Package: BASiCS

Version: 1.4.7

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BASiCS_1.4.7.tar.gz

StartedAt: 2019-04-15 22:20:24 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:25:02 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 278.4 seconds

RetCode: 0

Status:  OK

CheckDir: BASiCS.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings BASiCS_1.4.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/BASiCS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BASiCS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  10.8Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
BASiCS_MCMC 7.396   0.16   7.646
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/BASiCS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL BASiCS
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘BASiCS’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c general_utils.cpp -o general_utils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -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++) {
                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -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++) {
                  ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2 -Wall -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++) {
                     ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o BASiCS.so 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 -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/BASiCS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BASiCS)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(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
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: 0x18805a0>
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: 0x1eaf2a8>
<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 
 41.172   0.456  41.811 

name	user	system	elapsed
BASiCS_Chain-methods	1.604	0.000	1.669
BASiCS_Chain	1.608	0.004	1.616
BASiCS_D_TestDE	0.196	0.044	0.578
BASiCS_DenoisedCounts	1.596	0.092	1.710
BASiCS_DenoisedRates	1.508	0.000	1.506
BASiCS_DetectHVG_LVG	0.156	0.036	0.210
BASiCS_Filter	0.092	0.004	0.102
BASiCS_LoadChain	0.764	0.108	0.880
BASiCS_MCMC	7.396	0.160	7.646
BASiCS_Sim	0.120	0.028	0.186
BASiCS_Summary-methods	0.168	0.048	0.234
BASiCS_Summary	0.980	0.084	1.092
BASiCS_TestDE	3.292	0.088	3.396
BASiCS_VarThresholdSearchHVG_LVG	0.160	0.036	0.211
BASiCS_VarianceDecomp	0.088	0.008	0.100
BASiCS_showFit-BASiCS_Chain-method	0.504	0.044	0.551
Summary-BASiCS_Chain-method	0.148	0.056	0.272
colnames-BASiCS_Chain-method	0.168	0.052	0.289
displayChainBASiCS-BASiCS_Chain-method	0.136	0.056	0.244
displaySummaryBASiCS-BASiCS_Summary-method	0.152	0.052	0.244
makeExampleBASiCS_Data	0.092	0.000	0.091
newBASiCS_Chain	1.680	0.128	1.809
newBASiCS_Data	0.244	0.000	0.244
plot-BASiCS_Chain-method	0.164	0.040	0.211
plot-BASiCS_Summary-method	0.172	0.044	0.267
rownames-BASiCS_Chain-method	0.164	0.052	0.266
subset-BASiCS_Chain-method	0.176	0.048	0.247