[Vegan-commits] r2805 - in pkg/vegan: inst tests

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2013-12-03 22:05:17 +0100 (Tue, 03 Dec 2013)
New Revision: 2805

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/tests/vegan-tests.R
Log:
comment out failing anova.cca tests, but keep the *.save file to remind us of the problems in every check

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-12-03 20:39:39 UTC (rev 2804)
+++ pkg/vegan/inst/ChangeLog	2013-12-03 21:05:17 UTC (rev 2805)
@@ -19,6 +19,16 @@
 	* add1.cca, drop1.cca, ordistep, ordiR2step: functions were
 	adapted to new anova.cca and this brought along similar changes in
 	API. 
+
+	* tests for cca/rda/capscale: commented out test that failed with
+	the anova.cca. Known issue was that 'by = "term"' and 'by =
+	"axis"' stop with error with missing data. This was designed and
+	and can be re-designed to handle missing data by listwise deletion
+	so that models will have the same number of observation for every
+	variable.  An unknown issue was that 'by = "margin"' failed in
+	capscale(). This may be a scoping issue an needs inspection. We
+	keep the old vegan-tests.Rout.save file so that we are reminded of
+	the problems at every check.
 	
 Version 2.1-39 (closed December 3, 2013)
 

Modified: pkg/vegan/tests/vegan-tests.R
===================================================================
--- pkg/vegan/tests/vegan-tests.R	2013-12-03 20:39:39 UTC (rev 2804)
+++ pkg/vegan/tests/vegan-tests.R	2013-12-03 21:05:17 UTC (rev 2805)
@@ -37,30 +37,35 @@
 ### data= argument
 ## cca/rda
 m <-  cca(fla, data=df,  na.action=na.exclude,  subset = Use != "Pasture" & spno > 7)
-anova(m, perm=100)
-anova(m, by="term", perm=100)
-anova(m, by="margin", perm=100)
-anova(m, by="axis", perm=100)
+anova(m, permutations=99)
+## vegan 2.1-40 cannot handle missing data in next two
+##anova(m, by="term", permutations=99)
+##anova(m, by="margin", permutations=99)
+anova(m, by="axis", permutations=99)
 ## capscale
 p <- capscale(fla, data=df, na.action=na.exclude, subset = Use != "Pasture" & spno > 7)
-anova(p, perm=100)
-anova(p, by="term", perm=100)
-anova(p, by="margin", perm=100)
-anova(p, by="axis", perm=100)
+anova(p, permutations=99)
+## vegan 2.1-40 cannot hndle missing data in next two
+##anova(p, by="term", permutations=99)
+##anova(p, by="margin", permutations=99)
+##anova(p, by="axis", permutations=99)
 ## see that capscale can be updated and also works with 'dist' input
 dis <- vegdist(dune)
 p <- update(p, dis ~ .)
-anova(p, perm=100)
-anova(p, by="term", perm=100)
-anova(p, by="margin", perm=100)
-anova(p, by="axis", perm=100)
+anova(p, permutations=99)
+## vegan 2.1-40 cannot handle missing data in next three
+##anova(p, by="term", permutations=99)
+##anova(p, by="margin", permutations=99)
+##anova(p, by="axis", permutations=99)
 ### attach()ed data frame instead of data=
 attach(df)
 q <- cca(fla, na.action = na.omit, subset = Use != "Pasture" & spno > 7)
-anova(q, perm=100)
-anova(q, by="term", perm=100)
-anova(q, by="margin", perm=100)
-anova(q, by="axis", perm=100)
+anova(q, permutations=99)
+## commented tests below fail in vegan 2.1-40 because number of
+## observations changes
+##anova(q, by="term", permutations=99) 
+##anova(q, by="margin", permutations=99)
+anova(q, by="axis", permutations=99)
 ### Check that constrained ordination functions can be embedded.
 ### The data.frame 'df' is still attach()ed.
 foo <- function(bar, Y, X, ...)
@@ -77,7 +82,7 @@
 detach(df)
 ### Check that statistics match in partial constrained ordination
 m <- cca(dune ~ A1 + Moisture + Condition(Management), dune.env, subset = A1 > 3)
-tab <- anova(m, by = "axis", perm.max = 100)
+tab <- anova(m, by = "axis", permutations = 99)
 m
 tab
 all.equal(tab[,2], c(m$CCA$eig, m$CA$tot.chi), check.attributes=FALSE)