[Lme4-commits] r1809 - pkg/lme4.0/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 17 17:34:32 CEST 2013
Author: bbolker
Date: 2013-04-17 17:34:31 +0200 (Wed, 17 Apr 2013)
New Revision: 1809
Modified:
pkg/lme4.0/tests/lmer-1.R
pkg/lme4.0/tests/lmer-1.Rout.save
pkg/lme4.0/tests/nlmer.R
pkg/lme4.0/tests/nlmer.Rout.save
pkg/lme4.0/tests/simulate.R
Log:
test fix from Ruth Ripley; precision downgrades for tests
Modified: pkg/lme4.0/tests/lmer-1.R
===================================================================
--- pkg/lme4.0/tests/lmer-1.R 2013-04-09 23:45:28 UTC (rev 1808)
+++ pkg/lme4.0/tests/lmer-1.R 2013-04-17 15:34:31 UTC (rev 1809)
@@ -121,10 +121,10 @@
op <- options(digits=4)
fixef(M2.)
cov2cor(vcov(M2.))
- ## discrepancies have occured at digit 140.641x;
+ ## discrepancies have occured at digit 140.64x;
## digits= doesn't handle it properly since other
## elements have smaller magnitudes
- round(c(unlist(VarCorr(M2.))),3)
+ round(c(unlist(VarCorr(M2.))),2)
options(op)
## summary(M2.)
M2 <- lmer (y ~ x + ( x | group))
Modified: pkg/lme4.0/tests/lmer-1.Rout.save
===================================================================
--- pkg/lme4.0/tests/lmer-1.Rout.save 2013-04-09 23:45:28 UTC (rev 1808)
+++ pkg/lme4.0/tests/lmer-1.Rout.save 2013-04-17 15:34:31 UTC (rev 1809)
@@ -453,12 +453,12 @@
[,1] [,2]
[1,] 1.0000 -0.9961
[2,] -0.9961 1.0000
-> ## discrepancies have occured at digit 140.641x;
+> ## discrepancies have occured at digit 140.64x;
> ## digits= doesn't handle it properly since other
> ## elements have smaller magnitudes
-> round(c(unlist(VarCorr(M2.))),3)
- group1 group2 group3 group4
-140.641 -1.424 -1.424 0.014
+> round(c(unlist(VarCorr(M2.))),2)
+group1 group2 group3 group4
+140.64 -1.42 -1.42 0.01
> options(op)
> ## summary(M2.)
> M2 <- lmer (y ~ x + ( x | group))
@@ -643,8 +643,8 @@
> if(.unsafe.BLAS) rm(identical)
>
> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
-Time elapsed: 7.204 2.836 10.664 0.012 0.096
+Time elapsed: 5.608 1.612 7.891 0 0.024
>
> proc.time()
user system elapsed
- 7.216 2.936 10.666
+ 5.608 1.636 7.892
Modified: pkg/lme4.0/tests/nlmer.R
===================================================================
--- pkg/lme4.0/tests/nlmer.R 2013-04-09 23:45:28 UTC (rev 1808)
+++ pkg/lme4.0/tests/nlmer.R 2013-04-17 15:34:31 UTC (rev 1809)
@@ -21,10 +21,12 @@
options(op)
showProc.time() # ~ 5.7s {dual-opteron 2814, on 64b, no optim.}
+op <- options(digits=3)
(nm3 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
(lKe|Subject) + (lKa|Subject) + (lCl|Subject),
Theoph, start = Th.start))
showProc.time() # ~ 3.2s
+options(op)
## dropping lKe from random effects:
(nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
Modified: pkg/lme4.0/tests/nlmer.Rout.save
===================================================================
--- pkg/lme4.0/tests/nlmer.Rout.save 2013-04-09 23:45:28 UTC (rev 1808)
+++ pkg/lme4.0/tests/nlmer.Rout.save 2013-04-17 15:34:31 UTC (rev 1809)
@@ -63,36 +63,38 @@
lCl 0.671 -0.141
> options(op)
> showProc.time() # ~ 5.7s {dual-opteron 2814, on 64b, no optim.}
-Time elapsed: 5.432 0.012 5.456
+Time elapsed: 4.908 0 4.899
>
+> op <- options(digits=3)
> (nm3 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
+ (lKe|Subject) + (lKa|Subject) + (lCl|Subject),
+ Theoph, start = Th.start))
Nonlinear mixed model fit by the Laplace approximation
Formula: conc ~ SSfol(Dose, Time, lKe, lKa, lCl) ~ (lKe | Subject) + (lKa | Subject) + (lCl | Subject)
Data: Theoph
- AIC BIC logLik deviance
- 146.1 166.3 -66.07 132.1
+ AIC BIC logLik deviance
+ 146 166 -66.1 132
Random effects:
Groups Name Variance Std.Dev.
- Subject lKe 0.000000 0.00000
- Subject lKa 0.227490 0.47696
- Subject lCl 0.015738 0.12545
- Residual 0.591692 0.76921
+ Subject lKe 0.0000 0.000
+ Subject lKa 0.2275 0.477
+ Subject lCl 0.0157 0.125
+ Residual 0.5917 0.769
Number of obs: 132, groups: Subject, 12
Fixed effects:
Estimate Std. Error t value
-lKe -2.47500 0.05641 -43.88
-lKa 0.47408 0.15291 3.10
-lCl -3.23538 0.05236 -61.79
+lKe -2.4750 0.0564 -43.9
+lKa 0.4741 0.1529 3.1
+lCl -3.2354 0.0524 -61.8
Correlation of Fixed Effects:
lKe lKa
lKa -0.264
lCl 0.671 -0.133
> showProc.time() # ~ 3.2s
-Time elapsed: 4.536 0.128 4.692
+Time elapsed: 6.1 0 6.25
+> options(op)
>
> ## dropping lKe from random effects:
> (nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
@@ -121,7 +123,7 @@
lKa -0.264
lCl 0.671 -0.141
> showProc.time()
-Time elapsed: 3.233 0.068 3.381
+Time elapsed: 2.641 0 2.653
>
> (nm5 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
+ (lKa|Subject) + (lCl|Subject),
@@ -149,7 +151,7 @@
lKa -0.264
lCl 0.671 -0.133
> showProc.time()
-Time elapsed: 2.8 0.068 2.95
+Time elapsed: 2.508 0.028 2.548
>
> e3 <- expand(nm3)
> stopifnot(identical(sapply(e3, class),
@@ -175,8 +177,8 @@
+ )
>
> showProc.time()
-Time elapsed: 0.04 0.04 0.08
+Time elapsed: 0.036 0.02 0.059
>
> proc.time()
user system elapsed
- 19.713 2.692 23.289
+ 18.905 1.248 20.864
Modified: pkg/lme4.0/tests/simulate.R
===================================================================
--- pkg/lme4.0/tests/simulate.R 2013-04-09 23:45:28 UTC (rev 1808)
+++ pkg/lme4.0/tests/simulate.R 2013-04-17 15:34:31 UTC (rev 1809)
@@ -10,7 +10,7 @@
##' @author Ben Bolker, Feb.2011; Martin Maechler, Aug.2011
pboot <- function(m0,m1, nsim = 1, seed=NULL) {
smat <- simulate(m0, nsim=nsim, seed=seed)
- 2 * apply(smat, 2, function(s) logLik(refit(m1,s)) - logLik(refit(m0,s)))
+ 2 * sapply(smat, function(s) logLik(refit(m1,s)) - logLik(refit(m0,s)))
}
set.seed(54321)
@@ -44,9 +44,10 @@
## FIXME: fails on more recent R 3.0.0, maybe 2.15.3?
## with downdated X'X problem ...
-## r1 <- pboot(gm0,gm1, 10)
-## showProc.time()
-## summary(r1)
+## 17 April 2013; not a problem anymore?
+r1 <- pboot(gm0,gm1, 10)
+showProc.time()
+summary(r1)
## FIXME: want real Poisson example, but will have to simulate one instead for now
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