diff --git a/docs/articles/a1_bayesdfa.html b/docs/articles/a1_bayesdfa.html index 45dcec4..e218d08 100644 --- a/docs/articles/a1_bayesdfa.html +++ b/docs/articles/a1_bayesdfa.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 @@ -607,7 +607,7 @@

DFA model with weightsglm, 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 -weights are included by modifying each variance to be \[(sigma^2) / w_i\]. As a concrete example, +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.

Our simulated standard errors are the same for all surveys – except @@ -622,12 +622,18 @@

DFA model with weights df <- data.frame(obs = c(sim_dat$y_sim), time = sort(rep(1:20,4)), ts = rep(1:4,20)) -df$se <- runif(nrow(df), 0.3, 0.5) -df$se[which(df$ts == 2)] = 0.04 +df$se <- runif(nrow(df), 0.6, 0.8) +df$se[which(df$ts == 2)] = 0.2

Next we can generate the weights (this is redundant, and “se” could -be used instead in the function call below)

+be used instead in the function call below). Because the weights are +used as an offset, \[\sigma^2 / w_i\], +we don’t want to use the SE alone as a weight but make them inversely +related to the SE. As a quick note, the scale of these may affect +estimation and some additional normalization may be needed (rather than +standard errors, it may be more helpful to think about the sample size +each data point represents).

-df$weights <- df$se
+df$weights <- (1 / df$se)^2

And fit the model with the weights argument

 f2 <- fit_dfa(
@@ -638,8 +644,8 @@ 
DFA model with weights## 
 ## SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1).
 ## Chain 1: 
-## Chain 1: Gradient evaluation took 4.9e-05 seconds
-## Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
+## 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: Adjust your expectations accordingly!
 ## Chain 1: 
 ## Chain 1: 
@@ -656,9 +662,9 @@ 
DFA model with weights## Chain 1: Iteration: 450 / 500 [ 90%]  (Sampling)
 ## Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
 ## Chain 1: 
-## Chain 1:  Elapsed Time: 12.3963 seconds (Warm-up)
-## Chain 1:                3.3721 seconds (Sampling)
-## Chain 1:                15.7684 seconds (Total)
+## Chain 1:  Elapsed Time: 120.552 seconds (Warm-up)
+## Chain 1:                22.6953 seconds (Sampling)
+## Chain 1:                143.247 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
@@ -668,139 +674,139 @@ 
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]        0.1   0.4   0.6   0.3 0.2  1.00       99       73
-## x[2,1]        1.1   1.6   2.2   1.6 0.3  1.00       97       41
-## x[1,2]        0.6   1.1   1.5   1.1 0.3  1.01       92       61
-## x[2,2]        0.7   1.4   2.1   1.4 0.5  0.99       65      102
-## x[1,3]       -0.9  -0.5  -0.1  -0.5 0.2  1.00      124       66
-## x[2,3]        0.6   1.1   1.9   1.2 0.4  1.00      119      108
-## x[1,4]       -1.9  -1.3  -0.9  -1.4 0.3  1.04       43       30
-## x[2,4]        1.4   2.2   3.1   2.2 0.5  1.00      145      146
-## x[1,5]       -0.5   0.0   0.3   0.0 0.2  1.05      110       97
-## x[2,5]        0.9   1.4   2.3   1.5 0.4  1.03      177       70
-## x[1,6]       -1.9  -1.4  -0.9  -1.4 0.3  1.02       48       38
-## x[2,6]        0.1   0.8   1.5   0.8 0.4  1.00       71       77
-## x[1,7]       -0.8  -0.4  -0.2  -0.4 0.2  1.00      138       81
-## x[2,7]       -0.5   0.0   0.4  -0.1 0.3  1.00      138       86
-## x[1,8]       -0.5  -0.2   0.0  -0.2 0.2  0.99      132       85
-## x[2,8]       -1.0  -0.4   0.0  -0.5 0.3  0.99      151      121
-## x[1,9]        0.6   0.9   1.3   1.0 0.2  1.01       75       56
-## x[2,9]       -2.1  -1.3  -0.6  -1.3 0.5  1.02      121      134
-## x[1,10]       0.3   0.6   1.0   0.6 0.2  1.03       87       34
-## x[2,10]      -3.4  -2.6  -1.8  -2.6 0.5  1.00       86       78
-## x[1,11]       0.5   0.9   1.4   0.9 0.3  1.03       50       68
-## x[2,11]      -3.8  -2.8  -1.9  -2.8 0.6  1.00      100      106
-## x[1,12]      -0.5  -0.2   0.1  -0.2 0.2  1.00      189      103
-## x[2,12]      -2.8  -1.8  -1.2  -1.9 0.5  1.01      118       95
-## x[1,13]      -1.8  -1.2  -0.8  -1.2 0.3  1.02       42       81
-## x[2,13]      -1.3  -0.6   0.1  -0.6 0.4  1.02       85       89
-## x[1,14]      -2.1  -1.5  -1.1  -1.5 0.3  1.03       39       63
-## x[2,14]      -1.4  -0.5   0.0  -0.6 0.4  0.99       67       86
-## x[1,15]      -1.2  -0.8  -0.4  -0.8 0.2  1.00       62       68
-## x[2,15]      -1.4  -0.8  -0.2  -0.8 0.4  1.00       63       52
-## x[1,16]       0.7   1.1   1.5   1.1 0.3  1.05       55       74
-## x[2,16]      -0.3   0.2   0.7   0.2 0.3  1.00       95       61
-## x[1,17]       0.3   0.6   0.9   0.6 0.2  1.02       62       25
-## x[2,17]      -0.6  -0.2   0.2  -0.2 0.3  1.01      132      138
-## x[1,18]       0.2   0.5   0.8   0.5 0.2  1.01      144       84
-## x[2,18]      -0.2   0.2   0.8   0.3 0.3  1.01      104      104
-## x[1,19]       0.3   0.6   1.0   0.6 0.2  1.01       82       74
-## x[2,19]       0.6   1.1   1.7   1.1 0.3  1.00       86      100
-## x[1,20]       0.6   0.9   1.4   1.0 0.2  1.04       37       52
-## x[2,20]       0.9   1.5   2.2   1.5 0.4  1.01       70       86
-## Z[1,1]       -1.5  -1.1  -0.7  -1.1 0.2  1.04       33       38
-## Z[2,1]       -0.9   0.2   1.3   0.2 0.6  1.00      260       68
-## Z[3,1]       -0.5  -0.2   0.1  -0.2 0.2  0.99       58       71
-## Z[4,1]        0.6   0.8   1.1   0.8 0.2  1.03       35       84
-## Z[1,2]        0.0   0.0   0.0   0.0 0.0  1.00      125      125
-## Z[2,2]        0.0   0.6   1.1   0.6 0.3  1.00      111       66
-## Z[3,2]        0.5   0.7   0.9   0.7 0.1  1.01       64       28
-## Z[4,2]       -0.6  -0.4  -0.3  -0.4 0.1  1.02       65       81
-## log_lik[1]   -0.5   0.5   0.9   0.4 0.7  1.01       42       38
-## log_lik[2]   -1.9  -1.7  -1.4  -1.7 0.1  1.02       49      100
-## log_lik[3]   -1.1   0.5   1.0   0.2 0.7  0.99       87       81
-## log_lik[4]   -0.4   0.6   0.9   0.5 0.4  1.02      120      103
-## log_lik[5]   -1.3   0.2   0.5   0.0 0.6  1.02       52       61
-## log_lik[6]   -2.1  -1.7  -1.5  -1.7 0.2  1.01       56      105
-## log_lik[7]   -1.0   0.4   0.7   0.2 0.5  1.02       53      101
-## log_lik[8]   -1.4   0.3   0.6   0.1 0.6  1.00       93      133
-## log_lik[9]   -3.7  -0.6   0.4  -1.0 1.3  1.00      128       60
-## log_lik[10]  -1.9  -1.6  -1.5  -1.7 0.1  1.04       38       69
-## log_lik[11]  -1.8   0.2   0.6  -0.1 0.8  1.00      185      108
-## log_lik[12]  -4.8  -1.7   0.0  -1.9 1.6  1.01       64      134
-## log_lik[13]  -1.6   0.3   0.8   0.0 0.8  1.00      128       85
-## log_lik[14]  -2.5  -1.8  -1.5  -1.8 0.3  1.00       63       50
-## log_lik[15]  -1.6   0.5   1.0   0.2 0.9  1.00      105       85
-## log_lik[16]  -4.5  -0.9   0.6  -1.3 1.7  1.01      163      106
-## log_lik[17]  -2.1   0.3   0.7  -0.1 1.0  1.01      100       82
-## log_lik[18]  -1.9  -1.7  -1.5  -1.7 0.1  1.03       55       86
-## log_lik[19]  -0.5   0.3   0.6   0.2 0.4  1.06       22       26
-## log_lik[20]  -0.1   0.8   1.0   0.7 0.3  1.08       13      130
-## log_lik[21]  -1.2   0.3   0.7   0.0 0.8  1.02       55       70
-## log_lik[22]  -2.1  -1.7  -1.5  -1.7 0.2  1.02       28       69
-## log_lik[23]  -0.7   0.5   0.9   0.4 0.5  1.02       54       44
-## log_lik[24]  -0.6   0.7   0.9   0.5 0.5  1.03       55       62
-## log_lik[25]  -0.9   0.4   0.8   0.2 0.6  1.01       71       45
-## log_lik[26]  -1.9  -1.6  -1.5  -1.7 0.1  1.08       13      107
-## log_lik[27]  -0.5   0.6   1.0   0.5 0.5  1.02      105      134
-## log_lik[28]  -0.1   0.7   0.9   0.5 0.4  1.01       68       69
-## log_lik[29]  -0.7   0.5   0.7   0.3 0.5  0.99      106      106
-## log_lik[30]  -1.9  -1.7  -1.5  -1.7 0.1  1.08       17       70
-## log_lik[31]  -0.6   0.2   0.5   0.1 0.4  1.03       58       48
-## log_lik[32]  -0.9   0.5   1.0   0.4 0.5  1.01      106       82
-## log_lik[33]  -3.3   0.3   0.9  -0.2 1.3  1.01       69       80
-## log_lik[34]  -2.0  -1.7  -1.5  -1.7 0.2  1.01       38       69
-## log_lik[35]  -2.5  -0.1   0.5  -0.4 1.1  1.08      201      104
-## log_lik[36]  -4.0  -0.7   0.4  -1.1 1.4  0.99      223      134
-## log_lik[37]  -1.4   0.5   0.8   0.2 0.7  1.00      106      141
-## log_lik[38]  -2.1  -1.7  -1.5  -1.7 0.2  1.01       51       81
-## log_lik[39]  -0.7   0.5   0.9   0.4 0.6  1.02       71       72
-## log_lik[40]  -1.1   0.1   0.6   0.0 0.6  1.00      192       89
-## log_lik[41]  -0.8   0.5   0.8   0.3 0.6  1.00      163      105
-## log_lik[42]  -2.1  -1.7  -1.5  -1.8 0.2  1.01       47       85
-## log_lik[43]  -0.9   0.7   1.0   0.4 0.6  1.05       38      104
-## log_lik[44]  -1.7   0.1   0.6  -0.2 0.8  1.01      159      103
-## log_lik[45]  -0.7   0.4   0.7   0.3 0.5  1.04       89      131
-## log_lik[46]  -2.0  -1.7  -1.5  -1.7 0.2  1.03       58       83
-## log_lik[47]  -1.1   0.2   0.6   0.0 0.6  1.02      123       62
-## log_lik[48]  -0.5   0.6   0.9   0.4 0.5  1.00       91       69
-## log_lik[49]  -1.2   0.4   0.8   0.2 0.7  1.01       58       60
-## log_lik[50]  -2.0  -1.7  -1.5  -1.7 0.2  1.03       33       61
-## log_lik[51]  -0.8   0.4   0.7   0.3 0.6  1.01       85       81
-## log_lik[52]  -0.9   0.5   0.9   0.3 0.7  1.01      149       86
-## log_lik[53]  -0.9   0.4   0.9   0.2 0.6  1.00       85       79
-## log_lik[54]  -2.0  -1.7  -1.5  -1.7 0.2  1.01       33       76
-## log_lik[55]  -0.6   0.6   1.0   0.4 0.6  1.02       83      108
-## log_lik[56]  -0.6   0.5   0.8   0.4 0.5  1.01       91       85
-## log_lik[57]  -1.4   0.1   0.5  -0.1 0.7  1.07       35       81
-## log_lik[58]  -2.0  -1.7  -1.5  -1.7 0.1  1.02       44      134
-## log_lik[59]  -0.8   0.4   0.8   0.3 0.5  1.03       80       78
-## log_lik[60]  -0.5   0.3   0.6   0.2 0.3  1.02       54       83
-## log_lik[61]  -5.7  -1.2   0.5  -1.8 1.9  0.99      195       90
-## log_lik[62]  -2.1  -1.7  -1.5  -1.7 0.2  1.02       51       58
-## log_lik[63]  -1.3   0.4   0.8   0.1 0.8  1.02      177      101
-## log_lik[64]  -6.5  -2.3  -0.2  -2.5 1.9  1.00       89      103
-## log_lik[65]  -0.7   0.4   0.7   0.2 0.4  1.03       73      108
-## log_lik[66]  -1.9  -1.6  -1.4  -1.6 0.1  1.07       20       70
-## log_lik[67]  -0.3   0.6   0.9   0.4 0.4  1.02      119      126
-## log_lik[68]  -0.1   0.7   1.0   0.6 0.4  1.05       31       51
-## log_lik[69]  -0.9   0.4   0.8   0.3 0.6  1.00      116       72
-## log_lik[70]  -1.9  -1.7  -1.5  -1.7 0.1  1.07       19       81
-## log_lik[71]  -0.4   0.5   0.8   0.4 0.4  1.08       60      104
-## log_lik[72]  -0.9   0.4   0.7   0.2 0.5  1.01       70       71
-## log_lik[73]  -0.8   0.4   0.8   0.2 0.5  1.07       17       43
-## log_lik[74]  -1.9  -1.7  -1.5  -1.7 0.1  1.05       34       85
-## log_lik[75]  -0.6   0.7   1.0   0.5 0.5  1.01       90       85
-## log_lik[76]  -0.2   0.4   0.6   0.3 0.3  1.06       69       97
-## log_lik[77]  -1.4   0.6   0.9   0.3 0.9  1.03       70       99
-## log_lik[78]  -2.1  -1.7  -1.5  -1.7 0.2  1.01       66      137
-## log_lik[79]  -1.5   0.5   1.0   0.2 1.0  1.01       99       83
-## log_lik[80]  -2.3  -0.4   0.5  -0.6 0.9  1.00      164      108
-## xstar[1,1]   -0.5   1.1   2.7   1.1 1.0  0.99      110      108
-## xstar[2,1]    0.1   1.6   3.4   1.6 1.1  1.01      125      135
-## sigma[1]      0.1   0.1   0.1   0.1 0.0  1.09       12       84
-## lp__        -41.0 -24.3 -13.7 -25.9 9.0  1.19        5       60
+##               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
 ## 
 ## 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/articles/a2_combining_data.html b/docs/articles/a2_combining_data.html
index b75670e..041b08f 100644
--- a/docs/articles/a2_combining_data.html
+++ b/docs/articles/a2_combining_data.html
@@ -34,7 +34,7 @@
       
       
         bayesdfa
-        1.2.0
+        1.3.0
diff --git a/docs/articles/a3_covariates.html b/docs/articles/a3_covariates.html index f56addc..64f2af4 100644 --- a/docs/articles/a3_covariates.html +++ b/docs/articles/a3_covariates.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/articles/a4_smooth.html b/docs/articles/a4_smooth.html index a14784f..1563c96 100644 --- a/docs/articles/a4_smooth.html +++ b/docs/articles/a4_smooth.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/articles/a5_estimate_process_sigma.html b/docs/articles/a5_estimate_process_sigma.html index 9c3ecec..22bf4fc 100644 --- a/docs/articles/a5_estimate_process_sigma.html +++ b/docs/articles/a5_estimate_process_sigma.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/articles/a6_compositional.html b/docs/articles/a6_compositional.html index a2b7417..4809baa 100644 --- a/docs/articles/a6_compositional.html +++ b/docs/articles/a6_compositional.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/articles/a7_bigdata.html b/docs/articles/a7_bigdata.html index c96b797..6b82501 100644 --- a/docs/articles/a7_bigdata.html +++ b/docs/articles/a7_bigdata.html @@ -34,7 +34,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/news/index.html b/docs/news/index.html index 83b0a40..c30c5dd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ bayesdfa - 1.2.0 + 1.3.0 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 41a092b..5ae0667 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -9,5 +9,5 @@ articles: a5_estimate_process_sigma: a5_estimate_process_sigma.html a6_compositional: a6_compositional.html a7_bigdata: a7_bigdata.html -last_built: 2023-06-15T13:26Z +last_built: 2023-06-15T18:34Z diff --git a/docs/reference/dfa_fitted.html b/docs/reference/dfa_fitted.html index d00c847..03c1578 100644 --- a/docs/reference/dfa_fitted.html +++ b/docs/reference/dfa_fitted.html @@ -117,8 +117,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000202 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.02 seconds. +#> 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: 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: 0.015988 seconds (Warm-up) -#> Chain 1: 0.019211 seconds (Sampling) -#> Chain 1: 0.035199 seconds (Total) +#> Chain 1: Elapsed Time: 0.011398 seconds (Warm-up) +#> Chain 1: 0.042844 seconds (Sampling) +#> Chain 1: 0.054242 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 @@ -162,138 +162,138 @@

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 1.87 4 13 -#> x[2,1] 0.0 0.0 0.0 0.0 0.0 2.06 3 13 -#> x[1,2] -0.1 -0.1 -0.1 -0.1 0.0 2.06 4 13 -#> x[2,2] 1.2 1.2 1.2 1.2 0.0 2.06 4 13 -#> x[1,3] -1.5 -1.5 -1.5 -1.5 0.0 2.06 3 13 -#> x[2,3] -0.5 -0.4 -0.4 -0.4 0.0 2.06 3 13 -#> x[1,4] -1.3 -1.3 -1.3 -1.3 0.0 2.06 3 13 -#> x[2,4] -1.7 -1.7 -1.7 -1.7 0.0 2.06 3 13 -#> x[1,5] -2.3 -2.3 -2.3 -2.3 0.0 2.06 3 13 -#> x[2,5] -1.2 -1.2 -1.2 -1.2 0.0 2.06 3 13 -#> x[1,6] -3.9 -3.9 -3.9 -3.9 0.0 2.06 3 13 -#> x[2,6] -0.1 -0.1 -0.1 -0.1 0.0 2.06 3 13 -#> x[1,7] -2.3 -2.2 -2.2 -2.2 0.0 2.06 3 13 -#> x[2,7] -1.4 -1.4 -1.3 -1.4 0.0 2.06 3 13 -#> x[1,8] -2.4 -2.4 -2.3 -2.4 0.0 2.06 3 13 -#> x[2,8] -1.0 -1.0 -0.9 -1.0 0.0 2.06 3 13 -#> x[1,9] -2.0 -2.0 -1.9 -2.0 0.0 2.06 3 13 -#> x[2,9] -0.4 -0.4 -0.3 -0.3 0.0 2.06 3 13 -#> x[1,10] -1.7 -1.6 -1.6 -1.6 0.0 2.06 3 13 -#> x[2,10] 0.7 0.7 0.8 0.7 0.0 2.06 3 13 -#> x[1,11] -0.3 -0.2 -0.2 -0.2 0.0 2.06 3 13 -#> x[2,11] 0.6 0.6 0.7 0.6 0.0 2.06 3 13 -#> x[1,12] 1.3 1.3 1.4 1.3 0.0 2.06 3 13 -#> x[2,12] -0.8 -0.8 -0.7 -0.8 0.0 2.06 3 13 -#> x[1,13] 0.7 0.8 0.8 0.7 0.1 2.06 3 13 -#> x[2,13] 0.2 0.3 0.4 0.3 0.1 2.06 3 13 -#> x[1,14] 1.8 1.9 1.9 1.9 0.1 2.06 3 13 -#> x[2,14] -0.4 -0.4 -0.2 -0.3 0.1 2.06 3 13 -#> x[1,15] 2.5 2.6 2.7 2.6 0.1 2.06 3 13 -#> x[2,15] -2.0 -1.9 -1.8 -1.9 0.1 2.06 3 13 -#> x[1,16] 4.0 4.1 4.2 4.1 0.1 2.06 3 13 -#> x[2,16] -1.7 -1.6 -1.5 -1.6 0.1 2.06 3 13 -#> x[1,17] 5.3 5.5 5.5 5.4 0.1 2.06 3 13 -#> x[2,17] -3.5 -3.4 -3.3 -3.4 0.1 2.06 3 13 -#> x[1,18] 6.3 6.4 6.5 6.4 0.1 2.06 3 13 -#> x[2,18] -4.9 -4.8 -4.7 -4.8 0.1 2.06 3 13 -#> x[1,19] 5.8 5.9 6.0 5.9 0.1 2.06 3 13 -#> x[2,19] -4.1 -4.1 -3.9 -4.1 0.1 2.06 3 13 -#> x[1,20] 3.9 4.0 4.1 4.0 0.1 2.06 3 13 -#> x[2,20] -5.3 -5.2 -5.1 -5.2 0.1 2.06 3 13 -#> Z[1,1] -98.0 -98.0 -98.0 -98.0 0.0 2.06 4 13 -#> Z[2,1] 24.0 24.7 25.1 24.7 0.4 2.06 3 13 -#> Z[3,1] -28.3 -28.1 -27.9 -28.1 0.2 2.06 3 13 -#> Z[4,1] -48.4 -47.9 -47.2 -47.9 0.4 2.06 3 13 +#> 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] -96.7 -96.7 -96.7 -96.7 0.0 1.58 4 13 -#> Z[3,2] -51.4 -51.3 -50.9 -51.2 0.2 2.06 4 13 -#> Z[4,2] 29.8 30.2 30.4 30.2 0.2 2.06 3 13 -#> log_lik[1] -57.2 -52.1 -45.5 -52.2 4.3 2.06 3 13 -#> log_lik[2] -7.8 -7.5 -6.9 -7.4 0.3 2.06 3 13 -#> log_lik[3] -7.6 -7.1 -6.6 -7.1 0.4 2.06 3 13 -#> log_lik[4] -17.2 -15.7 -13.9 -15.8 1.2 2.06 3 13 -#> log_lik[5] -4.0 -3.9 -3.9 -3.9 0.0 2.06 4 13 -#> log_lik[6] -54.5 -50.1 -44.5 -50.2 3.7 2.06 3 13 -#> log_lik[7] -15.4 -14.2 -12.8 -14.3 1.0 2.06 3 13 -#> log_lik[8] -10.0 -9.5 -8.8 -9.5 0.5 2.06 3 13 -#> log_lik[9] -76.9 -70.4 -61.9 -70.5 5.5 2.06 3 13 -#> log_lik[10] -3.6 -3.6 -3.5 -3.6 0.0 1.71 4 13 -#> log_lik[11] -18.5 -16.7 -14.4 -16.8 1.5 2.06 3 13 -#> log_lik[12] -15.0 -13.9 -12.7 -14.0 0.8 2.06 3 13 -#> log_lik[13] -58.5 -54.1 -48.5 -54.2 3.7 2.06 3 13 -#> log_lik[14] -68.1 -60.2 -50.5 -60.6 6.5 2.06 3 13 -#> log_lik[15] -59.2 -52.8 -44.6 -53.0 5.4 2.06 3 13 -#> log_lik[16] -3.8 -3.7 -3.6 -3.7 0.1 2.06 3 13 -#> log_lik[17] -173.3 -158.9 -140.3 -159.2 12.1 2.06 3 13 -#> log_lik[18] -16.4 -14.5 -12.2 -14.6 1.5 2.06 3 13 -#> log_lik[19] -59.9 -53.4 -44.9 -53.5 5.5 2.06 3 13 -#> log_lik[20] -21.1 -19.6 -18.1 -19.7 1.1 2.06 3 13 -#> log_lik[21] -496.1 -451.9 -394.8 -452.9 37.3 2.06 3 13 -#> log_lik[22] -28.9 -27.0 -24.7 -27.1 1.6 2.06 3 13 -#> log_lik[23] -49.5 -44.0 -37.0 -44.2 4.6 2.06 3 13 -#> log_lik[24] -119.9 -108.2 -93.8 -108.6 9.6 2.06 3 13 -#> log_lik[25] -161.1 -148.6 -132.6 -149.0 10.5 2.06 3 13 -#> log_lik[26] -25.7 -22.5 -18.1 -22.5 2.8 2.06 3 13 -#> log_lik[27] -65.6 -58.4 -48.9 -58.6 6.2 2.06 3 13 -#> log_lik[28] -17.6 -16.7 -15.8 -16.8 0.7 2.06 3 13 -#> log_lik[29] -184.5 -170.5 -152.2 -170.9 11.9 2.06 3 13 -#> log_lik[30] -8.1 -7.1 -5.9 -7.2 0.8 2.06 3 13 -#> log_lik[31] -51.0 -45.3 -37.9 -45.5 4.8 2.06 3 13 -#> log_lik[32] -26.8 -25.2 -23.4 -25.3 1.3 2.06 3 13 -#> log_lik[33] -129.5 -120.7 -109.2 -121.0 7.5 2.06 3 13 -#> log_lik[34] -4.5 -4.0 -3.8 -4.1 0.3 2.06 3 13 -#> log_lik[35] -23.3 -20.8 -17.5 -20.9 2.1 2.06 3 13 -#> log_lik[36] -26.0 -24.7 -23.1 -24.8 1.1 2.06 3 13 -#> log_lik[37] -88.2 -83.2 -77.0 -83.6 4.1 2.06 3 13 -#> log_lik[38] -43.8 -42.5 -41.3 -42.6 0.9 2.06 3 13 -#> log_lik[39] -3.7 -3.7 -3.6 -3.7 0.0 2.06 4 13 -#> log_lik[40] -37.0 -34.9 -32.5 -35.1 1.7 2.06 3 13 -#> log_lik[41] -5.5 -4.7 -4.3 -4.8 0.4 2.06 3 13 -#> log_lik[42] -17.6 -15.9 -15.3 -16.1 0.8 2.06 3 13 -#> log_lik[43] -5.4 -5.4 -5.4 -5.4 0.0 0.98 9 13 -#> log_lik[44] -6.6 -6.0 -5.6 -6.0 0.3 2.06 3 13 -#> log_lik[45] -68.0 -57.7 -44.9 -57.8 8.6 2.06 3 13 -#> log_lik[46] -49.1 -40.4 -28.9 -40.5 7.4 2.06 3 13 -#> log_lik[47] -3.5 -3.5 -3.4 -3.5 0.0 2.06 3 13 -#> log_lik[48] -33.5 -28.1 -21.2 -28.2 4.5 2.06 3 13 -#> log_lik[49] -25.1 -20.7 -15.1 -20.7 3.7 2.06 3 13 -#> log_lik[50] -4.6 -3.6 -3.4 -3.8 0.4 2.06 3 13 -#> log_lik[51] -7.7 -7.5 -7.4 -7.6 0.1 2.06 4 13 -#> log_lik[52] -6.9 -5.8 -4.6 -5.9 0.8 2.06 3 13 -#> log_lik[53] -126.4 -107.7 -83.8 -107.8 15.7 2.06 3 13 -#> log_lik[54] -29.5 -23.4 -15.2 -23.4 5.3 2.06 3 13 -#> log_lik[55] -7.5 -7.3 -7.2 -7.3 0.1 2.06 4 13 -#> log_lik[56] -41.4 -34.4 -25.4 -34.4 5.9 2.06 3 13 -#> log_lik[57] -247.4 -212.9 -168.9 -213.3 28.9 2.06 3 13 -#> log_lik[58] -235.2 -200.0 -152.2 -200.1 30.5 2.06 3 13 -#> log_lik[59] -5.5 -5.2 -4.7 -5.2 0.3 2.06 3 13 -#> log_lik[60] -129.0 -109.4 -83.8 -109.5 16.6 2.06 3 13 -#> log_lik[61] -588.4 -512.8 -416.1 -513.9 63.4 2.06 3 13 -#> log_lik[62] -250.0 -211.4 -159.0 -211.7 33.4 2.06 3 13 -#> log_lik[63] -7.1 -6.9 -6.8 -7.0 0.1 1.87 4 13 -#> log_lik[64] -225.0 -191.9 -149.2 -192.3 27.8 2.06 3 13 -#> log_lik[65] -1014.2 -889.4 -729.5 -891.7 104.7 2.06 3 13 -#> log_lik[66] -780.8 -675.1 -533.0 -676.3 91.0 2.06 3 13 -#> log_lik[67] -5.0 -4.8 -4.4 -4.8 0.2 2.06 4 13 -#> log_lik[68] -484.2 -417.4 -330.4 -418.3 56.4 2.06 3 13 -#> log_lik[69] -1403.0 -1234.1 -1017.9 -1237.4 141.7 2.06 3 13 -#> log_lik[70] -1408.6 -1228.1 -985.3 -1230.0 155.5 2.06 3 13 -#> log_lik[71] -19.3 -17.5 -14.2 -17.4 1.8 2.06 3 13 -#> log_lik[72] -747.2 -647.2 -516.2 -648.3 84.7 2.06 3 13 -#> log_lik[73] -1193.6 -1047.2 -859.8 -1050.0 122.8 2.06 3 13 -#> log_lik[74] -1040.8 -902.9 -717.3 -904.5 118.8 2.06 3 13 -#> log_lik[75] -9.2 -8.6 -7.2 -8.5 0.7 2.06 3 13 -#> log_lik[76] -594.8 -513.3 -407.0 -514.4 68.8 2.06 3 13 -#> log_lik[77] -553.7 -479.1 -385.3 -480.8 62.0 2.06 3 13 -#> log_lik[78] -1285.3 -1121.1 -900.7 -1123.1 141.1 2.06 3 13 -#> log_lik[79] -84.8 -75.9 -61.8 -75.6 8.4 2.06 3 13 -#> log_lik[80] -440.0 -378.4 -297.1 -378.9 52.3 2.06 3 13 -#> xstar[1,1] 2.3 3.9 5.4 3.8 1.1 0.98 13 13 -#> xstar[2,1] -7.1 -5.3 -3.8 -5.2 1.2 0.91 13 13 -#> sigma[1] 12.1 12.7 13.7 12.7 0.6 2.06 3 13 -#> lp__ -28676.7 -26708.9 -24112.0 -26733.3 1676.3 2.06 3 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 #> #> 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 dacefb9..79afe9f 100644 --- a/docs/reference/dfa_loadings.html +++ b/docs/reference/dfa_loadings.html @@ -129,8 +129,8 @@

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 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: @@ -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: 0.056592 seconds (Warm-up) -#> Chain 1: 0.815923 seconds (Sampling) -#> Chain 1: 0.872515 seconds (Total) +#> Chain 1: Elapsed Time: 0.042954 seconds (Warm-up) +#> Chain 1: 0.392739 seconds (Sampling) +#> Chain 1: 0.435693 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/dfa_trends.html b/docs/reference/dfa_trends.html index db500dd..fee2c6c 100644 --- a/docs/reference/dfa_trends.html +++ b/docs/reference/dfa_trends.html @@ -113,8 +113,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.76 seconds. +#> 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: 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: 0.011702 seconds (Warm-up) -#> Chain 1: 0.010977 seconds (Sampling) -#> Chain 1: 0.022679 seconds (Total) +#> Chain 1: Elapsed Time: 0.004706 seconds (Warm-up) +#> Chain 1: 0.005915 seconds (Sampling) +#> Chain 1: 0.010621 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 9dba8e5..3227cf2 100644 --- a/docs/reference/find_dfa_trends.html +++ b/docs/reference/find_dfa_trends.html @@ -153,8 +153,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6.7e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.67 seconds. +#> 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: 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: 0.006656 seconds (Warm-up) -#> Chain 1: 0.525723 seconds (Sampling) -#> Chain 1: 0.532379 seconds (Total) +#> Chain 1: Elapsed Time: 0.003748 seconds (Warm-up) +#> Chain 1: 0.242068 seconds (Sampling) +#> Chain 1: 0.245816 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 9e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.9 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: @@ -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: 0.044923 seconds (Warm-up) -#> Chain 1: 0.042976 seconds (Sampling) -#> Chain 1: 0.087899 seconds (Total) +#> Chain 1: Elapsed Time: 0.018711 seconds (Warm-up) +#> Chain 1: 0.020826 seconds (Sampling) +#> Chain 1: 0.039537 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 25ab599..072bf55 100644 --- a/docs/reference/find_inverted_chains.html +++ b/docs/reference/find_inverted_chains.html @@ -115,8 +115,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds. +#> 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: 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: 0.004587 seconds (Warm-up) -#> Chain 1: 0.015671 seconds (Sampling) -#> Chain 1: 0.020258 seconds (Total) +#> Chain 1: Elapsed Time: 0.002599 seconds (Warm-up) +#> Chain 1: 0.007209 seconds (Sampling) +#> Chain 1: 0.009808 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 2). #> Chain 2: -#> Chain 2: Gradient evaluation took 6e-05 seconds -#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.6 seconds. +#> 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: 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: 0.002598 seconds (Warm-up) -#> Chain 2: 0.008402 seconds (Sampling) -#> Chain 2: 0.011 seconds (Total) +#> Chain 2: Elapsed Time: 0.002685 seconds (Warm-up) +#> Chain 2: 0.004633 seconds (Sampling) +#> Chain 2: 0.007318 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 6253015..ba00d80 100644 --- a/docs/reference/find_regimes.html +++ b/docs/reference/find_regimes.html @@ -138,8 +138,8 @@

Examples

#> #> SAMPLING FOR MODEL 'regime_1' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 2.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds. +#> 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: 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: 0.002538 seconds (Warm-up) -#> Chain 1: 0.002198 seconds (Sampling) -#> Chain 1: 0.004736 seconds (Total) +#> Chain 1: Elapsed Time: 0.001218 seconds (Warm-up) +#> Chain 1: 0.000924 seconds (Sampling) +#> Chain 1: 0.002142 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 0.000196 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.96 seconds. +#> 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: 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: 0.643403 seconds (Warm-up) -#> Chain 1: 0.644215 seconds (Sampling) -#> Chain 1: 1.28762 seconds (Total) +#> Chain 1: Elapsed Time: 0.33669 seconds (Warm-up) +#> Chain 1: 0.321606 seconds (Sampling) +#> Chain 1: 0.658296 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 @@ -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 15:26:43 2023. +#> Samples were drawn using NUTS(diag_e) at Thu Jun 15 20:34:28 2023. #> 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.html b/docs/reference/find_swans.html index 85d7453..feacef6 100644 --- a/docs/reference/find_swans.html +++ b/docs/reference/find_swans.html @@ -127,8 +127,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7.5e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.75 seconds. +#> 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: 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: 0.401828 seconds (Warm-up) -#> Chain 1: 0.005841 seconds (Sampling) -#> Chain 1: 0.407669 seconds (Total) +#> Chain 1: Elapsed Time: 0.240815 seconds (Warm-up) +#> Chain 1: 0.002819 seconds (Sampling) +#> Chain 1: 0.243634 seconds (Total) #> Chain 1: #> Warning: There were 25 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup diff --git a/docs/reference/fit_dfa.html b/docs/reference/fit_dfa.html index e4b798d..b8207a1 100644 --- a/docs/reference/fit_dfa.html +++ b/docs/reference/fit_dfa.html @@ -319,8 +319,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6.7e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.67 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: @@ -345,9 +345,9 @@

Examples

#> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.010289 seconds (Warm-up) -#> Chain 1: 0.155572 seconds (Sampling) -#> Chain 1: 0.165861 seconds (Total) +#> Chain 1: Elapsed Time: 0.006447 seconds (Warm-up) +#> Chain 1: 0.107739 seconds (Sampling) +#> Chain 1: 0.114186 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 fbed922..226f6c1 100644 --- a/docs/reference/fit_regimes.html +++ b/docs/reference/fit_regimes.html @@ -133,8 +133,8 @@

Examples

#> #> SAMPLING FOR MODEL 'regime_1' 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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 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: 0.001475 seconds (Warm-up) -#> Chain 1: 0.001228 seconds (Sampling) -#> Chain 1: 0.002703 seconds (Total) +#> Chain 1: Elapsed Time: 0.001149 seconds (Warm-up) +#> Chain 1: 0.001079 seconds (Sampling) +#> Chain 1: 0.002228 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 15:26:57 2023. +#> Samples were drawn using NUTS(diag_e) at Thu Jun 15 20:34:33 2023. #> 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/loo.html b/docs/reference/loo.html index f481d12..cccf1a6 100644 --- a/docs/reference/loo.html +++ b/docs/reference/loo.html @@ -125,8 +125,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.63 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: 0.009508 seconds (Warm-up) -#> Chain 1: 0.562214 seconds (Sampling) -#> Chain 1: 0.571722 seconds (Total) +#> Chain 1: Elapsed Time: 0.006716 seconds (Warm-up) +#> Chain 1: 0.328732 seconds (Sampling) +#> Chain 1: 0.335448 seconds (Total) #> Chain 1: #> Warning: There were 2 divergent transitions after warmup. See #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup diff --git a/docs/reference/plot_fitted-1.png b/docs/reference/plot_fitted-1.png index ed2d6c6..8ae7361 100644 Binary files a/docs/reference/plot_fitted-1.png and b/docs/reference/plot_fitted-1.png differ diff --git a/docs/reference/plot_fitted.html b/docs/reference/plot_fitted.html index 5c2245e..898440e 100644 --- a/docs/reference/plot_fitted.html +++ b/docs/reference/plot_fitted.html @@ -125,8 +125,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds. +#> 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: 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: 0.014846 seconds (Warm-up) -#> Chain 1: 0.061652 seconds (Sampling) -#> Chain 1: 0.076498 seconds (Total) +#> Chain 1: Elapsed Time: 0.007462 seconds (Warm-up) +#> Chain 1: 0.029935 seconds (Sampling) +#> Chain 1: 0.037397 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.html b/docs/reference/plot_loadings.html index b0ec884..65d96fd 100644 --- a/docs/reference/plot_loadings.html +++ b/docs/reference/plot_loadings.html @@ -136,8 +136,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.6 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: @@ -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: 0.062456 seconds (Warm-up) -#> Chain 1: 0.759719 seconds (Sampling) -#> Chain 1: 0.822175 seconds (Total) +#> Chain 1: Elapsed Time: 0.031472 seconds (Warm-up) +#> Chain 1: 0.383423 seconds (Sampling) +#> Chain 1: 0.414895 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/plot_regime_model.html b/docs/reference/plot_regime_model.html index d8ffc4d..936ccf5 100644 --- a/docs/reference/plot_regime_model.html +++ b/docs/reference/plot_regime_model.html @@ -134,8 +134,8 @@

Examples

#> #> SAMPLING FOR MODEL 'hmm_gaussian' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000144 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.44 seconds. +#> 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: 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: 0.385931 seconds (Warm-up) -#> Chain 1: 0.456577 seconds (Sampling) -#> Chain 1: 0.842508 seconds (Total) +#> Chain 1: Elapsed Time: 0.235185 seconds (Warm-up) +#> Chain 1: 0.27697 seconds (Sampling) +#> Chain 1: 0.512155 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 fc84328..1eadad5 100644 --- a/docs/reference/plot_trends.html +++ b/docs/reference/plot_trends.html @@ -123,8 +123,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6.5e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.65 seconds. +#> 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: 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: 0.008094 seconds (Warm-up) -#> Chain 1: 0.005716 seconds (Sampling) -#> Chain 1: 0.01381 seconds (Total) +#> Chain 1: Elapsed Time: 0.005253 seconds (Warm-up) +#> Chain 1: 0.007281 seconds (Sampling) +#> Chain 1: 0.012534 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/rotate_trends.html b/docs/reference/rotate_trends.html index cc850fe..fc0b5ed 100644 --- a/docs/reference/rotate_trends.html +++ b/docs/reference/rotate_trends.html @@ -108,8 +108,8 @@

Examples

#> #> 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 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: @@ -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: 0.007431 seconds (Warm-up) -#> Chain 1: 0.180205 seconds (Sampling) -#> Chain 1: 0.187636 seconds (Total) +#> Chain 1: Elapsed Time: 0.007536 seconds (Warm-up) +#> Chain 1: 0.109812 seconds (Sampling) +#> Chain 1: 0.117348 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/trend_cor.html b/docs/reference/trend_cor.html index 768ca8a..3c892b1 100644 --- a/docs/reference/trend_cor.html +++ b/docs/reference/trend_cor.html @@ -161,8 +161,8 @@

Examples

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds. +#> 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: 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: 0.018319 seconds (Warm-up) -#> Chain 1: 0.508265 seconds (Sampling) -#> Chain 1: 0.526584 seconds (Total) +#> Chain 1: Elapsed Time: 0.015496 seconds (Warm-up) +#> Chain 1: 0.318609 seconds (Sampling) +#> Chain 1: 0.334105 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 @@ -300,8 +300,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds. +#> 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: 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: 0.006072 seconds (Warm-up) -#> Chain 1: 0.003867 seconds (Sampling) -#> Chain 1: 0.009939 seconds (Total) +#> Chain 1: Elapsed Time: 0.005817 seconds (Warm-up) +#> Chain 1: 0.003467 seconds (Sampling) +#> Chain 1: 0.009284 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 1.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.12 seconds. +#> 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: 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: 0.007949 seconds (Warm-up) -#> Chain 1: 0.003614 seconds (Sampling) -#> Chain 1: 0.011563 seconds (Total) +#> Chain 1: Elapsed Time: 0.00412 seconds (Warm-up) +#> Chain 1: 0.003064 seconds (Sampling) +#> Chain 1: 0.007184 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 @@ -383,9 +383,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006607 seconds (Warm-up) -#> Chain 1: 0.003077 seconds (Sampling) -#> Chain 1: 0.009684 seconds (Total) +#> Chain 1: Elapsed Time: 0.005732 seconds (Warm-up) +#> Chain 1: 0.002684 seconds (Sampling) +#> Chain 1: 0.008416 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 @@ -393,8 +393,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -411,9 +411,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005042 seconds (Warm-up) -#> Chain 1: 0.003779 seconds (Sampling) -#> Chain 1: 0.008821 seconds (Total) +#> Chain 1: Elapsed Time: 0.004293 seconds (Warm-up) +#> Chain 1: 0.003458 seconds (Sampling) +#> Chain 1: 0.007751 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 +424,8 @@

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: @@ -442,9 +442,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008387 seconds (Warm-up) -#> Chain 1: 0.005475 seconds (Sampling) -#> Chain 1: 0.013862 seconds (Total) +#> Chain 1: Elapsed Time: 0.00405 seconds (Warm-up) +#> Chain 1: 0.002739 seconds (Sampling) +#> Chain 1: 0.006789 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 +455,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -473,9 +473,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005959 seconds (Warm-up) -#> Chain 1: 0.005937 seconds (Sampling) -#> Chain 1: 0.011896 seconds (Total) +#> Chain 1: Elapsed Time: 0.004658 seconds (Warm-up) +#> Chain 1: 0.003139 seconds (Sampling) +#> Chain 1: 0.007797 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 @@ -486,8 +486,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -504,9 +504,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008332 seconds (Warm-up) -#> Chain 1: 0.004162 seconds (Sampling) -#> Chain 1: 0.012494 seconds (Total) +#> Chain 1: Elapsed Time: 0.004471 seconds (Warm-up) +#> Chain 1: 0.003623 seconds (Sampling) +#> Chain 1: 0.008094 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 +517,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' 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: @@ -535,9 +535,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008396 seconds (Warm-up) -#> Chain 1: 0.004506 seconds (Sampling) -#> Chain 1: 0.012902 seconds (Total) +#> Chain 1: Elapsed Time: 0.004553 seconds (Warm-up) +#> Chain 1: 0.002928 seconds (Sampling) +#> Chain 1: 0.007481 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 @@ -569,9 +569,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.009141 seconds (Warm-up) -#> Chain 1: 0.006223 seconds (Sampling) -#> Chain 1: 0.015364 seconds (Total) +#> Chain 1: Elapsed Time: 0.004722 seconds (Warm-up) +#> Chain 1: 0.003233 seconds (Sampling) +#> Chain 1: 0.007955 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 +582,8 @@

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 1.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -600,9 +600,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004804 seconds (Warm-up) -#> Chain 1: 0.005351 seconds (Sampling) -#> Chain 1: 0.010155 seconds (Total) +#> Chain 1: Elapsed Time: 0.004277 seconds (Warm-up) +#> Chain 1: 0.002968 seconds (Sampling) +#> Chain 1: 0.007245 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 @@ -631,9 +631,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004876 seconds (Warm-up) -#> Chain 1: 0.005862 seconds (Sampling) -#> Chain 1: 0.010738 seconds (Total) +#> Chain 1: Elapsed Time: 0.004169 seconds (Warm-up) +#> Chain 1: 0.003179 seconds (Sampling) +#> Chain 1: 0.007348 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 +644,8 @@

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 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: @@ -662,9 +662,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005808 seconds (Warm-up) -#> Chain 1: 0.005322 seconds (Sampling) -#> Chain 1: 0.01113 seconds (Total) +#> Chain 1: Elapsed Time: 0.00384 seconds (Warm-up) +#> Chain 1: 0.00309 seconds (Sampling) +#> Chain 1: 0.00693 seconds (Total) #> Chain 1: #> Warning: The largest R-hat is 1.12, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -678,8 +678,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. +#> 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: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -696,9 +696,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007318 seconds (Warm-up) -#> Chain 1: 0.005714 seconds (Sampling) -#> Chain 1: 0.013032 seconds (Total) +#> Chain 1: Elapsed Time: 0.0044 seconds (Warm-up) +#> Chain 1: 0.003328 seconds (Sampling) +#> Chain 1: 0.007728 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 @@ -709,8 +709,8 @@

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 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: @@ -727,9 +727,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005162 seconds (Warm-up) -#> Chain 1: 0.005034 seconds (Sampling) -#> Chain 1: 0.010196 seconds (Total) +#> Chain 1: Elapsed Time: 0.003971 seconds (Warm-up) +#> Chain 1: 0.002547 seconds (Sampling) +#> Chain 1: 0.006518 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 +740,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -758,9 +758,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00655 seconds (Warm-up) -#> Chain 1: 0.004744 seconds (Sampling) -#> Chain 1: 0.011294 seconds (Total) +#> Chain 1: Elapsed Time: 0.004593 seconds (Warm-up) +#> Chain 1: 0.003597 seconds (Sampling) +#> Chain 1: 0.00819 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 @@ -789,9 +789,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006668 seconds (Warm-up) -#> Chain 1: 0.006062 seconds (Sampling) -#> Chain 1: 0.01273 seconds (Total) +#> Chain 1: Elapsed Time: 0.004481 seconds (Warm-up) +#> Chain 1: 0.003432 seconds (Sampling) +#> Chain 1: 0.007913 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 @@ -820,9 +820,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008947 seconds (Warm-up) -#> Chain 1: 0.004449 seconds (Sampling) -#> Chain 1: 0.013396 seconds (Total) +#> Chain 1: Elapsed Time: 0.00593 seconds (Warm-up) +#> Chain 1: 0.003002 seconds (Sampling) +#> Chain 1: 0.008932 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 +833,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -851,9 +851,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005045 seconds (Warm-up) -#> Chain 1: 0.005981 seconds (Sampling) -#> Chain 1: 0.011026 seconds (Total) +#> Chain 1: Elapsed Time: 0.003715 seconds (Warm-up) +#> Chain 1: 0.003092 seconds (Sampling) +#> Chain 1: 0.006807 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 +864,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -882,9 +882,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005222 seconds (Warm-up) -#> Chain 1: 0.005494 seconds (Sampling) -#> Chain 1: 0.010716 seconds (Total) +#> Chain 1: Elapsed Time: 0.005217 seconds (Warm-up) +#> Chain 1: 0.004779 seconds (Sampling) +#> Chain 1: 0.009996 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 +895,8 @@

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: @@ -913,9 +913,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007594 seconds (Warm-up) -#> Chain 1: 0.006264 seconds (Sampling) -#> Chain 1: 0.013858 seconds (Total) +#> Chain 1: Elapsed Time: 0.003978 seconds (Warm-up) +#> Chain 1: 0.003167 seconds (Sampling) +#> Chain 1: 0.007145 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 +926,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -944,9 +944,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007964 seconds (Warm-up) -#> Chain 1: 0.004678 seconds (Sampling) -#> Chain 1: 0.012642 seconds (Total) +#> Chain 1: Elapsed Time: 0.004054 seconds (Warm-up) +#> Chain 1: 0.003391 seconds (Sampling) +#> Chain 1: 0.007445 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 +957,8 @@

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 1.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -975,9 +975,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00785 seconds (Warm-up) -#> Chain 1: 0.003838 seconds (Sampling) -#> Chain 1: 0.011688 seconds (Total) +#> Chain 1: Elapsed Time: 0.006235 seconds (Warm-up) +#> Chain 1: 0.004832 seconds (Sampling) +#> Chain 1: 0.011067 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 @@ -988,8 +988,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' 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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1006,9 +1006,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.009047 seconds (Warm-up) -#> Chain 1: 0.005452 seconds (Sampling) -#> Chain 1: 0.014499 seconds (Total) +#> Chain 1: Elapsed Time: 0.00475 seconds (Warm-up) +#> Chain 1: 0.002736 seconds (Sampling) +#> Chain 1: 0.007486 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 +1019,8 @@

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 1.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1037,9 +1037,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005632 seconds (Warm-up) -#> Chain 1: 0.003411 seconds (Sampling) -#> Chain 1: 0.009043 seconds (Total) +#> Chain 1: Elapsed Time: 0.008324 seconds (Warm-up) +#> Chain 1: 0.004725 seconds (Sampling) +#> Chain 1: 0.013049 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 +1050,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1068,9 +1068,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006871 seconds (Warm-up) -#> Chain 1: 0.005562 seconds (Sampling) -#> Chain 1: 0.012433 seconds (Total) +#> Chain 1: Elapsed Time: 0.00426 seconds (Warm-up) +#> Chain 1: 0.002904 seconds (Sampling) +#> Chain 1: 0.007164 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 @@ -1087,8 +1087,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1105,9 +1105,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006436 seconds (Warm-up) -#> Chain 1: 0.006374 seconds (Sampling) -#> Chain 1: 0.01281 seconds (Total) +#> Chain 1: Elapsed Time: 0.005423 seconds (Warm-up) +#> Chain 1: 0.006591 seconds (Sampling) +#> Chain 1: 0.012014 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 +1118,8 @@

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 1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1136,9 +1136,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006894 seconds (Warm-up) -#> Chain 1: 0.007132 seconds (Sampling) -#> Chain 1: 0.014026 seconds (Total) +#> Chain 1: Elapsed Time: 0.00396 seconds (Warm-up) +#> Chain 1: 0.003734 seconds (Sampling) +#> Chain 1: 0.007694 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 +1149,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' 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 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: @@ -1167,9 +1167,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008789 seconds (Warm-up) -#> Chain 1: 0.004699 seconds (Sampling) -#> Chain 1: 0.013488 seconds (Total) +#> Chain 1: Elapsed Time: 0.005119 seconds (Warm-up) +#> Chain 1: 0.003674 seconds (Sampling) +#> Chain 1: 0.008793 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 +1180,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1198,9 +1198,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007724 seconds (Warm-up) -#> Chain 1: 0.005802 seconds (Sampling) -#> Chain 1: 0.013526 seconds (Total) +#> Chain 1: Elapsed Time: 0.004585 seconds (Warm-up) +#> Chain 1: 0.002968 seconds (Sampling) +#> Chain 1: 0.007553 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 @@ -1214,8 +1214,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.14 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: @@ -1232,9 +1232,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.009145 seconds (Warm-up) -#> Chain 1: 0.005921 seconds (Sampling) -#> Chain 1: 0.015066 seconds (Total) +#> Chain 1: Elapsed Time: 0.004664 seconds (Warm-up) +#> Chain 1: 0.002985 seconds (Sampling) +#> Chain 1: 0.007649 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 @@ -1245,8 +1245,8 @@

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: @@ -1263,9 +1263,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007339 seconds (Warm-up) -#> Chain 1: 0.003224 seconds (Sampling) -#> Chain 1: 0.010563 seconds (Total) +#> Chain 1: Elapsed Time: 0.004817 seconds (Warm-up) +#> Chain 1: 0.003531 seconds (Sampling) +#> Chain 1: 0.008348 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 @@ -1279,8 +1279,8 @@

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 1.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1297,9 +1297,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005886 seconds (Warm-up) -#> Chain 1: 0.004304 seconds (Sampling) -#> Chain 1: 0.01019 seconds (Total) +#> Chain 1: Elapsed Time: 0.004939 seconds (Warm-up) +#> Chain 1: 0.003643 seconds (Sampling) +#> Chain 1: 0.008582 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 @@ -1313,8 +1313,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1331,9 +1331,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006821 seconds (Warm-up) -#> Chain 1: 0.006403 seconds (Sampling) -#> Chain 1: 0.013224 seconds (Total) +#> Chain 1: Elapsed Time: 0.004155 seconds (Warm-up) +#> Chain 1: 0.003377 seconds (Sampling) +#> Chain 1: 0.007532 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 @@ -1362,9 +1362,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005521 seconds (Warm-up) -#> Chain 1: 0.007836 seconds (Sampling) -#> Chain 1: 0.013357 seconds (Total) +#> Chain 1: Elapsed Time: 0.007592 seconds (Warm-up) +#> Chain 1: 0.006328 seconds (Sampling) +#> Chain 1: 0.01392 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 @@ -1375,8 +1375,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1393,9 +1393,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004138 seconds (Warm-up) -#> Chain 1: 0.003531 seconds (Sampling) -#> Chain 1: 0.007669 seconds (Total) +#> Chain 1: Elapsed Time: 0.004204 seconds (Warm-up) +#> Chain 1: 0.003007 seconds (Sampling) +#> Chain 1: 0.007211 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 +1406,8 @@

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 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: @@ -1424,9 +1424,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004606 seconds (Warm-up) -#> Chain 1: 0.005278 seconds (Sampling) -#> Chain 1: 0.009884 seconds (Total) +#> Chain 1: Elapsed Time: 0.003976 seconds (Warm-up) +#> Chain 1: 0.003396 seconds (Sampling) +#> Chain 1: 0.007372 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 +1437,8 @@

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 1.1e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1455,9 +1455,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00776 seconds (Warm-up) -#> Chain 1: 0.004529 seconds (Sampling) -#> Chain 1: 0.012289 seconds (Total) +#> Chain 1: Elapsed Time: 0.005451 seconds (Warm-up) +#> Chain 1: 0.003302 seconds (Sampling) +#> Chain 1: 0.008753 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 +1468,8 @@

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 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: @@ -1486,9 +1486,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.008549 seconds (Warm-up) -#> Chain 1: 0.003655 seconds (Sampling) -#> Chain 1: 0.012204 seconds (Total) +#> Chain 1: Elapsed Time: 0.004771 seconds (Warm-up) +#> Chain 1: 0.004268 seconds (Sampling) +#> Chain 1: 0.009039 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 @@ -1499,8 +1499,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1517,9 +1517,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007843 seconds (Warm-up) -#> Chain 1: 0.003357 seconds (Sampling) -#> Chain 1: 0.0112 seconds (Total) +#> Chain 1: Elapsed Time: 0.005298 seconds (Warm-up) +#> Chain 1: 0.002981 seconds (Sampling) +#> Chain 1: 0.008279 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 @@ -1533,8 +1533,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1551,9 +1551,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006636 seconds (Warm-up) -#> Chain 1: 0.005557 seconds (Sampling) -#> Chain 1: 0.012193 seconds (Total) +#> Chain 1: Elapsed Time: 0.00433 seconds (Warm-up) +#> Chain 1: 0.002801 seconds (Sampling) +#> Chain 1: 0.007131 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 +1564,8 @@

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: @@ -1582,9 +1582,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007294 seconds (Warm-up) -#> Chain 1: 0.00483 seconds (Sampling) -#> Chain 1: 0.012124 seconds (Total) +#> Chain 1: Elapsed Time: 0.00376 seconds (Warm-up) +#> Chain 1: 0.003069 seconds (Sampling) +#> Chain 1: 0.006829 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 +1595,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1613,9 +1613,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.006141 seconds (Warm-up) -#> Chain 1: 0.004949 seconds (Sampling) -#> Chain 1: 0.01109 seconds (Total) +#> Chain 1: Elapsed Time: 0.004083 seconds (Warm-up) +#> Chain 1: 0.003106 seconds (Sampling) +#> Chain 1: 0.007189 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 +1626,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1644,9 +1644,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00641 seconds (Warm-up) -#> Chain 1: 0.004396 seconds (Sampling) -#> Chain 1: 0.010806 seconds (Total) +#> Chain 1: Elapsed Time: 0.004754 seconds (Warm-up) +#> Chain 1: 0.003369 seconds (Sampling) +#> Chain 1: 0.008123 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 @@ -1660,8 +1660,8 @@

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 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: @@ -1678,9 +1678,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00777 seconds (Warm-up) -#> Chain 1: 0.003456 seconds (Sampling) -#> Chain 1: 0.011226 seconds (Total) +#> Chain 1: Elapsed Time: 0.004555 seconds (Warm-up) +#> Chain 1: 0.003008 seconds (Sampling) +#> Chain 1: 0.007563 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 +1694,8 @@

Examples

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds. +#> 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: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1712,9 +1712,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005892 seconds (Warm-up) -#> Chain 1: 0.003323 seconds (Sampling) -#> Chain 1: 0.009215 seconds (Total) +#> Chain 1: Elapsed Time: 0.004181 seconds (Warm-up) +#> Chain 1: 0.002933 seconds (Sampling) +#> Chain 1: 0.007114 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 +1725,8 @@

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 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: @@ -1743,9 +1743,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007449 seconds (Warm-up) -#> Chain 1: 0.006789 seconds (Sampling) -#> Chain 1: 0.014238 seconds (Total) +#> Chain 1: Elapsed Time: 0.004106 seconds (Warm-up) +#> Chain 1: 0.003448 seconds (Sampling) +#> Chain 1: 0.007554 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 +1756,8 @@

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 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: @@ -1774,9 +1774,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005147 seconds (Warm-up) -#> Chain 1: 0.004684 seconds (Sampling) -#> Chain 1: 0.009831 seconds (Total) +#> Chain 1: Elapsed Time: 0.004343 seconds (Warm-up) +#> Chain 1: 0.004019 seconds (Sampling) +#> Chain 1: 0.008362 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 +1787,8 @@

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 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: @@ -1805,9 +1805,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.009134 seconds (Warm-up) -#> Chain 1: 0.004397 seconds (Sampling) -#> Chain 1: 0.013531 seconds (Total) +#> Chain 1: Elapsed Time: 0.004541 seconds (Warm-up) +#> Chain 1: 0.003651 seconds (Sampling) +#> Chain 1: 0.008192 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 +1818,8 @@

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 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: @@ -1836,9 +1836,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.007992 seconds (Warm-up) -#> Chain 1: 0.006434 seconds (Sampling) -#> Chain 1: 0.014426 seconds (Total) +#> Chain 1: Elapsed Time: 0.004077 seconds (Warm-up) +#> Chain 1: 0.003211 seconds (Sampling) +#> Chain 1: 0.007288 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 +1849,8 @@

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 8e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1867,9 +1867,9 @@

Examples

#> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00779 seconds (Warm-up) -#> Chain 1: 0.006204 seconds (Sampling) -#> Chain 1: 0.013994 seconds (Total) +#> Chain 1: Elapsed Time: 0.005153 seconds (Warm-up) +#> Chain 1: 0.003348 seconds (Sampling) +#> Chain 1: 0.008501 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 diff --git a/vignettes/a1_bayesdfa.Rmd b/vignettes/a1_bayesdfa.Rmd index ff1b81b..b30f5bd 100644 --- a/vignettes/a1_bayesdfa.Rmd +++ b/vignettes/a1_bayesdfa.Rmd @@ -336,11 +336,11 @@ sim_dat <- sim_dfa( df <- data.frame(obs = c(sim_dat$y_sim), time = sort(rep(1:20,4)), ts = rep(1:4,20)) -df$se <- runif(nrow(df), 0.3, 0.5) -df$se[which(df$ts == 2)] = 0.04 +df$se <- runif(nrow(df), 0.6, 0.8) +df$se[which(df$ts == 2)] = 0.2 ``` -Next we can generate the weights (this is redundant, and "se" could be used instead in the function call below). Because the weights are used as an offset, $$\sigma^2 / w_i$$, we don't want to use the SE alone as a weight but make them inversely related to the SE. +Next we can generate the weights (this is redundant, and "se" could be used instead in the function call below). Because the weights are used as an offset, $$\sigma^2 / w_i$$, we don't want to use the SE alone as a weight but make them inversely related to the SE. As a quick note, the scale of these may affect estimation and some additional normalization may be needed (rather than standard errors, it may be more helpful to think about the sample size each data point represents). ```{r} df$weights <- (1 / df$se)^2