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@@ -112,6 +112,5 @@ dask-worker-space | |
| # osx | ||
| .DS_Store | ||
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|
||
| # R | ||
| .RData | ||
| .Rhistory | ||
| # Github codespaces | ||
| pythonenv3.8 | ||
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| @@ -1,26 +1,17 @@ | ||
| # Minimal makefile for Sphinx documentation | ||
| # | ||
| install: | ||
| @python setup.py install | ||
|
|
||
| # You can set these variables from the command line. | ||
| SPHINXOPTS = | ||
| SPHINXBUILD = sphinx-build | ||
| SPHINXPROJ = jMetalPy | ||
| SOURCEDIR = docs/source | ||
| BUILDDIR = build | ||
| clean: | ||
| @rm -rf build dist .eggs *.egg-info | ||
| @find . -type d -name '.mypy_cache' -exec rm -rf {} + | ||
| @find . -type d -name '__pycache__' -exec rm -rf {} + | ||
|
|
||
| # Put it first so that "make" without argument is like "make help". | ||
| help: | ||
| @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
| black: clean | ||
| @isort --profile black jmetal/ examples/ | ||
| @black jmetal/ | ||
|
|
||
| .PHONY: help Makefile | ||
| lint: | ||
| @mypy jmetal/ --show-error-codes | ||
|
|
||
| # "make github" option to build gh-pages | ||
| github: | ||
| @make html | ||
| @cp -a $(BUILDDIR)/html/. docs | ||
| @rm -r $(BUILDDIR) | ||
|
|
||
| # Catch-all target: route all unknown targets to Sphinx using the new | ||
| # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). | ||
| %: Makefile | ||
| @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
| tests: | ||
| @python -m unittest discover --quiet |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,68 +1,75 @@ | ||
| from jmetal.lab.experiment import generate_boxplot, generate_latex_tables, compute_mean_indicator, compute_wilcoxon | ||
| from jmetal.lab.experiment import ( | ||
| compute_mean_indicator, | ||
| compute_wilcoxon, | ||
| generate_boxplot, | ||
| generate_latex_tables, | ||
| ) | ||
| from jmetal.lab.statistical_test.bayesian import * | ||
| from jmetal.lab.statistical_test.functions import * | ||
| from jmetal.lab.visualization import CDplot, plot_posterior | ||
|
|
||
| if __name__ == '__main__': | ||
| if __name__ == "__main__": | ||
| # Generate Median & IQR tables | ||
| generate_latex_tables(filename='QualityIndicatorSummary.csv') | ||
| generate_latex_tables(filename="QualityIndicatorSummary.csv") | ||
|
|
||
| # Generate boxplots | ||
| generate_boxplot(filename='QualityIndicatorSummary.csv') | ||
| generate_boxplot(filename="QualityIndicatorSummary.csv") | ||
|
|
||
| # Wilcoxon | ||
| compute_wilcoxon(filename='QualityIndicatorSummary.csv') | ||
| compute_wilcoxon(filename="QualityIndicatorSummary.csv") | ||
|
|
||
| # Statistical lab | ||
|
|
||
| avg = compute_mean_indicator(filename='QualityIndicatorSummary.csv', indicator_name='HV') | ||
| avg = compute_mean_indicator(filename="QualityIndicatorSummary.csv", indicator_name="HV") | ||
| print(avg) | ||
|
|
||
| # Non-parametric test | ||
| print('-------- Sign Test --------') | ||
| print(sign_test(avg[['NSGAII', 'SMPSO']])) | ||
| print('-------- Friedman Test --------') | ||
| print("-------- Sign Test --------") | ||
| print(sign_test(avg[["NSGAII", "SMPSO"]])) | ||
| print("-------- Friedman Test --------") | ||
| print(friedman_test(avg)) | ||
| print('-------- Friedman Aligned Rank Test --------') | ||
| print("-------- Friedman Aligned Rank Test --------") | ||
| print(friedman_aligned_rank_test(avg)) | ||
| print('-------- Quade Test --------') | ||
| print("-------- Quade Test --------") | ||
| print(quade_test(avg)) | ||
|
|
||
| # Post-hoc tests | ||
| print('-------- Friedman Post-Hoc Test --------') | ||
| z, p_val, adj_pval = friedman_ph_test(avg, control=0, apv_procedure='Bonferroni') | ||
| print('z values \n', z) | ||
| print('p-values \n', p_val) | ||
| print('adjusted p-values \n', adj_pval) | ||
| print('-------- Friedman Aligned Rank Post-Hoc Test --------') | ||
| z, p_val, adj_pval = friedman_aligned_ph_test(avg, apv_procedure='Shaffer') | ||
| print('z values \n', z) | ||
| print('p-values \n', p_val) | ||
| print('adjusted p-values \n', adj_pval) | ||
| print('-------- QuadeTest Post-Hoc Test --------') | ||
| z, p_val, adj_pval = quade_ph_test(avg, apv_procedure='Holm') | ||
| print('z values \n', z) | ||
| print('p-values \n', p_val) | ||
| print('adjusted p-values \n', adj_pval) | ||
| print("-------- Friedman Post-Hoc Test --------") | ||
| z, p_val, adj_pval = friedman_ph_test(avg, control=0, apv_procedure="Bonferroni") | ||
| print("z values \n", z) | ||
| print("p-values \n", p_val) | ||
| print("adjusted p-values \n", adj_pval) | ||
| print("-------- Friedman Aligned Rank Post-Hoc Test --------") | ||
| z, p_val, adj_pval = friedman_aligned_ph_test(avg, apv_procedure="Shaffer") | ||
| print("z values \n", z) | ||
| print("p-values \n", p_val) | ||
| print("adjusted p-values \n", adj_pval) | ||
| print("-------- QuadeTest Post-Hoc Test --------") | ||
| z, p_val, adj_pval = quade_ph_test(avg, apv_procedure="Holm") | ||
| print("z values \n", z) | ||
| print("p-values \n", p_val) | ||
| print("adjusted p-values \n", adj_pval) | ||
|
|
||
| # Plot critical distance | ||
|
|
||
| CDplot(avg.T, alpha=0.15, higher_is_better=True) | ||
|
|
||
| print('-------- Bayesian Sign Test --------') | ||
| bst, DProcess = bayesian_sign_test(avg[['NSGAII', 'SMPSO']], rope_limits=[-0.002, 0.002], | ||
| prior_strength=0.5, return_sample=True) | ||
| plot_posterior(DProcess, higher_is_better=True, alg_names=['NSGAII', 'SMPSO']) | ||
| print("-------- Bayesian Sign Test --------") | ||
| bst, DProcess = bayesian_sign_test( | ||
| avg[["NSGAII", "SMPSO"]], rope_limits=[-0.002, 0.002], prior_strength=0.5, return_sample=True | ||
| ) | ||
| plot_posterior(DProcess, higher_is_better=True, alg_names=["NSGAII", "SMPSO"]) | ||
|
|
||
| print('Pr(NSGAII < SMPSO) = %.3f' % bst[0]) | ||
| print('Pr(NSGAII ~= SMPSO) = %.3f' % bst[1]) | ||
| print('Pr(NSGAII > SMPSO) = %.3f' % bst[2]) | ||
| print("Pr(NSGAII < SMPSO) = %.3f" % bst[0]) | ||
| print("Pr(NSGAII ~= SMPSO) = %.3f" % bst[1]) | ||
| print("Pr(NSGAII > SMPSO) = %.3f" % bst[2]) | ||
|
|
||
| print('-------- Bayesian Signed Rank Test --------') | ||
| bst, DProcess = bayesian_signed_rank_test(avg[['NSGAII', 'SMPSO']], rope_limits=[-0.002, 0.002], | ||
| prior_strength=0.5, return_sample=True) | ||
| plot_posterior(DProcess, higher_is_better=True, alg_names=['NSGAII', 'SMPSO']) | ||
| print("-------- Bayesian Signed Rank Test --------") | ||
| bst, DProcess = bayesian_signed_rank_test( | ||
| avg[["NSGAII", "SMPSO"]], rope_limits=[-0.002, 0.002], prior_strength=0.5, return_sample=True | ||
| ) | ||
| plot_posterior(DProcess, higher_is_better=True, alg_names=["NSGAII", "SMPSO"]) | ||
|
|
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| print('Pr(NSGAII < SMPSO) = %.3f' % bst[0]) | ||
| print('Pr(NSGAII ~= SMPSO) = %.3f' % bst[1]) | ||
| print('Pr(NSGAII > SMPSO) = %.3f' % bst[2]) | ||
| print("Pr(NSGAII < SMPSO) = %.3f" % bst[0]) | ||
| print("Pr(NSGAII ~= SMPSO) = %.3f" % bst[1]) | ||
| print("Pr(NSGAII > SMPSO) = %.3f" % bst[2]) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,25 @@ | ||
| from jmetal.algorithm.multiobjective.gde3 import GDE3 | ||
| from jmetal.problem import ZDT1 | ||
| from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file | ||
| from jmetal.util.solution import ( | ||
| print_function_values_to_file, | ||
| print_variables_to_file, | ||
| read_solutions, | ||
| ) | ||
| from jmetal.util.termination_criterion import StoppingByKeyboard | ||
|
|
||
| if __name__ == '__main__': | ||
| if __name__ == "__main__": | ||
| problem = ZDT1() | ||
| problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf') | ||
| problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf") | ||
|
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| algorithm = GDE3( | ||
| problem=problem, | ||
| population_size=100, | ||
| cr=0.5, | ||
| f=0.5, | ||
| termination_criterion=StoppingByKeyboard() | ||
| ) | ||
| algorithm = GDE3(problem=problem, population_size=100, cr=0.5, f=0.5, termination_criterion=StoppingByKeyboard()) | ||
|
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| algorithm.run() | ||
| front = algorithm.get_result() | ||
|
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| # Save results to file | ||
| print_function_values_to_file(front, 'FUN.' + algorithm.label) | ||
| print_variables_to_file(front, 'VAR.'+ algorithm.label) | ||
| print_function_values_to_file(front, "FUN." + algorithm.label) | ||
| print_variables_to_file(front, "VAR." + algorithm.label) | ||
|
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| print(f'Algorithm: ${algorithm.get_name()}') | ||
| print(f'Problem: ${problem.get_name()}') | ||
| print(f'Computing time: ${algorithm.total_computing_time}') | ||
| print(f"Algorithm: ${algorithm.get_name()}") | ||
| print(f"Problem: ${problem.get_name()}") | ||
| print(f"Computing time: ${algorithm.total_computing_time}") |
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