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[ENH] Adds PLS example datasets #44

Merged
merged 32 commits into from
Sep 26, 2019
Merged

[ENH] Adds PLS example datasets #44

merged 32 commits into from
Sep 26, 2019

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rmarkello
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Begins to include example datasets for performing PLS and showcasing the different flavors / types. Will be a work-in-progress for a while, as the goal is to have these for the user documentation (#19).

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coveralls commented Dec 11, 2018

Coverage Status

Coverage decreased (-0.6%) to 97.551% when pulling 98aeb96 on examples into e750ee1 on master.

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codecov-io commented Dec 17, 2018

Codecov Report

Merging #44 into master will decrease coverage by 0.6%.
The diff coverage is 92.08%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #44      +/-   ##
==========================================
- Coverage   98.16%   97.55%   -0.61%     
==========================================
  Files          21       24       +3     
  Lines        1087     1184      +97     
==========================================
+ Hits         1067     1155      +88     
- Misses         20       29       +9
Impacted Files Coverage Δ
pyls/info.py 100% <ø> (ø) ⬆️
pyls/io.py 95% <ø> (ø) ⬆️
pyls/types/meancentered.py 100% <ø> (ø) ⬆️
pyls/types/behavioral.py 97.05% <ø> (ø) ⬆️
pyls/matlab/__init__.py 100% <100%> (ø) ⬆️
pyls/base.py 95.87% <100%> (+0.78%) ⬆️
pyls/__init__.py 100% <100%> (ø) ⬆️
pyls/structures.py 100% <100%> (ø) ⬆️
pyls/tests/test_examples.py 100% <100%> (ø)
pyls/examples/__init__.py 100% <100%> (ø)
... and 7 more

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@rmarkello rmarkello force-pushed the examples branch 2 times, most recently from 5967325 to 127331f Compare December 18, 2018 21:35
Including functions for loading example datasets and structure for
adding new examples
Found the URLs required! Will need to rethink how I want to do this
since the FC data are all separate files and the behavioral data
requires some wrangling...
Now fully loadable (files uploaded to Dropbox -- will have to host
scripts for creation elsewhere).
As well as ability to query that information with `query_dataset()`
Can just use urllib for the little that we need
Have to use np.genfromtxt with CSV files that would otherwise be loaded
with pandas (if pandas isn't available).
Wasn't testing a few lines of code that really should have been
tested...
Independently zscores (not scipy.stats.zscore) to retain input data
structures (e.g., pandas dataframes). Good for documentation
demonstration purposes to show cross-correlation matrices.

Minor update to compute.efficient_corr to use np.clip, as well.
Still very much a WIP, but...coming along to a degree?
Some minor maintenance that makes working with the documentation a bit
easier (e.g., 'make clean html') and some updates to the user guide!
@rmarkello rmarkello changed the title [WIP, ENH] Adds PLS example datasets [ENH] Adds PLS example datasets Sep 26, 2019
@rmarkello rmarkello merged commit b433d7e into master Sep 26, 2019
@rmarkello rmarkello deleted the examples branch September 26, 2019 13:28
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3 participants