improve print and summary; add corpcor to dependencies in actions checks

.github/workflows/R-CMD-check-rstan.yaml

@@ -55,6 +55,7 @@ jobs:
               lubridate
               wrswoR
               tweedie
+              corpcor
               splines2
               scoringRules
               matrixStats

.github/workflows/R-CMD-check.yaml

@@ -53,6 +53,7 @@ jobs:
               lubridate
               wrswoR
               tweedie
+              corpcor
               splines2
               scoringRules
               matrixStats

R/print.mvgam.R

@@ -29,34 +29,43 @@ cat(paste0(object$family, '\n'))
 cat("\nLink function:\n")
 cat(paste0(family_links(object$family), '\n'))
 
-
-cat("\nTrend model:\n")
-if(inherits(object$trend_model, 'mvgam_trend')){
-  print(object$trend_model$label)
-  cat('\n')
-} else {
-  cat(paste0(object$trend_model, '\n'))
+if(!inherits(object, 'jsdgam')){
+  cat("\nTrend model:\n")
+  if(inherits(object$trend_model, 'mvgam_trend')){
+    print(object$trend_model$label)
+    cat('\n')
+  } else {
+    cat(paste0(object$trend_model, '\n'))
+  }
 }
 
 if(object$use_lv){
-  cat("N latent factors:\n")
+  cat("\nN latent factors:\n")
   cat(object$n_lv, '\n')
 
 }
 
-cat('\nN series:\n')
-cat(NCOL(object$ytimes), '\n')
-
+if(inherits(object, 'jsdgam')){
+  cat('\nN species:\n')
+  cat(NCOL(object$ytimes), '\n')
+} else {
+  cat('\nN series:\n')
+  cat(NCOL(object$ytimes), '\n')
+}
 
 if(!is.null(object$upper_bounds)){
   cat('\nUpper bounds:\n')
   cat(object$upper_bounds, '\n')
 
 }
 
-cat('\nN timepoints:\n')
-cat(NROW(object$ytimes), '\n')
-
+if(inherits(object, 'jsdgam')){
+  cat('\nN sites:\n')
+  cat(NROW(object$ytimes), '\n')
+} else {
+  cat('\nN timepoints:\n')
+  cat(NROW(object$ytimes), '\n')
+}
 
 if(object$fit_engine == 'jags'){
   cat('\nStatus:\n')

R/residual_cor.R

@@ -54,7 +54,7 @@
 #' directly associated, but they are still correlated *through* other species. In other words, they
 #' are conditionally independent given the other species. It is important that the precision matrix
 #' does not exhibit the exact same properties of the correlation e.g., the diagonal elements are
-#' not equal to 1. Nevertheless, relatively larger values of precision imply a stronger
+#' not equal to 1. Nevertheless, relatively larger values of precision may imply stronger
 #' direct relationships between two species.
 #'
 #' In addition to the residual correlation and precision matrices, the median or mean point estimator

R/summary.mvgam.R

@@ -81,14 +81,16 @@ cat(paste0(object$family, '\n'))
 cat("\nLink function:\n")
 cat(paste0(family_links(object$family), '\n'))
 
-cat("\nTrend model:\n")
-if(inherits(object$trend_model, 'mvgam_trend')){
-  print(object$trend_model$label)
-} else {
-  cat(paste0(object$trend_model, '\n'))
+if(!inherits(object, 'jsdgam')){
+  cat("\nTrend model:\n")
+  if(inherits(object$trend_model, 'mvgam_trend')){
+    print(object$trend_model$label)
+    cat('\n')
+  } else {
+    cat(paste0(object$trend_model, '\n'))
+  }
 }
 
-
 if(object$use_lv){
   if(!is.null(object$trend_call)){
     cat("\nN process models:\n")
@@ -99,16 +101,26 @@ if(object$use_lv){
   }
 }
 
-cat('\nN series:\n')
-cat(NCOL(object$ytimes), '\n')
+if(inherits(object, 'jsdgam')){
+  cat('\nN species:\n')
+  cat(NCOL(object$ytimes), '\n')
+} else {
+  cat('\nN series:\n')
+  cat(NCOL(object$ytimes), '\n')
+}
 
 if(!is.null(object$upper_bounds)){
   cat('\nUpper bounds:\n')
   cat(object$upper_bounds, '\n')
 }
 
-cat('\nN timepoints:\n')
-cat(NROW(object$ytimes), '\n')
+if(inherits(object, 'jsdgam')){
+  cat('\nN sites:\n')
+  cat(NROW(object$ytimes), '\n')
+} else {
+  cat('\nN timepoints:\n')
+  cat(NROW(object$ytimes), '\n')
+}
 
 if(object$fit_engine == 'jags'){
   cat('\nStatus:\n')
@@ -825,14 +837,16 @@ summary.mvgam_prefit = function(object, ...){
   cat(paste0(family_links(object$family), '\n'))
 
 
-  cat("\nTrend model:\n")
-  if(inherits(object$trend_model, 'mvgam_trend')){
-    cat(paste0(print(object$trend_model$label), '\n'))
-  } else {
-    cat(paste0(object$trend_model, '\n'))
+  if(!inherits(object, 'jsdgam')){
+    cat("\nTrend model:\n")
+    if(inherits(object$trend_model, 'mvgam_trend')){
+      print(object$trend_model$label)
+      cat('\n')
+    } else {
+      cat(paste0(object$trend_model, '\n'))
+    }
   }
 
-
   if(object$use_lv){
     if(!is.null(object$trend_call)){
       cat("\nN process models:\n")
@@ -846,12 +860,22 @@ summary.mvgam_prefit = function(object, ...){
 
   }
 
-  cat('\n\nN series:')
-  cat(NCOL(object$ytimes), '\n')
+  if(inherits(object, 'jsdgam')){
+    cat('\nN species:\n')
+    cat(NCOL(object$ytimes), '\n')
+  } else {
+    cat('\nN series:\n')
+    cat(NCOL(object$ytimes), '\n')
+  }
 
 
-  cat('\n\nN timepoints:')
-  cat(NROW(object$ytimes), '\n')
+  if(inherits(object, 'jsdgam')){
+    cat('\nN sites:\n')
+    cat(NROW(object$ytimes), '\n')
+  } else {
+    cat('\nN timepoints:\n')
+    cat(NROW(object$ytimes), '\n')
+  }
 
 
   cat('\nStatus:')