diff --git a/docs/articles/a1_bayesdfa.html b/docs/articles/a1_bayesdfa.html index 73b78a1..9269e4c 100644 --- a/docs/articles/a1_bayesdfa.html +++ b/docs/articles/a1_bayesdfa.html @@ -102,7 +102,7 @@

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

-

2024-10-18

+

2024-10-19

Source: vignettes/a1_bayesdfa.Rmd @@ -643,8 +643,8 @@

DFA model with weights## ## SAMPLING FOR MODEL 'dfa' NOW (CHAIN 1). ## Chain 1: -## Chain 1: Gradient evaluation took 4.7e-05 seconds -## Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.47 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: @@ -661,9 +661,9 @@

DFA model with weights## Chain 1: Iteration: 450 / 500 [ 90%] (Sampling) ## Chain 1: Iteration: 500 / 500 [100%] (Sampling) ## Chain 1: -## Chain 1: Elapsed Time: 25.292 seconds (Warm-up) -## Chain 1: 4.311 seconds (Sampling) -## Chain 1: 29.603 seconds (Total) +## Chain 1: Elapsed Time: 26.684 seconds (Warm-up) +## Chain 1: 4.183 seconds (Sampling) +## Chain 1: 30.867 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/docs/articles/a2_combining_data.html b/docs/articles/a2_combining_data.html
index 479ff35..f17b46c 100644
--- a/docs/articles/a2_combining_data.html
+++ b/docs/articles/a2_combining_data.html
@@ -102,7 +102,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a2_combining_data.Rmd
       
diff --git a/docs/articles/a3_covariates.html b/docs/articles/a3_covariates.html
index 7dfa5e2..d2e70da 100644
--- a/docs/articles/a3_covariates.html
+++ b/docs/articles/a3_covariates.html
@@ -103,7 +103,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a3_covariates.Rmd
       
diff --git a/docs/articles/a4_smooth.html b/docs/articles/a4_smooth.html
index d0c6e21..70f4f20 100644
--- a/docs/articles/a4_smooth.html
+++ b/docs/articles/a4_smooth.html
@@ -102,7 +102,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a4_smooth.Rmd
       
diff --git a/docs/articles/a5_estimate_process_sigma.html b/docs/articles/a5_estimate_process_sigma.html
index 40b357e..9b5d7d2 100644
--- a/docs/articles/a5_estimate_process_sigma.html
+++ b/docs/articles/a5_estimate_process_sigma.html
@@ -103,7 +103,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a5_estimate_process_sigma.Rmd
       
diff --git a/docs/articles/a6_compositional.html b/docs/articles/a6_compositional.html
index 5c895fb..aa5af79 100644
--- a/docs/articles/a6_compositional.html
+++ b/docs/articles/a6_compositional.html
@@ -103,7 +103,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a6_compositional.Rmd
       
diff --git a/docs/articles/a7_bigdata.html b/docs/articles/a7_bigdata.html
index d107295..da83186 100644
--- a/docs/articles/a7_bigdata.html
+++ b/docs/articles/a7_bigdata.html
@@ -103,7 +103,7 @@ 
Eric J. Ward,
 Sean C. Anderson, Mary E. Hunsicker, Mike A. Litzow, Luis A. Damiano,
 Mark D. Scheuerell, Elizabeth E. Holmes, Nick Tolimieri

             
-            
2024-10-18

+            
2024-10-19

       
       Source: vignettes/a7_bigdata.Rmd
       
diff --git a/docs/index.html b/docs/index.html
index 39434e9..9b08c89 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -116,7 +116,7 @@ 
Overview
 
Vignettes
 

-
We’ve put together several vignettes for using the bayesdfa package.
Overview
Combining data
Compositional models
Including covariates
Estimating process variance
DFA for big data

+
We’ve put together several vignettes for using the bayesdfa package.
Overview
Combining data
Including covariates
Smooth trend models
Estimating process variance
Compositional models
DFA for big data.

 
Additional examples can be found in the course that Eli Holmes, Mark Scheuerell, and Eric Ward teach at the University of Washington:
Course webpage
Lab book

 
 

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 91dbdb1..63bee6d 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: 2024-10-18T23:33Z
+last_built: 2024-10-19T13:26Z
 
diff --git a/docs/reference/dfa_fitted.html b/docs/reference/dfa_fitted.html
index d486680..3a0fe1a 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 0.000137 seconds
-#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.37 seconds.
+#> Chain 1: Gradient evaluation took 0.000141 seconds
+#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.41 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: 0.02 seconds (Warm-up)
-#> Chain 1:                0.169 seconds (Sampling)
-#> Chain 1:                0.189 seconds (Total)
+#> Chain 1:  Elapsed Time: 0.021 seconds (Warm-up)
+#> Chain 1:                0.167 seconds (Sampling)
+#> Chain 1:                0.188 seconds (Total)
 #> Chain 1: 
 #> Warning: There were 11 divergent transitions after warmup. See
 #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
diff --git a/docs/reference/dfa_loadings.html b/docs/reference/dfa_loadings.html
index 5860063..2e09144 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 4.2e-05 seconds
-#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 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: 
@@ -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: 0.035 seconds (Warm-up)
-#> Chain 1:                0.366 seconds (Sampling)
-#> Chain 1:                0.401 seconds (Total)
+#> Chain 1:  Elapsed Time: 0.033 seconds (Warm-up)
+#> Chain 1:                0.355 seconds (Sampling)
+#> Chain 1:                0.388 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 aacc534..f7e64a4 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 3.7e-05 seconds
-#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
+#> Chain 1: Gradient evaluation took 3.6e-05 seconds
+#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds.
 #> Chain 1: Adjust your expectations accordingly!
 #> Chain 1: 
 #> Chain 1: 
@@ -139,9 +139,9 @@ 
Examples

 #> Chain 1: Iteration: 45 / 50 [ 90%]  (Sampling)
 #> Chain 1: Iteration: 50 / 50 [100%]  (Sampling)
 #> Chain 1: 
-#> Chain 1:  Elapsed Time: 0.01 seconds (Warm-up)
-#> Chain 1:                0.005 seconds (Sampling)
-#> Chain 1:                0.015 seconds (Total)
+#> Chain 1:  Elapsed Time: 0.009 seconds (Warm-up)
+#> Chain 1:                0.004 seconds (Sampling)
+#> Chain 1:                0.013 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 6e558e9..77c253a 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 4.8e-05 seconds
-#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
+#> Chain 1: Gradient evaluation took 4.9e-05 seconds
+#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
 #> Chain 1: Adjust your expectations accordingly!
 #> Chain 1: 
 #> Chain 1: 
@@ -180,8 +180,8 @@ 
Examples

 #> Chain 1: Iteration: 50 / 50 [100%]  (Sampling)
 #> Chain 1: 
 #> Chain 1:  Elapsed Time: 0.008 seconds (Warm-up)
-#> Chain 1:                0.241 seconds (Sampling)
-#> Chain 1:                0.249 seconds (Total)
+#> Chain 1:                0.233 seconds (Sampling)
+#> Chain 1:                0.241 seconds (Total)
 #> Chain 1: 
 #> Warning: There were 5 divergent transitions after warmup. See
 #> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
@@ -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: 0.023 seconds (Warm-up)
-#> Chain 1:                0.021 seconds (Sampling)
-#> Chain 1:                0.044 seconds (Total)
+#> Chain 1:  Elapsed Time: 0.028 seconds (Warm-up)
+#> Chain 1:                0.022 seconds (Sampling)
+#> Chain 1:                0.05 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