tra-analysis/analysis-master/tra_analysis/CorrelationTest.py

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tra-analysis v 3.0.0 aggregate PR (#73) * reflected doc changes to README.md Signed-off-by: Arthur Lu <learthurgo@gmail.com> * tra_analysis v 2.1.0-alpha.1 Signed-off-by: Arthur Lu <learthurgo@gmail.com> * changed setup.py to use __version__ from source added Topic and keywords Signed-off-by: Arthur Lu <learthurgo@gmail.com> * updated Supported Platforms in README.md Signed-off-by: Arthur Lu <learthurgo@gmail.com> * moved required files back to parent Signed-off-by: Arthur Lu <learthurgo@gmail.com> * moved security back to parent Signed-off-by: Arthur Lu <learthurgo@gmail.com> * moved security back to parent moved contributing back to parent Signed-off-by: Arthur Lu <learthurgo@gmail.com> * add PR template Signed-off-by: Arthur Lu <learthurgo@gmail.com> * moved to parent folder Signed-off-by: Arthur Lu <learthurgo@gmail.com> * moved meta files to .github folder Signed-off-by: Arthur Lu <learthurgo@gmail.com> * Analysis.py v 3.0.1 Signed-off-by: Arthur Lu <learthurgo@gmail.com> * updated test_analysis for submodules, and added missing numpy import in Sort.py * fixed item one of Issue #58 Signed-off-by: Arthur Lu <learthurgo@gmail.com> * readded cache searching in postCreateCommand Signed-off-by: Arthur Lu <learthurgo@gmail.com> * added myself as an author * feat: created kivy gui boilerplate * added Kivy to requirements.txt Signed-off-by: Arthur Lu <learthurgo@gmail.com> * feat: gui with placeholders * fix: changed config.json path * migrated docker base image to debian Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * style: spaces to tabs * migrated to ubuntu Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * fixed issues Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * fix: docker build? * fix: use ubuntu bionic * fix: get kivy installed * @ltcptgeneral can't spell * optim dockerfile for not installing unused packages * install basic stuff while building the container * use prebuilt image for development * install pylint on base image * rename and use new kivy * tests: added tests for Array and CorrelationTest Both are not working due to errors * use new thing * use 20.04 base * symlink pip3 to pip * use pip instead of pip3 * equation.Expression.py v 0.0.1-alpha added corresponding .pyc to .gitignore * parser.py v 0.0.2-alpha * added pyparsing to requirements.txt * parser v 0.0.4-alpha * Equation v 0.0.1-alpha * added Equation to tra_analysis imports * tests: New unit tests for submoduling (#66) * feat: created kivy gui boilerplate * migrated docker base image to debian Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * migrated to ubuntu Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * fixed issues Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * fix: docker build? * fix: use ubuntu bionic * fix: get kivy installed * @ltcptgeneral can't spell * optim dockerfile for not installing unused packages * install basic stuff while building the container * use prebuilt image for development * install pylint on base image * rename and use new kivy * tests: added tests for Array and CorrelationTest Both are not working due to errors * fix: Array no longer has *args and CorrelationTest functions no longer have self in the arguments * use new thing * use 20.04 base * symlink pip3 to pip * use pip instead of pip3 * tra_analysis v 2.1.0-alpha.2 SVM v 1.0.1 added unvalidated SVM unit tests Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * fixed version number Signed-off-by: ltcptgeneral <learthurgo@gmail.com> * tests: added tests for ClassificationMetric * partially fixed and commented out svm unit tests * fixed some SVM unit tests * added installing pytest to devcontainer.json * fix: small fixes to KNN Namely, removing self from parameters and passing correct arguments to KNeighborsClassifier constructor * fix, test: Added tests for KNN and NaiveBayes. Also made some small fixes in KNN, NaiveBayes, and RegressionMetric * test: finished unit tests except for StatisticalTest Also made various small fixes and style changes * StatisticalTest v 1.0.1 * fixed RegressionMetric unit test temporarily disabled CorrelationTest unit tests * tra_analysis v 2.1.0-alpha.3 * readded __all__ * fix: floating point issues in unit tests for CorrelationTest Co-authored-by: AGawde05 <agawde05@gmail.com> Co-authored-by: ltcptgeneral <learthurgo@gmail.com> Co-authored-by: Dev Singh <dev@devksingh.com> Co-authored-by: jzpan1 <panzhenyu2014@gmail.com> * fixed depreciated escape sequences * ficed tests, indent, import in test_analysis * changed version to 3.0.0 added backwards compatibility * ficed pytest install in container * removed GUI changes Signed-off-by: Arthur Lu <learthurgo@gmail.com> * incremented version to rc.1 (release candidate 1) Signed-off-by: Arthur Lu <learthurgo@gmail.com> * fixed NaiveBayes __changelog__ Signed-off-by: Arthur Lu <learthurgo@gmail.com> * fix: __setitem__ == to single = * Array v 1.0.1 * Revert "Array v 1.0.1" This reverts commit 59783b79f7451586bc9741794589e00f0c625348. * Array v 1.0.1 * Array.py v 1.0.2 added more Array unit tests * cleaned .gitignore tra_analysis v 3.0.0-rc2 Signed-off-by: Arthur Lu <learthurgo@gmail.com> * added *.pyc to gitignore finished subdividing test_analysis * feat: gui layout + basic func * Froze and removed superscript (data-analysis) * remove data-analysis deps install for devcontainer * tukey pairwise comparison and multicomparison but no critical q-values * quick patch for devcontainer.json * better fix for devcontainer.json * fixed some styling in StatisticalTest removed print statement in StatisticalTest unit tests * update analysis tests to be more effecient * don't use loop for test_nativebayes * removed useless secondary docker files * tra-analysis v 3.0.0 Co-authored-by: James Pan <panzhenyu2014@gmail.com> Co-authored-by: AGawde05 <agawde05@gmail.com> Co-authored-by: zpan1 <72054510+zpan1@users.noreply.github.com> Co-authored-by: Dev Singh <dev@devksingh.com> Co-authored-by: = <=> Co-authored-by: Dev Singh <dsingh@imsa.edu> Co-authored-by: zpan1 <zpan@imsa.edu>
2021-04-29 00:33:50 +00:00
# Titan Robotics Team 2022: CorrelationTest submodule
# Written by Arthur Lu
# Notes:
# this should be imported as a python module using 'from tra_analysis import CorrelationTest'
# setup:
__version__ = "1.0.1"
__changelog__ = """changelog:
1.0.1:
- fixed __all__
1.0.0:
- ported analysis.CorrelationTest() here
- removed classness
"""
__author__ = (
"Arthur Lu <learthurgo@gmail.com>",
)
__all__ = [
"anova_oneway",
"pearson",
"spearman",
"point_biserial",
"kendall",
"kendall_weighted",
"mgc",
]
import scipy
from scipy import stats
def anova_oneway(*args): #expects arrays of samples
results = scipy.stats.f_oneway(*args)
return {"f-value": results[0], "p-value": results[1]}
def pearson(x, y):
results = scipy.stats.pearsonr(x, y)
return {"r-value": results[0], "p-value": results[1]}
def spearman(a, b = None, axis = 0, nan_policy = 'propagate'):
results = scipy.stats.spearmanr(a, b = b, axis = axis, nan_policy = nan_policy)
return {"r-value": results[0], "p-value": results[1]}
def point_biserial(x, y):
results = scipy.stats.pointbiserialr(x, y)
return {"r-value": results[0], "p-value": results[1]}
def kendall(x, y, initial_lexsort = None, nan_policy = 'propagate', method = 'auto'):
results = scipy.stats.kendalltau(x, y, initial_lexsort = initial_lexsort, nan_policy = nan_policy, method = method)
return {"tau": results[0], "p-value": results[1]}
def kendall_weighted(x, y, rank = True, weigher = None, additive = True):
results = scipy.stats.weightedtau(x, y, rank = rank, weigher = weigher, additive = additive)
return {"tau": results[0], "p-value": results[1]}
def mgc(x, y, compute_distance = None, reps = 1000, workers = 1, is_twosamp = False, random_state = None):
results = scipy.stats.multiscale_graphcorr(x, y, compute_distance = compute_distance, reps = reps, workers = workers, is_twosamp = is_twosamp, random_state = random_state)
return {"k-value": results[0], "p-value": results[1], "data": results[2]} # unsure if MGC test returns a k value