[Lme4-commits] r1504 - pkg/lme4Eigen/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 10 21:53:54 CET 2012
Author: dmbates
Date: 2012-01-10 21:53:54 +0100 (Tue, 10 Jan 2012)
New Revision: 1504
Modified:
pkg/lme4Eigen/tests/drop.R
pkg/lme4Eigen/tests/lmer-1.R
pkg/lme4Eigen/tests/lmer2_ex.R
pkg/lme4Eigen/tests/nlmer-conv.R
pkg/lme4Eigen/tests/nlmer.R
Log:
Add examples and use nAGQ in glmer when appropriate. Change tolPwrss in nlmer and bump maxfun.
Modified: pkg/lme4Eigen/tests/drop.R
===================================================================
--- pkg/lme4Eigen/tests/drop.R 2012-01-10 20:51:55 UTC (rev 1503)
+++ pkg/lme4Eigen/tests/drop.R 2012-01-10 20:53:54 UTC (rev 1504)
@@ -9,6 +9,6 @@
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
- family = binomial, data = cbpp)
+ family = binomial, data = cbpp, nAGQ=25L)
drop1(gm1, test="Chisq")
Modified: pkg/lme4Eigen/tests/lmer-1.R
===================================================================
--- pkg/lme4Eigen/tests/lmer-1.R 2012-01-10 20:51:55 UTC (rev 1503)
+++ pkg/lme4Eigen/tests/lmer-1.R 2012-01-10 20:53:54 UTC (rev 1504)
@@ -123,14 +123,16 @@
## now
#bobyqa(m1e, control = list(iprint = 2L))
m1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), cbpp, binomial, nAGQ=25L)
+dput(unname(fixef(m1)))
+dput(deviance(m1))
stopifnot(is((cm1 <- coef(m1)), "coef.mer"),
dim(cm1$herd) == c(15,4),
all.equal(fixef(m1), ## these values are from an Ubuntu 11.10 amd64 system
c(-1.39922135307046, -0.991415396352428,
-1.12781521322006, -1.57947198508598),
- tol = 1.e-7,
+ tol = 1.e-5,
check.attr=FALSE),
- all.equal(deviance(m1), 100.010030539916, tol=1e-7)
+ all.equal(deviance(m1), 100.010030539916, tol=1e-9)
)
## Simple example by Andrew Gelman (2006-01-10) ----
@@ -311,8 +313,8 @@
m1 <- lmer(y ~ x1 + x2|ff , data = D)
m2 <- lmer(y ~ x1 + (x2|ff), data = D)
m3 <- lmer(y ~ (x2|ff) + x1, data = D)
-stopifnot(identical(ranef(m0), ranef(m1)),
- identical(ranef(m2), ranef(m3)),
+stopifnot(all.equal(ranef(m0), ranef(m1)),
+ all.equal(ranef(m2), ranef(m3)),
inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D), error = function(e)e),
"error"))
@@ -321,14 +323,14 @@
## Reordering of grouping factors should not change the internal structure
#Pm1 <- lmer1(strength ~ (1|batch) + (1|sample), Pastes, doFit = FALSE)
#Pm2 <- lmer1(strength ~ (1|sample) + (1|batch), Pastes, doFit = FALSE)
-P2.1 <- lmer (strength ~ (1|batch) + (1|sample), Pastes, doFit = FALSE)
-P2.2 <- lmer (strength ~ (1|sample) + (1|batch), Pastes, doFit = FALSE)
+#P2.1 <- lmer (strength ~ (1|batch) + (1|sample), Pastes, devFunOnly = TRUE)
+#P2.2 <- lmer (strength ~ (1|sample) + (1|batch), Pastes, devFunOnly = TRUE)
## The environments of Pm1 and Pm2 should be identical except for
## "call" and "frame":
-stopifnot(## all.EQ(env(Pm1), env(Pm2)),
- all.EQ(S4_2list(P2.1),
- S4_2list(P2.2)))
+#stopifnot(## all.EQ(env(Pm1), env(Pm2)),
+# all.EQ(S4_2list(P2.1),
+# S4_2list(P2.2)))
## glmer - Modeling overdispersion as "mixture" aka
## ----- - *ONE* random effect *PER OBSERVATION" -- example inspired by Ben Bolker:
@@ -368,7 +370,7 @@
}
dd <- rPoisGLMMi(12, 20)
m0 <- glmer(y~x + (1|f), family="poisson", data=dd)
-(m1 <- glmer(y~x + (1|f) + (1|obs), family="poisson", data=dd))
+(m1 <- glmer(y~x + (1|f) + (1|obs), family="poisson", data=dd))# must use Laplace
anova(m0, m1)
showProc.time()
Modified: pkg/lme4Eigen/tests/lmer2_ex.R
===================================================================
--- pkg/lme4Eigen/tests/lmer2_ex.R 2012-01-10 20:51:55 UTC (rev 1503)
+++ pkg/lme4Eigen/tests/lmer2_ex.R 2012-01-10 20:53:54 UTC (rev 1504)
@@ -11,6 +11,7 @@
y2 <- y + RE
})
+if (FALSE) { # need to adapt to new structure
##' <description>
##'
@@ -75,5 +76,6 @@
## but higher tolerance works:
chkLmers(y ~ 0+lagoon + (1|habitat), data = dat., tol = 2e-4, verbose=TRUE)
+}
proc.time()
sessionInfo()
Modified: pkg/lme4Eigen/tests/nlmer-conv.R
===================================================================
--- pkg/lme4Eigen/tests/nlmer-conv.R 2012-01-10 20:51:55 UTC (rev 1503)
+++ pkg/lme4Eigen/tests/nlmer-conv.R 2012-01-10 20:53:54 UTC (rev 1504)
@@ -9,15 +9,15 @@
(nm2 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0+lKe+lKa+lCl+(0+lKe+lKa+lCl|Subject),
- Theoph, start = Th.start, verb = TRUE))
+ Theoph, start = Th.start, control=list(maxfun=100000L)))
(nm3 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0+lKe+lKa+lCl+(0+lKe|Subject)+(0+lKa|Subject)
+(0+lCl|Subject),
- Theoph, start = Th.start, verbose = 1))
+ Theoph, start = Th.start, control=list(maxfun=100000L)))
## dropping lKe from random effects:
(nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0+lKe+lKa+lCl+(0+lKa+lCl|Subject),
- Theoph, start = Th.start, verbose = 1))
+ Theoph, start = Th.start, control=list(maxfun=100000L)))
(nm5 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0+lKe+lKa+lCl+(0+lKa|Subject)+(0+lCl|Subject),
- Theoph, start = Th.start, verbose = 1))
+ Theoph, start = Th.start, control=list(maxfun=100000L)))
Modified: pkg/lme4Eigen/tests/nlmer.R
===================================================================
--- pkg/lme4Eigen/tests/nlmer.R 2012-01-10 20:51:55 UTC (rev 1503)
+++ pkg/lme4Eigen/tests/nlmer.R 2012-01-10 20:53:54 UTC (rev 1504)
@@ -6,16 +6,22 @@
(nm1 <- nlmer(circumference ~ SSlogis(age, Asym, xmid, scal) ~
0 + Asym + xmid + scal + (0 + Asym|Tree),
Orange,
- start = c(Asym = 200, xmid = 725, scal = 350),
- verbose = 1L))
+ start = c(Asym = 200, xmid = 725, scal = 350)))
fixef(nm1)
## 'Theoph' Data modeling
+Th.start <- c(lKe = -2.5, lKa = 0.5, lCl = -3)
-Th.start <- c(lKe = -2.5, lKa = 0.5, lCl = -3)
+system.time(nm3 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
+ 0 + lKe + lKa + lCl + (0 + lKe|Subject) +
+ (0 + lKa|Subject) + (0 + lCl|Subject),
+ Theoph, start = Th.start,
+ verbose = 4L)) # ~ 3.2s
+fixef(nm3)
+
system.time(nm2 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0 + lKe + lKa + lCl +
- (0 + lKe+lKa+lCl|Subject), verb = 1,
+ (0 + lKe+lKa+lCl|Subject), verb = 4L, tolPwrss = 1e-3,
Theoph, start = Th.start)) # ~ 5.7s {dual-opteron 2814, on 64b, no optim.}
fixef(nm2)
@@ -23,19 +29,19 @@
0 + lKe + lKa + lCl + (0 + lKe|Subject) +
(0 + lKa|Subject) + (0 + lCl|Subject),
Theoph, start = Th.start,
- verbose = 1L)) # ~ 3.2s
+ verbose = 4L)) # ~ 3.2s
fixef(nm3)
## dropping lKe from random effects:
system.time(nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0 + lKe + lKa + lCl + (0+lKa+lCl|Subject),
- Theoph, start = Th.start, verbose = 1L))
+ Theoph, start = Th.start, verbose = 4L))
fixef(nm4)
sigma(nm4)
system.time(nm5 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
0 +lKe + lKa + lCl + (0 + lKa|Subject) +
- (0 + lCl|Subject), verbose = 1L,
+ (0 + lCl|Subject), verbose = 4L,
Theoph, start = Th.start))
fixef(nm5)
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