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CHECK report for BASiCS on tokay1

This page was generated on 2019-04-13 11:28:22 -0400 (Sat, 13 Apr 2019).

Package 101/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BASiCS 1.4.7
Catalina A. Vallejos , Nils Eling
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/BASiCS
Branch: RELEASE_3_8
Last Commit: 56a7c64
Last Changed Date: 2019-03-22 06:17:40 -0400 (Fri, 22 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BASiCS
Version: 1.4.7
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BASiCS_1.4.7.tar.gz
StartedAt: 2019-04-13 00:37:58 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:44:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 397.3 seconds
RetCode: 0
Status:  OK  
CheckDir: BASiCS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BASiCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BASiCS_1.4.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BASiCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BASiCS' version '1.4.7'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'BASiCS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.8-bioc/R/library/BASiCS/libs/i386/BASiCS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
Examples with CPU or elapsed time > 5s
            user system elapsed
BASiCS_MCMC 5.64   0.14    5.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
BASiCS_MCMC  5.7   0.13    5.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.Rcheck/00check.log'
for details.

Installation output

BASiCS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BASiCS_1.4.7.tar.gz && rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BASiCS.buildbin-libdir BASiCS_1.4.7.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BASiCS_1.4.7.zip && rm BASiCS_1.4.7.tar.gz BASiCS_1.4.7.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2367k  100 2367k    0     0  13.4M      0 --:--:-- --:--:-- --:--:-- 13.7M

install for i386

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=1; i < myu.size(); i++) {
                  ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BASiCS'
    finding HTML links ... done
    BASiCS-deprecated                       html  
    BASiCS_Chain-methods                    html  
    BASiCS_Chain                            html  
    BASiCS_D_TestDE                         html  
    BASiCS_DenoisedCounts                   html  
    finding level-2 HTML links ... done

    BASiCS_DenoisedRates                    html  
    BASiCS_DetectHVG_LVG                    html  
    BASiCS_Filter                           html  
    BASiCS_LoadChain                        html  
    BASiCS_MCMC                             html  
    BASiCS_Sim                              html  
    BASiCS_Summary-methods                  html  
    BASiCS_Summary                          html  
    BASiCS_TestDE                           html  
    BASiCS_VarThresholdSearchHVG_LVG        html  
    BASiCS_VarianceDecomp                   html  
    BASiCS_showFit-BASiCS_Chain-method      html  
    ChainRNA                                html  
    ChainRNAReg                             html  
    ChainSC                                 html  
    ChainSCReg                              html  
    Summary-BASiCS_Chain-method             html  
    colnames-BASiCS_Chain-method            html  
    displayChainBASiCS-BASiCS_Chain-method
                                            html  
    displaySummaryBASiCS-BASiCS_Summary-method
                                            html  
    makeExampleBASiCS_Data                  html  
    newBASiCS_Chain                         html  
    newBASiCS_Data                          html  
    plot-BASiCS_Chain-method                html  
    plot-BASiCS_Summary-method              html  
    rownames-BASiCS_Chain-method            html  
    subset-BASiCS_Chain-method              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=1; i < myu.size(); i++) {
                  ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i < ConstrainGene.size(); i++) {
                   ^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i < NotConstrainGene.size(); i++) {
                     ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_1.4.7.zip
* DONE (BASiCS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BASiCS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BASiCS.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(testthat)
> library(BASiCS)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: ggplot2
    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.1823
delta (gene 1): 1.15149
phi (cell 1): 0.963952
s (cell 1): 0.613943
nu (cell 1): 0.189188
theta (batch 1): 0.448946
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.9449
delta (gene 1): 0.759247
phi (cell 1): 0.958731
s (cell 1): 0.359771
nu (cell 1): 0.198295
theta (batch 1): 0.326796
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.90978
delta (gene 1): 1.54192
phi (cell 1): 0.944349
s (cell 1): 0.419055
nu (cell 1): 0.19383
theta (batch 1): 0.452359
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.94074
delta (gene 1): 1.49811
phi (cell 1): 0.93278
s (cell 1): 0.118873
nu (cell 1): 0.190914
theta (batch 1): 0.389401
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.64432
delta (gene 1): 1.24193
phi (cell 1): 0.93485
s (cell 1): 0.422776
nu (cell 1): 0.187127
theta (batch 1): 0.385258
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.7848
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.48
Average acceptance rate among delta[i]'s: 0.6952
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.36
Average acceptance rate among nu[j]'s: 0.656
Maximum acceptance rate among nu[j]'s: 0.88
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.92
Maximum acceptance rate among theta[k]'s: 0.96
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.9765
delta (gene 1): 1.72649
phi (cell 1): 0.959693
s (cell 1): 0.701896
nu (cell 1): 0.190595
theta (batch 1): 0.226352
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.06609
delta (gene 1): 1.4053
phi (cell 1): 0.976277
s (cell 1): 0.142306
nu (cell 1): 0.190266
theta (batch 1): 0.266355
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.1
delta (gene 1): 1.08018
phi (cell 1): 0.989084
s (cell 1): 0.301713
nu (cell 1): 0.192387
theta (batch 1): 0.18372
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 8.03007
delta (gene 1): 1.16585
phi (cell 1): 0.995183
s (cell 1): 0.233543
nu (cell 1): 0.193327
theta (batch 1): 0.147823
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.70306
delta (gene 1): 0.73963
phi (cell 1): 0.992061
s (cell 1): 0.347739
nu (cell 1): 0.18833
theta (batch 1): 0.166263
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.7744
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.6864
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Acceptance rate for phi (joint): 0.88
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.684
Maximum acceptance rate among nu[j]'s: 0.96
 
 
Minimum acceptance rate among theta[k]'s: 0.72
Average acceptance rate among theta[k]'s: 0.82
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.53346
delta (gene 1): 1.70383
s (cell 1): 0.14535
nu (cell 1): 0.506156
theta (batch 1): 0.982882
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.34788
delta (gene 1): 0.688184
s (cell 1): 0.533996
nu (cell 1): 0.520455
theta (batch 1): 0.856624
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.36791
delta (gene 1): 1.06097
s (cell 1): 0.612262
nu (cell 1): 0.528142
theta (batch 1): 0.775602
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.20284
delta (gene 1): 0.94544
s (cell 1): 0.70471
nu (cell 1): 0.538134
theta (batch 1): 0.891055
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.9494
delta (gene 1): 2.26372
s (cell 1): 1.53428
nu (cell 1): 0.556274
theta (batch 1): 1.62842
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.48
Average acceptance rate among mu[i]'s: 0.7776
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.6792
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.958667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.86
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 16.0188
delta (gene 1): 0.742407
s (cell 1): 0.662619
nu (cell 1): 0.95277
theta (batch 1): 1.10052
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 29.622
delta (gene 1): 1.5628
s (cell 1): 0.398639
nu (cell 1): 0.961675
theta (batch 1): 0.849276
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 23.2387
delta (gene 1): 1.18968
s (cell 1): 0.910105
nu (cell 1): 0.964826
theta (batch 1): 1.01081
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 22.4653
delta (gene 1): 0.882127
s (cell 1): 0.516601
nu (cell 1): 0.96197
theta (batch 1): 0.917532
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.0972
delta (gene 1): 0.856072
s (cell 1): 0.229178
nu (cell 1): 0.972111
theta (batch 1): 1.03815
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.7568
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.5904
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.72
Average acceptance rate among nu[jk]'s: 0.936
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.8
Maximum acceptance rate among theta[k]'s: 0.8
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 15.484
delta (gene 1): 1.16451
s (cell 1): 3.8094
nu (cell 1): 0.943411
theta (batch 1): 0.869848
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.5464
delta (gene 1): 0.924271
s (cell 1): 1.39591
nu (cell 1): 0.923135
theta (batch 1): 1.24997
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 14.2655
delta (gene 1): 0.772748
s (cell 1): 3.21281
nu (cell 1): 0.926473
theta (batch 1): 0.737701
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 15.2376
delta (gene 1): 0.717673
s (cell 1): 1.12654
nu (cell 1): 0.92525
theta (batch 1): 0.695046
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.84699
delta (gene 1): 1.17675
s (cell 1): 1.42195
nu (cell 1): 0.934952
theta (batch 1): 0.396758
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.32
Average acceptance rate among mu[i]'s: 0.768
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.44
Average acceptance rate among delta[i]'s: 0.6328
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Minimum acceptance rate among nu[jk]'s: 0.72
Average acceptance rate among nu[jk]'s: 0.94
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.88
Maximum acceptance rate among theta[k]'s: 0.88
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.1397
delta (gene 1): 1.39174
phi (cell 1): 0.966536
s (cell 1): 0.157224
nu (cell 1): 0.189188
theta (batch 1): 0.387808
betas:    0.0587  -0.2528   0.8921   0.2698   0.5536  -0.1842   0.5830   0.2157  -0.2752   0.2387   0.4639  -0.4665

sigma: 0.326869
lambda (gene 1): 1.77417
epsilon (gene 1): 0.111672
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.0963
delta (gene 1): 1.10812
phi (cell 1): 0.964215
s (cell 1): 0.219344
nu (cell 1): 0.193286
theta (batch 1): 0.219869
betas:    0.7889  -0.3287   0.1202   0.2554  -0.1062   0.0653  -0.0515  -0.3250   0.2133   0.0008  -0.8170   0.7331

sigma: 0.248213
lambda (gene 1): 1.0674
epsilon (gene 1): 0.153561
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.5424
delta (gene 1): 1.68992
phi (cell 1): 0.974689
s (cell 1): 0.356965
nu (cell 1): 0.187714
theta (batch 1): 0.153783
betas:    0.0574  -0.0261   0.1359   0.4023  -0.4251   0.4753   0.2540  -0.6990  -0.4517  -0.3854  -0.4539  -0.1190

sigma: 0.236951
lambda (gene 1): 0.612708
epsilon (gene 1): 0.267293
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.20446
delta (gene 1): 0.904086
phi (cell 1): 0.976654
s (cell 1): 0.155822
nu (cell 1): 0.188413
theta (batch 1): 0.147269
betas:   -0.2435   0.0527   0.1532  -0.6836   1.1023  -0.4862   0.2645  -0.2271  -0.6523   0.2594  -0.8638  -1.0214

sigma: 0.30994
lambda (gene 1): 1.72742
epsilon (gene 1): -0.207856
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 8.15378
delta (gene 1): 0.725008
phi (cell 1): 0.96564
s (cell 1): 0.173282
nu (cell 1): 0.192181
theta (batch 1): 0.221186
betas:   -0.1869  -0.2943   1.4766  -0.1831   0.2354   0.6061   0.3967  -0.2594   0.2633   0.0337   0.3621  -0.3413

sigma: 0.346018
lambda (gene 1): 1.68848
epsilon (gene 1): -0.447329
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.7584
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.32
Average acceptance rate among delta[i]'s: 0.6656
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.622667
Maximum acceptance rate among nu[j]'s: 0.88
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.84
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.5071
delta (gene 1): 1.66356
phi (cell 1): 0.963741
s (cell 1): 0.890288
nu (cell 1): 0.189188
theta (batch 1): 0.569577
betas:    0.8618  -0.4583   0.6226  -0.1527   0.0912   0.5639   0.0156   1.0115  -0.9131  -0.1174   1.0609  -0.8734

sigma: 0.36928
lambda (gene 1): 1.08974
epsilon (gene 1): -0.10019
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.39901
delta (gene 1): 1.67495
phi (cell 1): 0.96552
s (cell 1): 0.488109
nu (cell 1): 0.192011
theta (batch 1): 0.490617
betas:    0.6608  -0.3539   0.2834   0.0918   0.6556  -0.2515  -0.0316  -0.0762   0.0676  -0.7336   0.4028  -0.4932

sigma: 0.28579
lambda (gene 1): 0.275559
epsilon (gene 1): 0.505918
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.70966
delta (gene 1): 0.708728
phi (cell 1): 0.985096
s (cell 1): 0.364519
nu (cell 1): 0.195652
theta (batch 1): 0.154592
betas:   -0.0496  -0.2739   0.0429  -0.0178   0.6991  -0.0333   0.4834  -0.1974   0.1581  -0.1237   0.0144  -0.4892

sigma: 0.194432
lambda (gene 1): 1.39428
epsilon (gene 1): -0.392233
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.0493
delta (gene 1): 1.7606
phi (cell 1): 0.989638
s (cell 1): 0.25513
nu (cell 1): 0.195163
theta (batch 1): 0.218958
betas:    0.2115  -0.3273   1.3837  -0.5805   0.6261   0.4424  -0.1598  -0.1427   0.8767  -0.0977  -0.2667   0.4098

sigma: 0.310315
lambda (gene 1): 0.424222
epsilon (gene 1): 0.454063
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.20317
delta (gene 1): 1.19075
phi (cell 1): 0.98873
s (cell 1): 0.391416
nu (cell 1): 0.192803
theta (batch 1): 0.248405
betas:    0.0143  -0.1055   0.8425   0.2064   0.0284  -0.0660   0.1897  -0.1737  -0.6685  -0.5543  -0.7620   0.0750

sigma: 0.246724
lambda (gene 1): 2.10768
epsilon (gene 1): 0.315488
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.52
Average acceptance rate among mu[i]'s: 0.7624
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.6592
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.629333
Maximum acceptance rate among nu[j]'s: 0.92
 
 
Minimum acceptance rate among theta[k]'s: 0.96
Average acceptance rate among theta[k]'s: 0.98
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.37967
delta (gene 1): 1.72649
s (cell 1): 0.782461
nu (cell 1): 0.515171
theta (batch 1): 0.817757
betas:    0.2430  -0.1908  -0.8754   0.6812   0.6029  -0.0155   0.0750  -0.0593   0.4478  -0.8451   0.0619  -0.0197

sigma: 0.363814
lambda (gene 1): 3.47766
epsilon (gene 1): 0.113152
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.46829
delta (gene 1): 1.43592
s (cell 1): 1.44913
nu (cell 1): 0.502849
theta (batch 1): 0.748963
betas:    0.3936  -0.5619   0.3886  -0.5285   0.7809   0.2030  -0.1109   0.2391  -0.2348   0.1898   0.1388  -0.4435

sigma: 0.21646
lambda (gene 1): 0.756427
epsilon (gene 1): 0.188622
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.97195
delta (gene 1): 1.06668
s (cell 1): 0.822497
nu (cell 1): 0.494005
theta (batch 1): 0.557189
betas:   -0.3513  -0.1468   1.0847   0.4634  -0.5565   0.9797  -0.3929   0.2304  -0.5419  -0.1182  -0.3578  -0.0724

sigma: 0.333834
lambda (gene 1): 0.44644
epsilon (gene 1): 0.188223
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 2.75654
delta (gene 1): 1.38118
s (cell 1): 0.443902
nu (cell 1): 0.466552
theta (batch 1): 1.1505
betas:   -0.1989  -0.4704  -0.0172  -0.1345   0.5138   0.4146   0.4232   0.0385  -0.1102   0.6282  -0.3128   0.0508

sigma: 0.287442
lambda (gene 1): 0.965035
epsilon (gene 1): 0.105948
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.8763
delta (gene 1): 1.42676
s (cell 1): 1.41504
nu (cell 1): 0.494691
theta (batch 1): 1.65652
betas:    0.2624  -0.4239   0.0343  -0.1219   0.3651  -0.7314   0.4759   0.2018   0.2218  -0.8755   0.7847  -0.1595

sigma: 0.377378
lambda (gene 1): 0.611034
epsilon (gene 1): 0.632183
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.48
Average acceptance rate among mu[i]'s: 0.7496
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.6752
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.946667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.84
Average acceptance rate among theta[k]'s: 0.86
Maximum acceptance rate among theta[k]'s: 0.88
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 12.974
delta (gene 1): 2.10806
s (cell 1): 0.779886
nu (cell 1): 0.945268
theta (batch 1): 0.637459
betas:   -0.3619  -0.0951   0.5528  -0.1336   0.5982  -0.0540   0.5008  -0.3050  -0.0414   0.4276  -0.5497  -0.5956

sigma: 0.223037
lambda (gene 1): 0.473511
epsilon (gene 1): 0.728402
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.6328
delta (gene 1): 0.974484
s (cell 1): 0.568827
nu (cell 1): 0.922705
theta (batch 1): 0.743622
betas:   -0.0599  -0.1987   0.7607   0.4101   0.4360   0.1242   0.0493   0.2653  -0.4365  -0.0589  -0.4153  -0.2739

sigma: 0.214803
lambda (gene 1): 1.77527
epsilon (gene 1): -0.076247
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.174
delta (gene 1): 0.970747
s (cell 1): 2.05193
nu (cell 1): 0.931289
theta (batch 1): 0.671897
betas:    0.4059  -0.4005   0.3917   0.4096   0.5308  -0.2726   0.3263   0.4794  -0.2963  -0.0690  -0.1016  -0.0246

sigma: 0.305187
lambda (gene 1): 1.55256
epsilon (gene 1): 0.0770614
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 59.1238
delta (gene 1): 1.47973
s (cell 1): 0.502719
nu (cell 1): 0.924117
theta (batch 1): 0.887035
betas:    0.8208  -0.2947   1.3781   0.1273  -0.3316   0.6581  -0.6244   0.2962  -0.9287   0.1869  -0.6936  -0.5943

sigma: 0.27595
lambda (gene 1): 1.19947
epsilon (gene 1): 0.256193
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 38.4477
delta (gene 1): 1.52158
s (cell 1): 0.944273
nu (cell 1): 0.941864
theta (batch 1): 0.680793
betas:    1.7902  -0.7549   0.6094   0.0327  -0.2341   0.5792   0.1763  -0.5668   0.2043   0.0280   0.4331   0.6245

sigma: 0.317137
lambda (gene 1): 0.648869
epsilon (gene 1): 0.202017
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.32
Average acceptance rate among mu[i]'s: 0.6752
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.5944
Maximum acceptance rate among delta[i]'s: 0.8
 
 
Minimum acceptance rate among nu[jk]'s: 0.76
Average acceptance rate among nu[jk]'s: 0.922667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.84
Maximum acceptance rate among theta[k]'s: 0.88
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 18.5343
delta (gene 1): 1.20446
s (cell 1): 1.3798
nu (cell 1): 0.927389
theta (batch 1): 0.714085
betas:   -0.1215  -0.1502   0.0018   0.6359  -0.1468   1.0651  -0.8814   0.4548  -0.1361  -1.0002  -0.2049  -0.0096

sigma: 0.251752
lambda (gene 1): 1.53954
epsilon (gene 1): 0.119676
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 14.1889
delta (gene 1): 1.33933
s (cell 1): 1.73594
nu (cell 1): 0.925327
theta (batch 1): 0.655469
betas:    0.6109  -0.4770   0.8240   0.2665   0.3805   0.1986  -0.0300   0.2450   0.3324   0.0306   0.3288  -0.3239

sigma: 0.209444
lambda (gene 1): 1.08325
epsilon (gene 1): 0.334843
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.1711
delta (gene 1): 0.943706
s (cell 1): 0.453942
nu (cell 1): 0.906057
theta (batch 1): 0.687912
betas:    0.2837  -0.3003   1.3994  -0.0134   0.4715  -0.1288   0.5282   0.2471  -0.8315  -0.0330  -0.0684  -0.2067

sigma: 0.236154
lambda (gene 1): 0.809167
epsilon (gene 1): -0.199496
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 20.292
delta (gene 1): 1.22264
s (cell 1): 0.827296
nu (cell 1): 0.893782
theta (batch 1): 0.527292
betas:    0.1436  -0.3270   0.4339   0.6975  -0.1110   0.8383  -0.0880   0.4675  -0.6774   0.5196   0.1672  -0.2062

sigma: 0.331722
lambda (gene 1): 1.37037
epsilon (gene 1): -0.045675
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.7775
delta (gene 1): 1.20188
s (cell 1): 0.760507
nu (cell 1): 0.884977
theta (batch 1): 0.68969
betas:   -0.1300  -0.3571   0.4999   0.8587   0.7262   0.2372   0.0971   0.1637   0.2113  -0.0976   0.3861   0.1082

sigma: 0.216667
lambda (gene 1): 1.51499
epsilon (gene 1): 0.176961
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.6944
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.6144
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.76
Average acceptance rate among nu[jk]'s: 0.946667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.84
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.96
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.88025
delta (gene 1): 1.35453
s (cell 1): 1.24758
nu (cell 1): 0.591016
theta (batch 1): 0.382241
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.30239
delta (gene 1): 1.13589
s (cell 1): 0.952532
nu (cell 1): 0.603502
theta (batch 1): 0.628488
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.12911
delta (gene 1): 1.08339
s (cell 1): 0.544108
nu (cell 1): 0.595019
theta (batch 1): 0.531377
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 2.89422
delta (gene 1): 1.24921
s (cell 1): 0.680775
nu (cell 1): 0.571118
theta (batch 1): 0.589861
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.50123
delta (gene 1): 0.995004
s (cell 1): 0.738163
nu (cell 1): 0.543385
theta (batch 1): 0.406926
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.16
Average acceptance rate among mu[i]'s: 0.693143
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.48
Average acceptance rate among delta[i]'s: 0.704
Maximum acceptance rate among delta[i]'s: 0.96
 
 
Minimum acceptance rate among nu[jk]'s: 0.8
Average acceptance rate among nu[jk]'s: 0.918667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.19861
delta (gene 1): 1.72649
phi (cell 1): 0.959311
s (cell 1): 0.284997
nu (cell 1): 0.189188
theta (batch 1): 0.612703
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.50062
delta (gene 1): 1.05696
phi (cell 1): 0.954246
s (cell 1): 0.39526
nu (cell 1): 0.190014
theta (batch 1): 0.703926
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.67026
delta (gene 1): 0.817779
phi (cell 1): 0.966748
s (cell 1): 0.424078
nu (cell 1): 0.199087
theta (batch 1): 0.416005
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 16.3695
delta (gene 1): 1.13048
phi (cell 1): 0.944188
s (cell 1): 0.73483
nu (cell 1): 0.199107
theta (batch 1): 0.356171
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.07619
delta (gene 1): 2.31572
phi (cell 1): 0.953499
s (cell 1): 0.516729
nu (cell 1): 0.193889
theta (batch 1): 0.271176
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.764
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.7008
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Acceptance rate for phi (joint): 0.96
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.626667
Maximum acceptance rate among nu[j]'s: 0.96
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.76
Maximum acceptance rate among theta[k]'s: 0.76
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.454
Average acceptance rate among mu[i]'s: 0.65608
Maximum acceptance rate among mu[i]'s: 0.834
 
 
Minimum acceptance rate among delta[i]'s: 0.464
Average acceptance rate among delta[i]'s: 0.5502
Maximum acceptance rate among delta[i]'s: 0.714
 
 
Acceptance rate for phi (joint): 0.884
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.540933
Maximum acceptance rate among nu[j]'s: 0.72
 
 
Minimum acceptance rate among theta[k]'s: 0.75
Average acceptance rate among theta[k]'s: 0.75
Maximum acceptance rate among theta[k]'s: 0.75
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.772
Maximum acceptance rate among mu[i]'s: 0.95
 
 
Minimum acceptance rate among delta[i]'s: 0.5
Average acceptance rate among delta[i]'s: 0.678
Maximum acceptance rate among delta[i]'s: 0.85
 
 
Acceptance rate for phi (joint): 0.95
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.668333
Maximum acceptance rate among nu[j]'s: 0.85
 
 
Minimum acceptance rate among theta[k]'s: 0.75
Average acceptance rate among theta[k]'s: 0.75
Maximum acceptance rate among theta[k]'s: 0.75
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.432
Average acceptance rate among mu[i]'s: 0.65752
Maximum acceptance rate among mu[i]'s: 0.838
 
 
Minimum acceptance rate among delta[i]'s: 0.388
Average acceptance rate among delta[i]'s: 0.54484
Maximum acceptance rate among delta[i]'s: 0.698
 
 
Acceptance rate for phi (joint): 0.882
 
 
Minimum acceptance rate among nu[j]'s: 0.448
Average acceptance rate among nu[j]'s: 0.530467
Maximum acceptance rate among nu[j]'s: 0.7
 
 
Minimum acceptance rate among theta[k]'s: 0.81
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.848
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.404
Average acceptance rate among mu[i]'s: 0.6282
Maximum acceptance rate among mu[i]'s: 0.83
 
 
Minimum acceptance rate among delta[i]'s: 0.446
Average acceptance rate among delta[i]'s: 0.49484
Maximum acceptance rate among delta[i]'s: 0.576
 
 
Minimum acceptance rate among nu[jk]'s: 0.804
Average acceptance rate among nu[jk]'s: 0.9198
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.786
Average acceptance rate among theta[k]'s: 0.796
Maximum acceptance rate among theta[k]'s: 0.806
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.404
Average acceptance rate among mu[i]'s: 0.6282
Maximum acceptance rate among mu[i]'s: 0.83
 
 
Minimum acceptance rate among delta[i]'s: 0.446
Average acceptance rate among delta[i]'s: 0.49484
Maximum acceptance rate among delta[i]'s: 0.576
 
 
Minimum acceptance rate among nu[jk]'s: 0.804
Average acceptance rate among nu[jk]'s: 0.9198
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.786
Average acceptance rate among theta[k]'s: 0.796
Maximum acceptance rate among theta[k]'s: 0.806
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.741
Maximum acceptance rate among mu[i]'s: 0.9
 
 
Minimum acceptance rate among delta[i]'s: 0.425
Average acceptance rate among delta[i]'s: 0.6165
Maximum acceptance rate among delta[i]'s: 0.75
 
 
Minimum acceptance rate among nu[jk]'s: 0.85
Average acceptance rate among nu[jk]'s: 0.951667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.85
Maximum acceptance rate among theta[k]'s: 0.9
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.468
Average acceptance rate among mu[i]'s: 0.65876
Maximum acceptance rate among mu[i]'s: 0.824
 
 
Minimum acceptance rate among delta[i]'s: 0.472
Average acceptance rate among delta[i]'s: 0.54948
Maximum acceptance rate among delta[i]'s: 0.628
 
 
Minimum acceptance rate among nu[jk]'s: 0.862
Average acceptance rate among nu[jk]'s: 0.939133
Maximum acceptance rate among nu[jk]'s: 0.994
 
 
Minimum acceptance rate among theta[k]'s: 0.808
Average acceptance rate among theta[k]'s: 0.81
Maximum acceptance rate among theta[k]'s: 0.812
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.468
Average acceptance rate among mu[i]'s: 0.65876
Maximum acceptance rate among mu[i]'s: 0.824
 
 
Minimum acceptance rate among delta[i]'s: 0.472
Average acceptance rate among delta[i]'s: 0.54948
Maximum acceptance rate among delta[i]'s: 0.628
 
 
Minimum acceptance rate among nu[jk]'s: 0.862
Average acceptance rate among nu[jk]'s: 0.939133
Maximum acceptance rate among nu[jk]'s: 0.994
 
 
Minimum acceptance rate among theta[k]'s: 0.808
Average acceptance rate among theta[k]'s: 0.81
Maximum acceptance rate among theta[k]'s: 0.812
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.61168
Maximum acceptance rate among mu[i]'s: 0.774
 
 
Minimum acceptance rate among delta[i]'s: 0.414
Average acceptance rate among delta[i]'s: 0.4972
Maximum acceptance rate among delta[i]'s: 0.57
 
 
Minimum acceptance rate among nu[jk]'s: 0.792
Average acceptance rate among nu[jk]'s: 0.919867
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.814
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.844
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.61168
Maximum acceptance rate among mu[i]'s: 0.774
 
 
Minimum acceptance rate among delta[i]'s: 0.414
Average acceptance rate among delta[i]'s: 0.4972
Maximum acceptance rate among delta[i]'s: 0.57
 
 
Minimum acceptance rate among nu[jk]'s: 0.792
Average acceptance rate among nu[jk]'s: 0.919867
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.814
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.844
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.714
Maximum acceptance rate among mu[i]'s: 0.875
 
 
Minimum acceptance rate among delta[i]'s: 0.425
Average acceptance rate among delta[i]'s: 0.619
Maximum acceptance rate among delta[i]'s: 0.825
 
 
Minimum acceptance rate among nu[jk]'s: 0.85
Average acceptance rate among nu[jk]'s: 0.956667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.875
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.925
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.434
Average acceptance rate among mu[i]'s: 0.60812
Maximum acceptance rate among mu[i]'s: 0.816
 
 
Minimum acceptance rate among delta[i]'s: 0.418
Average acceptance rate among delta[i]'s: 0.52908
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Acceptance rate for phi (joint): 0.87
 
 
Minimum acceptance rate among nu[j]'s: 0.434
Average acceptance rate among nu[j]'s: 0.536733
Maximum acceptance rate among nu[j]'s: 0.712
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.78
Maximum acceptance rate among theta[k]'s: 0.8
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.758
Maximum acceptance rate among mu[i]'s: 0.95
 
 
Minimum acceptance rate among delta[i]'s: 0.375
Average acceptance rate among delta[i]'s: 0.6405
Maximum acceptance rate among delta[i]'s: 0.775
 
 
Acceptance rate for phi (joint): 0.975
 
 
Minimum acceptance rate among nu[j]'s: 0.45
Average acceptance rate among nu[j]'s: 0.643333
Maximum acceptance rate among nu[j]'s: 0.9
 
 
Minimum acceptance rate among theta[k]'s: 0.875
Average acceptance rate among theta[k]'s: 0.875
Maximum acceptance rate among theta[k]'s: 0.875
 
-----------------------------------------------------
 
new("standardGeneric", .Data = function (x, y, ...) 
standardGeneric("plot"), generic = "plot", package = "graphics", 
    group = list(), valueClass = character(0), signature = c("x", 
    "y"), default = new("derivedDefaultMethod", .Data = function (x, 
        y, ...) 
    UseMethod("plot"), target = new("signature", .Data = "ANY", 
        names = "x", package = "methods"), defined = new("signature", 
        .Data = "ANY", names = "x", package = "methods"), generic = "plot"), 
    skeleton = (new("derivedDefaultMethod", .Data = function (x, 
        y, ...) 
    UseMethod("plot"), target = new("signature", .Data = "ANY", 
        names = "x", package = "methods"), defined = new("signature", 
        .Data = "ANY", names = "x", package = "methods"), generic = "plot"))(x, 
        y, ...))
<environment: 0x0227b2a8>
attr(,"generic")
[1] "plot"
attr(,"generic")attr(,"package")
[1] "graphics"
attr(,"package")
[1] "graphics"
attr(,"group")
list()
attr(,"valueClass")
character(0)
attr(,"signature")
[1] "x" "y"
attr(,"default")
Method Definition (Class "derivedDefaultMethod"):

function (x, y, ...) 
UseMethod("plot")
<bytecode: 0x027159c0>
<environment: namespace:graphics>

Signatures:
        x    
target  "ANY"
defined "ANY"
attr(,"skeleton")
(new("derivedDefaultMethod", .Data = function (x, y, ...) 
UseMethod("plot"), target = new("signature", .Data = "ANY", names = "x", 
    package = "methods"), defined = new("signature", .Data = "ANY", 
    names = "x", package = "methods"), generic = "plot"))(x, 
    y, ...)
attr(,"class")
[1] "standardGeneric"
attr(,"class")attr(,"package")
[1] "methods"
== testthat results  ===========================================================
OK: 171 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  32.85    1.17   34.09

BASiCS.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(testthat)
> library(BASiCS)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: ggplot2
    Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
    Bioconductor, please visit:
    https://github.com/catavallejos/BASiCS/wiki.
> 
> test_check("BASiCS")
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.1823
delta (gene 1): 1.15149
phi (cell 1): 0.963952
s (cell 1): 0.613943
nu (cell 1): 0.189188
theta (batch 1): 0.448946
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.9449
delta (gene 1): 0.759247
phi (cell 1): 0.958731
s (cell 1): 0.359771
nu (cell 1): 0.198295
theta (batch 1): 0.326796
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.90978
delta (gene 1): 1.54192
phi (cell 1): 0.944349
s (cell 1): 0.419055
nu (cell 1): 0.19383
theta (batch 1): 0.452359
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.94074
delta (gene 1): 1.49811
phi (cell 1): 0.93278
s (cell 1): 0.118873
nu (cell 1): 0.190914
theta (batch 1): 0.389401
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.64432
delta (gene 1): 1.24193
phi (cell 1): 0.93485
s (cell 1): 0.422776
nu (cell 1): 0.187127
theta (batch 1): 0.385258
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.7848
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.48
Average acceptance rate among delta[i]'s: 0.6952
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.36
Average acceptance rate among nu[j]'s: 0.656
Maximum acceptance rate among nu[j]'s: 0.88
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.92
Maximum acceptance rate among theta[k]'s: 0.96
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.9765
delta (gene 1): 1.72649
phi (cell 1): 0.959693
s (cell 1): 0.701896
nu (cell 1): 0.190595
theta (batch 1): 0.226352
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.06609
delta (gene 1): 1.4053
phi (cell 1): 0.976277
s (cell 1): 0.142306
nu (cell 1): 0.190266
theta (batch 1): 0.266355
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.1
delta (gene 1): 1.08018
phi (cell 1): 0.989084
s (cell 1): 0.301713
nu (cell 1): 0.192387
theta (batch 1): 0.18372
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 8.03007
delta (gene 1): 1.16585
phi (cell 1): 0.995183
s (cell 1): 0.233543
nu (cell 1): 0.193327
theta (batch 1): 0.147823
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.70306
delta (gene 1): 0.73963
phi (cell 1): 0.992061
s (cell 1): 0.347739
nu (cell 1): 0.18833
theta (batch 1): 0.166263
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.7744
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.6864
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Acceptance rate for phi (joint): 0.88
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.684
Maximum acceptance rate among nu[j]'s: 0.96
 
 
Minimum acceptance rate among theta[k]'s: 0.72
Average acceptance rate among theta[k]'s: 0.82
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.53346
delta (gene 1): 1.70383
s (cell 1): 0.14535
nu (cell 1): 0.506156
theta (batch 1): 0.982882
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.34788
delta (gene 1): 0.688184
s (cell 1): 0.533996
nu (cell 1): 0.520455
theta (batch 1): 0.856624
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.36791
delta (gene 1): 1.06097
s (cell 1): 0.612262
nu (cell 1): 0.528142
theta (batch 1): 0.775602
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.20284
delta (gene 1): 0.94544
s (cell 1): 0.70471
nu (cell 1): 0.538134
theta (batch 1): 0.891055
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.9494
delta (gene 1): 2.26372
s (cell 1): 1.53428
nu (cell 1): 0.556274
theta (batch 1): 1.62842
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.48
Average acceptance rate among mu[i]'s: 0.7776
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.6792
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.958667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.86
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 16.0188
delta (gene 1): 0.742407
s (cell 1): 0.662619
nu (cell 1): 0.95277
theta (batch 1): 1.10052
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 29.622
delta (gene 1): 1.5628
s (cell 1): 0.398639
nu (cell 1): 0.961675
theta (batch 1): 0.849276
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 23.2387
delta (gene 1): 1.18968
s (cell 1): 0.910105
nu (cell 1): 0.964826
theta (batch 1): 1.01081
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 22.4653
delta (gene 1): 0.882127
s (cell 1): 0.516601
nu (cell 1): 0.96197
theta (batch 1): 0.917532
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.0972
delta (gene 1): 0.856072
s (cell 1): 0.229178
nu (cell 1): 0.972111
theta (batch 1): 1.03815
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.7568
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.5904
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.72
Average acceptance rate among nu[jk]'s: 0.936
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.8
Maximum acceptance rate among theta[k]'s: 0.8
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 15.484
delta (gene 1): 1.16451
s (cell 1): 3.8094
nu (cell 1): 0.943411
theta (batch 1): 0.869848
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.5464
delta (gene 1): 0.924271
s (cell 1): 1.39591
nu (cell 1): 0.923135
theta (batch 1): 1.24997
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 14.2655
delta (gene 1): 0.772748
s (cell 1): 3.21281
nu (cell 1): 0.926473
theta (batch 1): 0.737701
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 15.2376
delta (gene 1): 0.717673
s (cell 1): 1.12654
nu (cell 1): 0.92525
theta (batch 1): 0.695046
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 4.84699
delta (gene 1): 1.17675
s (cell 1): 1.42195
nu (cell 1): 0.934952
theta (batch 1): 0.396758
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.32
Average acceptance rate among mu[i]'s: 0.768
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.44
Average acceptance rate among delta[i]'s: 0.6328
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Minimum acceptance rate among nu[jk]'s: 0.72
Average acceptance rate among nu[jk]'s: 0.94
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.88
Maximum acceptance rate among theta[k]'s: 0.88
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.1397
delta (gene 1): 1.39174
phi (cell 1): 0.966536
s (cell 1): 0.157224
nu (cell 1): 0.189188
theta (batch 1): 0.387808
betas:    0.0587  -0.2528   0.8921   0.2698   0.5536  -0.1842   0.5830   0.2157  -0.2752   0.2387   0.4639  -0.4665

sigma: 0.326869
lambda (gene 1): 1.77417
epsilon (gene 1): 0.111672
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.0963
delta (gene 1): 1.10812
phi (cell 1): 0.964215
s (cell 1): 0.219344
nu (cell 1): 0.193286
theta (batch 1): 0.219869
betas:    0.7889  -0.3287   0.1202   0.2554  -0.1062   0.0653  -0.0515  -0.3250   0.2133   0.0008  -0.8170   0.7331

sigma: 0.248213
lambda (gene 1): 1.0674
epsilon (gene 1): 0.153561
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.5424
delta (gene 1): 1.68992
phi (cell 1): 0.974689
s (cell 1): 0.356965
nu (cell 1): 0.187714
theta (batch 1): 0.153783
betas:    0.0574  -0.0261   0.1359   0.4023  -0.4251   0.4753   0.2540  -0.6990  -0.4517  -0.3854  -0.4539  -0.1190

sigma: 0.236951
lambda (gene 1): 0.612708
epsilon (gene 1): 0.267293
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.20446
delta (gene 1): 0.904086
phi (cell 1): 0.976654
s (cell 1): 0.155822
nu (cell 1): 0.188413
theta (batch 1): 0.147269
betas:   -0.2435   0.0527   0.1532  -0.6836   1.1023  -0.4862   0.2645  -0.2271  -0.6523   0.2594  -0.8638  -1.0214

sigma: 0.30994
lambda (gene 1): 1.72742
epsilon (gene 1): -0.207856
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 8.15378
delta (gene 1): 0.725008
phi (cell 1): 0.96564
s (cell 1): 0.173282
nu (cell 1): 0.192181
theta (batch 1): 0.221186
betas:   -0.1869  -0.2943   1.4766  -0.1831   0.2354   0.6061   0.3967  -0.2594   0.2633   0.0337   0.3621  -0.3413

sigma: 0.346018
lambda (gene 1): 1.68848
epsilon (gene 1): -0.447329
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.7584
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.32
Average acceptance rate among delta[i]'s: 0.6656
Maximum acceptance rate among delta[i]'s: 0.88
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.622667
Maximum acceptance rate among nu[j]'s: 0.88
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.84
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.5071
delta (gene 1): 1.66356
phi (cell 1): 0.963741
s (cell 1): 0.890288
nu (cell 1): 0.189188
theta (batch 1): 0.569577
betas:    0.8618  -0.4583   0.6226  -0.1527   0.0912   0.5639   0.0156   1.0115  -0.9131  -0.1174   1.0609  -0.8734

sigma: 0.36928
lambda (gene 1): 1.08974
epsilon (gene 1): -0.10019
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 6.39901
delta (gene 1): 1.67495
phi (cell 1): 0.96552
s (cell 1): 0.488109
nu (cell 1): 0.192011
theta (batch 1): 0.490617
betas:    0.6608  -0.3539   0.2834   0.0918   0.6556  -0.2515  -0.0316  -0.0762   0.0676  -0.7336   0.4028  -0.4932

sigma: 0.28579
lambda (gene 1): 0.275559
epsilon (gene 1): 0.505918
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 5.70966
delta (gene 1): 0.708728
phi (cell 1): 0.985096
s (cell 1): 0.364519
nu (cell 1): 0.195652
theta (batch 1): 0.154592
betas:   -0.0496  -0.2739   0.0429  -0.0178   0.6991  -0.0333   0.4834  -0.1974   0.1581  -0.1237   0.0144  -0.4892

sigma: 0.194432
lambda (gene 1): 1.39428
epsilon (gene 1): -0.392233
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 10.0493
delta (gene 1): 1.7606
phi (cell 1): 0.989638
s (cell 1): 0.25513
nu (cell 1): 0.195163
theta (batch 1): 0.218958
betas:    0.2115  -0.3273   1.3837  -0.5805   0.6261   0.4424  -0.1598  -0.1427   0.8767  -0.0977  -0.2667   0.4098

sigma: 0.310315
lambda (gene 1): 0.424222
epsilon (gene 1): 0.454063
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.20317
delta (gene 1): 1.19075
phi (cell 1): 0.98873
s (cell 1): 0.391416
nu (cell 1): 0.192803
theta (batch 1): 0.248405
betas:    0.0143  -0.1055   0.8425   0.2064   0.0284  -0.0660   0.1897  -0.1737  -0.6685  -0.5543  -0.7620   0.0750

sigma: 0.246724
lambda (gene 1): 2.10768
epsilon (gene 1): 0.315488
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.52
Average acceptance rate among mu[i]'s: 0.7624
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.4
Average acceptance rate among delta[i]'s: 0.6592
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Acceptance rate for phi (joint): 0.92
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.629333
Maximum acceptance rate among nu[j]'s: 0.92
 
 
Minimum acceptance rate among theta[k]'s: 0.96
Average acceptance rate among theta[k]'s: 0.98
Maximum acceptance rate among theta[k]'s: 1
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.37967
delta (gene 1): 1.72649
s (cell 1): 0.782461
nu (cell 1): 0.515171
theta (batch 1): 0.817757
betas:    0.2430  -0.1908  -0.8754   0.6812   0.6029  -0.0155   0.0750  -0.0593   0.4478  -0.8451   0.0619  -0.0197

sigma: 0.363814
lambda (gene 1): 3.47766
epsilon (gene 1): 0.113152
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.46829
delta (gene 1): 1.43592
s (cell 1): 1.44913
nu (cell 1): 0.502849
theta (batch 1): 0.748963
betas:    0.3936  -0.5619   0.3886  -0.5285   0.7809   0.2030  -0.1109   0.2391  -0.2348   0.1898   0.1388  -0.4435

sigma: 0.21646
lambda (gene 1): 0.756427
epsilon (gene 1): 0.188622
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.97195
delta (gene 1): 1.06668
s (cell 1): 0.822497
nu (cell 1): 0.494005
theta (batch 1): 0.557189
betas:   -0.3513  -0.1468   1.0847   0.4634  -0.5565   0.9797  -0.3929   0.2304  -0.5419  -0.1182  -0.3578  -0.0724

sigma: 0.333834
lambda (gene 1): 0.44644
epsilon (gene 1): 0.188223
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 2.75654
delta (gene 1): 1.38118
s (cell 1): 0.443902
nu (cell 1): 0.466552
theta (batch 1): 1.1505
betas:   -0.1989  -0.4704  -0.0172  -0.1345   0.5138   0.4146   0.4232   0.0385  -0.1102   0.6282  -0.3128   0.0508

sigma: 0.287442
lambda (gene 1): 0.965035
epsilon (gene 1): 0.105948
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.8763
delta (gene 1): 1.42676
s (cell 1): 1.41504
nu (cell 1): 0.494691
theta (batch 1): 1.65652
betas:    0.2624  -0.4239   0.0343  -0.1219   0.3651  -0.7314   0.4759   0.2018   0.2218  -0.8755   0.7847  -0.1595

sigma: 0.377378
lambda (gene 1): 0.611034
epsilon (gene 1): 0.632183
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -8.59865
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.48
Average acceptance rate among mu[i]'s: 0.7496
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.6752
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.84
Average acceptance rate among nu[jk]'s: 0.946667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.84
Average acceptance rate among theta[k]'s: 0.86
Maximum acceptance rate among theta[k]'s: 0.88
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 12.974
delta (gene 1): 2.10806
s (cell 1): 0.779886
nu (cell 1): 0.945268
theta (batch 1): 0.637459
betas:   -0.3619  -0.0951   0.5528  -0.1336   0.5982  -0.0540   0.5008  -0.3050  -0.0414   0.4276  -0.5497  -0.5956

sigma: 0.223037
lambda (gene 1): 0.473511
epsilon (gene 1): 0.728402
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 11.6328
delta (gene 1): 0.974484
s (cell 1): 0.568827
nu (cell 1): 0.922705
theta (batch 1): 0.743622
betas:   -0.0599  -0.1987   0.7607   0.4101   0.4360   0.1242   0.0493   0.2653  -0.4365  -0.0589  -0.4153  -0.2739

sigma: 0.214803
lambda (gene 1): 1.77527
epsilon (gene 1): -0.076247
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.174
delta (gene 1): 0.970747
s (cell 1): 2.05193
nu (cell 1): 0.931289
theta (batch 1): 0.671897
betas:    0.4059  -0.4005   0.3917   0.4096   0.5308  -0.2726   0.3263   0.4794  -0.2963  -0.0690  -0.1016  -0.0246

sigma: 0.305187
lambda (gene 1): 1.55256
epsilon (gene 1): 0.0770614
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 59.1238
delta (gene 1): 1.47973
s (cell 1): 0.502719
nu (cell 1): 0.924117
theta (batch 1): 0.887035
betas:    0.8208  -0.2947   1.3781   0.1273  -0.3316   0.6581  -0.6244   0.2962  -0.9287   0.1869  -0.6936  -0.5943

sigma: 0.27595
lambda (gene 1): 1.19947
epsilon (gene 1): 0.256193
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 38.4477
delta (gene 1): 1.52158
s (cell 1): 0.944273
nu (cell 1): 0.941864
theta (batch 1): 0.680793
betas:    1.7902  -0.7549   0.6094   0.0327  -0.2341   0.5792   0.1763  -0.5668   0.2043   0.0280   0.4331   0.6245

sigma: 0.317137
lambda (gene 1): 0.648869
epsilon (gene 1): 0.202017
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.32
Average acceptance rate among mu[i]'s: 0.6752
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.5944
Maximum acceptance rate among delta[i]'s: 0.8
 
 
Minimum acceptance rate among nu[jk]'s: 0.76
Average acceptance rate among nu[jk]'s: 0.922667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.84
Maximum acceptance rate among theta[k]'s: 0.88
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 18.5343
delta (gene 1): 1.20446
s (cell 1): 1.3798
nu (cell 1): 0.927389
theta (batch 1): 0.714085
betas:   -0.1215  -0.1502   0.0018   0.6359  -0.1468   1.0651  -0.8814   0.4548  -0.1361  -1.0002  -0.2049  -0.0096

sigma: 0.251752
lambda (gene 1): 1.53954
epsilon (gene 1): 0.119676
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 14.1889
delta (gene 1): 1.33933
s (cell 1): 1.73594
nu (cell 1): 0.925327
theta (batch 1): 0.655469
betas:    0.6109  -0.4770   0.8240   0.2665   0.3805   0.1986  -0.0300   0.2450   0.3324   0.0306   0.3288  -0.3239

sigma: 0.209444
lambda (gene 1): 1.08325
epsilon (gene 1): 0.334843
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.1711
delta (gene 1): 0.943706
s (cell 1): 0.453942
nu (cell 1): 0.906057
theta (batch 1): 0.687912
betas:    0.2837  -0.3003   1.3994  -0.0134   0.4715  -0.1288   0.5282   0.2471  -0.8315  -0.0330  -0.0684  -0.2067

sigma: 0.236154
lambda (gene 1): 0.809167
epsilon (gene 1): -0.199496
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 20.292
delta (gene 1): 1.22264
s (cell 1): 0.827296
nu (cell 1): 0.893782
theta (batch 1): 0.527292
betas:    0.1436  -0.3270   0.4339   0.6975  -0.1110   0.8383  -0.0880   0.4675  -0.6774   0.5196   0.1672  -0.2062

sigma: 0.331722
lambda (gene 1): 1.37037
epsilon (gene 1): -0.045675
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 13.7775
delta (gene 1): 1.20188
s (cell 1): 0.760507
nu (cell 1): 0.884977
theta (batch 1): 0.68969
betas:   -0.1300  -0.3571   0.4999   0.8587   0.7262   0.2372   0.0971   0.1637   0.2113  -0.0976   0.3861   0.1082

sigma: 0.216667
lambda (gene 1): 1.51499
epsilon (gene 1): 0.176961
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -10
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.6944
Maximum acceptance rate among mu[i]'s: 0.92
 
 
Minimum acceptance rate among delta[i]'s: 0.36
Average acceptance rate among delta[i]'s: 0.6144
Maximum acceptance rate among delta[i]'s: 0.84
 
 
Minimum acceptance rate among nu[jk]'s: 0.76
Average acceptance rate among nu[jk]'s: 0.946667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.84
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.96
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.88025
delta (gene 1): 1.35453
s (cell 1): 1.24758
nu (cell 1): 0.591016
theta (batch 1): 0.382241
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.30239
delta (gene 1): 1.13589
s (cell 1): 0.952532
nu (cell 1): 0.603502
theta (batch 1): 0.628488
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.12911
delta (gene 1): 1.08339
s (cell 1): 0.544108
nu (cell 1): 0.595019
theta (batch 1): 0.531377
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 2.89422
delta (gene 1): 1.24921
s (cell 1): 0.680775
nu (cell 1): 0.571118
theta (batch 1): 0.589861
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 3.50123
delta (gene 1): 0.995004
s (cell 1): 0.738163
nu (cell 1): 0.543385
theta (batch 1): 0.406926
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSnu (cell 1): -9.04345
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.16
Average acceptance rate among mu[i]'s: 0.693143
Maximum acceptance rate among mu[i]'s: 1
 
 
Minimum acceptance rate among delta[i]'s: 0.48
Average acceptance rate among delta[i]'s: 0.704
Maximum acceptance rate among delta[i]'s: 0.96
 
 
Minimum acceptance rate among nu[jk]'s: 0.8
Average acceptance rate among nu[jk]'s: 0.918667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.88
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.92
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
Iteration 0 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.19861
delta (gene 1): 1.72649
phi (cell 1): 0.959311
s (cell 1): 0.284997
nu (cell 1): 0.189188
theta (batch 1): 0.612703
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 10 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.50062
delta (gene 1): 1.05696
phi (cell 1): 0.954246
s (cell 1): 0.39526
nu (cell 1): 0.190014
theta (batch 1): 0.703926
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 20 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 7.67026
delta (gene 1): 0.817779
phi (cell 1): 0.966748
s (cell 1): 0.424078
nu (cell 1): 0.199087
theta (batch 1): 0.416005
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
-----------------------------------------------------
Iteration 30 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 16.3695
delta (gene 1): 1.13048
phi (cell 1): 0.944188
s (cell 1): 0.73483
nu (cell 1): 0.199107
theta (batch 1): 0.356171
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
-----------------------------------------------------
Iteration 40 out of 50 has been completed.
-----------------------------------------------------
Current draws for selected parameters are displayed below.
mu (gene 1): 9.07619
delta (gene 1): 2.31572
phi (cell 1): 0.953499
s (cell 1): 0.516729
nu (cell 1): 0.193889
theta (batch 1): 0.271176
-----------------------------------------------------
Current proposal variances for Metropolis Hastings updates (log-scale).
LSmu (gene 1): -4
LSdelta (gene 1): -2
LSphi: 11
LSnu (cell 1): -6.80438
LStheta (batch 1): -4
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.56
Average acceptance rate among mu[i]'s: 0.764
Maximum acceptance rate among mu[i]'s: 0.96
 
 
Minimum acceptance rate among delta[i]'s: 0.52
Average acceptance rate among delta[i]'s: 0.7008
Maximum acceptance rate among delta[i]'s: 0.92
 
 
Acceptance rate for phi (joint): 0.96
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.626667
Maximum acceptance rate among nu[j]'s: 0.96
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.76
Maximum acceptance rate among theta[k]'s: 0.76
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.454
Average acceptance rate among mu[i]'s: 0.65608
Maximum acceptance rate among mu[i]'s: 0.834
 
 
Minimum acceptance rate among delta[i]'s: 0.464
Average acceptance rate among delta[i]'s: 0.5502
Maximum acceptance rate among delta[i]'s: 0.714
 
 
Acceptance rate for phi (joint): 0.884
 
 
Minimum acceptance rate among nu[j]'s: 0.44
Average acceptance rate among nu[j]'s: 0.540933
Maximum acceptance rate among nu[j]'s: 0.72
 
 
Minimum acceptance rate among theta[k]'s: 0.75
Average acceptance rate among theta[k]'s: 0.75
Maximum acceptance rate among theta[k]'s: 0.75
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.772
Maximum acceptance rate among mu[i]'s: 0.95
 
 
Minimum acceptance rate among delta[i]'s: 0.5
Average acceptance rate among delta[i]'s: 0.678
Maximum acceptance rate among delta[i]'s: 0.85
 
 
Acceptance rate for phi (joint): 0.95
 
 
Minimum acceptance rate among nu[j]'s: 0.4
Average acceptance rate among nu[j]'s: 0.668333
Maximum acceptance rate among nu[j]'s: 0.85
 
 
Minimum acceptance rate among theta[k]'s: 0.75
Average acceptance rate among theta[k]'s: 0.75
Maximum acceptance rate among theta[k]'s: 0.75
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.432
Average acceptance rate among mu[i]'s: 0.65752
Maximum acceptance rate among mu[i]'s: 0.838
 
 
Minimum acceptance rate among delta[i]'s: 0.388
Average acceptance rate among delta[i]'s: 0.54484
Maximum acceptance rate among delta[i]'s: 0.698
 
 
Acceptance rate for phi (joint): 0.882
 
 
Minimum acceptance rate among nu[j]'s: 0.448
Average acceptance rate among nu[j]'s: 0.530467
Maximum acceptance rate among nu[j]'s: 0.7
 
 
Minimum acceptance rate among theta[k]'s: 0.81
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.848
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.404
Average acceptance rate among mu[i]'s: 0.6282
Maximum acceptance rate among mu[i]'s: 0.83
 
 
Minimum acceptance rate among delta[i]'s: 0.446
Average acceptance rate among delta[i]'s: 0.49484
Maximum acceptance rate among delta[i]'s: 0.576
 
 
Minimum acceptance rate among nu[jk]'s: 0.804
Average acceptance rate among nu[jk]'s: 0.9198
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.786
Average acceptance rate among theta[k]'s: 0.796
Maximum acceptance rate among theta[k]'s: 0.806
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.404
Average acceptance rate among mu[i]'s: 0.6282
Maximum acceptance rate among mu[i]'s: 0.83
 
 
Minimum acceptance rate among delta[i]'s: 0.446
Average acceptance rate among delta[i]'s: 0.49484
Maximum acceptance rate among delta[i]'s: 0.576
 
 
Minimum acceptance rate among nu[jk]'s: 0.804
Average acceptance rate among nu[jk]'s: 0.9198
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.786
Average acceptance rate among theta[k]'s: 0.796
Maximum acceptance rate among theta[k]'s: 0.806
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.4
Average acceptance rate among mu[i]'s: 0.741
Maximum acceptance rate among mu[i]'s: 0.9
 
 
Minimum acceptance rate among delta[i]'s: 0.425
Average acceptance rate among delta[i]'s: 0.6165
Maximum acceptance rate among delta[i]'s: 0.75
 
 
Minimum acceptance rate among nu[jk]'s: 0.85
Average acceptance rate among nu[jk]'s: 0.951667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.8
Average acceptance rate among theta[k]'s: 0.85
Maximum acceptance rate among theta[k]'s: 0.9
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.468
Average acceptance rate among mu[i]'s: 0.65876
Maximum acceptance rate among mu[i]'s: 0.824
 
 
Minimum acceptance rate among delta[i]'s: 0.472
Average acceptance rate among delta[i]'s: 0.54948
Maximum acceptance rate among delta[i]'s: 0.628
 
 
Minimum acceptance rate among nu[jk]'s: 0.862
Average acceptance rate among nu[jk]'s: 0.939133
Maximum acceptance rate among nu[jk]'s: 0.994
 
 
Minimum acceptance rate among theta[k]'s: 0.808
Average acceptance rate among theta[k]'s: 0.81
Maximum acceptance rate among theta[k]'s: 0.812
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.468
Average acceptance rate among mu[i]'s: 0.65876
Maximum acceptance rate among mu[i]'s: 0.824
 
 
Minimum acceptance rate among delta[i]'s: 0.472
Average acceptance rate among delta[i]'s: 0.54948
Maximum acceptance rate among delta[i]'s: 0.628
 
 
Minimum acceptance rate among nu[jk]'s: 0.862
Average acceptance rate among nu[jk]'s: 0.939133
Maximum acceptance rate among nu[jk]'s: 0.994
 
 
Minimum acceptance rate among theta[k]'s: 0.808
Average acceptance rate among theta[k]'s: 0.81
Maximum acceptance rate among theta[k]'s: 0.812
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.61168
Maximum acceptance rate among mu[i]'s: 0.774
 
 
Minimum acceptance rate among delta[i]'s: 0.414
Average acceptance rate among delta[i]'s: 0.4972
Maximum acceptance rate among delta[i]'s: 0.57
 
 
Minimum acceptance rate among nu[jk]'s: 0.792
Average acceptance rate among nu[jk]'s: 0.919867
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.814
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.844
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.44
Average acceptance rate among mu[i]'s: 0.61168
Maximum acceptance rate among mu[i]'s: 0.774
 
 
Minimum acceptance rate among delta[i]'s: 0.414
Average acceptance rate among delta[i]'s: 0.4972
Maximum acceptance rate among delta[i]'s: 0.57
 
 
Minimum acceptance rate among nu[jk]'s: 0.792
Average acceptance rate among nu[jk]'s: 0.919867
Maximum acceptance rate among nu[jk]'s: 0.978
 
 
Minimum acceptance rate among theta[k]'s: 0.814
Average acceptance rate among theta[k]'s: 0.829
Maximum acceptance rate among theta[k]'s: 0.844
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.714
Maximum acceptance rate among mu[i]'s: 0.875
 
 
Minimum acceptance rate among delta[i]'s: 0.425
Average acceptance rate among delta[i]'s: 0.619
Maximum acceptance rate among delta[i]'s: 0.825
 
 
Minimum acceptance rate among nu[jk]'s: 0.85
Average acceptance rate among nu[jk]'s: 0.956667
Maximum acceptance rate among nu[jk]'s: 1
 
 
Minimum acceptance rate among theta[k]'s: 0.875
Average acceptance rate among theta[k]'s: 0.9
Maximum acceptance rate among theta[k]'s: 0.925
 
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 1000 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 1000 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.434
Average acceptance rate among mu[i]'s: 0.60812
Maximum acceptance rate among mu[i]'s: 0.816
 
 
Minimum acceptance rate among delta[i]'s: 0.418
Average acceptance rate among delta[i]'s: 0.52908
Maximum acceptance rate among delta[i]'s: 0.672
 
 
Acceptance rate for phi (joint): 0.87
 
 
Minimum acceptance rate among nu[j]'s: 0.434
Average acceptance rate among nu[j]'s: 0.536733
Maximum acceptance rate among nu[j]'s: 0.712
 
 
Minimum acceptance rate among theta[k]'s: 0.76
Average acceptance rate among theta[k]'s: 0.78
Maximum acceptance rate among theta[k]'s: 0.8
 
-----------------------------------------------------
 
-----------------------------------------------------
MCMC sampler has been started: 50 iterations to go.
-----------------------------------------------------
-----------------------------------------------------
End of Burn-in period.
-----------------------------------------------------
 
-----------------------------------------------------
-----------------------------------------------------
All 50 MCMC iterations have been completed.
-----------------------------------------------------
-----------------------------------------------------
 
-----------------------------------------------------
Please see below a summary of the overall acceptance rates.
-----------------------------------------------------
 
Minimum acceptance rate among mu[i]'s: 0.475
Average acceptance rate among mu[i]'s: 0.758
Maximum acceptance rate among mu[i]'s: 0.95
 
 
Minimum acceptance rate among delta[i]'s: 0.375
Average acceptance rate among delta[i]'s: 0.6405
Maximum acceptance rate among delta[i]'s: 0.775
 
 
Acceptance rate for phi (joint): 0.975
 
 
Minimum acceptance rate among nu[j]'s: 0.45
Average acceptance rate among nu[j]'s: 0.643333
Maximum acceptance rate among nu[j]'s: 0.9
 
 
Minimum acceptance rate among theta[k]'s: 0.875
Average acceptance rate among theta[k]'s: 0.875
Maximum acceptance rate among theta[k]'s: 0.875
 
-----------------------------------------------------
 
new("standardGeneric", .Data = function (x, y, ...) 
standardGeneric("plot"), generic = "plot", package = "graphics", 
    group = list(), valueClass = character(0), signature = c("x", 
    "y"), default = new("derivedDefaultMethod", .Data = function (x, 
        y, ...) 
    UseMethod("plot"), target = new("signature", .Data = "ANY", 
        names = "x", package = "methods"), defined = new("signature", 
        .Data = "ANY", names = "x", package = "methods"), generic = "plot"), 
    skeleton = (new("derivedDefaultMethod", .Data = function (x, 
        y, ...) 
    UseMethod("plot"), target = new("signature", .Data = "ANY", 
        names = "x", package = "methods"), defined = new("signature", 
        .Data = "ANY", names = "x", package = "methods"), generic = "plot"))(x, 
        y, ...))
<environment: 0x0000000005e4a7e8>
attr(,"generic")
[1] "plot"
attr(,"generic")attr(,"package")
[1] "graphics"
attr(,"package")
[1] "graphics"
attr(,"group")
list()
attr(,"valueClass")
character(0)
attr(,"signature")
[1] "x" "y"
attr(,"default")
Method Definition (Class "derivedDefaultMethod"):

function (x, y, ...) 
UseMethod("plot")
<bytecode: 0x0000000005afcd18>
<environment: namespace:graphics>

Signatures:
        x    
target  "ANY"
defined "ANY"
attr(,"skeleton")
(new("derivedDefaultMethod", .Data = function (x, y, ...) 
UseMethod("plot"), target = new("signature", .Data = "ANY", names = "x", 
    package = "methods"), defined = new("signature", .Data = "ANY", 
    names = "x", package = "methods"), generic = "plot"))(x, 
    y, ...)
attr(,"class")
[1] "standardGeneric"
attr(,"class")attr(,"package")
[1] "methods"
== testthat results  ===========================================================
OK: 171 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.70    0.28   34.04

Example timings

BASiCS.Rcheck/examples_i386/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods1.060.001.07
BASiCS_Chain1.610.001.63
BASiCS_D_TestDE0.300.050.54
BASiCS_DenoisedCounts1.440.001.44
BASiCS_DenoisedRates1.310.001.31
BASiCS_DetectHVG_LVG0.170.000.17
BASiCS_Filter0.050.000.05
BASiCS_LoadChain0.590.000.59
BASiCS_MCMC5.640.145.79
BASiCS_Sim0.050.000.04
BASiCS_Summary-methods0.160.000.16
BASiCS_Summary0.610.000.61
BASiCS_TestDE2.530.092.63
BASiCS_VarThresholdSearchHVG_LVG0.210.000.20
BASiCS_VarianceDecomp0.070.020.10
BASiCS_showFit-BASiCS_Chain-method0.400.010.40
Summary-BASiCS_Chain-method0.140.030.17
colnames-BASiCS_Chain-method0.150.000.16
displayChainBASiCS-BASiCS_Chain-method0.160.000.16
displaySummaryBASiCS-BASiCS_Summary-method0.150.020.17
makeExampleBASiCS_Data0.070.000.06
newBASiCS_Chain1.230.001.24
newBASiCS_Data0.170.000.17
plot-BASiCS_Chain-method0.130.030.15
plot-BASiCS_Summary-method0.140.030.18
rownames-BASiCS_Chain-method0.160.000.15
subset-BASiCS_Chain-method0.140.020.16

BASiCS.Rcheck/examples_x64/BASiCS-Ex.timings

nameusersystemelapsed
BASiCS_Chain-methods0.830.020.84
BASiCS_Chain1.390.001.39
BASiCS_D_TestDE0.190.010.20
BASiCS_DenoisedCounts1.340.001.35
BASiCS_DenoisedRates1.270.001.26
BASiCS_DetectHVG_LVG0.140.000.14
BASiCS_Filter0.060.000.07
BASiCS_LoadChain0.600.000.59
BASiCS_MCMC5.700.135.83
BASiCS_Sim0.050.000.04
BASiCS_Summary-methods0.170.000.18
BASiCS_Summary0.760.000.76
BASiCS_TestDE2.460.082.53
BASiCS_VarThresholdSearchHVG_LVG0.150.000.16
BASiCS_VarianceDecomp0.070.010.08
BASiCS_showFit-BASiCS_Chain-method0.390.020.40
Summary-BASiCS_Chain-method0.120.030.16
colnames-BASiCS_Chain-method0.160.000.16
displayChainBASiCS-BASiCS_Chain-method0.140.020.15
displaySummaryBASiCS-BASiCS_Summary-method0.140.010.16
makeExampleBASiCS_Data0.050.000.05
newBASiCS_Chain1.290.001.29
newBASiCS_Data0.160.000.15
plot-BASiCS_Chain-method0.140.020.16
plot-BASiCS_Summary-method0.170.000.17
rownames-BASiCS_Chain-method0.140.010.16
subset-BASiCS_Chain-method0.140.020.16