 2.06 3 13 -#> log_lik[39] -4.3 -1.7 -0.6 -2.0 1.3 1.87 4 13 -#> log_lik[40] -4.3 -1.3 -0.6 -2.0 1.4 2.06 4 13 -#> xstar[1,1] -2.1 -0.5 1.3 -0.6 1.2 1.00 9 13 -#> xstar[2,1] -2.0 -0.4 1.2 -0.3 1.2 1.12 8 13 +#> log_lik[35] -4.3 -1.0 -0.4 -1.8 1.5 2.06 3 13 +#> log_lik[36] -4.3 -1.6 -0.6 -1.9 1.4 1.71 4 13 +#> log_lik[37] -4.3 -2.0 -0.7 -2.2 1.4 1.87 4 13 +#> log_lik[38] -4.3 -1.2 -0.4 -1.8 1.5 2.06 3 13 +#> log_lik[39] -4.3 -1.4 -0.5 -2.0 1.4 1.87 4 13 +#> log_lik[40] -4.3 -1.2 -0.7 -2.0 1.4 2.06 4 13 +#> xstar[1,1] -2.1 -0.8 1.3 -0.6 1.2 0.96 10 13 +#> xstar[2,1] -1.7 -0.4 1.2 -0.3 1.1 1.25 6 13 #> sigma[1] 0.6 1.0 29.7 7.5 11.8 2.06 3 13 -#> lp__ -203.1 -43.1 -19.4 -78.8 72.9 2.06 3 13 +#> lp__ -203.1 -43.1 -17.1 -78.4 73.2 2.06 3 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 diff --git a/docs/reference/plot_regime_model-1.png b/docs/reference/plot_regime_model-1.png index 5e12cc6..fb2be1a 100644 Binary files a/docs/reference/plot_regime_model-1.png and b/docs/reference/plot_regime_model-1.png differ diff --git a/docs/reference/plot_regime_model-2.png b/docs/reference/plot_regime_model-2.png index 785a53a..d61a31c 100644 Binary files a/docs/reference/plot_regime_model-2.png and b/docs/reference/plot_regime_model-2.png differ diff --git a/docs/reference/plot_regime_model-3.png b/docs/reference/plot_regime_model-3.png index 692dbfa..50e633f 100644 Binary files a/docs/reference/plot_regime_model-3.png and b/docs/reference/plot_regime_model-3.png differ diff --git a/docs/reference/plot_regime_model.html b/docs/reference/plot_regime_model.html index 936ccf5..a33caa6 100644 --- a/docs/reference/plot_regime_model.html +++ b/docs/reference/plot_regime_model.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -134,8 +134,8 @@

Examples

#> #> SAMPLING FOR MODEL 'hmm_gaussian' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000122 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.22 seconds. +#> Chain 1: Gradient evaluation took 8.2e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -160,9 +160,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.235185 seconds (Warm-up) -#> Chain 1: 0.27697 seconds (Sampling) -#> Chain 1: 0.512155 seconds (Total) +#> Chain 1: Elapsed Time: 0.244 seconds (Warm-up) +#> Chain 1: 0.311 seconds (Sampling) +#> Chain 1: 0.555 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is NA, indicating chains have not mixed. #> Running the chains for more iterations may help. See diff --git a/docs/reference/plot_trends.html b/docs/reference/plot_trends.html index 1eadad5..b76687f 100644 --- a/docs/reference/plot_trends.html +++ b/docs/reference/plot_trends.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -123,8 +123,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds. +#> Chain 1: Gradient evaluation took 3.9e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -149,9 +149,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005253 seconds (Warm-up) -#> Chain 1: 0.007281 seconds (Sampling) -#> Chain 1: 0.012534 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.005 seconds (Sampling) +#> Chain 1: 0.009 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low diff --git a/docs/reference/predicted.html b/docs/reference/predicted.html index a198679..b33edb6 100644 --- a/docs/reference/predicted.html +++ b/docs/reference/predicted.html @@ -18,7 +18,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/rotate_trends.html b/docs/reference/rotate_trends.html index fc0b5ed..0d3ee0f 100644 --- a/docs/reference/rotate_trends.html +++ b/docs/reference/rotate_trends.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -108,8 +108,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 3.9e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds. +#> Chain 1: Gradient evaluation took 3.8e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -134,9 +134,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007536 seconds (Warm-up) -#> Chain 1: 0.109812 seconds (Sampling) -#> Chain 1: 0.117348 seconds (Total) +#> Chain 1: Elapsed Time: 0.008 seconds (Warm-up) +#> Chain 1: 0.115 seconds (Sampling) +#> Chain 1: 0.123 seconds (Total) #> Chain 1: #> Warning: There were 16 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup diff --git a/docs/reference/sim_dfa.html b/docs/reference/sim_dfa.html index 5351780..812e9bb 100644 --- a/docs/reference/sim_dfa.html +++ b/docs/reference/sim_dfa.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 diff --git a/docs/reference/trend_cor-1.png b/docs/reference/trend_cor-1.png index 8615b05..69f94e7 100644 Binary files a/docs/reference/trend_cor-1.png and b/docs/reference/trend_cor-1.png differ diff --git a/docs/reference/trend_cor-2.png b/docs/reference/trend_cor-2.png index 99787c2..0060c43 100644 Binary files a/docs/reference/trend_cor-2.png and b/docs/reference/trend_cor-2.png differ diff --git a/docs/reference/trend_cor.html b/docs/reference/trend_cor.html index 3c892b1..ad45a03 100644 --- a/docs/reference/trend_cor.html +++ b/docs/reference/trend_cor.html @@ -17,7 +17,7 @@ bayesdfa - 1.3.0 + 1.3.2 @@ -161,8 +161,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds. +#> Chain 1: Gradient evaluation took 3.6e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -187,9 +187,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.015496 seconds (Warm-up) -#> Chain 1: 0.318609 seconds (Sampling) -#> Chain 1: 0.334105 seconds (Total) +#> Chain 1: Elapsed Time: 0.013 seconds (Warm-up) +#> Chain 1: 0.312 seconds (Sampling) +#> Chain 1: 0.325 seconds (Total) #> Chain 1: #> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> https://mc-stan.org/misc/warnings.html#bfmi-low @@ -206,88 +206,88 @@

Examples

#> Inference for the input samples (1 chains: each with iter = 25; warmup = 12): #> #> Q5 Q50 Q95 Mean SD Rhat Bulk_ESS Tail_ESS -#> x[1,1] -1.6 -0.3 0.9 -0.4 0.9 1.30 6 13 -#> x[1,2] -0.7 0.6 1.3 0.4 0.8 1.47 5 13 -#> x[1,3] 0.0 1.1 1.9 0.9 0.7 1.71 4 13 -#> x[1,4] 0.3 0.9 2.0 1.1 0.7 2.06 4 13 +#> x[1,1] -1.6 0.0 0.9 -0.4 0.9 1.37 6 13 +#> x[1,2] -0.7 0.8 1.4 0.5 0.8 1.58 4 13 +#> x[1,3] 0.0 1.1 2.2 1.0 0.8 1.87 4 13 +#> x[1,4] 0.3 0.9 2.1 1.1 0.7 2.06 4 13 #> x[1,5] -0.2 0.5 1.4 0.6 0.6 2.06 4 13 -#> x[1,6] -0.5 0.2 0.9 0.1 0.5 0.92 13 13 -#> x[1,7] -0.3 0.2 1.1 0.4 0.5 1.71 8 13 -#> x[1,8] -0.4 0.0 1.2 0.2 0.6 0.93 12 13 -#> x[1,9] 0.0 0.4 0.8 0.4 0.3 1.45 5 13 -#> x[1,10] -1.0 0.2 0.7 0.0 0.6 1.45 5 13 -#> x[1,11] -2.2 -1.4 -0.6 -1.4 0.6 1.20 6 13 -#> x[1,12] -2.5 -1.3 0.3 -1.2 1.1 2.06 4 13 -#> x[1,13] -1.8 -0.9 0.8 -0.7 1.1 2.06 4 13 -#> x[1,14] -0.8 -0.4 0.3 -0.3 0.4 0.96 13 13 -#> x[1,15] -0.8 0.5 0.9 0.2 0.6 1.09 12 13 -#> Z[1,1] -4.9 -0.9 7.8 0.0 6.2 1.87 13 13 -#> Z[2,1] 0.0 0.5 1.1 0.5 0.4 1.33 13 13 -#> Z[3,1] -1.7 -0.7 1.0 -0.5 0.9 1.71 11 13 +#> x[1,6] -0.5 0.2 0.7 0.1 0.5 0.92 13 13 +#> x[1,7] -0.3 0.2 1.1 0.4 0.5 2.06 7 13 +#> x[1,8] -0.4 0.0 1.3 0.3 0.6 0.93 12 13 +#> x[1,9] -0.1 0.4 0.9 0.4 0.4 1.15 10 13 +#> x[1,10] -1.0 0.2 0.7 -0.1 0.7 1.71 4 13 +#> x[1,11] -2.5 -1.5 -0.6 -1.5 0.7 1.47 4 13 +#> x[1,12] -3.0 -1.6 0.3 -1.4 1.3 2.06 4 13 +#> x[1,13] -1.8 -1.4 0.8 -0.7 1.1 2.06 4 13 +#> x[1,14] -1.0 -0.5 0.3 -0.5 0.4 1.08 11 13 +#> x[1,15] -0.8 0.5 0.9 0.3 0.6 1.09 13 13 +#> Z[1,1] -4.9 -0.6 7.8 0.1 6.2 2.06 13 13 +#> Z[2,1] 0.0 0.5 1.1 0.5 0.4 1.58 13 13 +#> Z[3,1] -1.7 -0.7 1.0 -0.5 0.8 2.06 9 13 #> Z[4,1] -0.7 -0.2 0.7 -0.1 0.5 1.71 9 13 -#> log_lik[1] -4.5 -0.8 -0.5 -1.8 1.6 1.71 4 13 -#> log_lik[2] -3.7 -1.0 -0.5 -1.5 1.2 1.39 5 13 -#> log_lik[3] -3.7 -1.0 -0.5 -1.5 1.2 1.71 4 13 -#> log_lik[4] -3.7 -1.1 -0.7 -1.6 1.1 1.07 10 13 -#> log_lik[5] -3.8 -1.8 -0.7 -2.1 1.1 1.87 4 13 -#> log_lik[6] -3.7 -0.9 -0.7 -1.6 1.1 1.48 5 13 -#> log_lik[7] -3.7 -1.0 -0.5 -1.5 1.1 1.71 4 13 +#> log_lik[1] -4.5 -0.8 -0.4 -1.7 1.6 2.06 4 13 +#> log_lik[2] -3.7 -1.0 -0.5 -1.5 1.1 1.39 5 13 +#> log_lik[3] -3.7 -1.1 -0.4 -1.6 1.2 1.48 4 13 +#> log_lik[4] -3.7 -1.1 -0.7 -1.5 1.1 1.19 10 13 +#> log_lik[5] -3.8 -1.7 -1.0 -2.1 1.1 2.06 4 13 +#> log_lik[6] -3.7 -1.0 -0.7 -1.6 1.1 1.32 5 13 +#> log_lik[7] -3.7 -1.0 -0.5 -1.5 1.2 1.87 4 13 #> log_lik[8] -3.7 -1.5 -1.1 -2.0 0.9 1.18 7 13 -#> log_lik[9] -3.7 -1.1 -0.4 -1.6 1.2 2.06 4 13 -#> log_lik[10] -3.7 -0.6 -0.5 -1.4 1.2 1.71 4 13 -#> log_lik[11] -3.7 -1.4 -0.5 -1.6 1.1 2.06 4 13 -#> log_lik[12] -3.7 -0.8 -0.5 -1.4 1.2 1.71 5 13 -#> log_lik[13] -3.9 -1.2 -0.4 -1.6 1.2 1.58 4 13 -#> log_lik[14] -3.7 -2.3 -1.1 -2.3 0.9 1.30 5 13 -#> log_lik[15] -3.7 -1.5 -0.5 -1.6 1.1 1.33 5 13 +#> log_lik[9] -3.7 -1.1 -0.4 -1.7 1.1 2.06 4 13 +#> log_lik[10] -3.7 -1.0 -0.5 -1.4 1.2 1.58 4 13 +#> log_lik[11] -3.7 -1.4 -0.5 -1.5 1.2 2.06 4 13 +#> log_lik[12] -3.7 -0.7 -0.5 -1.4 1.2 1.87 5 13 +#> log_lik[13] -3.9 -0.8 -0.4 -1.4 1.3 2.06 4 13 +#> log_lik[14] -3.7 -2.3 -1.0 -2.3 0.9 1.22 6 13 +#> log_lik[15] -3.7 -1.0 -0.4 -1.5 1.2 1.58 4 13 #> log_lik[16] -3.7 -0.8 -0.5 -1.3 1.2 1.87 4 13 -#> log_lik[17] -3.7 -0.9 -0.5 -1.5 1.2 1.58 5 13 -#> log_lik[18] -3.7 -0.8 -0.5 -1.3 1.2 1.30 5 13 -#> log_lik[19] -3.7 -1.0 -0.5 -1.5 1.1 1.58 4 13 -#> log_lik[20] -3.7 -1.2 -1.0 -1.7 1.0 1.08 8 13 -#> log_lik[21] -3.8 -0.8 -0.4 -1.6 1.3 1.71 4 13 +#> log_lik[17] -3.7 -0.9 -0.5 -1.5 1.2 1.71 5 13 +#> log_lik[18] -3.7 -0.8 -0.5 -1.4 1.2 1.16 6 13 +#> log_lik[19] -3.7 -0.9 -0.5 -1.5 1.2 1.71 4 13 +#> log_lik[20] -3.7 -1.2 -1.0 -1.7 1.0 1.14 9 13 +#> log_lik[21] -3.8 -0.8 -0.4 -1.5 1.3 2.06 4 13 #> log_lik[22] -3.7 -0.8 -0.5 -1.4 1.2 1.58 4 13 -#> log_lik[23] -3.7 -0.9 -0.5 -1.5 1.2 1.71 4 13 +#> log_lik[23] -3.7 -0.9 -0.6 -1.5 1.1 1.58 4 13 #> log_lik[24] -3.7 -0.7 -0.4 -1.3 1.2 2.06 4 13 -#> log_lik[25] -4.1 -0.8 -0.4 -1.5 1.4 1.87 4 13 -#> log_lik[26] -3.7 -0.8 -0.4 -1.3 1.2 2.06 4 13 +#> log_lik[25] -4.1 -0.8 -0.4 -1.5 1.4 2.06 4 13 +#> log_lik[26] -3.7 -0.8 -0.5 -1.3 1.2 2.06 4 13 #> log_lik[27] -3.7 -0.7 -0.4 -1.4 1.2 2.06 4 13 #> log_lik[28] -3.7 -0.6 -0.4 -1.3 1.2 1.87 4 13 -#> log_lik[29] -3.7 -1.1 -0.6 -1.5 1.1 1.21 6 13 -#> log_lik[30] -3.7 -0.9 -0.5 -1.4 1.2 1.48 5 13 -#> log_lik[31] -3.7 -1.2 -0.7 -1.7 1.1 1.19 7 13 -#> log_lik[32] -3.7 -0.6 -0.5 -1.3 1.2 1.58 4 13 -#> log_lik[33] -3.8 -0.6 -0.4 -1.3 1.3 1.58 5 13 -#> log_lik[34] -3.7 -1.2 -0.8 -1.6 1.0 1.08 8 13 +#> log_lik[29] -3.7 -1.1 -0.6 -1.5 1.1 1.30 5 13 +#> log_lik[30] -3.7 -0.9 -0.5 -1.5 1.2 1.48 5 13 +#> log_lik[31] -3.7 -1.3 -0.6 -1.7 1.1 1.19 6 13 +#> log_lik[32] -3.7 -0.6 -0.5 -1.3 1.2 1.71 4 13 +#> log_lik[33] -3.8 -0.7 -0.4 -1.3 1.3 1.71 5 13 +#> log_lik[34] -3.7 -1.2 -0.7 -1.6 1.1 1.14 7 13 #> log_lik[35] -3.7 -0.8 -0.5 -1.4 1.2 1.71 4 13 -#> log_lik[36] -3.7 -0.9 -0.8 -1.5 1.1 1.06 8 13 -#> log_lik[37] -3.7 -0.9 -0.5 -1.4 1.2 1.71 4 13 -#> log_lik[38] -3.7 -0.8 -0.4 -1.3 1.2 1.71 4 13 -#> log_lik[39] -3.7 -0.9 -0.5 -1.6 1.2 1.31 5 13 -#> log_lik[40] -3.7 -1.0 -0.6 -1.4 1.1 1.71 4 13 -#> log_lik[41] -4.6 -1.0 -0.4 -1.7 1.6 1.39 5 13 -#> log_lik[42] -3.7 -2.1 -0.9 -2.2 0.9 1.45 5 13 +#> log_lik[36] -3.7 -0.9 -0.8 -1.5 1.1 1.19 8 13 +#> log_lik[37] -3.7 -0.9 -0.4 -1.4 1.2 1.71 4 13 +#> log_lik[38] -3.7 -0.9 -0.4 -1.4 1.2 1.47 5 13 +#> log_lik[39] -3.7 -0.9 -0.4 -1.5 1.2 1.39 5 13 +#> log_lik[40] -3.7 -0.9 -0.7 -1.4 1.1 2.06 4 13 +#> log_lik[41] -4.6 -0.9 -0.5 -1.7 1.6 1.58 4 13 +#> log_lik[42] -3.7 -2.1 -0.9 -2.1 1.0 1.71 4 13 #> log_lik[43] -4.3 -1.2 -0.5 -1.9 1.6 1.71 5 13 -#> log_lik[44] -4.7 -3.4 -1.3 -3.3 1.2 1.05 13 13 -#> log_lik[45] -4.0 -1.7 -0.5 -1.9 1.4 1.87 6 13 -#> log_lik[46] -3.7 -0.7 -0.6 -1.5 1.2 1.58 6 13 -#> log_lik[47] -3.7 -0.9 -0.5 -1.7 1.3 1.58 4 13 -#> log_lik[48] -7.4 -4.9 -2.4 -4.7 1.9 1.05 13 13 -#> log_lik[49] -4.0 -0.9 -0.5 -1.7 1.4 1.87 4 13 -#> log_lik[50] -3.7 -1.2 -0.5 -1.6 1.1 2.06 4 13 -#> log_lik[51] -3.7 -1.4 -0.5 -1.7 1.1 1.19 6 13 -#> log_lik[52] -3.7 -0.9 -0.7 -1.5 1.1 1.71 4 13 -#> log_lik[53] -3.8 -0.9 -0.5 -1.4 1.2 2.06 4 13 -#> log_lik[54] -3.7 -0.8 -0.4 -1.3 1.2 1.58 4 13 +#> log_lik[44] -4.8 -3.4 -1.3 -3.3 1.2 1.00 13 13 +#> log_lik[45] -4.0 -1.1 -0.5 -1.9 1.5 1.71 5 13 +#> log_lik[46] -3.7 -1.0 -0.5 -1.5 1.2 1.38 5 13 +#> log_lik[47] -3.7 -0.7 -0.5 -1.6 1.3 1.58 4 13 +#> log_lik[48] -7.2 -4.8 -2.4 -4.6 1.7 0.99 13 13 +#> log_lik[49] -4.0 -0.9 -0.5 -1.7 1.4 2.06 4 13 +#> log_lik[50] -3.7 -1.1 -0.6 -1.6 1.1 2.06 4 13 +#> log_lik[51] -3.7 -0.9 -0.5 -1.5 1.2 1.58 4 13 +#> log_lik[52] -3.7 -0.9 -0.7 -1.5 1.1 1.87 4 13 +#> log_lik[53] -3.8 -0.9 -0.4 -1.4 1.2 2.06 4 13 +#> log_lik[54] -3.7 -0.8 -0.5 -1.3 1.2 1.47 5 13 #> log_lik[55] -3.7 -0.9 -0.5 -1.4 1.2 2.06 4 13 -#> log_lik[56] -3.7 -2.2 -1.4 -2.4 0.9 1.45 8 13 -#> log_lik[57] -5.0 -1.3 -0.6 -2.1 1.8 1.58 5 13 -#> log_lik[58] -3.7 -2.3 -0.8 -2.2 1.1 0.98 10 13 -#> log_lik[59] -4.1 -1.3 -0.5 -1.8 1.4 1.48 5 13 -#> log_lik[60] -3.7 -2.0 -0.9 -2.1 1.0 1.71 8 13 -#> xstar[1,1] -2.2 0.7 2.1 0.4 1.5 1.21 13 13 +#> log_lik[56] -3.7 -2.6 -1.4 -2.4 0.9 1.30 10 13 +#> log_lik[57] -5.0 -1.3 -0.6 -2.1 1.8 1.71 5 13 +#> log_lik[58] -3.7 -1.8 -0.8 -2.1 1.0 1.24 10 13 +#> log_lik[59] -4.1 -1.3 -0.6 -1.8 1.4 1.48 5 13 +#> log_lik[60] -3.7 -1.7 -0.9 -2.0 1.0 1.87 8 13 +#> xstar[1,1] -1.2 1.1 2.1 0.6 1.2 1.01 13 13 #> sigma[1] 0.6 0.7 15.9 3.5 5.7 1.58 4 13 -#> lp__ -315.4 -60.3 -46.3 -110.6 108.8 2.06 4 13 +#> lp__ -315.4 -60.3 -46.3 -109.8 109.3 2.06 4 13 #> #> For each parameter, Bulk_ESS and Tail_ESS are crude measures of #> effective sample size for bulk and tail quantities respectively (an ESS > 100 @@ -300,8 +300,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds. +#> Chain 1: Gradient evaluation took 9e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -318,9 +318,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005817 seconds (Warm-up) -#> Chain 1: 0.003467 seconds (Sampling) -#> Chain 1: 0.009284 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is 1.09, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -334,8 +334,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -352,9 +352,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00412 seconds (Warm-up) -#> Chain 1: 0.003064 seconds (Sampling) -#> Chain 1: 0.007184 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.006 seconds (Sampling) +#> Chain 1: 0.009 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -365,8 +365,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -383,18 +383,21 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005732 seconds (Warm-up) -#> Chain 1: 0.002684 seconds (Sampling) -#> Chain 1: 0.008416 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess +#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#tail-ess #> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -411,9 +414,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004293 seconds (Warm-up) -#> Chain 1: 0.003458 seconds (Sampling) -#> Chain 1: 0.007751 seconds (Total) +#> Chain 1: Elapsed Time: 0.005 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.008 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -424,8 +427,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -442,9 +445,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00405 seconds (Warm-up) -#> Chain 1: 0.002739 seconds (Sampling) -#> Chain 1: 0.006789 seconds (Total) +#> Chain 1: Elapsed Time: 0.012 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.015 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -455,8 +458,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 7e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -473,10 +476,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004658 seconds (Warm-up) -#> Chain 1: 0.003139 seconds (Sampling) -#> Chain 1: 0.007797 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.15, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -486,8 +492,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 7e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -504,9 +510,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004471 seconds (Warm-up) -#> Chain 1: 0.003623 seconds (Sampling) -#> Chain 1: 0.008094 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -517,8 +523,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -535,11 +541,11 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004553 seconds (Warm-up) -#> Chain 1: 0.002928 seconds (Sampling) -#> Chain 1: 0.007481 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.08, indicating chains have not mixed. +#> Warning: The largest R-hat is 1.13, indicating chains have not mixed. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -551,8 +557,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -569,9 +575,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004722 seconds (Warm-up) -#> Chain 1: 0.003233 seconds (Sampling) -#> Chain 1: 0.007955 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -582,8 +588,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 7e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -600,10 +606,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004277 seconds (Warm-up) -#> Chain 1: 0.002968 seconds (Sampling) -#> Chain 1: 0.007245 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.06, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -613,8 +622,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -631,9 +640,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004169 seconds (Warm-up) -#> Chain 1: 0.003179 seconds (Sampling) -#> Chain 1: 0.007348 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -644,8 +653,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -662,11 +671,11 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00384 seconds (Warm-up) -#> Chain 1: 0.00309 seconds (Sampling) -#> Chain 1: 0.00693 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.005 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.12, indicating chains have not mixed. +#> Warning: The largest R-hat is 1.14, indicating chains have not mixed. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -678,8 +687,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -696,10 +705,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.0044 seconds (Warm-up) -#> Chain 1: 0.003328 seconds (Sampling) -#> Chain 1: 0.007728 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.13, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -709,8 +721,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -727,9 +739,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003971 seconds (Warm-up) -#> Chain 1: 0.002547 seconds (Sampling) -#> Chain 1: 0.006518 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -740,8 +752,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -758,9 +770,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004593 seconds (Warm-up) -#> Chain 1: 0.003597 seconds (Sampling) -#> Chain 1: 0.00819 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -771,8 +783,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -789,9 +801,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004481 seconds (Warm-up) -#> Chain 1: 0.003432 seconds (Sampling) -#> Chain 1: 0.007913 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -802,8 +814,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -820,9 +832,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00593 seconds (Warm-up) -#> Chain 1: 0.003002 seconds (Sampling) -#> Chain 1: 0.008932 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -833,8 +845,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -851,9 +863,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003715 seconds (Warm-up) -#> Chain 1: 0.003092 seconds (Sampling) -#> Chain 1: 0.006807 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.005 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -864,8 +876,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -882,9 +894,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005217 seconds (Warm-up) -#> Chain 1: 0.004779 seconds (Sampling) -#> Chain 1: 0.009996 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -895,8 +907,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -913,9 +925,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003978 seconds (Warm-up) -#> Chain 1: 0.003167 seconds (Sampling) -#> Chain 1: 0.007145 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -926,8 +938,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -944,9 +956,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004054 seconds (Warm-up) -#> Chain 1: 0.003391 seconds (Sampling) -#> Chain 1: 0.007445 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -957,8 +969,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -975,10 +987,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006235 seconds (Warm-up) -#> Chain 1: 0.004832 seconds (Sampling) -#> Chain 1: 0.011067 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.06, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -988,8 +1003,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1006,9 +1021,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00475 seconds (Warm-up) -#> Chain 1: 0.002736 seconds (Sampling) -#> Chain 1: 0.007486 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1019,8 +1034,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1037,9 +1052,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008324 seconds (Warm-up) -#> Chain 1: 0.004725 seconds (Sampling) -#> Chain 1: 0.013049 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1050,8 +1065,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1068,10 +1083,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00426 seconds (Warm-up) -#> Chain 1: 0.002904 seconds (Sampling) -#> Chain 1: 0.007164 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.07, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1087,8 +1105,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1105,9 +1123,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005423 seconds (Warm-up) -#> Chain 1: 0.006591 seconds (Sampling) -#> Chain 1: 0.012014 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.004 seconds (Sampling) +#> Chain 1: 0.008 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1118,8 +1136,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1136,9 +1154,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00396 seconds (Warm-up) -#> Chain 1: 0.003734 seconds (Sampling) -#> Chain 1: 0.007694 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.005 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1149,8 +1167,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1167,9 +1185,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005119 seconds (Warm-up) -#> Chain 1: 0.003674 seconds (Sampling) -#> Chain 1: 0.008793 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1180,8 +1198,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1198,13 +1216,10 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004585 seconds (Warm-up) -#> Chain 1: 0.002968 seconds (Sampling) -#> Chain 1: 0.007553 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.05, indicating chains have not mixed. -#> Running the chains for more iterations may help. See -#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1214,8 +1229,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1232,10 +1247,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004664 seconds (Warm-up) -#> Chain 1: 0.002985 seconds (Sampling) -#> Chain 1: 0.007649 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.1, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1245,8 +1263,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1263,13 +1281,10 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004817 seconds (Warm-up) -#> Chain 1: 0.003531 seconds (Sampling) -#> Chain 1: 0.008348 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.05, indicating chains have not mixed. -#> Running the chains for more iterations may help. See -#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1279,8 +1294,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1297,13 +1312,10 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004939 seconds (Warm-up) -#> Chain 1: 0.003643 seconds (Sampling) -#> Chain 1: 0.008582 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.14, indicating chains have not mixed. -#> Running the chains for more iterations may help. See -#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1313,8 +1325,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1331,9 +1343,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004155 seconds (Warm-up) -#> Chain 1: 0.003377 seconds (Sampling) -#> Chain 1: 0.007532 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1344,8 +1356,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1362,10 +1374,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007592 seconds (Warm-up) -#> Chain 1: 0.006328 seconds (Sampling) -#> Chain 1: 0.01392 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.08, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1375,8 +1390,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1393,9 +1408,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004204 seconds (Warm-up) -#> Chain 1: 0.003007 seconds (Sampling) -#> Chain 1: 0.007211 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1406,8 +1421,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1424,9 +1439,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003976 seconds (Warm-up) -#> Chain 1: 0.003396 seconds (Sampling) -#> Chain 1: 0.007372 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1437,8 +1452,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1455,9 +1470,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005451 seconds (Warm-up) -#> Chain 1: 0.003302 seconds (Sampling) -#> Chain 1: 0.008753 seconds (Total) +#> Chain 1: Elapsed Time: 0.005 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.008 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1468,8 +1483,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1486,10 +1501,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004771 seconds (Warm-up) -#> Chain 1: 0.004268 seconds (Sampling) -#> Chain 1: 0.009039 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.11, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1499,8 +1517,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1517,13 +1535,10 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005298 seconds (Warm-up) -#> Chain 1: 0.002981 seconds (Sampling) -#> Chain 1: 0.008279 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.08, indicating chains have not mixed. -#> Running the chains for more iterations may help. See -#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1533,8 +1548,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1551,9 +1566,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00433 seconds (Warm-up) -#> Chain 1: 0.002801 seconds (Sampling) -#> Chain 1: 0.007131 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1564,8 +1579,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1582,9 +1597,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00376 seconds (Warm-up) -#> Chain 1: 0.003069 seconds (Sampling) -#> Chain 1: 0.006829 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1595,8 +1610,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1613,9 +1628,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004083 seconds (Warm-up) -#> Chain 1: 0.003106 seconds (Sampling) -#> Chain 1: 0.007189 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1626,8 +1641,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1644,13 +1659,10 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004754 seconds (Warm-up) -#> Chain 1: 0.003369 seconds (Sampling) -#> Chain 1: 0.008123 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: -#> Warning: The largest R-hat is 1.05, indicating chains have not mixed. -#> Running the chains for more iterations may help. See -#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess @@ -1660,8 +1672,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1678,9 +1690,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004555 seconds (Warm-up) -#> Chain 1: 0.003008 seconds (Sampling) -#> Chain 1: 0.007563 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is 1.08, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -1694,8 +1706,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 7e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1712,9 +1724,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004181 seconds (Warm-up) -#> Chain 1: 0.002933 seconds (Sampling) -#> Chain 1: 0.007114 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1725,8 +1737,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1743,9 +1755,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004106 seconds (Warm-up) -#> Chain 1: 0.003448 seconds (Sampling) -#> Chain 1: 0.007554 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.002 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1756,8 +1768,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1774,9 +1786,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004343 seconds (Warm-up) -#> Chain 1: 0.004019 seconds (Sampling) -#> Chain 1: 0.008362 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1787,8 +1799,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1805,9 +1817,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004541 seconds (Warm-up) -#> Chain 1: 0.003651 seconds (Sampling) -#> Chain 1: 0.008192 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1818,8 +1830,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1836,9 +1848,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004077 seconds (Warm-up) -#> Chain 1: 0.003211 seconds (Sampling) -#> Chain 1: 0.007288 seconds (Total) +#> Chain 1: Elapsed Time: 0.003 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.006 seconds (Total) #> Chain 1: #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See @@ -1849,8 +1861,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1867,10 +1879,13 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005153 seconds (Warm-up) -#> Chain 1: 0.003348 seconds (Sampling) -#> Chain 1: 0.008501 seconds (Total) +#> Chain 1: Elapsed Time: 0.004 seconds (Warm-up) +#> Chain 1: 0.003 seconds (Sampling) +#> Chain 1: 0.007 seconds (Total) #> Chain 1: +#> Warning: The largest R-hat is 1.05, indicating chains have not mixed. +#> Running the chains for more iterations may help. See +#> https://mc-stan.org/misc/warnings.html#r-hat #> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. #> Running the chains for more iterations may help. See #> https://mc-stan.org/misc/warnings.html#bulk-ess