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Refactor prof.to.features #84
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hechth
merged 166 commits into
RECETOX:master
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maximskorik:refactor_prof.to.features
Aug 17, 2022
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b006c19
setup remote
wverastegui b099d9e
Update
wverastegui ae0be7d
extracted functions into top level
hechth e573714
Refactoring
wverastegui 91746c2
renamed and extracted variables
hechth 70152c6
Started adding documentation and reworked base.curve variable
7e93cb6
add gaussian test cases
maximskorik c956608
mark a bug
maximskorik fef6835
change variable
maximskorik 49fa52a
remove nested conditionals
maximskorik 10daab0
simplify argument checks
maximskorik af430cf
reformat conditionals
maximskorik 2386d55
change feature-matrix var name
maximskorik 72238de
change var name
maximskorik 14fac74
wrap input validation
maximskorik 678a330
wrap bandwidth preprocessing
maximskorik d07b3ae
add colnames; slice dataframes by colnames
maximskorik 55ff10c
add more slicing by colname
maximskorik 416df7f
add slicing `this.features` by colnames
maximskorik f70a310
rename `nrowa`
maximskorik 573be8d
reformat oneline conditionals
maximskorik a4a5f97
remove redundant assignment
maximskorik 5390232
rename undescriptive variable
maximskorik 91c82dc
remove fallacious conditional (it's always FALSE)
maximskorik 60119d1
Removed compute base curve function
hechth 091ca25
remove commented out code
maximskorik 572ebaa
Removed parallel code section from test
hechth 145e31f
Renamed all.times to delta_rt which is the actual content of the vari…
hechth bc9b0c9
wrap gaussian peak computing
maximskorik eb24305
simplify iterable
maximskorik f1ac061
rename `this`
maximskorik 16ee586
rename `nrow_this` and `this.inte`
maximskorik f8342d4
remove failing test case
maximskorik 4b4863c
Added documentation for compute target times and renamed variable
hechth c67e22d
adjusted namespace
hechth dca7449
rename `this.features`
maximskorik 35770aa
remove empty row
maximskorik 6ccafec
index by colname
maximskorik 72f4519
rename variables
maximskorik d6f1543
Revert "remove redundant assignment"
maximskorik c4fe18a
rename variables
maximskorik b46d66c
reformat with `styler`
maximskorik 42b1de5
add more formatting
maximskorik 0afe180
extract plotting
maximskorik fc7e916
add link to remote data
maximskorik ee6d1d2
refactored find.tol.time function
hechth 8ced53c
Further improved documentation and removed unnecessary functions
hechth d520cde
Added further documentation and renamed variables
hechth 9004c22
Fixing other test cases
hechth a49291d
added coments
wverastegui 133a1bc
Finalized find.tol.time
hechth f7e54ab
started find.turn.point
hechth 00ce47e
remove outcommented code
maximskorik e62fc9f
reformat conditionals
maximskorik 8d899c0
reformat conditional
maximskorik 5449b1e
rename `plot` function
maximskorik 1550e82
refactor `compute_bounds`
maximskorik f4f0d3d
add built-in infinite values check
maximskorik dbc1be0
extract to `compute_dx`
maximskorik ed76ef1
remove unnecessary conditional
maximskorik c6e1da7
slice by colname
maximskorik 6abf2dc
rename `rt_curve`
maximskorik 83fcf63
extract `chr_profile` computation
maximskorik 7071fbb
refactor input to `bigauss.mix`
maximskorik e81974b
more descriptive `rt_range` indexing
maximskorik dd5e26b
refactor `bigauss.mix`
maximskorik 4053a31
roxygenise comments
maximskorik fa5141c
mark uncovered function
maximskorik 1cc32fc
roxygenise comments
maximskorik 6fed10d
mark uncovered function
maximskorik 0dd4a9c
refactor `rev_cum_sum`
maximskorik 5cc86aa
refactor bounds computation
maximskorik 6c8d82a
rearrange `compute_dx`
maximskorik 4707b23
use built-in func for dx computation
maximskorik 2f50190
use element wise min function for masking
maximskorik 957a3b9
fix wrong threshold computation
maximskorik 126120a
add docstring
maximskorik fbdd303
Adapted to new combine.seq implementation
hechth 0da9aa5
Merge branch 'refactor_prof.to.features' of https://github.com/maxims…
maximskorik e54f576
Merge remote-tracking branch 'origin/master' into 74_continue
hechth e93a9d3
Refactored find.turn.point.R
wverastegui 91547dd
post merge cleanup
hechth a5f4c21
Refactored find.turn.point.R
wverastegui b68615b
fetch upstream recetox-aplcms
maximskorik 1464c88
use built-in pipe
maximskorik e8ee226
Merge branch 'master' of https://github.com/maximskorik/recetox-aplcm…
maximskorik 4de2598
Merge branch 'refactor_prof.to.features' of https://github.com/maxims…
maximskorik 29c0485
extract `compute_scale`
maximskorik 75b39a1
refactored find turn points with pastecs library
wverastegui 0bdeaf3
final refactorings
824fcae
Updated changelog file
wverastegui 821bb9a
updated variable name
hechth 2b642b0
add return statement
maximskorik 8e1f381
Finalized documentation
hechth e5cde42
Added final documentation sections.
8587a61
Merge branch 'master' into 77_refactor_R_aplcms
hechth 3788061
tiny refactor
hechth 1ae9674
mode plotting to plot.R
maximskorik 5372762
make onliner
maximskorik daf8f70
move `plot_peak_summary` to plot.R
maximskorik 0eb8d57
move another plotting to plot.R
maximskorik 66d7879
move plotting
maximskorik 9c3df64
reformatting
hechth e44e2c9
refactor sorting
maximskorik 60086e9
add comment
maximskorik 01ed54a
Changed test case to actually check the recovered tables
8beafb4
fixed typo
hechth 4e91d2d
Adapted to tibble and properly added rows to dataframes
hechth 5db5d2f
extracted function to compute cores and starting on fixing hybrid tes…
hechth d11743b
temporarily disabled two step hybrid
hechth 215afdc
Merge branch 'master' into 74_continue
hechth 63beaed
Merge branch 'master' of https://github.com/maximskorik/recetox-aplcm…
maximskorik 45c120d
add compute_mu_sc from `hecht/74_continue`
maximskorik 5d24c20
document `validate_inputs`
maximskorik ea72c84
document `process_bandwidth`
maximskorik bbeddbe
Merge branch '74_continue' of https://github.com/hechth/recetox-aplcm…
maximskorik 7116111
resolve conflicts from `recover.weaker`
maximskorik 9db30a3
add `compute_mu_sc_std` to `prof.to.features`
maximskorik 503441a
rename vars
maximskorik d888751
try to incorporate `compute_mu_sc_std` further
maximskorik 02df343
add documentation
maximskorik b3b5014
move function for plotting to utils
maximskorik 46f5532
describe params
maximskorik 88604a0
remove redundant param
maximskorik 13928c8
Reformatted file and adjusted variable name
hechth 7cd24d9
Fixed bug with vscDebugger
hechth 9192974
Adapted function name to better reflect functionality
7c8c114
Adapted to new variable name
hechth 4f3cec6
added r-httpgd package for plotting
hechth 96c64ae
Reverted to refactored version without turnpoint(). Updated changelog…
wverastegui e4b9d3c
Merge branch 'master' into 77_refactor_R_aplcms
hechth 9df570d
Update conda/environment-dev.yaml
hechth fa06229
Update conda/meta.yaml
hechth 9fbe94b
document `compute_chromatographic_profile`
maximskorik 39e45e8
document `bigauss.esti`
maximskorik 77fea0a
add comment and remove redundant argument
maximskorik 830932f
replace `order` with `sort`
maximskorik 106f675
document `bigauss.mix`
maximskorik eefb795
extract initiation step
maximskorik 9f73188
reuse `compute_dx`
maximskorik 7937e44
fix `compute_mu_sc_std` usage
maximskorik c9932de
extract e-step computation
maximskorik 82b49bf
document `normix`; remove unused arg
maximskorik 852e2c9
Update DESCRIPTION
hechth 79aa394
fixed adjust.time, feature.align and extract_features test cases
hechth a037131
document `normix.bic`
maximskorik 878dd6f
add punctuation
maximskorik c354bdc
fixed unsupervised and hybrid test cases
hechth ac41bcb
add docs; add more descriptive varname
maximskorik ceb2927
complete `compute_gaussian_peak_shape` docs
maximskorik 1ab7709
mark uncovered functions
maximskorik 054f62f
Added missing function exports
hechth 54ff3c0
add more docstrings
maximskorik 0cfaaf4
capitalize first words of docs
maximskorik 38bec5b
update NAMESPACE
maximskorik fd19277
change argname
maximskorik c0bd74f
change to proper argname
maximskorik f84f147
Merge branch '74_continue' into 77_refactor_R_aplcms
hechth 6c7cf2f
addressed comment
hechth 05c213a
pinned r-arrow version as 9.0.0 fails
hechth 51fa953
moved arrange out of loop
hechth 804f16b
reverted change
hechth 952b7d9
Fixed extract features and unsupervised test case
hechth bbf3237
Fixed documentation
hechth 8bb7965
Merge branch '77_refactor_R_aplcms' into refactor_prof.to.features
hechth d37acc5
Added export statements
hechth File filter
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It is actually called
magrittr
and there is a new R pipe operator|>
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Forgot about that one. Replaced with
|>
in 1464c88.