[Lme4-commits] r1704 - in pkg/lme4: . testsx

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

Author: bbolker
Date: 2012-04-11 02:31:30 +0200 (Wed, 11 Apr 2012)
New Revision: 1704

Added:
   pkg/lme4/testsx/
   pkg/lme4/testsx/colonizer_rand.RData
   pkg/lme4/testsx/randcrabdata.RData
   pkg/lme4/testsx/testcolonizer.R
   pkg/lme4/testsx/testcrab.R
Log:

  new tests (not run routinely)



Added: pkg/lme4/testsx/colonizer_rand.RData
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(Binary files differ)


Property changes on: pkg/lme4/testsx/colonizer_rand.RData
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Added: svn:mime-type
   + application/octet-stream

Added: pkg/lme4/testsx/randcrabdata.RData
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(Binary files differ)


Property changes on: pkg/lme4/testsx/randcrabdata.RData
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Added: svn:mime-type
   + application/octet-stream

Added: pkg/lme4/testsx/testcolonizer.R
===================================================================
--- pkg/lme4/testsx/testcolonizer.R	                        (rev 0)
+++ pkg/lme4/testsx/testcolonizer.R	2012-04-11 00:31:30 UTC (rev 1704)
@@ -0,0 +1,15 @@
+library(lme4.0)
+load("colonizer_rand.RData")
+m1 <- glmer(form1,data=randdat,
+      family=poisson)
+m2 <- glmer(form2,data=randdat,
+      family=poisson)
+detach("package:lme4.0")
+library(lme4)
+try(m1 <- glmer(form1,data=randdat,
+      family=poisson,verbose=10L))
+try(m1 <- glmer(form1,data=randdat,
+      family=poisson,verbose=10L,tolPwrss=1e-13))
+try(m2 <- glmer(form2,data=randdat,
+      family=poisson,verbose=10L))
+

Added: pkg/lme4/testsx/testcrab.R
===================================================================
--- pkg/lme4/testsx/testcrab.R	                        (rev 0)
+++ pkg/lme4/testsx/testcrab.R	2012-04-11 00:31:30 UTC (rev 1704)
@@ -0,0 +1,42 @@
+load("randcrabdata.RData")
+## randdata0: simulated data, in form suitable for plotting
+## randdata: simulated data, in form suitable for analysis
+
+fr  ## alive/dead formula
+fr2 ## proportion alive formula (use with weights=initial.snail.density)
+
+library(ggplot2)
+library(grid)
+zmargin <- opts(panel.margin=unit(0,"lines"))
+theme_update(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)+
+    facet_grid(.~ttt)+zmargin+
+    geom_boxplot(fill=NA,outlier.colour=NULL,outlier.shape=3)+  ## set outliers to same colour as points
+    ## (hard to see which are outliers, but it doesn't really matter in this case)
+    scale_size_discrete("# obs",range=c(2,5))
+
+
+library(lme4)
+if (packageVersion("lme4")>"0.999375-42") {
+    ## using development lme4 ...
+    try(glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata))
+    try(glmer1B <- glmer(fr,family ="binomial", data=randdata))
+    if (require("lme4.0")) {
+        detach("package:lme4")
+        ## prop/weights formulation
+        glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata)
+        ## alive/dead formulation
+        glmer1B <- glmer(fr,family ="binomial", data=randdata)
+    }
+} else {
+    ## CRAN version of lme4
+    glmer1 <- glmer(fr2,weights=initial.snail.density,family ="binomial", data=randdata)
+    glmer1B <- glmer(fr,family ="binomial", data=randdata)
+}
+    
+fixef(glmer1)
+fixef(glmer1B)
+## note in this case that variances are not converging to zero
+VarCorr(glmer1)