[R-gregmisc-commits] r2138 - in pkg/gmodels: . test

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

Author: warnes
Date: 2016-08-15 21:11:04 +0200 (Mon, 15 Aug 2016)
New Revision: 2138

Added:
   pkg/gmodels/test/
   pkg/gmodels/test/lme-test.R
   pkg/gmodels/test/test_estimable_mlm.R
Log:
Add tests for mlm and (obsolete) lme

Added: pkg/gmodels/test/lme-test.R
===================================================================
--- pkg/gmodels/test/lme-test.R	                        (rev 0)
+++ pkg/gmodels/test/lme-test.R	2016-08-15 19:11:04 UTC (rev 2138)
@@ -0,0 +1,77 @@
+library(gmodels)
+library(lme4)
+set.seed(314159)
+
+sleepstudy$dayGroup <- cut(sleepstudy$Days, seq(-1,9,by=2), include=T)
+
+fm2 <- lmer(Reaction ~ dayGroup + (1|Subject) + (0+Days|Subject), sleepstudy)
+
+# ci example
+#!!# ci(fm2)
+
+
+# estimable examples
+#!!# estimable(fm2, c( 0, -1, 1, 0,  0 )  ) # list all terms
+#!!# estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1)) # just the nonzero terms
+#!!# estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1), n.sim=5000 ) # more simulations...
+
+
+# fit.contrast example
+#!!# fit.contrast( fm2, "dayGroup",
+#!!#               rbind("0-1 vs 3-4"=c(-1,0,1,0,0),
+#!!#                     "3-4 vs 5-6"=c(0,0,-1,1,0)
+#!!#                   ),
+#!!#             conf=0.95 )
+
+# Example from Ariel.Muldoon at oregonstate.edu
+homerange=c(
+        "male","1","fall","0.1",
+	"male","1","winter","0.3",
+	"male","1","spring","5.2",
+	"male","1","summer","3.1",
+	"male","2","fall","3.4",
+	"male","2","winter","1.3",
+	"male","2","spring","4.8",
+	"male","2","summer","4.3",
+	"male","3","fall","3.9",
+	"male","3","winter","3.8",
+	"male","3","spring","5.7",
+	"male","3","summer","2.0",
+	"male","4","fall","3.7",
+	"male","4","winter","4.3",
+	"male","4","spring","6.0",
+	"male","4","summer","1.8",
+	"female","5","fall","4.3",
+	"female","5","winter","1.9",
+	"female","5","spring","7.2",
+	"female","5","summer","6.9",
+	"female","6","fall","5.3",
+	"female","6","winter","4.3",
+	"female","6","spring","6.2",
+	"female","6","summer","4.8",
+	"female","7","fall","7.1",
+	"female","7","winter","4.9",
+	"female","7","spring","8.3",
+	"female","7","summer","7.7"
+	)
+ 
+homerange <- data.frame(matrix(homerange,ncol=4, byrow=T))
+names(homerange) <- c("sex", "animal", "season", "area")
+homerange$area = as.numeric(as.character(homerange$area))
+
+fit1 <- lmer(area ~ sex*season + (1|animal), data=homerange)
+summary(fit1)
+anova(fit1)
+ 
+
+#matrix to give estimable for making estimates
+
+spr <- rbind(c(1,0,1,0,0,0,0,0),
+             c(1,1,0,0,0,1,0,0),
+             c(1,0,0,1,0,0,0,0),
+             c(1,1,0,0,0,0,1,0),
+             c(1,0,0,0,1,0,0,0),
+             c(1,1,0,0,0,0,0,1))
+
+ 
+#!!# estimable(fit1, spr)

Added: pkg/gmodels/test/test_estimable_mlm.R
===================================================================
--- pkg/gmodels/test/test_estimable_mlm.R	                        (rev 0)
+++ pkg/gmodels/test/test_estimable_mlm.R	2016-08-15 19:11:04 UTC (rev 2138)
@@ -0,0 +1,15 @@
+library(gmodels)
+
+y <- cbind(rnorm(100), rnorm(100))
+
+x1 <- rnorm(100)
+x2 <- rnorm(100)
+
+cm <- t(matrix(c(0, 1,-1)))
+lm.1 <- lm(y ~ x1 + x2)
+
+estimable(lm.1, cm)
+
+## >> Error in coef(object) : object 'object' not found
+
+gmodels:::estimable.mlm(lm.1, cm)