[Lme4-commits] r1786 - pkg/lme4/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 8 21:38:32 CEST 2012
Author: bbolker
Date: 2012-07-08 21:38:31 +0200 (Sun, 08 Jul 2012)
New Revision: 1786
Added:
pkg/lme4/tests/boundary.R
pkg/lme4/tests/dat20101314.csv
pkg/lme4/tests/koller-data.R
Log:
tests for boundary-sticking behavior
Added: pkg/lme4/tests/boundary.R
===================================================================
--- pkg/lme4/tests/boundary.R (rev 0)
+++ pkg/lme4/tests/boundary.R 2012-07-08 19:38:31 UTC (rev 1786)
@@ -0,0 +1,30 @@
+## Stephane Laurent:
+dat <- read.csv("dat20101314.csv")
+library(lme4)
+fit <- lmer(y ~ (1|Operator)+(1|Part)+(1|Part:Operator), data=dat)
+fit_b <- lmer(y ~ (1|Operator)+(1|Part)+(1|Part:Operator), data=dat,
+ optimizer="bobyqa")
+fit_c <- lmer(y ~ (1|Operator)+(1|Part)+(1|Part:Operator), data=dat,
+ control=list(restart=FALSE))
+getME(fit_c,"theta") ## some are zero
+stopifnot(all.equal(getME(fit,"theta"),getME(fit_b,"theta"),tol=1e-6))
+
+
+## Manuel Koller
+source("koller-data.R")
+
+ldata <- getData(13)
+fm4 <- lmer(y ~ (1|Var2), ldata)
+getME(fm4,"theta")
+fm4b <- lmer(y ~ (1|Var2), ldata, control=list(restart=FALSE))
+getME(fm4b,"theta")
+fm4c <- lmer(y ~ (1|Var2), ldata, optimizer="bobyqa")
+stopifnot(all.equal(getME(fm4,"theta"),getME(fm4c,"theta"),tol=1e-4))
+
+## dd <- lmer(y ~ (1|Var2), ldata, devFunOnly=TRUE)
+## tvec <- 10^seq(-7,0,by=0.1)
+## dvec <- sapply(tvec,dd)
+## d0 <- dd(0)
+## plot(tvec,dvec,type="b")
+## plot(tvec,abs(dvec-d0),log="xy",col=ifelse(dvec<d0,"black","red"))
+
Added: pkg/lme4/tests/dat20101314.csv
===================================================================
--- pkg/lme4/tests/dat20101314.csv (rev 0)
+++ pkg/lme4/tests/dat20101314.csv 2012-07-08 19:38:31 UTC (rev 1786)
@@ -0,0 +1,46 @@
+"","Operator","Part","y"
+"1","A","P1",1.98353608160299
+"2","A","P1",2.00732095292274
+"3","A","P2",3.0749991860642
+"4","A","P2",3.10873748962838
+"5","A","P3",3.10259147754259
+"6","A","P3",3.1218519017369
+"7","H","P1",1.98645821273731
+"8","H","P1",1.98245215138499
+"9","H","P2",3.05996458578668
+"10","H","P2",3.08242270866658
+"11","H","P3",3.07070635017356
+"12","H","P3",3.04616336618396
+"13","B","P1",2.01140125992474
+"14","B","P2",3.16219985241226
+"15","B","P3",3.17248908910763
+"16","I","P1",2.02958667163046
+"17","I","P1",2.03750617769168
+"18","I","P2",3.10722354113837
+"19","I","P2",3.14463646758849
+"20","I","P3",3.14980086225833
+"21","I","P3",3.14796987608195
+"22","C","P1",2.0111473607758
+"23","C","P1",2.04559677186758
+"24","C","P2",3.13151922069791
+"25","C","P2",3.17781632049401
+"26","C","P3",3.11138686811249
+"27","C","P3",3.1244031385292
+"28","J","P1",2.06213053462212
+"29","J","P1",2.04785872740746
+"30","J","P2",3.12921603371435
+"31","J","P2",3.08574354980366
+"32","J","P3",3.11093297024656
+"33","J","P3",3.10771861052026
+"34","D","P1",1.9903388547876
+"35","D","P1",1.9778607292647
+"36","D","P2",3.05476621783899
+"37","D","P2",3.08762882022979
+"38","D","P3",3.06490702715964
+"39","D","P3",3.0651276340067
+"40","K","P1",1.96350449941429
+"41","K","P1",1.98851436583367
+"42","K","P2",3.06846787597901
+"43","K","P2",3.085126393163
+"44","K","P3",3.05210884681015
+"45","K","P3",3.05642838998105
Added: pkg/lme4/tests/koller-data.R
===================================================================
--- pkg/lme4/tests/koller-data.R (rev 0)
+++ pkg/lme4/tests/koller-data.R 2012-07-08 19:38:31 UTC (rev 1786)
@@ -0,0 +1,190 @@
+data <- structure(list(Var1 = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
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+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
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+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+ 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+ .Label = "i", class = "factor"),
+ Var2 = structure(c(1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L,
+ 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 15L, 20L, 1L, 2L,
+ 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L, 11L, 12L, 13L, 14L, 16L,
+ 17L, 18L, 19L, 15L, 20L, 1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L,
+ 5L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 15L, 20L,
+ 1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L, 11L, 12L, 13L, 14L,
+ 16L, 17L, 18L, 19L, 15L, 20L, 1L, 2L, 3L, 4L, 6L, 7L, 8L,
+ 9L, 5L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 15L,
+ 20L, 1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L, 11L, 12L, 13L,
+ 14L, 16L, 17L, 18L, 19L, 15L, 20L, 1L, 2L, 3L, 4L, 6L, 7L,
+ 8L, 9L, 5L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L,
+ 15L, 20L, 1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L, 11L, 12L,
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+ 15L, 20L, 1L, 2L, 3L, 4L, 6L, 7L, 8L, 9L, 5L, 10L, 11L, 12L,
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+ 13L, 14L, 16L, 17L, 18L, 19L, 15L, 20L),
+ .Label = c("I", "II", "III", "IV", "IX", "V", "VI", "VII",
+ "VIII", "X", "XI", "XII", "XIII", "XIV", "XIX", "XV", "XVI",
+ "XVII", "XVIII", "XX"), class = "factor"),
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+ -6.33651886787928, -1.66649793204419, 6.39995921794792, -6.68259735687546,
+ 6.08981926235198, -3.53583947340409, -1.21103587811449, 7.24975022684127,
+ 4.97801019029663, 3.14976379524903, 1.96758553600254, 8.43197057862052,
+ 3.33822717991332, 0.235378273638341, -10.1630873499494, 5.76230996838168,
+ -4.61549138480825, 8.20531094191712, 7.12941741404648, 6.00054322848315,
+ -5.48192520344437, -9.59876928907475, 1.7683225066202, -7.1390901352502,
+ 4.25471218768541, 1.80718924948737, -4.20866358864448, -2.44486024149221,
+ 3.91749495580739, -0.158740143510694, 1.47791160298965, -1.34641057801835,
+ -0.668352362532367, -8.17427466239714, -10.2034896388957,
+ -0.860308461006896, 3.75705378224295, -0.336485137456501,
+ 12.5132973642976, 3.49023309888176)),
+ .Names = c("Var1", "Var2", "y"), row.names = c(NA, -400L),
+ b = c(-4.36950232041146,
+ -0.0424473953245598, 5.56953719092376, -5.30334683089667, -1.10285116011549,
+ -0.252162996387152, 2.0499747831754, -1.74063623059889, 7.15605161270018,
+ -1.33699218239019, 0.888758869258693, 3.14516697594312, -2.35262555592678,
+ -4.94052004170718, 6.34707170732277, -10.0261204723322, 2.73257418977353,
+ -0.638617261850626, 3.2694706345968, 0.947216484246937), class = "data.frame")
+slim <- c(0.1, 40)
+npoints <- 31
+group <- 1
+obs <- which(data$Var2 == levels(data$Var2)[group])
+shifts <- rep(attr(data, 'b')[data$Var2[group]], npoints)
+scales <- seq(slim[1], slim[2], length.out = npoints)
+
+
+getData <- function(i) {
+ lb <- attr(data, 'b')[data$Var2[obs[1]]]
+ ldata <- data
+ ldata$y[obs] <- if (length(obs) == 1)
+ lb + shifts[i] else (ldata$y[obs] - lb)*scales[i] + shifts[i]
+ ldata
+}
+
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