[Lme4-commits] r1792 - pkg/lme4/testsx

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

Author: bbolker
Date: 2012-12-19 22:25:06 +0100 (Wed, 19 Dec 2012)
New Revision: 1792

Modified:
   pkg/lme4/testsx/testcrab.R
Log:

  updated, added coefplot2 and MCMCglmm stuff



Modified: pkg/lme4/testsx/testcrab.R
===================================================================
--- pkg/lme4/testsx/testcrab.R	2012-10-20 20:43:40 UTC (rev 1791)
+++ pkg/lme4/testsx/testcrab.R	2012-12-19 21:25:06 UTC (rev 1792)
@@ -7,8 +7,8 @@
 
 library(ggplot2)
 library(grid)
-zmargin <- opts(panel.margin=unit(0,"lines"))
-theme_update(theme_bw())
+zmargin <- theme(panel.margin=unit(0,"lines"))
+theme_set(theme_bw())
 g1 <- ggplot(randdata0,aes(x=snail.size,y=surv,colour=snail.size,fill=snail.size))+
     geom_hline(yintercept=1,colour="black")+
     stat_sum(aes(size=factor(..n..)),alpha=0.6)+
@@ -19,24 +19,53 @@
 
 
 library(lme4)
+## FIXME: this test doesn't quite work, CRAN-lme4 is now 0.999999-0
 if (packageVersion("lme4")>"0.999375-42") {
     ## using development lme4 ...
     try(glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata))
     ## pwrssUpdate did not converge
     try(glmer1B <- glmer(fr,family ="binomial", data=randdata))
     if (require("lme4.0")) {
-        detach("package:lme4")
+        detach("package:lme4",unload=TRUE)
         ## prop/weights formulation
         glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata)
         ## alive/dead formulation
         glmer1B <- glmer(fr,family ="binomial", data=randdata)
         coef(glmer1B)
+        fixef(glmer1B)
         detach("package:lme4.0")
     }
     if (require("glmmADMB")) {
         ## prop/weights formulation
-        glmer1B <- glmmadmb(fr,family ="binomial", data=randdata)
+        glmer1C <- glmmadmb(fr,family ="binomial", data=randdata)
     }
+     if (require("MCMCglmm")) {
+        ## prop/weights formulation
+         ff <- lme4:::nobars(fr)
+         ff <- ff[-2] ## delete response
+         X <- model.matrix(ff,data=randdata)
+         npar <- ncol(X)
+        fit1D <- MCMCglmm(cbind(final.snail.density, snails.lost) ~
+                          crab.speciesS + crab.speciesW + 
+                          crab.sizeS + crab.sizeM + snail.sizeS + crab.speciesS:crab.sizeS + 
+                          crab.speciesS:crab.sizeM + crab.speciesS:snail.sizeS +
+                          crab.speciesW:snail.sizeS + 
+                          crab.sizeS:snail.sizeS + crab.sizeM:snail.sizeS +
+                          crab.speciesS:crab.sizeS:snail.sizeS +
+                          crab.speciesS:crab.sizeM:snail.sizeS,
+                  random=~us(1+snail.size):plot,
+                          family="multinomial2",
+                          data=randdata,
+                          prior=list(B=list(mu=rep(0,npar),V=diag(npar)*1e3),
+                                     G=list(list(nu=10,V=diag(2))),
+                                     R=list(nu=10,V=1)),
+                          verbose=FALSE)
+    }
+    if (require("coefplot2")) {
+        cc2 <- coeftab(fit1D)
+        rownames(cc2) <- gsub("^Sol\\.","",rownames(cc2))
+        coefplot2(list(glmer1B,glmer1C,cc2),col=c(1,2,4))
+    }
 } else {
     ## CRAN version of lme4
     glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata)
@@ -47,3 +76,6 @@
 fixef(glmer1B)
 ## note in this case that variances are not converging to zero
 VarCorr(glmer1)
+
+if (FALSE) {
+    library(glmmADMB)