Merge branch 'master' of https://github.com/StijnVandenbulcke/msqrob2

NEWS.md

@@ -1,3 +1,8 @@
+# msqrob 1.6.2
+
+- Fixed issues related to residual degrees of freedom of overparameterized models.
+- Fixed issue relating to coldata variables as factors.
+
 # msqrob2 1.5.4
 
 - Removed the full lmer model that was accidently left in the statmodel object.

R/msqrob.R

@@ -378,6 +378,10 @@ msqrobLmer <- function(y,
     colnames(data) <- c(colnames(coldata),colnames(rowdata))
   }
 
+  # Drop levels that are absent, for all factors
+  for (i in colnames(data)) {
+      if (is.factor(data[[i]])) data[[i]] <- droplevels(data[[i]])
+  }
 
   #all possible variables are now in data,  now we can create the fixed object if we use ridge regression
   fixed <- model.matrix(nobars(formula), data = data)  

R/msqrobAggregate.R

@@ -140,10 +140,11 @@ setMethod(
           fun = aggregateFun
         )
 
+        x <- getWithColData(object, i)
         rowData(object[[name]])[[modelColumnName]] <- msqrobLmer(
-            y = assay(object[[i]]),
+            y = assay(x),
             formula = formula,
-            data = colData(object),
+            data = colData(x),
             rowdata = rowdata,
             robust = robust,
             ridge = ridge,