Ming Yuan
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/EBarrays |
| git_branch: RELEASE_3_13 |
| git_last_commit: 097b73e |
| git_last_commit_date: 2021-05-19 11:34:05 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the EBarrays package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBarrays.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 547/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EBarrays 2.56.0 (landing page) Ming Yuan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: EBarrays |
| Version: 2.56.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBarrays.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBarrays_2.56.0.tar.gz |
| StartedAt: 2021-10-14 22:36:58 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:38:23 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 85.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBarrays.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBarrays.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBarrays_2.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'EBarrays/DESCRIPTION' ... OK * this is package 'EBarrays' version '2.56.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'EBarrays' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'Biobase' 'lattice' 'methods' A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to 'lattice' which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.ebarraysEMfit See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE prepare_Rd: crit.fun.Rd:51: Dropping empty section \keyword prepare_Rd: ebplots.Rd:116-117: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/EBarrays/libs/i386/EBarrays.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/EBarrays/libs/x64/EBarrays.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test.R' OK ** running tests for arch 'x64' ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.Rcheck/00check.log' for details.
EBarrays.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EBarrays_2.56.0.tar.gz && rm -rf EBarrays.buildbin-libdir && mkdir EBarrays.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBarrays.buildbin-libdir EBarrays_2.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EBarrays_2.56.0.zip && rm EBarrays_2.56.0.tar.gz EBarrays_2.56.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 243k 100 243k 0 0 847k 0 --:--:-- --:--:-- --:--:-- 850k
install for i386
* installing *source* package 'EBarrays' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ebarrays.c -o ebarrays.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o EBarrays.dll tmp.def ebarrays.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.buildbin-libdir/00LOCK-EBarrays/00new/EBarrays/libs/i386
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EBarrays'
finding HTML links ... done
EBarrays-Internal html
crit.fun html
ebarraysFamily-class html
ebplots html
emfit html
gould html
postprob html
utilities html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'EBarrays' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ebarrays.c -o ebarrays.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o EBarrays.dll tmp.def ebarrays.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/EBarrays.buildbin-libdir/EBarrays/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBarrays' as EBarrays_2.56.0.zip
* DONE (EBarrays)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'EBarrays' successfully unpacked and MD5 sums checked
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EBarrays.Rcheck/tests_i386/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(EBarrays)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
> demo(ebarrays)
demo(ebarrays)
---- ~~~~~~~~
> library(EBarrays)
> ## EM algorithm
> ## Lognormal-Normal Demo
>
> ## mu10,sigma2,tau are parameters in the LNNB model; pde is the
> ## proportion of differentially expressed genes; n is the
> ## total number of genes; nr1 and nr2 are the number of replicate
> ## arrays in each group.
>
> lnnb.sim <- function(mu10, sigmasq, tausq, pde, n, nr1, nr2)
+ {
+ de <- sample(c(TRUE, FALSE), size = n, replace = TRUE, prob = c(pde, 1 - pde))
+ x <- matrix(NA, n, nr1)
+ y <- matrix(NA, n, nr2)
+ mu1 <- rnorm(n, mu10, sqrt(tausq))
+ mu2.de <- rnorm(n, mu10, sqrt(tausq))
+ mu2 <- mu1
+ mu2[de] <- mu2.de[de]
+ for(j in 1:nr1) {
+ x[, j] <- rnorm(n, mu1, sqrt(sigmasq))
+ }
+ for(j in 1:nr2) {
+ y[, j] <- rnorm(n, mu2, sqrt(sigmasq))
+ }
+ outmat <- exp(cbind(x, y))
+ list(mu1 = mu1, mu2 = mu2, outmat = outmat, de = de)
+ }
> ## simulating data with
> ## mu_0 = 2.33, sigma^2 = 0.1, tau^2 = 2
> ## P(DE) = 0.2
>
> sim.data1 <- lnnb.sim(2.33, 0.1, 2, 0.2, 2000, nr1 = 3, nr2 = 3)
> de.true1 <- sim.data1$de ## true indicators of differential expression
> sim.data2 <- lnnb.sim(1.33, 0.01, 2, 0.2, 2000, nr1 = 3, nr2 = 3)
> de.true2 <- sim.data2$de ## true indicators of differential expression
> testdata <- rbind(sim.data1$outmat,sim.data2$outmat)
> hypotheses <- ebPatterns(c("1 1 1 1 1 1", "1 1 1 2 2 2"))
> em.out <- emfit(testdata, family = "LNN", hypotheses,
+ cluster = 1:5,
+ type = 2,
+ verbose = TRUE,
+ num.iter = 10)
Checking for negative entries...
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 0.28 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 1.04 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 1.20 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 1.76 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 2.19 seconds user time
> em.out
EB model fit
Family: LNN ( Lognormal-Normal )
Model parameter estimates:
mu_0 sigma.2 tao_0.2
Cluster 1 2.370598 0.1003321 2.041651
Cluster 2 1.323206 0.0103339 1.943924
Estimated mixing proportions:
Pattern.1 Pattern.2
Cluster 1 0.4017568 0.09948277
Cluster 2 0.3940671 0.10469325
> post.out <- postprob(em.out, testdata)
> table(post.out$pattern[, 2] > .5, c(de.true1,de.true2))
FALSE TRUE
FALSE 3168 141
TRUE 24 667
> table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000)))
Cluster 1 Cluster 2
1 1869 63
2 131 1937
> plotMarginal(em.out,testdata)
> par(ask=TRUE)
> plotCluster(em.out,testdata)
> par(ask=FALSE)
> lnnmv.em.out <- emfit(testdata, family = "LNNMV", hypotheses, groupid=c(1,1,1,2,2,2),
+ verbose = TRUE,
+ num.iter = 10,
+ p.init = c(0.95, 0.05))
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 0.72 seconds user time
> lnnmv.em.out
EB model fit
Family: LNNMV ( Lognormal-Normal with modified variances )
Model parameter estimates:
mu_0 tao_0.2
1 1.85046 2.259741
Estimated mixing proportions:
Pattern.1 Pattern.2
p.temp 0.7825764 0.2174236
> post.out <- postprob(lnnmv.em.out, testdata, groupid=c(1,1,1,2,2,2))
> table(post.out$pattern[, 2] > .5, c(de.true1,de.true2))
FALSE TRUE
FALSE 3118 135
TRUE 74 673
There were 50 or more warnings (use warnings() to see the first 50)
>
>
>
> proc.time()
user system elapsed
9.04 0.25 9.29
|
EBarrays.Rcheck/tests_x64/test.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(EBarrays)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
> demo(ebarrays)
demo(ebarrays)
---- ~~~~~~~~
> library(EBarrays)
> ## EM algorithm
> ## Lognormal-Normal Demo
>
> ## mu10,sigma2,tau are parameters in the LNNB model; pde is the
> ## proportion of differentially expressed genes; n is the
> ## total number of genes; nr1 and nr2 are the number of replicate
> ## arrays in each group.
>
> lnnb.sim <- function(mu10, sigmasq, tausq, pde, n, nr1, nr2)
+ {
+ de <- sample(c(TRUE, FALSE), size = n, replace = TRUE, prob = c(pde, 1 - pde))
+ x <- matrix(NA, n, nr1)
+ y <- matrix(NA, n, nr2)
+ mu1 <- rnorm(n, mu10, sqrt(tausq))
+ mu2.de <- rnorm(n, mu10, sqrt(tausq))
+ mu2 <- mu1
+ mu2[de] <- mu2.de[de]
+ for(j in 1:nr1) {
+ x[, j] <- rnorm(n, mu1, sqrt(sigmasq))
+ }
+ for(j in 1:nr2) {
+ y[, j] <- rnorm(n, mu2, sqrt(sigmasq))
+ }
+ outmat <- exp(cbind(x, y))
+ list(mu1 = mu1, mu2 = mu2, outmat = outmat, de = de)
+ }
> ## simulating data with
> ## mu_0 = 2.33, sigma^2 = 0.1, tau^2 = 2
> ## P(DE) = 0.2
>
> sim.data1 <- lnnb.sim(2.33, 0.1, 2, 0.2, 2000, nr1 = 3, nr2 = 3)
> de.true1 <- sim.data1$de ## true indicators of differential expression
> sim.data2 <- lnnb.sim(1.33, 0.01, 2, 0.2, 2000, nr1 = 3, nr2 = 3)
> de.true2 <- sim.data2$de ## true indicators of differential expression
> testdata <- rbind(sim.data1$outmat,sim.data2$outmat)
> hypotheses <- ebPatterns(c("1 1 1 1 1 1", "1 1 1 2 2 2"))
> em.out <- emfit(testdata, family = "LNN", hypotheses,
+ cluster = 1:5,
+ type = 2,
+ verbose = TRUE,
+ num.iter = 10)
Checking for negative entries...
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 0.31 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 0.85 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 1.49 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 1.90 seconds user time
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 2.36 seconds user time
> em.out
EB model fit
Family: LNN ( Lognormal-Normal )
Model parameter estimates:
mu_0 sigma.2 tao_0.2
Cluster 1 1.373798 0.01013525 1.979309
Cluster 2 2.357468 0.10015473 2.016061
Estimated mixing proportions:
Pattern.1 Pattern.2
Cluster 1 0.3997553 0.1021728
Cluster 2 0.3972669 0.1008051
> post.out <- postprob(em.out, testdata)
> table(post.out$pattern[, 2] > .5, c(de.true1,de.true2))
FALSE TRUE
FALSE 3169 155
TRUE 27 649
> table((post.out$cluster[, 2] > .5)+1, c(rep("Cluster 1",2000),rep("Cluster 2",2000)))
Cluster 1 Cluster 2
1 138 1945
2 1862 55
> plotMarginal(em.out,testdata)
> par(ask=TRUE)
> plotCluster(em.out,testdata)
> par(ask=FALSE)
> lnnmv.em.out <- emfit(testdata, family = "LNNMV", hypotheses, groupid=c(1,1,1,2,2,2),
+ verbose = TRUE,
+ num.iter = 10,
+ p.init = c(0.95, 0.05))
Checking for negative entries...
Generating summary statistics for patterns.
This may take a few seconds...
Starting EM iterations (total 10 ).
This may take a while
Starting iteration 1 ...
Starting iteration 2 ...
Starting iteration 3 ...
Starting iteration 4 ...
Starting iteration 5 ...
Starting iteration 6 ...
Starting iteration 7 ...
Starting iteration 8 ...
Starting iteration 9 ...
Starting iteration 10 ...
Fit used 0.58 seconds user time
> lnnmv.em.out
EB model fit
Family: LNNMV ( Lognormal-Normal with modified variances )
Model parameter estimates:
mu_0 tao_0.2
1 1.870027 2.23832
Estimated mixing proportions:
Pattern.1 Pattern.2
p.temp 0.7815595 0.2184405
> post.out <- postprob(lnnmv.em.out, testdata, groupid=c(1,1,1,2,2,2))
> table(post.out$pattern[, 2] > .5, c(de.true1,de.true2))
FALSE TRUE
FALSE 3114 142
TRUE 82 662
There were 50 or more warnings (use warnings() to see the first 50)
>
>
>
> proc.time()
user system elapsed
9.45 0.07 9.53
|
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EBarrays.Rcheck/examples_i386/EBarrays-Ex.timings
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EBarrays.Rcheck/examples_x64/EBarrays-Ex.timings
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