Code

Refactor prof.to.features#84

Code

Merged

hechth merged 166 commits intoRECETOX:masterRECETOX/recetox-aplcms:masterfrom maximskorik:refactor_prof.to.featuresmaximskorik/recetox-aplcms:refactor_prof.to.featuresCopy head branch name to clipboardAug 17, 2022

+2,335-1,487

Commits

Commits on Jul 29, 2022

• setup remote

  wverastegui

  committed
  b006c19

• Update

  wverastegui

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  b099d9e

Commits on Aug 1, 2022

• extracted functions into top level

  hechth

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Commits on Aug 2, 2022

• Refactoring

  wverastegui

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  e573714

• renamed and extracted variables

  hechth

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  91746c2

• Started adding documentation and reworked base.curve variable

  

  root

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  70152c6

• add gaussian test cases

  maximskorik

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• mark a bug

  maximskorik

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  c956608

• change variable

  maximskorik

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  fef6835

• remove nested conditionals

  maximskorik

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  49fa52a

• simplify argument checks

  maximskorik

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  10daab0

• reformat conditionals

  maximskorik

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  af430cf

• change feature-matrix var name

  maximskorik

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  2386d55

• change var name

  maximskorik

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  72238de

• wrap input validation

  maximskorik

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  14fac74

• wrap bandwidth preprocessing

  maximskorik

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  678a330

• add colnames; slice dataframes by colnames

  maximskorik

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  d07b3ae

• add more slicing by colname

  maximskorik

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  55ff10c

• add slicing this.features by colnames

  maximskorik

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  416df7f

• rename nrowa

  maximskorik

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  f70a310

• reformat oneline conditionals

  maximskorik

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  573be8d

• remove redundant assignment

  maximskorik

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  a4a5f97

• rename undescriptive variable

  maximskorik

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• remove fallacious conditional (it's always FALSE)

  maximskorik

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  91c82dc

• Removed compute base curve function

  hechth

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  60119d1

• remove commented out code

  maximskorik

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  091ca25

• Removed parallel code section from test

  hechth

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  572ebaa

• Renamed all.times to delta_rt which is the actual content of the variable and renamed matching function

  hechth

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  145e31f

• wrap gaussian peak computing

  maximskorik

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  bc9b0c9

• simplify iterable

  maximskorik

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  eb24305

Commits on Aug 3, 2022

• rename this

  maximskorik

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  f1ac061

• rename nrow_this and this.inte

  maximskorik

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  16ee586

• remove failing test case

  maximskorik

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  f8342d4

• Added documentation for compute target times and renamed variable

  hechth

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  4b4863c

• adjusted namespace

  hechth

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  c67e22d

• rename this.features

  maximskorik

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  dca7449

• remove empty row

  maximskorik

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  35770aa

• index by colname

  maximskorik

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  6ccafec

• rename variables

  maximskorik

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  72f4519

• Revert "remove redundant assignment"

  Show description for d6f1543
  maximskorik

  committed
  d6f1543

• rename variables

  maximskorik

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  c4fe18a

• reformat with styler

  maximskorik

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  b46d66c

• add more formatting

  maximskorik

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  42b1de5

• extract plotting

  maximskorik

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  0afe180

• add link to remote data

  maximskorik

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  fc7e916

• refactored find.tol.time function

  hechth

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  ee6d1d2

• Further improved documentation and removed unnecessary functions

  hechth

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  8ced53c

Commits on Aug 4, 2022

• Added further documentation and renamed variables

  hechth

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  d520cde

• Fixing other test cases

  hechth

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• added coments

  wverastegui

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• Finalized find.tol.time

  hechth

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  133a1bc

• started find.turn.point

  hechth

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  f7e54ab

• remove outcommented code

  maximskorik

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  00ce47e

• reformat conditionals

  maximskorik

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• reformat conditional

  maximskorik

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• rename plot function

  maximskorik

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  5449b1e

• refactor compute_bounds

  maximskorik

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• add built-in infinite values check

  maximskorik

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  f4f0d3d

• extract to compute_dx

  maximskorik

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  dbc1be0

Commits on Aug 5, 2022

• remove unnecessary conditional

  maximskorik

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  ed76ef1

• slice by colname

  maximskorik

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  c6e1da7

• rename rt_curve

  maximskorik

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  6abf2dc

• extract chr_profile computation

  maximskorik

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  83fcf63

• refactor input to bigauss.mix

  maximskorik

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  7071fbb

• more descriptive rt_range indexing

  maximskorik

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  e81974b

• refactor bigauss.mix

  maximskorik

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  dd5e26b

• roxygenise comments

  maximskorik

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• mark uncovered function

  maximskorik

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• roxygenise comments

  maximskorik

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  1cc32fc

• mark uncovered function

  maximskorik

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  6fed10d

• refactor rev_cum_sum

  maximskorik

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  0dd4a9c

• refactor bounds computation

  maximskorik

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  5cc86aa

• rearrange compute_dx

  maximskorik

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  6c8d82a

• use built-in func for dx computation

  maximskorik

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  4707b23

• use element wise min function for masking

  maximskorik

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  2f50190

• fix wrong threshold computation

  maximskorik

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  957a3b9

• add docstring

  maximskorik

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  126120a

• Adapted to new combine.seq implementation

  hechth

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  fbdd303

• Merge branch 'refactor_prof.to.features' of https://github.com/maximskorik/recetox-aplcms into refactor_prof.to.features

  maximskorik

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• Merge remote-tracking branch 'origin/master' into 74_continue

  hechth

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  e54f576

• Refactored find.turn.point.R

  wverastegui

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• post merge cleanup

  hechth

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  91547dd

• Refactored find.turn.point.R

  wverastegui

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  a5f4c21

Commits on Aug 8, 2022

• fetch upstream recetox-aplcms

  Show description for b68615b
  

  3 peopleauthored
  b68615b

• use built-in pipe

  maximskorik

  committed
  1464c88

• Merge branch 'master' of https://github.com/maximskorik/recetox-aplcms into refactor_prof.to.features

  maximskorik

  committed
  e8ee226

• Merge branch 'refactor_prof.to.features' of https://github.com/maximskorik/recetox-aplcms into refactor_prof.to.features

  maximskorik

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  4de2598

• extract compute_scale

  maximskorik

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  29c0485

• refactored find turn points with pastecs library

  wverastegui

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• final refactorings

  

  root

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  0bdeaf3

• Updated changelog file

  wverastegui

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  824fcae

• updated variable name

  hechth

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• add return statement

  maximskorik

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• Finalized documentation

  hechth

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• Added final documentation sections.

  

  root

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  e5cde42

• Merge branch 'master' into 77_refactor_R_aplcms

  hechth

  authored
  8587a61

• tiny refactor

  hechth

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  3788061

• mode plotting to plot.R

  maximskorik

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  1ae9674

• make onliner

  maximskorik

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• move plot_peak_summary to plot.R

  maximskorik

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• move another plotting to plot.R

  maximskorik

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• move plotting

  maximskorik

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  66d7879

Commits on Aug 9, 2022

• reformatting

  hechth

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• refactor sorting

  maximskorik

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  e44e2c9

• add comment

  maximskorik

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  60086e9

Commits on Aug 10, 2022

• Changed test case to actually check the recovered tables

  

  root

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  01ed54a

• fixed typo

  hechth

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  8beafb4

• Adapted to tibble and properly added rows to dataframes

  hechth

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  4e91d2d

• extracted function to compute cores and starting on fixing hybrid test case

  hechth

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  5db5d2f

• temporarily disabled two step hybrid

  hechth

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  d11743b

• Merge branch 'master' into 74_continue

  hechth

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  215afdc

• Merge branch 'master' of https://github.com/maximskorik/recetox-aplcms into refactor_prof.to.features

  maximskorik

  committed
  63beaed

• add compute_mu_sc from hecht/74_continue

  maximskorik

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  45c120d

• document validate_inputs

  maximskorik

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  5d24c20

• document process_bandwidth

  maximskorik

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  ea72c84

• Merge branch '74_continue' of https://github.com/hechth/recetox-aplcms into refactor_prof.to.features

  maximskorik

  committed
  bbeddbe

• resolve conflicts from recover.weaker

  maximskorik

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  7116111

• add compute_mu_sc_std to prof.to.features

  maximskorik

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  9db30a3

• rename vars

  maximskorik

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  503441a

• try to incorporate compute_mu_sc_std further

  maximskorik

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  d888751

• add documentation

  maximskorik

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  02df343

• move function for plotting to utils

  maximskorik

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  b3b5014

• describe params

  maximskorik

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• remove redundant param

  maximskorik

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  88604a0

Commits on Aug 11, 2022

• Reformatted file and adjusted variable name

  hechth

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  13928c8

• Fixed bug with vscDebugger

  hechth

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  7cd24d9

• Adapted function name to better reflect functionality

  

  root

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  9192974

• Adapted to new variable name

  hechth

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  7c8c114

• added r-httpgd package for plotting

  hechth

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  4f3cec6

• Reverted to refactored version without turnpoint(). Updated changelog file.

  wverastegui

  committed
  96c64ae

• Merge branch 'master' into 77_refactor_R_aplcms

  hechth

  authored
  e4b9d3c

• Update conda/environment-dev.yaml

  hechth

  authored
  9df570d

• Update conda/meta.yaml

  hechth

  authored
  fa06229

• document compute_chromatographic_profile

  maximskorik

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  9fbe94b

• document bigauss.esti

  maximskorik

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  39e45e8

• add comment and remove redundant argument

  maximskorik

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  77fea0a

• replace order with sort

  maximskorik

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  830932f

• document bigauss.mix

  maximskorik

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  106f675

• extract initiation step

  maximskorik

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  eefb795

• reuse compute_dx

  maximskorik

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  9f73188

• fix compute_mu_sc_std usage

  maximskorik

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  7937e44

• extract e-step computation

  maximskorik

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• document normix; remove unused arg

  maximskorik

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  82b49bf

Commits on Aug 12, 2022

• Update DESCRIPTION

  hechth

  authored
  852e2c9

• fixed adjust.time, feature.align and extract_features test cases

  hechth

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  79aa394

• document normix.bic

  maximskorik

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  a037131

• add punctuation

  maximskorik

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  878dd6f

• fixed unsupervised and hybrid test cases

  hechth

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  c354bdc

• add docs; add more descriptive varname

  maximskorik

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  ac41bcb

• complete compute_gaussian_peak_shape docs

  maximskorik

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  ceb2927

• mark uncovered functions

  maximskorik

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  1ab7709

• Added missing function exports

  hechth

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  054f62f

• add more docstrings

  maximskorik

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• capitalize first words of docs

  maximskorik

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  0cfaaf4

• update NAMESPACE

  maximskorik

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• change argname

  maximskorik

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• change to proper argname

  maximskorik

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  c0bd74f

Commits on Aug 16, 2022

• Merge branch '74_continue' into 77_refactor_R_aplcms

  hechth

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  f84f147

• addressed comment

  hechth

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  6c7cf2f

• pinned r-arrow version as 9.0.0 fails

  hechth

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  05c213a

• moved arrange out of loop

  hechth

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  51fa953

• reverted change

  hechth

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  804f16b

• Fixed extract features and unsupervised test case

  hechth

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  952b7d9

• Fixed documentation

  hechth

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  bbf3237

• Merge branch '77_refactor_R_aplcms' into refactor_prof.to.features

  hechth

  committed
  8bb7965

Commits on Aug 17, 2022

• Added export statements

  hechth

  committed
  d37acc5