update the test code and expected output so that we switch back to se…

…quential tests as that was what was being tested prior to changes in #677

tests/vegan-tests.Rout.save

@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.1 (2024-06-14) -- "Race for Your Life"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: aarch64-apple-darwin20 (64-bit)
+Platform: aarch64-apple-darwin20
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -109,13 +109,13 @@ Residual  5   0.80011
 ---
 Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
 > ## adonis
-> adonis2(fla, data = dune.env)
+> adonis2(fla, data = dune.env, by = "terms")
 Permutation test for adonis under reduced model
 Terms added sequentially (first to last)
 Permutation: free
 Number of permutations: 999
 
-adonis2(formula = fla, data = dune.env)
+adonis2(formula = fla, data = dune.env, by = "terms")
             Df SumOfSqs      R2      F Pr(>F)   
 Management   3   1.4686 0.34161 3.0480  0.003 **
 poly(A1, 2)  2   0.5829 0.13559 1.8146  0.057 . 
@@ -410,13 +410,13 @@ Eigenvalues for unconstrained axes:
 > ## adonis must be done with detached 'df' or it will be used instead
 > ## of with(dune.env, ...)
 > detach(df)
-> with(dune.env, foo("adonis2", dune, Management))
+> with(dune.env, foo("adonis2", dune, Management, by = "terms"))
 Permutation test for adonis under reduced model
 Terms added sequentially (first to last)
 Permutation: free
 Number of permutations: 999
 
-bar(formula = Y ~ X)
+bar(formula = Y ~ X, by = "terms")
          Df SumOfSqs      R2      F Pr(>F)   
 X         3   1.4686 0.34161 2.7672  0.006 **
 Residual 16   2.8304 0.65839                 
@@ -425,13 +425,13 @@ Total    19   4.2990 1.00000
 Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
 > ## the test case reported in github issue #285 by @ktmbiome
 > var <- "Moisture"
-> adonis2(dune ~ dune.env[, var])
+> adonis2(dune ~ dune.env[, var], by = "terms")
 Permutation test for adonis under reduced model
 Terms added sequentially (first to last)
 Permutation: free
 Number of permutations: 999
 
-adonis2(formula = dune ~ dune.env[, var])
+adonis2(formula = dune ~ dune.env[, var], by = "terms")
                 Df SumOfSqs      R2      F Pr(>F)    
 dune.env[, var]  3   1.7282 0.40199 3.5851  0.001 ***
 Residual        16   2.5709 0.59801                  
@@ -1003,4 +1003,4 @@ Cumulative Proportion 0.9994867 1.0000000
 > 
 > proc.time()
    user  system elapsed 
-  1.418   0.063   1.482 
+  1.108   0.041   1.165