From 4a9afddc72b9988d736054edb7e402d94cabce72 Mon Sep 17 00:00:00 2001 From: Eric Ward Date: Tue, 25 May 2021 10:02:30 -0700 Subject: [PATCH] shorten string length in example --- CRAN-RELEASE | 4 +- R/dfa_cv.R | 24 +- docs/pkgdown.yml | 2 +- docs/reference/dfa_cv.html | 24 +- docs/reference/dfa_fitted.html | 10 +- docs/reference/dfa_loadings.html | 10 +- docs/reference/dfa_trends.html | 10 +- docs/reference/find_dfa_trends.html | 20 +- docs/reference/find_inverted_chains.html | 20 +- docs/reference/find_regimes.html | 18 +- docs/reference/find_swans.html | 10 +- docs/reference/fit_dfa.html | 10 +- docs/reference/fit_regimes.html | 6 +- docs/reference/loo.html | 10 +- docs/reference/plot_fitted.html | 10 +- docs/reference/plot_loadings.html | 10 +- docs/reference/plot_regime_model.html | 10 +- docs/reference/plot_trends.html | 10 +- docs/reference/rotate_trends.html | 10 +- docs/reference/trend_cor.html | 492 +++++++++++------------ man/dfa_cv.Rd | 24 +- src/RcppExports-507982db.o.tmp | 0 22 files changed, 384 insertions(+), 360 deletions(-) create mode 100644 src/RcppExports-507982db.o.tmp diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 04019aa..938ce69 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2021-05-18. -Once it is accepted, delete this file and tag the release (commit 037b6a9). +This package was submitted to CRAN on 2021-05-25. +Once it is accepted, delete this file and tag the release (commit d85e775). diff --git a/R/dfa_cv.R b/R/dfa_cv.R index fcd3168..2e13021 100644 --- a/R/dfa_cv.R +++ b/R/dfa_cv.R @@ -21,26 +21,34 @@ #' set.seed(42) #' s <- sim_dfa(num_trends = 1, num_years = 20, num_ts = 3) #' obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -#' long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), "time" = rep(1:20, 3)) -#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) +#' long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), +#' "time" = rep(1:20, 3)) +#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +#' sample = FALSE) #' # random folds #' fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) #' #' # folds can also be passed in #' fold_ids <- sample(1:5, size = nrow(long), replace = TRUE) -#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -#' fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, fold_ids = fold_ids) +#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +#' sample = FALSE) +#' fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, +#' fold_ids = fold_ids) #' #' # do an example of leave-time-out cross validation where years are dropped #' fold_ids <- long$time -#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -#' fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, fold_ids = fold_ids) +#' m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +#' sample = FALSE) +#' fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, +#' fold_ids = fold_ids) #' #' # example with covariates and long format data -#' obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, "covariate" = 1:2) +#' obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, +#' "covariate" = 1:2) #' obs_covar$value <- rnorm(nrow(obs_covar), 0, 0.1) #' obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -#' m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, data_shape = "long", sample = FALSE) +#' m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, +#' data_shape = "long", sample = FALSE) #' fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) #' } #' diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4d139d0..df5acd0 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,5 +7,5 @@ articles: compositional: compositional.html covariates: covariates.html estimate_process_sigma: estimate_process_sigma.html -last_built: 2021-05-25T13:09Z +last_built: 2021-05-25T16:39Z diff --git a/docs/reference/dfa_cv.html b/docs/reference/dfa_cv.html index cd3daac..ebff0b7 100644 --- a/docs/reference/dfa_cv.html +++ b/docs/reference/dfa_cv.html @@ -202,26 +202,34 @@

Examp set.seed(42) s <- sim_dfa(num_trends = 1, num_years = 20, num_ts = 3) obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), "time" = rep(1:20, 3)) -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) +long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), +"time" = rep(1:20, 3)) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) # random folds fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) # folds can also be passed in fold_ids <- sample(1:5, size = nrow(long), replace = TRUE) -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, fold_ids = fold_ids) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) +fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, +fold_ids = fold_ids) # do an example of leave-time-out cross validation where years are dropped fold_ids <- long$time -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, fold_ids = fold_ids) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) +fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, +fold_ids = fold_ids) # example with covariates and long format data -obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, "covariate" = 1:2) +obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, +"covariate" = 1:2) obs_covar$value <- rnorm(nrow(obs_covar), 0, 0.1) obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, data_shape = "long", sample = FALSE) +m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, +data_shape = "long", sample = FALSE) fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) } diff --git a/docs/reference/dfa_fitted.html b/docs/reference/dfa_fitted.html index 41fb158..43d4483 100644 --- a/docs/reference/dfa_fitted.html +++ b/docs/reference/dfa_fitted.html @@ -177,8 +177,8 @@

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#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 0.000125 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.25 seconds. +#> Chain 1: Gradient evaluation took 0.000159 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.59 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -203,9 +203,9 @@

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#> Warning: There were 11 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
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#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 2.9e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds. +#> Chain 1: Gradient evaluation took 2.8e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -213,9 +213,9 @@

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#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
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#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.6e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds. +#> Chain 1: Gradient evaluation took 4.5e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -199,9 +199,9 @@

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#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
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#> Warning: There were 5 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
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Examp #> factor on rank normalized split chains (at convergence, Rhat <= 1.05).

#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
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#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
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#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 3.5e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds. +#> Chain 1: Gradient evaluation took 3.4e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -199,15 +199,15 @@

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#> Warning: There were 2 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
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#> Warning: The largest R-hat is 1.43, indicating chains have not mixed. #> Running the chains for more iterations may help. See #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -240,8 +240,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> Warning: Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
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#> Warning: The largest R-hat is NA, indicating chains have not mixed. #> Running the chains for more iterations may help. See #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -491,7 +491,7 @@

Examp #> 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 Tue May 25 06:10:06 2021. +#> Samples were drawn using NUTS(diag_e) at Tue May 25 09:39:33 2021. #> 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 5508b4d..bb3be40 100644 --- a/docs/reference/find_swans.html +++ b/docs/reference/find_swans.html @@ -186,8 +186,8 @@

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#> Warning: There were 25 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
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#> Warning: There were 16 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
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#> Warning: The largest R-hat is 1.52, indicating chains have not mixed. #> Running the chains for more iterations may help. See #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -442,7 +442,7 @@

Examp #> 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 Tue May 25 06:10:10 2021. +#> Samples were drawn using NUTS(diag_e) at Tue May 25 09:39:37 2021. #> 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 457e83b..97acb45 100644 --- a/docs/reference/loo.html +++ b/docs/reference/loo.html @@ -189,8 +189,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.83 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: @@ -215,9 +215,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.004749 seconds (Warm-up) -#> Chain 1: 0.191317 seconds (Sampling) -#> Chain 1: 0.196066 seconds (Total) +#> Chain 1: Elapsed Time: 0.004791 seconds (Warm-up) +#> Chain 1: 0.18995 seconds (Sampling) +#> Chain 1: 0.194741 seconds (Total) #> Chain 1:

#> Warning: There were 2 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See diff --git a/docs/reference/plot_fitted.html b/docs/reference/plot_fitted.html index 1ceb84e..573cebd 100644 --- a/docs/reference/plot_fitted.html +++ b/docs/reference/plot_fitted.html @@ -178,8 +178,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds. +#> Chain 1: Gradient evaluation took 3.9e-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: @@ -204,9 +204,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005592 seconds (Warm-up) -#> Chain 1: 0.021775 seconds (Sampling) -#> Chain 1: 0.027367 seconds (Total) +#> Chain 1: Elapsed Time: 0.005062 seconds (Warm-up) +#> Chain 1: 0.018015 seconds (Sampling) +#> Chain 1: 0.023077 seconds (Total) #> Chain 1:

#> Warning: There were 19 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See diff --git a/docs/reference/plot_loadings.html b/docs/reference/plot_loadings.html index a72b335..f1a52e0 100644 --- a/docs/reference/plot_loadings.html +++ b/docs/reference/plot_loadings.html @@ -199,8 +199,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 3.2e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds. +#> Chain 1: Gradient evaluation took 3.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -225,9 +225,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.021759 seconds (Warm-up) -#> Chain 1: 0.209865 seconds (Sampling) -#> Chain 1: 0.231624 seconds (Total) +#> Chain 1: Elapsed Time: 0.020793 seconds (Warm-up) +#> Chain 1: 0.215966 seconds (Sampling) +#> Chain 1: 0.236759 seconds (Total) #> Chain 1:

#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> 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_regime_model.html b/docs/reference/plot_regime_model.html index 5634aa5..6c5e314 100644 --- a/docs/reference/plot_regime_model.html +++ b/docs/reference/plot_regime_model.html @@ -197,8 +197,8 @@

Examp

#> #> SAMPLING FOR MODEL 'hmm_gaussian' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.84 seconds. +#> Chain 1: Gradient evaluation took 7.7e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.77 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -223,9 +223,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.159431 seconds (Warm-up) -#> Chain 1: 0.173489 seconds (Sampling) -#> Chain 1: 0.33292 seconds (Total) +#> Chain 1: Elapsed Time: 0.156626 seconds (Warm-up) +#> Chain 1: 0.187727 seconds (Sampling) +#> Chain 1: 0.344353 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. diff --git a/docs/reference/plot_trends.html b/docs/reference/plot_trends.html index 77e20f8..56d5434 100644 --- a/docs/reference/plot_trends.html +++ b/docs/reference/plot_trends.html @@ -186,8 +186,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.8 seconds. +#> Chain 1: Gradient evaluation took 4.4e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -212,9 +212,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003483 seconds (Warm-up) -#> Chain 1: 0.003669 seconds (Sampling) -#> Chain 1: 0.007152 seconds (Total) +#> Chain 1: Elapsed Time: 0.003918 seconds (Warm-up) +#> Chain 1: 0.003903 seconds (Sampling) +#> Chain 1: 0.007821 seconds (Total) #> Chain 1:

#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.1, indicating chains have not mixed. #> Running the chains for more iterations may help. See diff --git a/docs/reference/rotate_trends.html b/docs/reference/rotate_trends.html index 2cccb57..6bbd783 100644 --- a/docs/reference/rotate_trends.html +++ b/docs/reference/rotate_trends.html @@ -172,8 +172,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 3.4e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds. +#> Chain 1: Gradient evaluation took 3.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -198,9 +198,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.005142 seconds (Warm-up) -#> Chain 1: 0.070047 seconds (Sampling) -#> Chain 1: 0.075189 seconds (Total) +#> Chain 1: Elapsed Time: 0.004758 seconds (Warm-up) +#> Chain 1: 0.063277 seconds (Sampling) +#> Chain 1: 0.068035 seconds (Total) #> Chain 1:

#> Warning: There were 16 divergent transitions after warmup. See #> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup #> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See diff --git a/docs/reference/trend_cor.html b/docs/reference/trend_cor.html index 6f7bfaa..cc680ae 100644 --- a/docs/reference/trend_cor.html +++ b/docs/reference/trend_cor.html @@ -221,8 +221,8 @@

Examp

#> #> SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4.3e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds. +#> Chain 1: Gradient evaluation took 3.3e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -247,9 +247,9 @@

Examp #> Chain 1: Iteration: 45 / 50 [ 90%] (Sampling) #> Chain 1: Iteration: 50 / 50 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.010906 seconds (Warm-up) -#> Chain 1: 0.191305 seconds (Sampling) -#> Chain 1: 0.202211 seconds (Total) +#> Chain 1: Elapsed Time: 0.008701 seconds (Warm-up) +#> Chain 1: 0.184442 seconds (Sampling) +#> Chain 1: 0.193143 seconds (Total) #> Chain 1:

#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See #> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.1, indicating chains have not mixed. #> Running the chains for more iterations may help. See @@ -353,8 +353,8 @@

Examp

#> #> 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 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: @@ -371,9 +371,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002798 seconds (Warm-up) -#> Chain 1: 0.002067 seconds (Sampling) -#> Chain 1: 0.004865 seconds (Total) +#> Chain 1: Elapsed Time: 0.00281 seconds (Warm-up) +#> Chain 1: 0.002143 seconds (Sampling) +#> Chain 1: 0.004953 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -383,8 +383,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 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: @@ -401,9 +401,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002513 seconds (Warm-up) -#> Chain 1: 0.001891 seconds (Sampling) -#> Chain 1: 0.004404 seconds (Total) +#> Chain 1: Elapsed Time: 0.00256 seconds (Warm-up) +#> Chain 1: 0.001953 seconds (Sampling) +#> Chain 1: 0.004513 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -411,8 +411,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -429,16 +429,16 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002251 seconds (Warm-up) -#> Chain 1: 0.001418 seconds (Sampling) -#> Chain 1: 0.003669 seconds (Total) +#> Chain 1: Elapsed Time: 0.002823 seconds (Warm-up) +#> Chain 1: 0.001908 seconds (Sampling) +#> Chain 1: 0.004731 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 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: @@ -455,9 +455,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002372 seconds (Warm-up) -#> Chain 1: 0.001688 seconds (Sampling) -#> Chain 1: 0.00406 seconds (Total) +#> Chain 1: Elapsed Time: 0.002888 seconds (Warm-up) +#> Chain 1: 0.002307 seconds (Sampling) +#> Chain 1: 0.005195 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -465,8 +465,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 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: @@ -483,9 +483,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002119 seconds (Warm-up) -#> Chain 1: 0.001444 seconds (Sampling) -#> Chain 1: 0.003563 seconds (Total) +#> Chain 1: Elapsed Time: 0.002726 seconds (Warm-up) +#> Chain 1: 0.00218 seconds (Sampling) +#> Chain 1: 0.004906 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -493,8 +493,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 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: @@ -511,9 +511,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002406 seconds (Warm-up) -#> Chain 1: 0.001734 seconds (Sampling) -#> Chain 1: 0.00414 seconds (Total) +#> Chain 1: Elapsed Time: 0.003615 seconds (Warm-up) +#> Chain 1: 0.002394 seconds (Sampling) +#> Chain 1: 0.006009 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -521,8 +521,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 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: @@ -539,9 +539,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002502 seconds (Warm-up) -#> Chain 1: 0.001838 seconds (Sampling) -#> Chain 1: 0.00434 seconds (Total) +#> Chain 1: Elapsed Time: 0.002914 seconds (Warm-up) +#> Chain 1: 0.00225 seconds (Sampling) +#> Chain 1: 0.005164 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -549,8 +549,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -567,9 +567,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002299 seconds (Warm-up) -#> Chain 1: 0.001566 seconds (Sampling) -#> Chain 1: 0.003865 seconds (Total) +#> Chain 1: Elapsed Time: 0.002784 seconds (Warm-up) +#> Chain 1: 0.001895 seconds (Sampling) +#> Chain 1: 0.004679 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -579,8 +579,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 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: @@ -597,9 +597,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002573 seconds (Warm-up) -#> Chain 1: 0.001835 seconds (Sampling) -#> Chain 1: 0.004408 seconds (Total) +#> Chain 1: Elapsed Time: 0.003067 seconds (Warm-up) +#> Chain 1: 0.002044 seconds (Sampling) +#> Chain 1: 0.005111 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -607,8 +607,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 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: @@ -625,9 +625,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002221 seconds (Warm-up) -#> Chain 1: 0.001523 seconds (Sampling) -#> Chain 1: 0.003744 seconds (Total) +#> Chain 1: Elapsed Time: 0.002676 seconds (Warm-up) +#> Chain 1: 0.001881 seconds (Sampling) +#> Chain 1: 0.004557 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -635,8 +635,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -653,9 +653,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002252 seconds (Warm-up) -#> Chain 1: 0.0016 seconds (Sampling) -#> Chain 1: 0.003852 seconds (Total) +#> Chain 1: Elapsed Time: 0.002637 seconds (Warm-up) +#> Chain 1: 0.001812 seconds (Sampling) +#> Chain 1: 0.004449 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -663,8 +663,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -681,9 +681,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002236 seconds (Warm-up) -#> Chain 1: 0.001985 seconds (Sampling) -#> Chain 1: 0.004221 seconds (Total) +#> Chain 1: Elapsed Time: 0.002023 seconds (Warm-up) +#> Chain 1: 0.001618 seconds (Sampling) +#> Chain 1: 0.003641 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -693,8 +693,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.1 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -711,9 +711,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002818 seconds (Warm-up) -#> Chain 1: 0.002051 seconds (Sampling) -#> Chain 1: 0.004869 seconds (Total) +#> Chain 1: Elapsed Time: 0.002506 seconds (Warm-up) +#> Chain 1: 0.001724 seconds (Sampling) +#> Chain 1: 0.00423 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -721,8 +721,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -739,9 +739,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002573 seconds (Warm-up) -#> Chain 1: 0.00165 seconds (Sampling) -#> Chain 1: 0.004223 seconds (Total) +#> Chain 1: Elapsed Time: 0.002181 seconds (Warm-up) +#> Chain 1: 0.001406 seconds (Sampling) +#> Chain 1: 0.003587 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -749,8 +749,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -767,9 +767,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002881 seconds (Warm-up) -#> Chain 1: 0.002095 seconds (Sampling) -#> Chain 1: 0.004976 seconds (Total) +#> Chain 1: Elapsed Time: 0.002363 seconds (Warm-up) +#> Chain 1: 0.001728 seconds (Sampling) +#> Chain 1: 0.004091 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -777,8 +777,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: 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: @@ -795,9 +795,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002698 seconds (Warm-up) -#> Chain 1: 0.002075 seconds (Sampling) -#> Chain 1: 0.004773 seconds (Total) +#> Chain 1: Elapsed Time: 0.002632 seconds (Warm-up) +#> Chain 1: 0.002069 seconds (Sampling) +#> Chain 1: 0.004701 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -805,8 +805,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 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: @@ -823,9 +823,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002996 seconds (Warm-up) -#> Chain 1: 0.001633 seconds (Sampling) -#> Chain 1: 0.004629 seconds (Total) +#> Chain 1: Elapsed Time: 0.002969 seconds (Warm-up) +#> Chain 1: 0.001656 seconds (Sampling) +#> Chain 1: 0.004625 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -833,8 +833,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -851,9 +851,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002308 seconds (Warm-up) -#> Chain 1: 0.001939 seconds (Sampling) -#> Chain 1: 0.004247 seconds (Total) +#> Chain 1: Elapsed Time: 0.002396 seconds (Warm-up) +#> Chain 1: 0.001975 seconds (Sampling) +#> Chain 1: 0.004371 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -861,8 +861,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 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: @@ -879,9 +879,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002423 seconds (Warm-up) -#> Chain 1: 0.001582 seconds (Sampling) -#> Chain 1: 0.004005 seconds (Total) +#> Chain 1: Elapsed Time: 0.002615 seconds (Warm-up) +#> Chain 1: 0.001788 seconds (Sampling) +#> Chain 1: 0.004403 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -889,8 +889,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 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: @@ -907,9 +907,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002396 seconds (Warm-up) -#> Chain 1: 0.00195 seconds (Sampling) -#> Chain 1: 0.004346 seconds (Total) +#> Chain 1: Elapsed Time: 0.002791 seconds (Warm-up) +#> Chain 1: 0.002432 seconds (Sampling) +#> Chain 1: 0.005223 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -917,8 +917,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -935,9 +935,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00209 seconds (Warm-up) -#> Chain 1: 0.001639 seconds (Sampling) -#> Chain 1: 0.003729 seconds (Total) +#> Chain 1: Elapsed Time: 0.00282 seconds (Warm-up) +#> Chain 1: 0.002166 seconds (Sampling) +#> Chain 1: 0.004986 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -945,8 +945,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: 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: @@ -963,9 +963,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002092 seconds (Warm-up) -#> Chain 1: 0.00171 seconds (Sampling) -#> Chain 1: 0.003802 seconds (Total) +#> Chain 1: Elapsed Time: 0.002849 seconds (Warm-up) +#> Chain 1: 0.002311 seconds (Sampling) +#> Chain 1: 0.00516 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -973,8 +973,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -991,9 +991,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002915 seconds (Warm-up) -#> Chain 1: 0.001398 seconds (Sampling) -#> Chain 1: 0.004313 seconds (Total) +#> Chain 1: Elapsed Time: 0.003323 seconds (Warm-up) +#> Chain 1: 0.00184 seconds (Sampling) +#> Chain 1: 0.005163 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1001,8 +1001,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -1019,9 +1019,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002576 seconds (Warm-up) -#> Chain 1: 0.001446 seconds (Sampling) -#> Chain 1: 0.004022 seconds (Total) +#> Chain 1: Elapsed Time: 0.003173 seconds (Warm-up) +#> Chain 1: 0.001851 seconds (Sampling) +#> Chain 1: 0.005024 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1047,9 +1047,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002531 seconds (Warm-up) -#> Chain 1: 0.001643 seconds (Sampling) -#> Chain 1: 0.004174 seconds (Total) +#> Chain 1: Elapsed Time: 0.002605 seconds (Warm-up) +#> Chain 1: 0.001852 seconds (Sampling) +#> Chain 1: 0.004457 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1062,8 +1062,8 @@

Examp

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1080,9 +1080,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002638 seconds (Warm-up) -#> Chain 1: 0.001956 seconds (Sampling) -#> Chain 1: 0.004594 seconds (Total) +#> Chain 1: Elapsed Time: 0.002917 seconds (Warm-up) +#> Chain 1: 0.002397 seconds (Sampling) +#> Chain 1: 0.005314 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1090,8 +1090,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 1.1e-05 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1108,9 +1108,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002282 seconds (Warm-up) -#> Chain 1: 0.00216 seconds (Sampling) -#> Chain 1: 0.004442 seconds (Total) +#> Chain 1: Elapsed Time: 0.002419 seconds (Warm-up) +#> Chain 1: 0.002183 seconds (Sampling) +#> Chain 1: 0.004602 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1118,8 +1118,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1136,9 +1136,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.00324 seconds (Warm-up) -#> Chain 1: 0.002252 seconds (Sampling) -#> Chain 1: 0.005492 seconds (Total) +#> Chain 1: Elapsed Time: 0.002409 seconds (Warm-up) +#> Chain 1: 0.001781 seconds (Sampling) +#> Chain 1: 0.00419 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1146,8 +1146,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> 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 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1164,9 +1164,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002503 seconds (Warm-up) -#> Chain 1: 0.001925 seconds (Sampling) -#> Chain 1: 0.004428 seconds (Total) +#> Chain 1: Elapsed Time: 0.002454 seconds (Warm-up) +#> Chain 1: 0.00151 seconds (Sampling) +#> Chain 1: 0.003964 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1176,8 +1176,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1194,9 +1194,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002822 seconds (Warm-up) -#> Chain 1: 0.001859 seconds (Sampling) -#> Chain 1: 0.004681 seconds (Total) +#> Chain 1: Elapsed Time: 0.002302 seconds (Warm-up) +#> Chain 1: 0.001542 seconds (Sampling) +#> Chain 1: 0.003844 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1204,8 +1204,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 8e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.08 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1222,9 +1222,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002775 seconds (Warm-up) -#> Chain 1: 0.00183 seconds (Sampling) -#> Chain 1: 0.004605 seconds (Total) +#> Chain 1: Elapsed Time: 0.002206 seconds (Warm-up) +#> Chain 1: 0.001509 seconds (Sampling) +#> Chain 1: 0.003715 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1234,8 +1234,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -1252,9 +1252,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003134 seconds (Warm-up) -#> Chain 1: 0.002323 seconds (Sampling) -#> Chain 1: 0.005457 seconds (Total) +#> Chain 1: Elapsed Time: 0.003108 seconds (Warm-up) +#> Chain 1: 0.002362 seconds (Sampling) +#> Chain 1: 0.00547 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1282,9 +1282,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002618 seconds (Warm-up) -#> Chain 1: 0.002055 seconds (Sampling) -#> Chain 1: 0.004673 seconds (Total) +#> Chain 1: Elapsed Time: 0.002697 seconds (Warm-up) +#> Chain 1: 0.002123 seconds (Sampling) +#> Chain 1: 0.00482 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1292,8 +1292,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 7e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1310,9 +1310,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002742 seconds (Warm-up) -#> Chain 1: 0.002585 seconds (Sampling) -#> Chain 1: 0.005327 seconds (Total) +#> Chain 1: Elapsed Time: 0.002865 seconds (Warm-up) +#> Chain 1: 0.00268 seconds (Sampling) +#> Chain 1: 0.005545 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1320,8 +1320,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. +#> Chain 1: Gradient evaluation took 1.7e-05 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1338,9 +1338,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.001912 seconds (Warm-up) -#> Chain 1: 0.001559 seconds (Sampling) -#> Chain 1: 0.003471 seconds (Total) +#> Chain 1: Elapsed Time: 0.002564 seconds (Warm-up) +#> Chain 1: 0.002002 seconds (Sampling) +#> Chain 1: 0.004566 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1348,8 +1348,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: 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: @@ -1366,9 +1366,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002058 seconds (Warm-up) -#> Chain 1: 0.001602 seconds (Sampling) -#> Chain 1: 0.00366 seconds (Total) +#> Chain 1: Elapsed Time: 0.002513 seconds (Warm-up) +#> Chain 1: 0.001965 seconds (Sampling) +#> Chain 1: 0.004478 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1376,8 +1376,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1394,9 +1394,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002723 seconds (Warm-up) -#> Chain 1: 0.001713 seconds (Sampling) -#> Chain 1: 0.004436 seconds (Total) +#> Chain 1: Elapsed Time: 0.003063 seconds (Warm-up) +#> Chain 1: 0.002079 seconds (Sampling) +#> Chain 1: 0.005142 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1404,8 +1404,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 4e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. +#> Chain 1: Gradient evaluation took 6e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1422,9 +1422,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002355 seconds (Warm-up) -#> Chain 1: 0.001802 seconds (Sampling) -#> Chain 1: 0.004157 seconds (Total) +#> Chain 1: Elapsed Time: 0.002749 seconds (Warm-up) +#> Chain 1: 0.001887 seconds (Sampling) +#> Chain 1: 0.004636 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1432,8 +1432,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1450,9 +1450,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002325 seconds (Warm-up) -#> Chain 1: 0.001563 seconds (Sampling) -#> Chain 1: 0.003888 seconds (Total) +#> Chain 1: Elapsed Time: 0.002257 seconds (Warm-up) +#> Chain 1: 0.001575 seconds (Sampling) +#> Chain 1: 0.003832 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1462,8 +1462,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 5e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1480,9 +1480,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002435 seconds (Warm-up) -#> Chain 1: 0.001488 seconds (Sampling) -#> Chain 1: 0.003923 seconds (Total) +#> Chain 1: Elapsed Time: 0.002329 seconds (Warm-up) +#> Chain 1: 0.001519 seconds (Sampling) +#> Chain 1: 0.003848 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1490,8 +1490,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1508,9 +1508,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.001989 seconds (Warm-up) -#> Chain 1: 0.001643 seconds (Sampling) -#> Chain 1: 0.003632 seconds (Total) +#> Chain 1: Elapsed Time: 0.002092 seconds (Warm-up) +#> Chain 1: 0.001635 seconds (Sampling) +#> Chain 1: 0.003727 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1518,8 +1518,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: Gradient evaluation took 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1536,9 +1536,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002566 seconds (Warm-up) +#> Chain 1: Elapsed Time: 0.00207 seconds (Warm-up) #> Chain 1: 0.001662 seconds (Sampling) -#> Chain 1: 0.004228 seconds (Total) +#> Chain 1: 0.003732 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1546,8 +1546,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> 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 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1564,9 +1564,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002763 seconds (Warm-up) -#> Chain 1: 0.001996 seconds (Sampling) -#> Chain 1: 0.004759 seconds (Total) +#> Chain 1: Elapsed Time: 0.002522 seconds (Warm-up) +#> Chain 1: 0.001802 seconds (Sampling) +#> Chain 1: 0.004324 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1576,8 +1576,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> 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 4e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1594,9 +1594,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.003244 seconds (Warm-up) -#> Chain 1: 0.002044 seconds (Sampling) -#> Chain 1: 0.005288 seconds (Total) +#> Chain 1: Elapsed Time: 0.00254 seconds (Warm-up) +#> Chain 1: 0.001581 seconds (Sampling) +#> Chain 1: 0.004121 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 #> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable. @@ -1606,8 +1606,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 9e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds. +#> Chain 1: Gradient evaluation took 5e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.05 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1624,9 +1624,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002671 seconds (Warm-up) -#> Chain 1: 0.001901 seconds (Sampling) -#> Chain 1: 0.004572 seconds (Total) +#> Chain 1: Elapsed Time: 0.00216 seconds (Warm-up) +#> Chain 1: 0.001549 seconds (Sampling) +#> Chain 1: 0.003709 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1634,8 +1634,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: Gradient evaluation took 3e-06 seconds +#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds. #> Chain 1: Adjust your expectations accordingly! #> Chain 1: #> Chain 1: @@ -1652,9 +1652,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002654 seconds (Warm-up) -#> Chain 1: 0.00215 seconds (Sampling) -#> Chain 1: 0.004804 seconds (Total) +#> Chain 1: Elapsed Time: 0.002034 seconds (Warm-up) +#> Chain 1: 0.001771 seconds (Sampling) +#> Chain 1: 0.003805 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1680,9 +1680,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002808 seconds (Warm-up) -#> Chain 1: 0.002502 seconds (Sampling) -#> Chain 1: 0.00531 seconds (Total) +#> Chain 1: Elapsed Time: 0.00234 seconds (Warm-up) +#> Chain 1: 0.002133 seconds (Sampling) +#> Chain 1: 0.004473 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1708,9 +1708,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002982 seconds (Warm-up) -#> Chain 1: 0.002035 seconds (Sampling) -#> Chain 1: 0.005017 seconds (Total) +#> Chain 1: Elapsed Time: 0.003005 seconds (Warm-up) +#> Chain 1: 0.002041 seconds (Sampling) +#> Chain 1: 0.005046 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1718,8 +1718,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> 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: @@ -1736,9 +1736,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002476 seconds (Warm-up) -#> Chain 1: 0.00203 seconds (Sampling) -#> Chain 1: 0.004506 seconds (Total) +#> Chain 1: Elapsed Time: 0.002598 seconds (Warm-up) +#> Chain 1: 0.00209 seconds (Sampling) +#> Chain 1: 0.004688 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. @@ -1746,8 +1746,8 @@

Examp #> http://mc-stan.org/misc/warnings.html#tail-ess

#> #> SAMPLING FOR MODEL 'corr' NOW (CHAIN 1). #> Chain 1: -#> Chain 1: Gradient evaluation took 6e-06 seconds -#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. +#> Chain 1: 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: @@ -1764,9 +1764,9 @@

Examp #> Chain 1: Iteration: 270 / 300 [ 90%] (Sampling) #> Chain 1: Iteration: 300 / 300 [100%] (Sampling) #> Chain 1: -#> Chain 1: Elapsed Time: 0.002979 seconds (Warm-up) -#> Chain 1: 0.001812 seconds (Sampling) -#> Chain 1: 0.004791 seconds (Total) +#> Chain 1: Elapsed Time: 0.003069 seconds (Warm-up) +#> Chain 1: 0.001986 seconds (Sampling) +#> Chain 1: 0.005055 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 #> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable. diff --git a/man/dfa_cv.Rd b/man/dfa_cv.Rd index a06d513..eed17ac 100644 --- a/man/dfa_cv.Rd +++ b/man/dfa_cv.Rd @@ -44,26 +44,34 @@ Apply cross validation to DFA model set.seed(42) s <- sim_dfa(num_trends = 1, num_years = 20, num_ts = 3) obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), "time" = rep(1:20, 3)) -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) +long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)), +"time" = rep(1:20, 3)) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) # random folds fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) # folds can also be passed in fold_ids <- sample(1:5, size = nrow(long), replace = TRUE) -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, fold_ids = fold_ids) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) +fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1, +fold_ids = fold_ids) # do an example of leave-time-out cross validation where years are dropped fold_ids <- long$time -m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", sample = FALSE) -fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, fold_ids = fold_ids) +m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long", +sample = FALSE) +fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1, +fold_ids = fold_ids) # example with covariates and long format data -obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, "covariate" = 1:2) +obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3, +"covariate" = 1:2) obs_covar$value <- rnorm(nrow(obs_covar), 0, 0.1) obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ]) -m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, data_shape = "long", sample = FALSE) +m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar, +data_shape = "long", sample = FALSE) fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1) } diff --git a/src/RcppExports-507982db.o.tmp b/src/RcppExports-507982db.o.tmp new file mode 100644 index 0000000..e69de29