Fix summary bug

Precompute Vignette models, use data in vignette specification
Fix to edge prior class

Author: MaartenMarsman

NEWS.md

@@ -2,20 +2,21 @@
 
 ## New features
 
-* NUTS and HMC options are not provided for sampling the bgm and bgmCompare model
+* NUTS and HMC options are now provided for sampling the bgm and bgmCompare model
 * Sampling for multiple chains can now be done in parallel
 * Markov chain diagnostics are now offered for the sampled parameters
 
 ## Other changes
 
 * Improved progress bar for parallel sampling
 * User interrupt for parallel sampling
-* More extensive summary and print options are provided
+* More extensive summary and print options are provided; integrates summary_SBM
+* Removed the options for modeling the main differences; main differences are now always estimated or selected similar to the old `main_difference_model = "collapse"` option.
 
 ## Bug fixes
 
-* Fixed a bug in the bgmCompare function with missing data handling
-* Fixed a bug in the SBM prior handling
+* Fixed an out-of-bounds bug in the bgmCompare function with missing data handling
+* Fixed a bug in the SBM prior computation
 
 # bgms 0.1.5.0
 

R/bgms-methods.R

@@ -117,7 +117,7 @@ print.summary.bgms <- function(x, digits = 3, ...) {
     cat("Inclusion probabilities:\n")
     ind <- head(x$indicator, 6)
     ind[] <- lapply(ind, function(col) ifelse(is.na(col), "", round(col, digits)))
-    print(ind, row.names = FALSE)
+    print(ind)
     if (nrow(x$indicator) > 6)
       cat("... (use `summary(fit)$indicator` to see full output)\n")
     cat("Note: NA values are suppressed in the print table. They occur when an indicator\n")

inst/extdata/fit_5items.rds

@@ -44,7 +44,7 @@ inline UpdateMethod update_method_from_string(const std::string& update_method)
 enum EdgePrior { Stochastic_Block, Beta_Bernoulli, Bernoulli, Not_Applicable };
 
 inline EdgePrior edge_prior_from_string(const std::string& edge_prior) {
-  if (edge_prior == "stochastic-block")
+  if (edge_prior == "Stochastic-Block")
     return Stochastic_Block;
 
   if (edge_prior == "Beta-Bernoulli")

inst/extdata/fit_boredom.rds

@@ -41,8 +41,10 @@ data_english = data_english[, 1:5]
 ```
 
 # Fitting a model
-
-```{r, cache=TRUE, results = "hide"}
+```{r, include=FALSE}
+  fit <- readRDS(system.file("extdata", "fit_boredom.rds", package = "bgms"))
+```
+```{r, eval = FALSE}
 fit = bgmCompare(x = data_french, y = data_english, seed = 1234)
 ```
 Note: During fitting, progress bars are shown in interactive sessions.