##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ELViS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ELViS_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ELViS.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELViS/DESCRIPTION’ ... OK
* this is package ‘ELViS’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘ELViS’ can be installed ... OK
* checking installed package size ... OK
* 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 code 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 whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
run_ELViS           20.464  0.389  22.331
integrative_heatmap 15.466  0.522  16.777
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ELViS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘ELViS’ ...
** this is package ‘ELViS’ version ‘1.3.0’
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ELViS)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(ELViS)
> 
> test_check("ELViS")
ELViS run starts.
1

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
1| done
2

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
2| done
3

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
4| done
5

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
5| done
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
3| done
4| done
5| done
6| done
1

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
1| done
2

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
2| done
3

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
4| done
5

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
5| done
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
3| done
4| done
5| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
6| done
Normalization done.

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4| done
5| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done
1
1
2
2
3
3
4
4
5
5
6
6
Segmentation done.
ELViS run starts.
1

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
1| done
2

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
2| done
3

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
4| done
5

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
5| done
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
3| done
4| done
5| done
6| done
1

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
1| done
2

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
2| done
3

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
4| done
5

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
5| done
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
3| done
4| done
5| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
6| done
Normalization done.

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4| done
5| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done
1
1
2
2
3
3
4
4
5
5
6
6
Segmentation done.
1

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
1| done
2

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
2| done
3

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
3| done
4

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
4| done
5

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
5| done
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
! Argument ncluster was not provided. Selecting values with BIC
i BIC-selected number of class : ncluster = 2
BIC-selected number of segment : nseg = 2
3| done
4| done
5| done
6| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
1| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
2| done

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using ncluster = 2L
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
! Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running Segmentation/Clustering algorithm -----------------------------------
i Running Segmentation/Clustering with lmin = 5, Kmax = 3 and ncluster = 2L
> Calculating initial segmentation without clustering
v Initial segmentation with no cluster calculated.
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
-- Segmentation/Clustering with ncluster = 2 
> Calculating initial segmentation without clustering
> Calculating initial segmentation without clustering
> Segmentation-Clustering for ncluster = 2 and nseg = 2/3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
v Segmentation-Clustering successful for ncluster = 2 and nseg = 2:3
> Segmentation-Clustering for ncluster = 2 and nseg = 3/3
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
v Smoothing successful for ncluster = 2
> Smoothing likelihood for ncluster = 2. This step can be lengthy.
> Calculating initial segmentation without clustering
v Segmentation/Clustering with ncluster = 2 successfully calculated.
BIC selected : nseg = 2
> Calculating initial segmentation without clustering
-- Segmentation/Clustering results ---------------------------------------------
v Best segmentation/clustering estimated with 2 clusters and 2 segments according to BIC
> Number of cluster should preferentially be selected according to biological
knowledge. Exploring the BIC plot with plot_BIC() can also provide advice to
select the number of clusters.
> Once number of clusters is selected, the number of segment cab be selected
according to BIC.
> Results of the segmentation/clustering may further be explored with plot()
and segmap()
3| done
4| done
5| done
6| done
1
1
2
2
3
3
4
4
5
5
6
6

-- Checking arguments ----------------------------------------------------------
v Segmentation with seg.var = c("z", "y")
v Using lmin = 300
v Using Kmax = 10
v Using scale.variable = FALSE
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("z", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "z"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
v Using subsample_by = 60
v subsampling by 60
v Adjusting lmin to subsampling. 
Dividing lmin by 60, with a minimum of 5
> After subsampling, lmin = 5. 
Corresponding to lmin = 300 on the original time scale
v Adjusting Kmax so that lmin*Kmax < nrow(x). Kmax = 3

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 3
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 3
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 2 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
n_cycle : 1
N_alt_ori
n_cycle : 1
N_alt_ori
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_auto/bin/samtools
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_auto/bin/samtools
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_1.21/bin/samtools
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_1.21/bin/samtools
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_1.21/bin/samtools
The path to samtools not provided.
Default samtools is used : /Users/biocbuild/Library/r-miniconda-arm64/envs/env_samtools_1.21/bin/samtools

-- Checking arguments ----------------------------------------------------------
! Argument seg.var missing
taking default value seg.var = c("x","y")
v Segmentation with seg.var = c("x", "y")
v Using lmin = 5
v Using Kmax = 2
! Argument scale.variable missing
Taking default value scale.variable = FALSE for segmentation().
i Argument diag.var was not provided
Taking default seg.var as diagnostic variables diag.var.
Setting diag.var = c("x", "y")
i Argument order.var was not provided
Taking default diag.var[1] as ordering variable order.var.
Setting order.var = "x"

-- Preparing and checking data -------------------------------------------------

-- Subsampling --

! Subsampling automatically activated. To disable it, provide subsample = FALSE
i Argument subsample_over was not provided
Taking default value for segmentation()
Setting subsample_over = 10000
v nrow(x) < subsample_over, no subsample needed

-- Scaling and final data check --

v No variable rescaling.
To activate, use scale.variable = TRUE
v Data have no repetition of nearly-identical values larger than lmin

-- Running segmentation algorithm ----------------------------------------------
i Running segmentation with lmin = 5 and Kmax = 2
> Calculating cost matrix
v Cost matrix calculated
> Calculating cost matrix
> Dynamic Programming
v Optimal segmentation calculated for all number of segments <= 2
> Dynamic Programming
> Calculating segment statistics
v Best segmentation estimated with 1 segments, according to Lavielle's criterium
Other number of segments may be selected by looking for likelihood breaks with
plot_likelihood()
Results of the segmentation may be explored with plot() and segmap()
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 101 ]
> 
> proc.time()
   user  system elapsed 
 17.546   1.017  19.919