[Lme4-commits] r1884 - in pkg/MEMSS: . man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 11 15:05:30 CET 2014
Author: walker
Date: 2014-03-11 15:05:29 +0100 (Tue, 11 Mar 2014)
New Revision: 1884
Added:
pkg/MEMSS/tests/Pixel.Rout.save
Removed:
pkg/MEMSS/tests/Pixel.Rout.save
Modified:
pkg/MEMSS/DESCRIPTION
pkg/MEMSS/man/Cefamandole.Rd
pkg/MEMSS/man/Fatigue.Rd
pkg/MEMSS/man/Gasoline.Rd
pkg/MEMSS/man/Glucose.Rd
pkg/MEMSS/man/Glucose2.Rd
pkg/MEMSS/man/Orange.Rd
pkg/MEMSS/man/Theoph.Rd
pkg/MEMSS/tests/Pixel.R
Log:
prepare for maintenance cran submission
Modified: pkg/MEMSS/DESCRIPTION
===================================================================
--- pkg/MEMSS/DESCRIPTION 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/DESCRIPTION 2014-03-11 14:05:29 UTC (rev 1884)
@@ -1,14 +1,16 @@
Package: MEMSS
-Version: 0.9-0
+Version: 0.9-2
Date: $Date$
Title: Data sets from Mixed-effects Models in S
Author: Douglas Bates <bates at stat.wisc.edu>,
Martin Maechler <maechler at R-project.org> and
Ben Bolker <bbolker at gmail.com>
-Maintainer: <lme4-authors at R-forge.wu-wien.ac.at>
+Contact: LME4 Authors <lme4-authors at lists.r-forge.r-project.org>
+Maintainer: Steve Walker <steve.walker at utoronto.ca>
Description: Data sets and sample analyses from Pinheiro and Bates,
"Mixed-effects Models in S and S-PLUS" (Springer, 2000).
-Depends: R(>= 2.12.0), lme4 (>= 0.999375-36), lattice
+Depends: R(>= 2.12.0), lme4 (>= 0.999375-36)
+Suggests: lattice
LazyData: yes
License: GPL (>=2)
Packaged: 2011-02-15 21:43:38 UTC; bates
Modified: pkg/MEMSS/man/Cefamandole.Rd
===================================================================
--- pkg/MEMSS/man/Cefamandole.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Cefamandole.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -35,6 +35,7 @@
Repeated Measurement Data}, Chapman and Hall, London.
}
\examples{
+require(lattice)
str(Cefamandole)
xyplot(conc ~ Time, Cefamandole, groups = Subject, type = c("g", "b"),
aspect = 'xy', scales = list(y = list(log = 2)),
Modified: pkg/MEMSS/man/Fatigue.Rd
===================================================================
--- pkg/MEMSS/man/Fatigue.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Fatigue.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -37,6 +37,7 @@
\emph{Technometrics}, \bold{35}, 161-174
}
\examples{
+require(lattice)
str(Fatigue)
xyplot(relLength ~ cycles | Path, Fatigue, type = c("g", "b"),
aspect = 'xy', xlab = "Number of test cycles (millions)",
Modified: pkg/MEMSS/man/Gasoline.Rd
===================================================================
--- pkg/MEMSS/man/Gasoline.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Gasoline.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -58,6 +58,7 @@
Statistics with S-PLUS (3rd ed)}, Springer, New York.
}
\examples{
+require(lattice)
str(Gasoline)
xyplot(yield ~ endpoint | Sample, Gasoline, aspect = 'xy',
main = "Gasoline data", xlab = "Endpoint (degrees F)",
Modified: pkg/MEMSS/man/Glucose.Rd
===================================================================
--- pkg/MEMSS/man/Glucose.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Glucose.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -27,6 +27,7 @@
Analysis}, Chapman and Hall, London.
}
\examples{
+require(lattice)
str(Glucose)
xyplot(conc ~ Time | Meal * Subject, Glucose)
}
Modified: pkg/MEMSS/man/Glucose2.Rd
===================================================================
--- pkg/MEMSS/man/Glucose2.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Glucose2.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -39,6 +39,7 @@
Analysis}, Chapman and Hall, London.
}
\examples{
+require(lattice)
str(Glucose2)
xyplot(glucose ~ Time | Subject, Glucose2, type = c("g", "b"),
groups = Date, aspect = 'xy', layout = c(4,2),
Modified: pkg/MEMSS/man/Orange.Rd
===================================================================
--- pkg/MEMSS/man/Orange.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Orange.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -32,6 +32,7 @@
in S and S-PLUS}, Springer.
}
\examples{
+require(lattice)
xyplot(circumference ~ age, Orange, groups = Tree, type = c("g", "b"),
auto.key = list(space = "right", lines = TRUE), aspect = "xy",
xlab = "Age (days since 1968/12/31)", ylab = "Circumference (mm)")
Modified: pkg/MEMSS/man/Theoph.Rd
===================================================================
--- pkg/MEMSS/man/Theoph.Rd 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/man/Theoph.Rd 2014-03-11 14:05:29 UTC (rev 1884)
@@ -53,6 +53,7 @@
}
\seealso{\code{\link{SSfol}}}
\examples{
+require(lattice)
xyplot(conc ~ Time | Subject, Theoph, aspect = 'xy',
xlab = "Time since drug administration (hr)",
ylab = "Theophylline concentration (mg/L)")
Modified: pkg/MEMSS/tests/Pixel.R
===================================================================
--- pkg/MEMSS/tests/Pixel.R 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/tests/Pixel.R 2014-03-11 14:05:29 UTC (rev 1884)
@@ -1,7 +1,7 @@
library(MEMSS)
-options(show.signif.stars = FALSE)
+options(show.signif.stars = FALSE, digits = 3)
m1 <- lmer(pixel ~ day + I(day^2) + (1|Dog:Side) + (day|Dog),
- Pixel, verbose = TRUE)
+ Pixel)
print(m1, corr = FALSE)
ranef(m1)
q("no")
Deleted: pkg/MEMSS/tests/Pixel.Rout.save
===================================================================
--- pkg/MEMSS/tests/Pixel.Rout.save 2014-03-11 10:41:15 UTC (rev 1883)
+++ pkg/MEMSS/tests/Pixel.Rout.save 2014-03-11 14:05:29 UTC (rev 1884)
@@ -1,124 +0,0 @@
-
-R version 2.13.0 Under development (unstable) (2011-01-27 r54122)
-Copyright (C) 2011 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> library(MEMSS)
-Loading required package: lme4
-Loading required package: Matrix
-Loading required package: lattice
-
-Attaching package: 'Matrix'
-
-The following object(s) are masked from 'package:base':
-
- det
-
-
-Attaching package: 'lme4'
-
-The following object(s) are masked from 'package:stats':
-
- AIC
-
-
-Attaching package: 'MEMSS'
-
-The following object(s) are masked from 'package:datasets':
-
- CO2, Orange, Theoph
-
-> options(show.signif.stars = FALSE)
-> m1 <- lmer(pixel ~ day + I(day^2) + (1|Dog:Side) + (day|Dog),
-+ Pixel, verbose = TRUE)
- 0: 873.72159: 0.723102 0.511310 0.0568329 0.00000
- 1: 871.66533: 0.764372 0.554115 0.265188 0.0790461
- 2: 852.35632: 1.10288 0.845433 0.152994 0.106287
- 3: 847.00713: 1.16858 0.874801 0.156863 -0.0635782
- 4: 843.28354: 1.28974 0.977631 0.124712 0.0245253
- 5: 839.18659: 1.39637 1.09183 0.170471 -0.0623283
- 6: 835.37182: 1.50827 1.23102 0.141225 -0.0263052
- 7: 833.06559: 1.61648 1.57796 0.163260 -0.0866104
- 8: 830.84987: 1.65466 1.92391 0.257306 -0.00783820
- 9: 828.14679: 1.68613 2.06592 0.192482 -0.0156918
- 10: 827.82345: 1.68819 2.06947 0.181224 -0.0514799
- 11: 827.28012: 1.69484 2.10213 0.175173 -0.0348203
- 12: 827.01905: 1.69435 2.17391 0.152650 -0.0408582
- 13: 825.44591: 1.73725 2.84064 0.174861 -0.0376152
- 14: 825.35061: 1.91511 2.84581 0.174449 -0.0392779
- 15: 825.28815: 1.87339 3.12798 0.166605 -0.0304982
- 16: 825.21125: 1.86755 3.15403 0.170668 -0.0367170
- 17: 825.21020: 1.87136 3.15349 0.170695 -0.0360639
- 18: 825.21019: 1.87143 3.15555 0.170648 -0.0360495
- 19: 825.21019: 1.87151 3.15585 0.170648 -0.0360509
- 20: 825.21019: 1.87152 3.15586 0.170649 -0.0360511
-> print(m1, corr = FALSE)
-Linear mixed model fit by REML
-Formula: pixel ~ day + I(day^2) + (1 | Dog:Side) + (day | Dog)
- Data: Pixel
- AIC BIC logLik deviance REMLdev
- 841.2 862.2 -412.6 827.3 825.2
-Random effects:
- Groups Name Variance Std.Dev. Corr
- Dog:Side (Intercept) 283.0551 16.8242
- Dog (Intercept) 804.8539 28.3699
- day 3.3994 1.8437 -0.555
- Residual 80.8131 8.9896
-Number of obs: 102, groups: Dog:Side, 20; Dog, 10
-
-Fixed effects:
- Estimate Std. Error t value
-(Intercept) 1073.33924 10.17170 105.52
-day 6.12959 0.87935 6.97
-I(day^2) -0.36735 0.03395 -10.82
-> ranef(m1)
-$`Dog:Side`
- (Intercept)
-A:L -5.967398
-A:R -11.773448
-B:L -4.052805
-B:R -9.803953
-C:L -7.974107
-C:R 3.734075
-D:L 2.111162
-D:R 2.852360
-E:L 3.308485
-E:R 7.111339
-F:L 10.906577
-F:R -9.905066
-G:L -5.905196
-G:R 21.116136
-H:L 8.125799
-H:R -7.414967
-I:L 11.172113
-I:R -17.049246
-J:L 31.610148
-J:R -22.202008
-
-$Dog
- (Intercept) day
-A -24.713033 -1.1955736
-B -23.581270 -0.4326202
-C -27.080727 2.1945475
-D -16.659734 3.0958617
-E 25.299329 -0.5610542
-F 10.823466 -1.0369111
-G 49.353936 -2.2740738
-H -7.054531 0.9902335
-I -5.753166 -0.6811398
-J 19.365730 -0.0992701
-
-> q("no")
Added: pkg/MEMSS/tests/Pixel.Rout.save
===================================================================
--- pkg/MEMSS/tests/Pixel.Rout.save (rev 0)
+++ pkg/MEMSS/tests/Pixel.Rout.save 2014-03-11 14:05:29 UTC (rev 1884)
@@ -0,0 +1,87 @@
+
+R Under development (unstable) (2014-03-08 r65144) -- "Unsuffered Consequences"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin10.8.0 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(MEMSS)
+Loading required package: lme4
+Loading required package: Matrix
+Loading required package: Rcpp
+
+Attaching package: 'MEMSS'
+
+The following objects are masked from 'package:datasets':
+
+ CO2, Orange, Theoph
+
+> options(show.signif.stars = FALSE, digits = 3)
+> m1 <- lmer(pixel ~ day + I(day^2) + (1|Dog:Side) + (day|Dog),
++ Pixel)
+> print(m1, corr = FALSE)
+Linear mixed model fit by REML ['lmerMod']
+Formula: pixel ~ day + I(day^2) + (1 | Dog:Side) + (day | Dog)
+ Data: Pixel
+REML criterion at convergence: 825
+Random effects:
+ Groups Name Std.Dev. Corr
+ Dog:Side (Intercept) 16.82
+ Dog (Intercept) 28.37
+ day 1.84 -0.55
+ Residual 8.99
+Number of obs: 102, groups: Dog:Side, 20; Dog, 10
+Fixed Effects:
+(Intercept) day I(day^2)
+ 1073.339 6.130 -0.367
+> ranef(m1)
+$`Dog:Side`
+ (Intercept)
+A:L -5.97
+A:R -11.77
+B:L -4.05
+B:R -9.80
+C:L -7.97
+C:R 3.73
+D:L 2.11
+D:R 2.85
+E:L 3.31
+E:R 7.11
+F:L 10.91
+F:R -9.90
+G:L -5.91
+G:R 21.12
+H:L 8.13
+H:R -7.42
+I:L 11.17
+I:R -17.05
+J:L 31.61
+J:R -22.20
+
+$Dog
+ (Intercept) day
+A -24.71 -1.1954
+B -23.58 -0.4324
+C -27.08 2.1948
+D -16.66 3.0960
+E 25.30 -0.5613
+F 10.82 -1.0370
+G 49.35 -2.2745
+H -7.05 0.9903
+I -5.75 -0.6811
+J 19.37 -0.0994
+
+> q("no")
+> proc.time()
+ user system elapsed
+ 2.468 0.074 2.568
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