From 6cbb5df00f90f86a3ea13c3d73359659e46c1c29 Mon Sep 17 00:00:00 2001 From: joethorley Date: Fri, 9 Aug 2024 00:09:45 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20poissonc?= =?UTF-8?q?onsulting/embr@c5302cddce7ce88db09870d7899c7ec92753870a=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 12 +- CODE_OF_CONDUCT.html | 12 +- CONTRIBUTING.html | 12 +- LICENSE-text.html | 12 +- LICENSE.html | 12 +- SUPPORT.html | 12 +- authors.html | 20 +- index.html | 12 +- news/index.html | 14 +- pkgdown.yml | 5 +- reference/IC.html | 24 +- reference/R2.html | 24 +- reference/R2.mb_analysis.html | 38 +- reference/add_analyses.html | 24 +- reference/add_models.html | 24 +- reference/analyse.character.html | 40 +- reference/analyse.html | 20 +- reference/analyse.mb_model.html | 38 +- reference/analyse.mb_models.html | 38 +- reference/analyse1.html | 36 +- reference/analyse_residuals.html | 18 +- reference/analyses.html | 22 +- reference/as.analyses.html | 20 +- reference/as.model.html | 20 +- reference/as.models.html | 20 +- reference/backwards.html | 32 +- reference/base_model.html | 24 +- reference/check_mb_analysis.html | 24 +- reference/check_mb_code.html | 24 +- reference/check_mb_model.html | 24 +- reference/check_model_pars.html | 30 +- reference/check_uniquely_named_list.html | 24 +- reference/code.html | 24 +- reference/coef.mb_analyses.html | 34 +- reference/coef.mb_analysis.html | 36 +- reference/coef.mb_meta_analyses.html | 34 +- reference/coef.mb_meta_analysis.html | 34 +- reference/coef_profile.html | 20 +- reference/coef_profile.mb_analyses.html | 38 +- reference/coef_profile.mb_analysis.html | 40 +- reference/coef_profile.mb_meta_analyses.html | 38 +- reference/coef_profile.mb_meta_analysis.html | 38 +- reference/comment_string.html | 24 +- reference/data_set.html | 30 +- reference/density99.html | 14 +- reference/drop_pars.html | 26 +- reference/elapsed.html | 20 +- reference/embr-package.html | 14 +- reference/estimates.mb_analysis.html | 30 +- reference/fitted.mb_analysis.html | 26 +- reference/get_analysis_mode.html | 22 +- reference/get_model.html | 18 +- reference/index.html | 14 +- reference/is.lmb_analysis.html | 22 +- reference/is.lmb_code.html | 22 +- reference/is.lmb_model.html | 22 +- reference/is.mb_analyses.html | 22 +- reference/is.mb_analysis.html | 22 +- reference/is.mb_code.html | 22 +- reference/is.mb_model.html | 22 +- reference/is.mb_models.html | 22 +- reference/is.mb_null_analysis.html | 22 +- reference/is.syntactic.html | 24 +- reference/is_bayesian.html | 24 +- reference/is_frequentist.html | 22 +- reference/is_namedlist.html | 22 +- reference/load_model.html | 22 +- reference/logLik.mb_analysis.html | 22 +- reference/logLik.mb_null_analysis.html | 22 +- reference/make_all_models.html | 24 +- reference/mb_code.html | 31 +- reference/mcmc_derive.mb_analyses.html | 46 +- reference/mcmc_derive.mb_analysis.html | 50 +- reference/mcmc_derive_data.mb_analyses.html | 48 +- reference/mcmc_derive_data.mb_analysis.html | 50 +- reference/model.html | 54 +- reference/models.html | 22 +- reference/modify_data.html | 26 +- reference/modify_new_data.html | 30 +- reference/monitor.html | 24 +- reference/new_analysis.html | 20 +- reference/new_expr-set.html | 24 +- reference/new_expr.html | 24 +- reference/ngens.html | 24 +- reference/nmodels.html | 24 +- reference/nterms.mb_analysis.html | 26 +- reference/nthin.html | 24 +- reference/params.html | 22 +- reference/plot.mb_analysis.html | 24 +- reference/plot_data.html | 20 +- reference/plot_residuals.html | 20 +- reference/posterior_predictive_check.html | 24 +- ...osterior_predictive_check.mb_analysis.html | 28 +- reference/predict.mb_analyses.html | 46 +- reference/predict.mb_analysis.html | 48 +- reference/random_effects.html | 24 +- reference/reanalyse.html | 20 +- reference/reanalyse.mb_analyses.html | 38 +- reference/reanalyse.mb_analysis.html | 38 +- reference/reanalyse.mb_meta_analyses.html | 38 +- reference/reanalyse.mb_meta_analysis.html | 38 +- reference/reanalyse1.html | 24 +- reference/reexports.html | 14 +- reference/residuals.mb_analysis.html | 28 +- reference/rm_comments.html | 24 +- reference/sample_size.html | 24 +- reference/scalar_nlist.html | 24 +- reference/sd_priors_by.html | 42 +- reference/select_rescale_data.html | 26 +- reference/set_analysis_mode.html | 26 +- reference/simulate_residuals.html | 24 +- reference/sort_by_ic.html | 24 +- reference/sort_nlist.html | 22 +- reference/template-set.html | 20 +- reference/template.html | 24 +- reference/terms.mb_analysis.html | 26 +- reference/update_model.html | 52 +- sitemap.xml | 468 +++++------------- 118 files changed, 1680 insertions(+), 1852 deletions(-) diff --git a/404.html b/404.html index f6629be..9f7175a 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -88,16 +88,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index d77aa63..ccd2d3c 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -3,7 +3,7 @@ - +
- +
@@ -129,15 +129,15 @@

Attribution -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 3758300..ec05711 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -3,7 +3,7 @@ - +
- +
@@ -92,15 +92,15 @@

Code of Conduct
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 8cdbada..8a3192f 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -3,7 +3,7 @@ - +
- +
@@ -65,15 +65,15 @@

License

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/LICENSE.html b/LICENSE.html index f8d4482..361a8a5 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -69,15 +69,15 @@

The MIT License (MIT)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/SUPPORT.html b/SUPPORT.html index d09bd30..ed5da41 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,15 +74,15 @@

Make a reprex -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/authors.html b/authors.html index 23deb36..6f4b60f 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -47,7 +47,7 @@

Authors and Citation

- +

Citation

- Source: DESCRIPTION + Source: DESCRIPTION

Thorley J, Müller K (2024). embr: Model Builder Utility Functions and Virtual Classes. -R package version 0.0.1.9037, https://github.com/poissonconsulting/embr. +R package version 0.0.1.9037, https://github.com/poissonconsulting/embr. 

@Manual{,
   title = {embr: Model Builder Utility Functions and Virtual Classes},
@@ -100,15 +100,15 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index 088e66e..bc5a606 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -168,16 +168,16 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.0.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/news/index.html b/news/index.html
index d140dc3..07e09f3 100644
--- a/news/index.html
+++ b/news/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

       
Changelog 

-      Source: NEWS.md
+      Source: NEWS.md
     

 
     

@@ -145,15 +145,15 @@ 
embr 0.0.1
-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 52ba4c5..4de88c7 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,5 @@
 pandoc: 3.1.11
-pkgdown: 2.0.9
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-17T21:58Z
-
+last_built: 2024-08-09T00:09Z
diff --git a/reference/IC.html b/reference/IC.html
index b8253b2..ef5342a 100644
--- a/reference/IC.html
+++ b/reference/IC.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Information Criterion

-    Source: R/IC.R
+    Source: R/IC.R
     
     

 
@@ -58,19 +58,19 @@ 
Information Criterion

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to calculate the IC for.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
The Information Criteron as a number.

+    
The Information Criteron as a number.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/R2.html b/reference/R2.html
index 811af2e..426679a 100644
--- a/reference/R2.html
+++ b/reference/R2.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
R2

-    Source: R/R2.R
+    Source: R/R2.R
     
     

 
@@ -58,19 +58,19 @@ 
R2

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
An index of the R2 value.

+    
An index of the R2 value.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/R2.mb_analysis.html b/reference/R2.mb_analysis.html
index ca6f08d..c2c2bb4 100644
--- a/reference/R2.mb_analysis.html
+++ b/reference/R2.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
R2

-    Source: R/R2.R
+    Source: R/R2.R
     
     

 
@@ -53,7 +53,7 @@ 
R2

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 R2(
   object,
   response,
@@ -68,43 +68,43 @@ 
R2

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
response

+
response

 
A string specifying the column in the data corresponding to the response.

 
 
-
marginal

+
marginal

 
A flag indicating whether to calculate the marginal or conditional R2 value.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused

 
 

     

     
Value

-    
-
-
A number of the R2 value.

+    
A number of the R2 value.

     

     

     
Details

@@ -124,15 +124,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/add_analyses.html b/reference/add_analyses.html
index 7e15213..b7fe087 100644
--- a/reference/add_analyses.html
+++ b/reference/add_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Add analyses

-    Source: R/add.R
+    Source: R/add.R
     
     

 
@@ -58,19 +58,19 @@ 
Add analyses

 
     

     
Arguments

-    
x

+
+
+
x

 
An mb_analysis or mb_analyses object.

 
 
-
x2

+
x2

 
n mb_analysis or mb_analyses object.

 
 

     

     
Value

-    
-
-
An object of class mb_analyses.

+    
An object of class mb_analyses.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/add_models.html b/reference/add_models.html
index 0259275..abbad96 100644
--- a/reference/add_models.html
+++ b/reference/add_models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Add model(s)

-    Source: R/add.R
+    Source: R/add.R
     
     

 
@@ -58,19 +58,19 @@ 
Add model(s)

 
     

     
Arguments

-    
x

+
+
+
x

 
An mb_model or mb_models object.

 
 
-
x2

+
x2

 
n mb_model or mb_models object.

 
 

     

     
Value

-    
-
-
An object of class mb_models.

+    
An object of class mb_models.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse.character.html b/reference/analyse.character.html
index 46fd452..264db4b 100644
--- a/reference/analyse.character.html
+++ b/reference/analyse.character.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Analyse

-    Source: R/analyse.R
+    Source: R/analyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Analyse

     

 
     

-    
# S3 method for character
+    
# S3 method for class 'character'
 analyse(
   x,
   data,
@@ -71,47 +71,49 @@ 
Analyse

 
     

     
Arguments

-    
x

+
+
+
x

 
An object inheriting from class mb_model or a list of such objects.

 
 
-
data

+
data

 
The data frame to analyse.

 
 
-
select_data

+
select_data

 
A named list specifying the columns to select and their associated classes and values as well as transformations and scaling options.

 
 
-
nchains

+
nchains

 
A count of the number of chains.

 
 
-
niters

+
niters

 
A count of the number of simulations to save per chain.

 
 
-
nthin

+
nthin

 
A count of the thining interval or NULL (in which case taken from model).

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print a model summary.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -128,15 +130,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse.html b/reference/analyse.html
index d56f5ec..dcbc8cd 100644
--- a/reference/analyse.html
+++ b/reference/analyse.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Analyse

-    Source: R/analyse.R
+    Source: R/analyse.R
     
     

 
@@ -58,11 +58,13 @@ 
Analyse

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to analyse.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse.mb_model.html b/reference/analyse.mb_model.html
index 95aafb9..6c0901e 100644
--- a/reference/analyse.mb_model.html
+++ b/reference/analyse.mb_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Analyse

-    Source: R/analyse.R
+    Source: R/analyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Analyse

     

 
     

-    
# S3 method for mb_model
+    
# S3 method for class 'mb_model'
 analyse(
   x,
   data,
@@ -70,43 +70,45 @@ 
Analyse

 
     

     
Arguments

-    
x

+
+
+
x

 
An object inheriting from class mb_model or a list of such objects.

 
 
-
data

+
data

 
The data frame to analyse.

 
 
-
nchains

+
nchains

 
A count of the number of chains.

 
 
-
niters

+
niters

 
A count of the number of simulations to save per chain.

 
 
-
nthin

+
nthin

 
A count of the thining interval or NULL (in which case taken from model).

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print a model summary.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse.mb_models.html b/reference/analyse.mb_models.html
index 0df41fd..7f31960 100644
--- a/reference/analyse.mb_models.html
+++ b/reference/analyse.mb_models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Analyse

-    Source: R/analyse.R
+    Source: R/analyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Analyse

     

 
     

-    
# S3 method for mb_models
+    
# S3 method for class 'mb_models'
 analyse(
   x,
   data,
@@ -70,43 +70,45 @@ 
Analyse

 
     

     
Arguments

-    
x

+
+
+
x

 
An object inheriting from class mb_model or a list of such objects.

 
 
-
data

+
data

 
The data frame to analyse.

 
 
-
nchains

+
nchains

 
A count of the number of chains.

 
 
-
niters

+
niters

 
A count of the number of simulations to save per chain.

 
 
-
nthin

+
nthin

 
A count of the thining interval or NULL (in which case taken from model).

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print a model summary.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse1.html b/reference/analyse1.html
index 09a0653..1c75763 100644
--- a/reference/analyse1.html
+++ b/reference/analyse1.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Analyse

-    Source: R/analyse.R
+    Source: R/analyse.R
     
     

 
@@ -69,43 +69,45 @@ 
Analyse

 
     

     
Arguments

-    
model

+
+
+
model

 
The mb_model to analyse.

 
 
-
data

+
data

 
The data.

 
 
-
loaded

+
loaded

 
The loaded model.

 
 
-
nchains

+
nchains

 
chains.

 
 
-
niters

+
niters

 
iters

 
 
-
nthin

+
nthin

 
thin

 
 
-
quiet

+
quiet

 
quiet

 
 
-
glance

+
glance

 
glance

 
 
-
parallel

+
parallel

 
parallel

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -122,15 +124,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyse_residuals.html b/reference/analyse_residuals.html
index cbf77ef..f3fceab 100644
--- a/reference/analyse_residuals.html
+++ b/reference/analyse_residuals.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Analyse Residuals

-    Source: R/residuals.R
+    Source: R/residuals.R
     
     

 
@@ -58,7 +58,9 @@ 
Analyse Residuals

 
     

     
Arguments

-    
x

+
+
+
x

 
The mb_analysis object to analyse the residuals for.

 
 

@@ -75,15 +77,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/analyses.html b/reference/analyses.html
index 1e560dc..8780cd1 100644
--- a/reference/analyses.html
+++ b/reference/analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
MB Analyses

-    Source: R/analyses.R
+    Source: R/analyses.R
     
     

 
@@ -58,15 +58,15 @@ 
MB Analyses

 
     

     
Arguments

-    
...

+
+
+
...

 
Named objects.

 
 

     

     
Value

-    
-
-
An object inheriting from class mb_analyses.

+    
An object inheriting from class mb_analyses.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/as.analyses.html b/reference/as.analyses.html
index 7a59d95..18c3a51 100644
--- a/reference/as.analyses.html
+++ b/reference/as.analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Coerce to an mb_analyses object

-    Source: R/as.R
+    Source: R/as.R
     
     

 
@@ -58,11 +58,13 @@ 
Coerce to an mb_analyses object

 
     

     
Arguments

-    
x

+
+
+
x

 
object to coerce.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/as.model.html b/reference/as.model.html
index 9a6d491..9b23b9e 100644
--- a/reference/as.model.html
+++ b/reference/as.model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Coerce to an mb_model object

-    Source: R/as.R
+    Source: R/as.R
     
     

 
@@ -58,11 +58,13 @@ 
Coerce to an mb_model object

 
     

     
Arguments

-    
x

+
+
+
x

 
object to coerce.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/as.models.html b/reference/as.models.html
index 680fafb..6643c1d 100644
--- a/reference/as.models.html
+++ b/reference/as.models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Coerce to an mb_models object

-    Source: R/as.R
+    Source: R/as.R
     
     

 
@@ -58,11 +58,13 @@ 
Coerce to an mb_models object

 
     

     
Arguments

-    
x

+
+
+
x

 
object to coerce.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/backwards.html b/reference/backwards.html
index de09638..6f15c4f 100644
--- a/reference/backwards.html
+++ b/reference/backwards.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Backwards

-    Source: R/backwards.R
+    Source: R/backwards.R
     
     

 
@@ -67,35 +67,35 @@ 
Backwards

 
     

     
Arguments

-    
model

+
+
+
model

 
An object.

 
 
-
data

+
data

 
Data.

 
 
-
drops

+
drops

 
A list of character vectors specifying the scalar parameters to consider.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A list of the analyses.

+    
A list of the analyses.

     

     

     
Details

@@ -117,15 +117,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/base_model.html b/reference/base_model.html
index aeb5f24..e424675 100644
--- a/reference/base_model.html
+++ b/reference/base_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Base Model

-    Source: R/base-model.R
+    Source: R/base-model.R
     
     

 
@@ -58,19 +58,19 @@ 
Base Model

 
     

     
Arguments

-    
model

+
+
+
model

 
The full model.

 
 
-
drops

+
drops

 
A list of character vectors specifying possible drops.

 
 

     

     
Value

-    
-
-
The base model (with all drops).

+    
The base model (with all drops).

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/check_mb_analysis.html b/reference/check_mb_analysis.html
index e2ad706..9d7b4a7 100644
--- a/reference/check_mb_analysis.html
+++ b/reference/check_mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Check MB Analysis

-    Source: R/check.R
+    Source: R/check.R
     
     

 
@@ -58,19 +58,19 @@ 
Check MB Analysis

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to check.

 
 
-
object_name

+
object_name

 
A string of the object name.

 
 

     

     
Value

-    
-
-
The object or throws an informative error.

+    
The object or throws an informative error.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/check_mb_code.html b/reference/check_mb_code.html
index 63aedcd..9e4ddd9 100644
--- a/reference/check_mb_code.html
+++ b/reference/check_mb_code.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Check MB Code

-    Source: R/check.R
+    Source: R/check.R
     
     

 
@@ -58,19 +58,19 @@ 
Check MB Code

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to check.

 
 
-
object_name

+
object_name

 
A string of the object name.

 
 

     

     
Value

-    
-
-
The object or throws an informative error.

+    
The object or throws an informative error.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/check_mb_model.html b/reference/check_mb_model.html
index 6c0d344..3d8f35e 100644
--- a/reference/check_mb_model.html
+++ b/reference/check_mb_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Check MB Model

-    Source: R/check.R
+    Source: R/check.R
     
     

 
@@ -58,19 +58,19 @@ 
Check MB Model

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to check.

 
 
-
object_name

+
object_name

 
A string of the object name.

 
 

     

     
Value

-    
-
-
The object or throws an informative error.

+    
The object or throws an informative error.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/check_model_pars.html b/reference/check_model_pars.html
index ad9899c..59a4b32 100644
--- a/reference/check_model_pars.html
+++ b/reference/check_model_pars.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Check Model Parameters

-    Source: R/check-model-parameters.R
+    Source: R/check-model-parameters.R
     
     

 
@@ -58,31 +58,31 @@ 
Check Model Parameters

 
     

     
Arguments

-    
x

+
+
+
x

 
The model code to check.

 
 
-
fixed

+
fixed

 
A string of a regular expression specifying the fixed parameters to monitor.

 
 
-
random

+
random

 
NULL or a character vector of the random effects.

 
 
-
derived

+
derived

 
NULL or a character vector of the derived parameters.

 
 
-
drops

+
drops

 
NULL or a character vector of the parameters to drop.

 
 

     

     
Value

-    
-
-
The possibly updated derived parameters.

+    
The possibly updated derived parameters.

     

 
   

@@ -97,15 +97,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/check_uniquely_named_list.html b/reference/check_uniquely_named_list.html
index 73ebcd3..c290ff4 100644
--- a/reference/check_uniquely_named_list.html
+++ b/reference/check_uniquely_named_list.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Check Uniquely Named List

-    Source: R/check.R
+    Source: R/check.R
     
     

 
@@ -58,19 +58,19 @@ 
Check Uniquely Named List

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to check.

 
 
-
x_name

+
x_name

 
A string of the objects name.

 
 

     

     
Value

-    
-
-
The original object or throws an informative error.

+    
The original object or throws an informative error.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/code.html b/reference/code.html
index ebda7c9..2bd2925 100644
--- a/reference/code.html
+++ b/reference/code.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Code

-    Source: R/code.R
+    Source: R/code.R
     
     

 
@@ -58,19 +58,19 @@ 
Code

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
An object inheriting from class mb_code.

+    
An object inheriting from class mb_code.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef.mb_analyses.html b/reference/coef.mb_analyses.html
index 8aa49bd..4cf51f7 100644
--- a/reference/coef.mb_analyses.html
+++ b/reference/coef.mb_analyses.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Coef TMB Analyses

-    Source: R/coef.R
+    Source: R/coef.R
     
     

 
@@ -55,7 +55,7 @@ 
Coef TMB Analyses

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 coef(
   object,
   param_type = "fixed",
@@ -68,35 +68,35 @@ 
Coef TMB Analyses

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analyses object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate for Bayesian models.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble of the coeffcient terms with the model averaged estimate, the
+    
A tidy tibble of the coeffcient terms with the model averaged estimate, the
 Akaike's weight and the proportion of models including the term.

     

 
@@ -112,15 +112,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef.mb_analysis.html b/reference/coef.mb_analysis.html
index 95bf005..704ca05 100644
--- a/reference/coef.mb_analysis.html
+++ b/reference/coef.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef JAGS Analysis

-    Source: R/coef.R
+    Source: R/coef.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef JAGS Analysis

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 coef(
   object,
   param_type = "fixed",
@@ -67,39 +67,39 @@ 
Coef JAGS Analysis

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analysis object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculating the estimate for Bayesian models.

 
 
-
simplify

+
simplify

 
A flag specifying whether to drop sd and zscore columns and return svalue instead of pvalue.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble of the coefficient terms.

+    
A tidy tibble of the coefficient terms.

     

     

     
Details

@@ -118,15 +118,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef.mb_meta_analyses.html b/reference/coef.mb_meta_analyses.html
index 4480ad8..3863445 100644
--- a/reference/coef.mb_meta_analyses.html
+++ b/reference/coef.mb_meta_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef TMB Meta Analyses

-    Source: R/coef.R
+    Source: R/coef.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef TMB Meta Analyses

     

 
     

-    
# S3 method for mb_meta_analyses
+    
# S3 method for class 'mb_meta_analyses'
 coef(
   object,
   param_type = "fixed",
@@ -66,35 +66,35 @@ 
Coef TMB Meta Analyses

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_meta_analyses object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble.

+    
A tidy tibble.

     

 
   

@@ -109,15 +109,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef.mb_meta_analysis.html b/reference/coef.mb_meta_analysis.html
index d64266a..14a0aff 100644
--- a/reference/coef.mb_meta_analysis.html
+++ b/reference/coef.mb_meta_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef TMB Meta Analysis

-    Source: R/coef.R
+    Source: R/coef.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef TMB Meta Analysis

     

 
     

-    
# S3 method for mb_meta_analysis
+    
# S3 method for class 'mb_meta_analysis'
 coef(
   object,
   param_type = "fixed",
@@ -66,35 +66,35 @@ 
Coef TMB Meta Analysis

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_meta_analysis object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble.

+    
A tidy tibble.

     

 
   

@@ -109,15 +109,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef_profile.html b/reference/coef_profile.html
index 61d87a6..c698ad4 100644
--- a/reference/coef_profile.html
+++ b/reference/coef_profile.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef Profile

-    Source: R/coef-profile.R
+    Source: R/coef-profile.R
     
     

 
@@ -58,11 +58,13 @@ 
Coef Profile

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef_profile.mb_analyses.html b/reference/coef_profile.mb_analyses.html
index 607fd16..bab288c 100644
--- a/reference/coef_profile.mb_analyses.html
+++ b/reference/coef_profile.mb_analyses.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef TMB Analyses

-    Source: R/coef-profile.R
+    Source: R/coef-profile.R
     
     

 
@@ -55,7 +55,7 @@ 
Coef TMB Analyses

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 coef_profile(
   object,
   param_type = "fixed",
@@ -70,43 +70,43 @@ 
Coef TMB Analyses

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analyses object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate for Bayesian models.

 
 
-
parallel

+
parallel

 
A flag indicating whether to using parallel backend provided by foreach.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble of the coeffcient terms with the model averaged estimate, the
+    
A tidy tibble of the coeffcient terms with the model averaged estimate, the
 Akaike's weight and the proportion of models including the term.

     

 
@@ -122,15 +122,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef_profile.mb_analysis.html b/reference/coef_profile.mb_analysis.html
index 3f6edbd..a19dd85 100644
--- a/reference/coef_profile.mb_analysis.html
+++ b/reference/coef_profile.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef Profile Analysis

-    Source: R/coef-profile.R
+    Source: R/coef-profile.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef Profile Analysis

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 coef_profile(
   object,
   param_type = "fixed",
@@ -69,47 +69,47 @@ 
Coef Profile Analysis

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analysis object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculating the estimate for Bayesian models.

 
 
-
parallel

+
parallel

 
A flag indicating whether to using parallel backend provided by foreach.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
simplify

+
simplify

 
A flag specifying whether to simplify with svalue.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble of the coefficient terms.

+    
A tidy tibble of the coefficient terms.

     

     

     
Details

@@ -128,15 +128,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef_profile.mb_meta_analyses.html b/reference/coef_profile.mb_meta_analyses.html
index 98eda30..c461df7 100644
--- a/reference/coef_profile.mb_meta_analyses.html
+++ b/reference/coef_profile.mb_meta_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef TMB Meta Analyses

-    Source: R/coef-profile.R
+    Source: R/coef-profile.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef TMB Meta Analyses

     

 
     

-    
# S3 method for mb_meta_analyses
+    
# S3 method for class 'mb_meta_analyses'
 coef_profile(
   object,
   param_type = "fixed",
@@ -68,43 +68,43 @@ 
Coef TMB Meta Analyses

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_meta_analyses object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate.

 
 
-
parallel

+
parallel

 
A flag indicating whether to using parallel backend provided by foreach.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble.

+    
A tidy tibble.

     

 
   

@@ -119,15 +119,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/coef_profile.mb_meta_analysis.html b/reference/coef_profile.mb_meta_analysis.html
index d2881b8..7ee7406 100644
--- a/reference/coef_profile.mb_meta_analysis.html
+++ b/reference/coef_profile.mb_meta_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Coef TMB Meta Analysis

-    Source: R/coef-profile.R
+    Source: R/coef-profile.R
     
     

 
@@ -53,7 +53,7 @@ 
Coef TMB Meta Analysis

     

 
     

-    
# S3 method for mb_meta_analysis
+    
# S3 method for class 'mb_meta_analysis'
 coef_profile(
   object,
   param_type = "fixed",
@@ -68,43 +68,43 @@ 
Coef TMB Meta Analysis

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_meta_analysis object.

 
 
-
param_type

+
param_type

 
A flag specifying whether 'fixed', 'random' or 'derived' terms.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
estimate

+
estimate

 
The function to use to calculate the estimate.

 
 
-
parallel

+
parallel

 
A flag indicating whether to using parallel backend provided by foreach.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A tidy tibble.

+    
A tidy tibble.

     

 
   

@@ -119,15 +119,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/comment_string.html b/reference/comment_string.html
index cc567f8..f645255 100644
--- a/reference/comment_string.html
+++ b/reference/comment_string.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Comment String

-    Source: R/comments.R
+    Source: R/comments.R
     
     

 
@@ -58,19 +58,19 @@ 
Comment String

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb code object.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A string of the regular expression.

+    
A string of the regular expression.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/data_set.html b/reference/data_set.html
index 2b0de55..e80d013 100644
--- a/reference/data_set.html
+++ b/reference/data_set.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Data Set

-    Source: R/data-set.R
+    Source: R/data-set.R
     
     

 
@@ -64,31 +64,31 @@ 
Data Set

 
     

     
Arguments

-    
x

+
+
+
x

 
The object.

 
 
-
modify

+
modify

 
A flag indicating whether to modify the data.

 
 
-
numericize_factors

+
numericize_factors

 
A flag indicating whether to convert factors to integers if modifying the data.

 
 
-
marginalize_random_effects

+
marginalize_random_effects

 
A flag indicating whether to set each factor in one or more random effects at its first level.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
The data set as a tibble.

+    
The data set as a tibble.

     

 
   

@@ -103,15 +103,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/density99.html b/reference/density99.html
index 20c41ba..f08addb 100644
--- a/reference/density99.html
+++ b/reference/density99.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Density99

-    Source: R/data.R
+    Source: R/data.R
     
     

 
@@ -73,15 +73,15 @@ 
Format

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/drop_pars.html b/reference/drop_pars.html
index 8d00b01..4dddc01 100644
--- a/reference/drop_pars.html
+++ b/reference/drop_pars.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Drop pars

-    Source: R/drop-parameters.R
+    Source: R/drop-parameters.R
     
     

 
@@ -58,23 +58,23 @@ 
Drop pars

 
     

     
Arguments

-    
x

+
+
+
x

 
The object.

 
 
-
pars

+
pars

 
A character vector of the pars to drop.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
The updated object.

+    
The updated object.

     

 
   

@@ -89,15 +89,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/elapsed.html b/reference/elapsed.html
index 3e1786c..8c6bafb 100644
--- a/reference/elapsed.html
+++ b/reference/elapsed.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Elapsed

-    Source: R/elapsed.R
+    Source: R/elapsed.R
     
     

 
@@ -58,11 +58,13 @@ 
Elapsed

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to calculate it for.

 
 
-
...

+
...

 
Not used.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/embr-package.html b/reference/embr-package.html
index 82efba6..534a048 100644
--- a/reference/embr-package.html
+++ b/reference/embr-package.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
embr: Model Builder Utility Functions and Virtual Classes

-    Source: R/embr-package.R
+    Source: R/embr-package.R
     
     

 
@@ -80,15 +80,15 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/estimates.mb_analysis.html b/reference/estimates.mb_analysis.html
index 2919340..980cba3 100644
--- a/reference/estimates.mb_analysis.html
+++ b/reference/estimates.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Estimates

-    Source: R/estimates.R
+    Source: R/estimates.R
     
     

 
@@ -53,33 +53,33 @@ 
Estimates

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 estimates(x, param_type = "fixed", ...)

     

 
     

     
Arguments

-    
x

+
+
+
x

 
An object.

 
 
-
param_type

+
param_type

 
A string indicating the type of terms to get the names for.

 
 
-
...

+
...

 
Other arguments passed to methods.

 
 

     

     
Value

-    
-
-
A list of uniquely named numeric objects.

+    
A list of uniquely named numeric objects.

     

     

     
See also

-    
Other MCMC manipulations: 
+    
Other MCMC manipulations:
 bind_chains(),
 bind_iterations(),
 collapse_chains(),
@@ -98,15 +98,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/fitted.mb_analysis.html b/reference/fitted.mb_analysis.html
index 3805afa..998cb1a 100644
--- a/reference/fitted.mb_analysis.html
+++ b/reference/fitted.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Fitted Values

-    Source: R/predict.R
+    Source: R/predict.R
     
     

 
@@ -53,25 +53,25 @@ 
Fitted Values

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 fitted(object, ...)

     

 
     

     
Arguments

-    
object

+
+
+
object

 
The MB analysis object.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
The analysis data set with the fitted values.

+    
The analysis data set with the fitted values.

     

     

     
Details

@@ -90,15 +90,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/get_analysis_mode.html b/reference/get_analysis_mode.html
index 13693c2..41b2007 100644
--- a/reference/get_analysis_mode.html
+++ b/reference/get_analysis_mode.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Get Analysis Mode

-    Source: R/get-analysis-mode.R
+    Source: R/get-analysis-mode.R
     
     

 
@@ -58,9 +58,7 @@ 
Get Analysis Mode

 
     

     
Value

-    
-
-
A named list of the current package options.

+    
A named list of the current package options.

     

     

     
Details

@@ -106,9 +104,9 @@ 
Details

 
     

     
Examples

-    
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 get_analysis_mode()
-}
+} # }
 

     

   

@@ -123,15 +121,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/get_model.html b/reference/get_model.html
index b8adcb6..7c2af37 100644
--- a/reference/get_model.html
+++ b/reference/get_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Retrieve model

-    Source: R/new-analysis.R
+    Source: R/new-analysis.R
     
     

 
@@ -58,7 +58,9 @@ 
Retrieve model

 
     

     
Arguments

-    
analysis

+
+
+
analysis

 
An object of class `"mb_analysis"`.

 
 

@@ -75,15 +77,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/index.html b/reference/index.html
index 6017836..620e963 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,9 +1,9 @@
 
-Function reference • embrPackage index • embr
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -479,15 +479,15 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.lmb_analysis.html b/reference/is.lmb_analysis.html
index 29f60da..0055c66 100644
--- a/reference/is.lmb_analysis.html
+++ b/reference/is.lmb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Is a LMB Analysis

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is a LMB Analysis

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.lmb_code.html b/reference/is.lmb_code.html
index f2b043b..8d38b9b 100644
--- a/reference/is.lmb_code.html
+++ b/reference/is.lmb_code.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is a LMB Code

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is a LMB Code

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.lmb_model.html b/reference/is.lmb_model.html
index a97b484..73e74a9 100644
--- a/reference/is.lmb_model.html
+++ b/reference/is.lmb_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is a LMB Model

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is a LMB Model

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_analyses.html b/reference/is.mb_analyses.html
index a120f84..3d48421 100644
--- a/reference/is.mb_analyses.html
+++ b/reference/is.mb_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Analyses?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Analyses?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_analysis.html b/reference/is.mb_analysis.html
index def01bb..463f9ac 100644
--- a/reference/is.mb_analysis.html
+++ b/reference/is.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Analysis?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Analysis?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_code.html b/reference/is.mb_code.html
index 01d7ec8..76fcaf5 100644
--- a/reference/is.mb_code.html
+++ b/reference/is.mb_code.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Code?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Code?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_model.html b/reference/is.mb_model.html
index 08b120c..802bcfe 100644
--- a/reference/is.mb_model.html
+++ b/reference/is.mb_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Model?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Model?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_models.html b/reference/is.mb_models.html
index f3df02a..9fb7f7a 100644
--- a/reference/is.mb_models.html
+++ b/reference/is.mb_models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Models?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Models?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.mb_null_analysis.html b/reference/is.mb_null_analysis.html
index 65bbe50..401b30a 100644
--- a/reference/is.mb_null_analysis.html
+++ b/reference/is.mb_null_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is MB Null Analysis?

-    Source: R/is.R
+    Source: R/is.R
     
     

 
@@ -58,15 +58,15 @@ 
Is MB Null Analysis?

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag indicating whether the test was positive.

+    
A flag indicating whether the test was positive.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is.syntactic.html b/reference/is.syntactic.html
index ec12932..15bd39a 100644
--- a/reference/is.syntactic.html
+++ b/reference/is.syntactic.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is syntactic

-    Source: R/utils.R
+    Source: R/utils.R
     
     

 
@@ -58,20 +58,20 @@ 
Is syntactic

 
     

     
Arguments

-    
x

+
+
+
x

 
A character of possible variable names.

 
 

     

     
Value

-    
-
-
A logical vector indicating whether a syntactically correct variable name.

+    
A logical vector indicating whether a syntactically correct variable name.

     

 
     

     
Examples

-    
is.syntactic(c("0", "x", "1x","x y", "x1"))
+    
is.syntactic(c("0", "x", "1x", "x y", "x1"))
 #> [1] FALSE  TRUE FALSE FALSE  TRUE
 

     

@@ -87,15 +87,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is_bayesian.html b/reference/is_bayesian.html
index c8a3e75..2d1b386 100644
--- a/reference/is_bayesian.html
+++ b/reference/is_bayesian.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Test if is bayesian

-    Source: R/is-paradigm.R
+    Source: R/is-paradigm.R
     
     

 
@@ -58,19 +58,19 @@ 
Test if is bayesian

 
     

     
Arguments

-    
x

+
+
+
x

 
the object.

 
 
-
...

+
...

 
Unused

 
 

     

     
Value

-    
-
-
A flag indicating wether bayesian.

+    
A flag indicating wether bayesian.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is_frequentist.html b/reference/is_frequentist.html
index 497fa81..d03557b 100644
--- a/reference/is_frequentist.html
+++ b/reference/is_frequentist.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Test if is frequentist

-    Source: R/is-paradigm.R
+    Source: R/is-paradigm.R
     
     

 
@@ -58,15 +58,15 @@ 
Test if is frequentist

 
     

     
Arguments

-    
x

+
+
+
x

 
the object.

 
 

     

     
Value

-    
-
-
A flag indicating whether frequentist

+    
A flag indicating whether frequentist

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/is_namedlist.html b/reference/is_namedlist.html
index 133241c..be1a165 100644
--- a/reference/is_namedlist.html
+++ b/reference/is_namedlist.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Is Named List

-    Source: R/utils.R
+    Source: R/utils.R
     
     

 
@@ -58,15 +58,15 @@ 
Is Named List

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to test.

 
 

     

     
Value

-    
-
-
A flag.

+    
A flag.

     

 
     

@@ -95,15 +95,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/load_model.html b/reference/load_model.html
index 7cee104..b8ef268 100644
--- a/reference/load_model.html
+++ b/reference/load_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Load Model

-    Source: R/load-model.R
+    Source: R/load-model.R
     
     

 
@@ -58,15 +58,17 @@ 
Load Model

 
     

     
Arguments

-    
x

+
+
+
x

 
The model to load.

 
 
-
quiet

+
quiet

 
A flag indicating whether to suppress warnings and output.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -83,15 +85,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/logLik.mb_analysis.html b/reference/logLik.mb_analysis.html
index e8954b5..98aba40 100644
--- a/reference/logLik.mb_analysis.html
+++ b/reference/logLik.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Log-Likelihood

-    Source: R/logLik.R
+    Source: R/logLik.R
     
     

 
@@ -53,17 +53,19 @@ 
Log-Likelihood

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 logLik(object, ...)

     

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analysis object.

 
 
-
...

+
...

 
unused.

 
 

@@ -80,15 +82,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/logLik.mb_null_analysis.html b/reference/logLik.mb_null_analysis.html
index d072c2e..13eb19a 100644
--- a/reference/logLik.mb_null_analysis.html
+++ b/reference/logLik.mb_null_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Log-Likelihood

-    Source: R/logLik.R
+    Source: R/logLik.R
     
     

 
@@ -53,17 +53,19 @@ 
Log-Likelihood

     

 
     

-    
# S3 method for mb_null_analysis
+    
# S3 method for class 'mb_null_analysis'
 logLik(object, ...)

     

 
     

     
Arguments

-    
object

+
+
+
object

 
The mb_analysis object.

 
 
-
...

+
...

 
unused.

 
 

@@ -80,15 +82,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/make_all_models.html b/reference/make_all_models.html
index cbc033c..3e860d2 100644
--- a/reference/make_all_models.html
+++ b/reference/make_all_models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Make All Models

-    Source: R/make-all-models.R
+    Source: R/make-all-models.R
     
     

 
@@ -58,19 +58,19 @@ 
Make All Models

 
     

     
Arguments

-    
model

+
+
+
model

 
The full model.

 
 
-
drops

+
drops

 
A list of character vectors specifying possible drops.

 
 

     

     
Value

-    
-
-
A list of objects inheriting from class mb_model.

+    
A list of objects inheriting from class mb_model.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/mb_code.html b/reference/mb_code.html
index e7da386..0c2edfb 100644
--- a/reference/mb_code.html
+++ b/reference/mb_code.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
MB Code

-    Source: R/mb-code.R
+    Source: R/mb-code.R
     
     

 
@@ -60,30 +60,30 @@ 
MB Code

 
     

     
Arguments

-    
template

+
+
+
template

 
A string, a braced `` expression (unquoted or quoted),
 or an object of class `"mb_code"`.

 
 
-
x

+
x

 
A string or a braced `` expression.

 
 
-
class

+
class

 
The class of the new object.

 
 

     

     
Value

-    
-
-
An object inheriting from class mb_code.

+    
An object inheriting from class mb_code.

     

 
     

     
Examples

     
x <- mb_code(
-"#include <TMB.hpp>
+  "#include <TMB.hpp>
 
 template<class Type>
 
@@ -99,7 +99,8 @@ 
Examples

 }
 return nll;
 }
-")
+"
+)
 class(x)
 #> [1] "tmb_code" "mb_code" 
 

@@ -116,15 +117,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/mcmc_derive.mb_analyses.html b/reference/mcmc_derive.mb_analyses.html
index 6f11fcf..9745aa0 100644
--- a/reference/mcmc_derive.mb_analyses.html
+++ b/reference/mcmc_derive.mb_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Derive

-    Source: R/derive.R
+    Source: R/derive.R
     
     

 
@@ -53,7 +53,7 @@ 
Derive

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 mcmc_derive(
   object,
   new_data = data_set(object),
@@ -72,59 +72,59 @@ 
Derive

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
A object of class mcmcr.

+    
A object of class mcmcr.

     

 
   

@@ -139,15 +139,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/mcmc_derive.mb_analysis.html b/reference/mcmc_derive.mb_analysis.html
index 4c1cc8e..6f01512 100644
--- a/reference/mcmc_derive.mb_analysis.html
+++ b/reference/mcmc_derive.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Derive

-    Source: R/derive.R
+    Source: R/derive.R
     
     

 
@@ -53,7 +53,7 @@ 
Derive

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 mcmc_derive(
   object,
   new_data = data_set(object),
@@ -74,67 +74,67 @@ 
Derive

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
ref_fun2

+
ref_fun2

 
A function whose first argument takes a vector of two numbers and returns a scalar of a metric of the difference between them.

 
 
-
random_effects

+
random_effects

 
A named list specifying the random effects and the associated factors.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
A object of class mcmcr.

+    
A object of class mcmcr.

     

 
   

@@ -149,15 +149,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/mcmc_derive_data.mb_analyses.html b/reference/mcmc_derive_data.mb_analyses.html
index 6af035a..3bb242f 100644
--- a/reference/mcmc_derive_data.mb_analyses.html
+++ b/reference/mcmc_derive_data.mb_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Derive Data

-    Source: R/derive-data.R
+    Source: R/derive-data.R
     
     

 
@@ -53,7 +53,7 @@ 
Derive Data

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 mcmc_derive_data(
   object,
   new_data = data_set(object),
@@ -73,63 +73,63 @@ 
Derive Data

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
ref_fun2

+
ref_fun2

 
A function whose first argument takes a vector of two numbers and returns a scalar of a metric of the difference between them.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
A object of class mcmc_data.

+    
A object of class mcmc_data.

     

 
   

@@ -144,15 +144,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/mcmc_derive_data.mb_analysis.html b/reference/mcmc_derive_data.mb_analysis.html
index 38fc9d1..e0c6557 100644
--- a/reference/mcmc_derive_data.mb_analysis.html
+++ b/reference/mcmc_derive_data.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Derive Data

-    Source: R/derive-data.R
+    Source: R/derive-data.R
     
     

 
@@ -53,7 +53,7 @@ 
Derive Data

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 mcmc_derive_data(
   object,
   new_data = data_set(object),
@@ -74,67 +74,67 @@ 
Derive Data

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
ref_fun2

+
ref_fun2

 
A function whose first argument takes a vector of two numbers and returns a scalar of a metric of the difference between them.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
random_effects

+
random_effects

 
A named list specifying the random effects and the associated factors.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
A object of class mcmc_data.

+    
A object of class mcmc_data.

     

 
   

@@ -149,15 +149,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/model.html b/reference/model.html
index 3c68170..b18605e 100644
--- a/reference/model.html
+++ b/reference/model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
MB Model

-    Source: R/model.R
+    Source: R/model.R
     
     

 
@@ -75,77 +75,77 @@ 
MB Model

 
     

     
Arguments

-    
x

+
+
+
x

 
A string, or an object inheriting from class `"mb_code"`.

 
 
-
...

+
...

 
Unused arguments.

 
 
-
code

+
code

 
Passed on to [mb_code()]. If `x` is not `NULL`, `code` must be `NULL`,
 and vice versa.

 
 
-
gen_inits

+
gen_inits

 
A single argument function taking the modified data and
 returning a named list of initial values.

 
 
-
random_effects

+
random_effects

 
A named list specifying the random effects and the associated factors.

 
 
-
fixed

+
fixed

 
A string of a regular expression specifying the fixed pars to monitor.

 
 
-
derived

+
derived

 
A character vector of the derived pars to monitor.

 
 
-
select_data

+
select_data

 
A named list specifying the columns to select and their associated classes and values as well as transformations and scaling options.

 
 
-
center

+
center

 
A character vector of the columns to center.

 
 
-
scale

+
scale

 
A character vector of the columns to scale (after centering).

 
 
-
modify_data

+
modify_data

 
A single argument function to modify the data (in list form) immediately prior to the analysis.

 
 
-
nthin

+
nthin

 
A count specifying the thinning interval.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationships.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
drops

+
drops

 
A list of character vector of possible scalar pars to drop (fix at 0).

 
 

     

     
Value

-    
-
-
An object inherting from class mb_model.

+    
An object inherting from class mb_model.

     

     

     
Details

@@ -155,7 +155,7 @@ 
Details

     

     
 
   

@@ -170,15 +170,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/models.html b/reference/models.html
index 013c92a..643dcd8 100644
--- a/reference/models.html
+++ b/reference/models.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
MB Models

-    Source: R/models.R
+    Source: R/models.R
     
     

 
@@ -58,15 +58,15 @@ 
MB Models

 
     

     
Arguments

-    
...

+
+
+
...

 
Named objects.

 
 

     

     
Value

-    
-
-
An object inheriting from class mb_models.

+    
An object inheriting from class mb_models.

     

 
   

@@ -81,15 +81,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/modify_data.html b/reference/modify_data.html
index 64675c8..edc210f 100644
--- a/reference/modify_data.html
+++ b/reference/modify_data.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Modify Data

-    Source: R/modify-data.R
+    Source: R/modify-data.R
     
     

 
@@ -58,23 +58,23 @@ 
Modify Data

 
     

     
Arguments

-    
data

+
+
+
data

 
The data to modify.

 
 
-
model

+
model

 
An object inheriting from class mb_model.

 
 
-
numericize_factors

+
numericize_factors

 
A flag indicating whether to convert factors to integer.

 
 

     

     
Value

-    
-
-
The modified data in list form.

+    
The modified data in list form.

     

 
   

@@ -89,15 +89,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/modify_new_data.html b/reference/modify_new_data.html
index bc1df0b..e7def03 100644
--- a/reference/modify_new_data.html
+++ b/reference/modify_new_data.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Modify New Data

-    Source: R/modify-data.R
+    Source: R/modify-data.R
     
     

 
@@ -64,31 +64,31 @@ 
Modify New Data

 
     

     
Arguments

-    
data

+
+
+
data

 
The data to modify.

 
 
-
data2

+
data2

 
The base data.

 
 
-
model

+
model

 
An object inheriting from class mb_model.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
numericize_factors

+
numericize_factors

 
A flag indicating whether to convert factors to integer.

 
 

     

     
Value

-    
-
-
The modified data in list form.

+    
The modified data in list form.

     

 
   

@@ -103,15 +103,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/monitor.html b/reference/monitor.html
index 00caf1a..833222a 100644
--- a/reference/monitor.html
+++ b/reference/monitor.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
pars to monitor

-    Source: R/monitor.R
+    Source: R/monitor.R
     
     

 
@@ -58,19 +58,19 @@ 
pars to monitor

 
     

     
Arguments

-    
object

+
+
+
object

 
An mb model object to get the pars for.

 
 
-
param_type

+
param_type

 
A string specifying the type of pars to get.

 
 

     

     
Value

-    
-
-
A character vector of the pars to monitor.

+    
A character vector of the pars to monitor.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/new_analysis.html b/reference/new_analysis.html
index fed463a..2f8fd90 100644
--- a/reference/new_analysis.html
+++ b/reference/new_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
MB Analysis

-    Source: R/new-analysis.R
+    Source: R/new-analysis.R
     
     

 
@@ -58,11 +58,13 @@ 
MB Analysis

 
     

     
Arguments

-    
x

+
+
+
x

 
A list.

 
 
-
class

+
class

 
The class of the new object.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/new_expr-set.html b/reference/new_expr-set.html
index 53e81f3..364e85b 100644
--- a/reference/new_expr-set.html
+++ b/reference/new_expr-set.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
new_expr set

-    Source: R/new-expr.R
+    Source: R/new-expr.R
     
     

 
@@ -58,19 +58,19 @@ 
new_expr set

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to set for.

 
 
-
value

+
value

 
The new value of new expr.

 
 

     

     
Value

-    
-
-
The modified object.

+    
The modified object.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/new_expr.html b/reference/new_expr.html
index b91ebee..a51c95a 100644
--- a/reference/new_expr.html
+++ b/reference/new_expr.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
new_expr

-    Source: R/new-expr.R
+    Source: R/new-expr.R
     
     

 
@@ -58,19 +58,19 @@ 
new_expr

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to get for.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
The new_expr

+    
The new_expr

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/ngens.html b/reference/ngens.html
index 1415088..72c22d7 100644
--- a/reference/ngens.html
+++ b/reference/ngens.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Total Number of MCMC simulations generated (including warmup)

-    Source: R/ngens.R
+    Source: R/ngens.R
     
     

 
@@ -58,19 +58,19 @@ 
Total Number of MCMC simulations generated (including warmup)

 
     

     
Arguments

-    
x

+
+
+
x

 
The object

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A count.

+    
A count.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/nmodels.html b/reference/nmodels.html
index af4ed2c..3b27cb3 100644
--- a/reference/nmodels.html
+++ b/reference/nmodels.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Number Models

-    Source: R/nmodels.R
+    Source: R/nmodels.R
     
     

 
@@ -58,19 +58,19 @@ 
Number Models

 
     

     
Arguments

-    
x

+
+
+
x

 
the object.

 
 
-
...

+
...

 
Named objects.

 
 

     

     
Value

-    
-
-
An integer of the number of models

+    
An integer of the number of models

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/nterms.mb_analysis.html b/reference/nterms.mb_analysis.html
index d79955b..4367aaa 100644
--- a/reference/nterms.mb_analysis.html
+++ b/reference/nterms.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Number of terms

-    Source: R/terms.R
+    Source: R/terms.R
     
     

 
@@ -53,25 +53,27 @@ 
Number of terms

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 nterms(x, param_type = "fixed", include_constant = TRUE, ...)

     

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to get the nterms for

 
 
-
param_type

+
param_type

 
A string indicating the type of terms to get the names for.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
...

+
...

 
unused

 
 

@@ -88,15 +90,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/nthin.html b/reference/nthin.html
index 3f727e7..cf655a7 100644
--- a/reference/nthin.html
+++ b/reference/nthin.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Thinning Rate

-    Source: R/nthin.R
+    Source: R/nthin.R
     
     

 
@@ -58,19 +58,19 @@ 
Thinning Rate

 
     

     
Arguments

-    
x

+
+
+
x

 
The object

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A count.

+    
A count.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/params.html b/reference/params.html
index 4f51156..8d74f83 100644
--- a/reference/params.html
+++ b/reference/params.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Parameter Descriptions

-    Source: R/params.R
+    Source: R/params.R
     
     

 
@@ -55,15 +55,17 @@ 
Parameter Descriptions

 
     

     
Arguments

-    
param_type

+
+
+
param_type

 
A string indicating the type of terms to get the names for.

 
 
-
type

+
type

 
A string of the residual type.

 
 
-
...

+
...

 
Unused.

 
 

@@ -80,15 +82,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plot.mb_analysis.html b/reference/plot.mb_analysis.html
index 0fb84e5..b4f95ce 100644
--- a/reference/plot.mb_analysis.html
+++ b/reference/plot.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Plot Analysis

-    Source: R/plot.R
+    Source: R/plot.R
     
     

 
@@ -53,21 +53,23 @@ 
Plot Analysis

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 plot(x, param_type = "fixed", ...)

     

 
     

     
Arguments

-    
x

+
+
+
x

 
The analysis object to plot

 
 
-
param_type

+
param_type

 
A string indicating the type of terms to get the names for.

 
 
-
...

+
...

 
Unused.

 
 

@@ -84,15 +86,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plot_data.html b/reference/plot_data.html
index 75e3d79..9e1d30d 100644
--- a/reference/plot_data.html
+++ b/reference/plot_data.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Plot Data

-    Source: R/plot-data.R
+    Source: R/plot-data.R
     
     

 
@@ -58,11 +58,13 @@ 
Plot Data

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to plot the data for.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/plot_residuals.html b/reference/plot_residuals.html
index 27a7b5b..44b6760 100644
--- a/reference/plot_residuals.html
+++ b/reference/plot_residuals.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Plot Residuals

-    Source: R/residuals.R
+    Source: R/residuals.R
     
     

 
@@ -58,11 +58,13 @@ 
Plot Residuals

 
     

     
Arguments

-    
x

+
+
+
x

 
The object to plot the residuals for.

 
 
-
...

+
...

 
Unused.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/posterior_predictive_check.html b/reference/posterior_predictive_check.html
index 05c5971..358a34e 100644
--- a/reference/posterior_predictive_check.html
+++ b/reference/posterior_predictive_check.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Posterior Predictive Check

-    Source: R/posterior-predictive-check.R
+    Source: R/posterior-predictive-check.R
     
     

 
@@ -58,19 +58,19 @@ 
Posterior Predictive Check

 
     

     
Arguments

-    
x

+
+
+
x

 
The object

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A tibble of the checks.

+    
A tibble of the checks.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/posterior_predictive_check.mb_analysis.html b/reference/posterior_predictive_check.mb_analysis.html
index ca54cdb..6bc2311 100644
--- a/reference/posterior_predictive_check.mb_analysis.html
+++ b/reference/posterior_predictive_check.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Posterior Predictive Check

-    Source: R/posterior-predictive-check.R
+    Source: R/posterior-predictive-check.R
     
     

 
@@ -53,30 +53,30 @@ 
Posterior Predictive Check

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 posterior_predictive_check(x, zeros = TRUE, ...)

     

 
     

     
Arguments

-    
x

+
+
+
x

 
The MB analysis object.

 
 
-
zeros

+
zeros

 
A flag specifying whether to perform a posterior predictive check
 on the number of zeros in the data.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
A tibble of the checks.

+    
A tibble of the checks.

     

 
   

@@ -91,15 +91,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/predict.mb_analyses.html b/reference/predict.mb_analyses.html
index 9d66a1c..b909102 100644
--- a/reference/predict.mb_analyses.html
+++ b/reference/predict.mb_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Predict

-    Source: R/predict.R
+    Source: R/predict.R
     
     

 
@@ -53,7 +53,7 @@ 
Predict

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 predict(
   object,
   new_data = data_set(object),
@@ -74,59 +74,61 @@ 
Predict

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
ref_fun2

+
ref_fun2

 
A function whose first argument takes a vector of two numbers and returns a scalar of a metric of the difference between them.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -143,15 +145,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/predict.mb_analysis.html b/reference/predict.mb_analysis.html
index f401a7a..2825e60 100644
--- a/reference/predict.mb_analysis.html
+++ b/reference/predict.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Predict

-    Source: R/predict.R
+    Source: R/predict.R
     
     

 
@@ -53,7 +53,7 @@ 
Predict

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 predict(
   object,
   new_data = data_set(object),
@@ -75,63 +75,65 @@ 
Predict

 
     

     
Arguments

-    
object

+
+
+
object

 
An object inheriting from class mb_analysis.

 
 
-
new_data

+
new_data

 
The data frame to calculate the predictions for.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationship.

 
 
-
new_values

+
new_values

 
A named list of new or replacement values to pass to new_expr.

 
 
-
term

+
term

 
A string of the term in new_expr.

 
 
-
conf_level

+
conf_level

 
A number specifying the confidence level. By default 0.95.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
ref_data

+
ref_data

 
A flag or a data frame with 1 row indicating the reference values for calculating the effects size.

 
 
-
ref_fun2

+
ref_fun2

 
A function whose first argument takes a vector of two numbers and returns a scalar of a metric of the difference between them.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
random_effects

+
random_effects

 
A named list specifying the random effects and the associated factors.

 
 
-
parallel

+
parallel

 
A flag indicating whether to do predictions using parallel backend provided by foreach.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -148,15 +150,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/random_effects.html b/reference/random_effects.html
index cda4773..e36e8c8 100644
--- a/reference/random_effects.html
+++ b/reference/random_effects.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Random Effects

-    Source: R/random-effects.R
+    Source: R/random-effects.R
     
     

 
@@ -58,19 +58,19 @@ 
Random Effects

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
The random effects as a sorted named list.

+    
The random effects as a sorted named list.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse.html b/reference/reanalyse.html
index 347640c..62d9944 100644
--- a/reference/reanalyse.html
+++ b/reference/reanalyse.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -58,11 +58,13 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse.mb_analyses.html b/reference/reanalyse.mb_analyses.html
index b5b85fc..13eba6c 100644
--- a/reference/reanalyse.mb_analyses.html
+++ b/reference/reanalyse.mb_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Reanalyse

     

 
     

-    
# S3 method for mb_analyses
+    
# S3 method for class 'mb_analyses'
 reanalyse(
   object,
   rhat = getOption("mb.rhat", 1.1),
@@ -70,43 +70,45 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
rhat

+
rhat

 
A number specifying the rhat threshold.

 
 
-
esr

+
esr

 
A number specifying the effective sampling rate.

 
 
-
nreanalyses

+
nreanalyses

 
A count between 1 and 7 specifying the maximum number of reanalyses.

 
 
-
duration

+
duration

 
The maximum total time to spend on analysis/reanalysis.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print summary of model.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse.mb_analysis.html b/reference/reanalyse.mb_analysis.html
index fc42d61..38d0d3e 100644
--- a/reference/reanalyse.mb_analysis.html
+++ b/reference/reanalyse.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Reanalyse

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 reanalyse(
   object,
   rhat = getOption("mb.rhat", 1.1),
@@ -70,43 +70,45 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
rhat

+
rhat

 
A number specifying the rhat threshold.

 
 
-
esr

+
esr

 
A number specifying the minimum effective sampling rate.

 
 
-
nreanalyses

+
nreanalyses

 
A count between 0 and 4 specifying the maximum number of reanalyses.

 
 
-
duration

+
duration

 
The maximum total time to spend on analysis and reanalysis.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print summary of model.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse.mb_meta_analyses.html b/reference/reanalyse.mb_meta_analyses.html
index 42e9724..aaba1be 100644
--- a/reference/reanalyse.mb_meta_analyses.html
+++ b/reference/reanalyse.mb_meta_analyses.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Reanalyse

     

 
     

-    
# S3 method for mb_meta_analyses
+    
# S3 method for class 'mb_meta_analyses'
 reanalyse(
   object,
   rhat = getOption("mb.rhat", 1.1),
@@ -70,43 +70,45 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
rhat

+
rhat

 
A number specifying the rhat threshold.

 
 
-
esr

+
esr

 
A number specifying the effective sampling rate.

 
 
-
nreanalyses

+
nreanalyses

 
A count between 1 and 7 specifying the maximum number of reanalyses.

 
 
-
duration

+
duration

 
The maximum total time to spend on analysis/reanalysis.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print summary of model.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse.mb_meta_analysis.html b/reference/reanalyse.mb_meta_analysis.html
index 54fb283..fd9741b 100644
--- a/reference/reanalyse.mb_meta_analysis.html
+++ b/reference/reanalyse.mb_meta_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -53,7 +53,7 @@ 
Reanalyse

     

 
     

-    
# S3 method for mb_meta_analysis
+    
# S3 method for class 'mb_meta_analysis'
 reanalyse(
   object,
   rhat = getOption("mb.rhat", 1.1),
@@ -70,43 +70,45 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
rhat

+
rhat

 
A number specifying the rhat threshold.

 
 
-
esr

+
esr

 
A number specifying the effective sampling rate.

 
 
-
nreanalyses

+
nreanalyses

 
A count between 1 and 7 specifying the maximum number of reanalyses.

 
 
-
duration

+
duration

 
The maximum total time to spend on analysis/reanalysis.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print summary of model.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 
-
...

+
...

 
Unused arguments.

 
 

@@ -123,15 +125,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reanalyse1.html b/reference/reanalyse1.html
index 0578131..c0cd143 100644
--- a/reference/reanalyse1.html
+++ b/reference/reanalyse1.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reanalyse

-    Source: R/reanalyse.R
+    Source: R/reanalyse.R
     
     

 
@@ -60,19 +60,21 @@ 
Reanalyse

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to reanalyse.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the reanalysis in parallel.

 
 
-
quiet

+
quiet

 
A flag indicating whether to capture output.

 
 
-
...

+
...

 
Additional arguments.

 
 

@@ -89,15 +91,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/reexports.html b/reference/reexports.html
index edbf882..91c6948 100644
--- a/reference/reexports.html
+++ b/reference/reexports.html
@@ -26,7 +26,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Objects exported from other packages

-    Source: R/augment.R, R/coef.R, R/derive-data.R, and 7 more
+    Source: R/augment.R, R/coef.R, R/derive-data.R, and 7 more
     
     

 
@@ -110,15 +110,15 @@ 
Objects exported from other packages

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/residuals.mb_analysis.html b/reference/residuals.mb_analysis.html
index eed158b..eff9e0e 100644
--- a/reference/residuals.mb_analysis.html
+++ b/reference/residuals.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Residuals

-    Source: R/residuals.R
+    Source: R/residuals.R
     
     

 
@@ -53,29 +53,29 @@ 
Residuals

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 residuals(object, type = NULL, ...)

     

 
     

     
Arguments

-    
object

+
+
+
object

 
The MB analysis object.

 
 
-
type

+
type

 
A string of the residual type.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
The analysis data set with the residual values.

+    
The analysis data set with the residual values.

     

     

     
Details

@@ -94,15 +94,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/rm_comments.html b/reference/rm_comments.html
index 56dc3fc..40309c3 100644
--- a/reference/rm_comments.html
+++ b/reference/rm_comments.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Removes comments from the template strings(s) of an mb object or a character vector.

-    Source: R/comments.R
+    Source: R/comments.R
     
     

 
@@ -58,19 +58,19 @@ 
Removes comments from the template strings(s) of an mb object or a character
 
     

     
Arguments

-    
object

+
+
+
object

 
The mb object or character vector.

 
 
-
...

+
...

 
Unused.

 
 

     

     
Value

-    
-
-
The mb object or character vector without comments in its template string(s).

+    
The mb object or character vector without comments in its template string(s).

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/sample_size.html b/reference/sample_size.html
index 7dc30f0..f212b3c 100644
--- a/reference/sample_size.html
+++ b/reference/sample_size.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Sample Size

-    Source: R/sample-size.R
+    Source: R/sample-size.R
     
     

 
@@ -58,19 +58,19 @@ 
Sample Size

 
     

     
Arguments

-    
object

+
+
+
object

 
The object to calculate the sample size for.

 
 
-
...

+
...

 
Not used.

 
 

     

     
Value

-    
-
-
A count of the sample size.

+    
A count of the sample size.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/scalar_nlist.html b/reference/scalar_nlist.html
index a8c48e1..d4586a8 100644
--- a/reference/scalar_nlist.html
+++ b/reference/scalar_nlist.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Scalar Named List

-    Source: R/utils.R
+    Source: R/utils.R
     
     

 
@@ -58,20 +58,20 @@ 
Scalar Named List

 
     

     
Arguments

-    
x

+
+
+
x

 
The named list to sort.

 
 

     

     
Value

-    
-
-
The sorted named list.

+    
The sorted named list.

     

 
     

     
Examples

-    
scalar_nlist(list(y = 2, x = 1, a = c(10,1)))
+    
scalar_nlist(list(y = 2, x = 1, a = c(10, 1)))
 #> $y
 #> [1] 2
 #> 
@@ -92,15 +92,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/sd_priors_by.html b/reference/sd_priors_by.html
index a5e4780..b8f0875 100644
--- a/reference/sd_priors_by.html
+++ b/reference/sd_priors_by.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Multiply Standard Deviation of Priors By

-    Source: R/sd-priors-by.R
+    Source: R/sd-priors-by.R
     
     

 
@@ -55,10 +55,10 @@ 
Multiply Standard Deviation of Priors By

     

     
sd_priors_by(x, by = 10, distributions = c("normal", "lognormal", "t"), ...)
 
-# S3 method for mb_model
+# S3 method for class 'mb_model'
 sd_priors_by(x, by = 10, distributions = c("normal", "lognormal", "t"), ...)
 
-# S3 method for mb_analysis
+# S3 method for class 'mb_analysis'
 sd_priors_by(
   x,
   by = 10,
@@ -73,48 +73,48 @@ 
Multiply Standard Deviation of Priors By

 
     

     
Arguments

-    
x

+
+
+
x

 
The object.

 
 
-
by

+
by

 
A double scalar of the multiplier.

 
 
-
distributions

+
distributions

 
A character vector of the distributions to adjust.
 Possible values are "laplace" (double exponential), "logistic", "lognormal", "normal", "t" and "nt" (non-central Student t).

 
 
-
...

+
...

 
Not used.

 
 
-
parallel

+
parallel

 
A flag indicating whether to perform the analysis in parallel if possible.

 
 
-
quiet

+
quiet

 
A flag indicating whether to disable tracing information.

 
 
-
glance

+
glance

 
A flag indicating whether to print a model summary.

 
 
-
beep

+
beep

 
A flag indicating whether to beep on completion of the analysis.

 
 

     

     
Value

-    
-
-
The updated object.

+    
The updated object.

     

     

     
Methods (by class)

-    
+
 
  • sd_priors_by(mb_model): Multiply Standard Deviation of Priors for an MB model
    • 
 
  • sd_priors_by(mb_analysis): Multiply Standard Deviation of Priors for an MB analysis
    • 
 

@@ -131,15 +131,15 @@ 
Methods (by class)

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/select_rescale_data.html b/reference/select_rescale_data.html
index 718e38e..84046e3 100644
--- a/reference/select_rescale_data.html
+++ b/reference/select_rescale_data.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Select and Rescale Data

-    Source: R/modify-data.R
+    Source: R/modify-data.R
     
     

 
@@ -58,23 +58,23 @@ 
Select and Rescale Data

 
     

     
Arguments

-    
data

+
+
+
data

 
The data to modify.

 
 
-
model

+
model

 
An object inheriting from class mb_model.

 
 
-
data2

+
data2

 
The base data.

 
 

     

     
Value

-    
-
-
The modified data in list form.

+    
The modified data in list form.

     

 
   

@@ -89,15 +89,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/set_analysis_mode.html b/reference/set_analysis_mode.html
index 738daa4..3609376 100644
--- a/reference/set_analysis_mode.html
+++ b/reference/set_analysis_mode.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Set Analysis Mode

-    Source: R/set-analysis-mode.R
+    Source: R/set-analysis-mode.R
     
     

 
@@ -58,15 +58,15 @@ 
Set Analysis Mode

 
     

     
Arguments

-    
mode

+
+
+
mode

 
A string of the analysis mode.

 
 

     

     
Value

-    
-
-
The old options.

+    
The old options.

     

     

     
Details

@@ -130,9 +130,9 @@ 
Details

 
     

     
Examples

-    
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 set_analysis_mode("reset")
-}
+} # }
 

     

   

@@ -147,15 +147,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/simulate_residuals.html b/reference/simulate_residuals.html
index ff61a63..256912e 100644
--- a/reference/simulate_residuals.html
+++ b/reference/simulate_residuals.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Simulate Residuals

-    Source: R/simulate-residuals.R
+    Source: R/simulate-residuals.R
     
     

 
@@ -60,19 +60,19 @@ 
Simulate Residuals

 
     

     
Arguments

-    
x

+
+
+
x

 
The MB analysis object.

 
 
-
type

+
type

 
A string of the residual type.

 
 

     

     
Value

-    
-
-
An mcmc_data of the simulated residuals.

+    
An mcmc_data of the simulated residuals.

     

     

     
See also

@@ -91,15 +91,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/sort_by_ic.html b/reference/sort_by_ic.html
index a56929b..95c48a0 100644
--- a/reference/sort_by_ic.html
+++ b/reference/sort_by_ic.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Sort Analyses by IC

-    Source: R/sort_by.R
+    Source: R/sort_by.R
     
     

 
@@ -58,19 +58,19 @@ 
Sort Analyses by IC

 
     

     
Arguments

-    
x

+
+
+
x

 
the object.

 
 
-
...

+
...

 
Unused

 
 

     

     
Value

-    
-
-
The sorted object

+    
The sorted object

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/sort_nlist.html b/reference/sort_nlist.html
index 63c32ae..a40147b 100644
--- a/reference/sort_nlist.html
+++ b/reference/sort_nlist.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Sort Named List

-    Source: R/utils.R
+    Source: R/utils.R
     
     

 
@@ -58,15 +58,15 @@ 
Sort Named List

 
     

     
Arguments

-    
x

+
+
+
x

 
The named list to sort.

 
 

     

     
Value

-    
-
-
The sorted named list.

+    
The sorted named list.

     

 
     

@@ -95,15 +95,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/template-set.html b/reference/template-set.html
index 5237c07..f646619 100644
--- a/reference/template-set.html
+++ b/reference/template-set.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Set Template

-    Source: R/template.R
+    Source: R/template.R
     
     

 
@@ -58,11 +58,13 @@ 
Set Template

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
value

+
value

 
A string of the new template

 
 

@@ -79,15 +81,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/template.html b/reference/template.html
index f14e7c5..2a73036 100644
--- a/reference/template.html
+++ b/reference/template.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Template

-    Source: R/template.R
+    Source: R/template.R
     
     

 
@@ -58,19 +58,19 @@ 
Template

 
     

     
Arguments

-    
object

+
+
+
object

 
The object.

 
 
-
...

+
...

 
Additional arguments.

 
 

     

     
Value

-    
-
-
The template model code as a string.

+    
The template model code as a string.

     

 
   

@@ -85,15 +85,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/terms.mb_analysis.html b/reference/terms.mb_analysis.html
index 8ad6ffe..d985ee6 100644
--- a/reference/terms.mb_analysis.html
+++ b/reference/terms.mb_analysis.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Terms

-    Source: R/terms.R
+    Source: R/terms.R
     
     

 
@@ -53,25 +53,27 @@ 
Terms

     

 
     

-    
# S3 method for mb_analysis
+    
# S3 method for class 'mb_analysis'
 terms(x, param_type = "fixed", include_constant = TRUE, ...)

     

 
     

     
Arguments

-    
x

+
+
+
x

 
The mb_analysis object.

 
 
-
param_type

+
param_type

 
A string indicating the type of terms to get the names for.

 
 
-
include_constant

+
include_constant

 
A flag specifying whether to include constant terms.

 
 
-
...

+
...

 
Not used.

 
 

@@ -88,15 +90,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/update_model.html b/reference/update_model.html
index a1d3c56..4d5cd29 100644
--- a/reference/update_model.html
+++ b/reference/update_model.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
Update MB Model

-    Source: R/update-model.R
+    Source: R/update-model.R
     
     

 
@@ -75,76 +75,76 @@ 
Update MB Model

 
     

     
Arguments

-    
model

+
+
+
model

 
The model to update.

 
 
-
code

+
code

 
A string of the model template or an object inheriting from class mb_code.

 
 
-
gen_inits

+
gen_inits

 
A single argument function taking the modified data and
 returning a named list of initial values.

 
 
-
random_effects

+
random_effects

 
A named list specifying the random effects and the associated factors.

 
 
-
fixed

+
fixed

 
A string of a regular expression specifying the fixed pars to monitor.

 
 
-
derived

+
derived

 
A character vector of the derived pars to monitor.

 
 
-
select_data

+
select_data

 
A named list specifying the columns to select and their associated classes and values as well as transformations and scaling options.

 
 
-
center

+
center

 
A character vector of the columns to center.

 
 
-
scale

+
scale

 
A character vector of the columns to scale (after centering).

 
 
-
modify_data

+
modify_data

 
A single argument function to modify the data (in list form) immediately prior to the analysis.

 
 
-
nthin

+
nthin

 
A count specifying the thinning interval.

 
 
-
new_expr

+
new_expr

 
A string of R code specifying the predictive relationships.

 
 
-
new_expr_vec

+
new_expr_vec

 
A flag specifying whether to vectorize the new_expr code.

 
 
-
modify_new_data

+
modify_new_data

 
A single argument function to modify new data (in list form) immediately prior to calculating new_expr.

 
 
-
drops

+
drops

 
A list of character vector of possible scalar pars to drop (fix at 0).

 
 
-
...

+
...

 
Unused arguments.

 
 

     

     
Value

-    
-
-
An object inheriting from class mb_model.

+    
An object inheriting from class mb_model.

     

 
   

@@ -159,15 +159,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/sitemap.xml b/sitemap.xml
index cd0b346..aa5d92b 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,351 +1,119 @@
-
-
-  
-    /404.html
-  
-  
-    /CODE_OF_CONDUCT.html
-  
-  
-    /CONTRIBUTING.html
-  
-  
-    /LICENSE-text.html
-  
-  
-    /LICENSE.html
-  
-  
-    /SUPPORT.html
-  
-  
-    /authors.html
-  
-  
-    /index.html
-  
-  
-    /news/index.html
-  
-  
-    /reference/IC.html
-  
-  
-    /reference/R2.html
-  
-  
-    /reference/R2.mb_analysis.html
-  
-  
-    /reference/add_analyses.html
-  
-  
-    /reference/add_models.html
-  
-  
-    /reference/analyse.character.html
-  
-  
-    /reference/analyse.html
-  
-  
-    /reference/analyse.mb_model.html
-  
-  
-    /reference/analyse.mb_models.html
-  
-  
-    /reference/analyse1.html
-  
-  
-    /reference/analyse_residuals.html
-  
-  
-    /reference/analyses.html
-  
-  
-    /reference/as.analyses.html
-  
-  
-    /reference/as.model.html
-  
-  
-    /reference/as.models.html
-  
-  
-    /reference/backwards.html
-  
-  
-    /reference/base_model.html
-  
-  
-    /reference/check_mb_analysis.html
-  
-  
-    /reference/check_mb_code.html
-  
-  
-    /reference/check_mb_model.html
-  
-  
-    /reference/check_model_pars.html
-  
-  
-    /reference/check_uniquely_named_list.html
-  
-  
-    /reference/code.html
-  
-  
-    /reference/coef.mb_analyses.html
-  
-  
-    /reference/coef.mb_analysis.html
-  
-  
-    /reference/coef.mb_meta_analyses.html
-  
-  
-    /reference/coef.mb_meta_analysis.html
-  
-  
-    /reference/coef_profile.html
-  
-  
-    /reference/coef_profile.mb_analyses.html
-  
-  
-    /reference/coef_profile.mb_analysis.html
-  
-  
-    /reference/coef_profile.mb_meta_analyses.html
-  
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-    /reference/coef_profile.mb_meta_analysis.html
-  
-  
-    /reference/comment_string.html
-  
-  
-    /reference/data_set.html
-  
-  
-    /reference/density99.html
-  
-  
-    /reference/drop_pars.html
-  
-  
-    /reference/elapsed.html
-  
-  
-    /reference/embr-package.html
-  
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-    /reference/estimates.mb_analysis.html
-  
-  
-    /reference/fitted.mb_analysis.html
-  
-  
-    /reference/get_analysis_mode.html
-  
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-    /reference/get_model.html
-  
-  
-    /reference/index.html
-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-  
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-    /reference/logLik.mb_null_analysis.html
-  
-  
-    /reference/make_all_models.html
-  
-  
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-  
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-  
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-  
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-  
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-  
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