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[NET-193] Fix for ResultRank tests #40

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pollaro merged 3 commits into from
Jun 25, 2024
Merged

[NET-193] Fix for ResultRank tests #40

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2f1e7a6
fix for result rank tests
pollaro Jun 25, 2024
4a32274
finally found all errors
pollaro Jun 25, 2024
106e402
another test fix
pollaro Jun 25, 2024
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72 changes: 40 additions & 32 deletions +nla/+net/ResultRank.m
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Original file line number Diff line number Diff line change
Expand Up @@ -27,75 +27,83 @@
function ranking_result = rank(obj)
import nla.TriMatrix nla.TriMatrixDiag

ranking_result = obj.permuted_network_results.copy();

for test_type = obj.permuted_network_results.test_methods
if ~isequal(test_type, "no_permutations") || ~isequal(obj.permuted_network_results.test_display_name, "Cohen's D")
if ~isequal(test_type, "no_permutations") && ~isequal(obj.permuted_network_results.test_display_name, "Cohen's D")

[ranking_statistic, probability, denominator] = obj.getTestParameters(test_type);
permutation_results = obj.permuted_network_results.permutation_results;
no_permutation_results = obj.permuted_network_results.no_permutations;
no_permutation_results = obj.nonpermuted_network_results;

% Eggebrecht ranking
obj.eggebrechtRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator)
ranking_result = obj.eggebrechtRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking_result);

if ~isequal(obj.permuted_network_results.test_name, "hypergeometric")
% Winkler Method ranking
obj.permuted_network_results.(test_type).winkler_p_value = TriMatrix(...
ranking_result.(test_type).winkler_p_value = TriMatrix(...
obj.number_of_networks, TriMatrixDiag.KEEP_DIAGONAL...
);
obj.winklerMethodRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator);
ranking_result = obj.winklerMethodRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking_result);

% Westfall Young ranking
obj.permuted_network_results.(test_type).westfall_young_p_value = TriMatrix(...
ranking_result.(test_type).westfall_young_p_value = TriMatrix(...
obj.number_of_networks, TriMatrixDiag.KEEP_DIAGONAL...
);
obj.westfallYoungMethodRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator);
ranking_result = obj.westfallYoungMethodRank(test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking_result);
end
end
end

ranking_result = obj.permuted_network_results.copy();
end

function eggebrechtRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator)
function ranking = eggebrechtRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking)

for index = 1:numel(no_permutation_results.(probability).v)
combined_probabilities = [...
permutation_results.(strcat(probability, "_permutations")).v(:);...
no_permutation_results.(probability).v(index)...
];
if isequal(test_type, "full_connectome")
combined_probabilities = [...
permutation_results.(strcat((probability), "_permutations")).v(:);...
no_permutation_results.(probability).v(index)...
];
else
combined_probabilities = [...
permutation_results.(strcat((probability), "_permutations")).v(index, :),...
no_permutation_results.(probability).v(index)...
];
end
[~, sorted_combined_probabilites] = sort(combined_probabilities);
obj.permuted_network_results.(test_type).p_value.v(index) = find(...
ranking.(test_type).(probability).v(index) = find(...
squeeze(sorted_combined_probabilites) == 1 + denominator...
) / (1 + denominator);

if ~isequal(obj.permuted_network_results.test_name, "hypergeometric")
combined_statistics = [permutation_results.(strcat(ranking_statistic, "_permutations")).v(:); no_permutation_results.(ranking_statistic).v(index)];
combined_statistics = [permutation_results.(strcat((ranking_statistic), "_permutations")).v(:); no_permutation_results.(ranking_statistic).v(index)];
[~, sorted_combined_statistics] = sort(combined_statistics);
obj.permuted_network_results.(test_type).statistic_p_value.v(index) = find(...
ranking.(test_type).(strcat("statistic_", (probability))).v(index) = find(...
squeeze(sorted_combined_statistics) == 1 + denominator...
) / (1 + denominator);
end
end
end

function winklerMethodRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator)
function ranking = winklerMethodRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking)

max_statistic_array = max(abs(permutation_results.(strcat(ranking_statistic, "_permutations")).v));
for index = 1:numel(no_permutation_results.(probability).v)
obj.permuted_network_results.(test_type).winkler_p_value.v(index) = sum(...
ranking.(test_type).winkler_p_value.v(index) = sum(...
squeeze(max_statistic_array) >= abs(no_permutation_results.(ranking_statistic).v(index))...
);
end
obj.permuted_network_results.(test_type).winkler_p_value.v =...
obj.permuted_network_results.(test_type).winkler_p_value.v ./ denominator;
ranking.(test_type).winkler_p_value.v =...
ranking.(test_type).winkler_p_value.v ./ denominator;
end

function westfallYoungMethodRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator)
function ranking = westfallYoungMethodRank(obj, test_type, permutation_results, no_permutation_results, ranking_statistic,...
probability, denominator, ranking)

% sort statistics in ascending order
[sorted_no_permutation_results, sorted_statistic_indexes] = sort(...
Expand All @@ -117,10 +125,10 @@ function westfallYoungMethodRank(obj, test_type, permutation_results, no_permuta
end
max_per_permutation_reducing_rows(1, :) = permutations_sorted_by_non_permuted(1, :);

obj.permuted_network_results.(test_type).westfall_young.p_value.v = mean(...
ranking.(test_type).westfall_young.p_value.v = mean(...
sorted_no_permutation_results < max_per_permutation_reducing_rows, 2);
obj.permuted_network_results.(test_type).westfall_young.p_value.v(sorted_statistic_indexes) =...
obj.permuted_network_results.(test_type).westfall_young.p_value.v;
ranking.(test_type).westfall_young.p_value.v(sorted_statistic_indexes) =...
ranking.(test_type).westfall_young.p_value.v;
end

function [ranking_statistic, probability, denominator] = getTestParameters(obj, test_type)
Expand All @@ -129,7 +137,7 @@ function westfallYoungMethodRank(obj, test_type, permutation_results, no_permuta
probability = "p_value";
denominator = obj.permutations * obj.number_of_network_pairs;
% Only use these for within network pair and not Chi-Squared and Hypergeometric.
if test_type == "within_network_pair" && ~any(...
if isequal(test_type, "within_network_pair") && ~any(...
strcmp(obj.permuted_network_results.test_name, obj.permuted_network_results.noncorrelation_input_tests)...
)
ranking_statistic = strcat("single_sample_", ranking_statistic);
Expand Down
2 changes: 1 addition & 1 deletion +nla/+net/unittests/NetworkTestResultTestCase.m
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ function loadInputData(testCase)
testCase.number_of_networks = 15;
testCase.test_data = TriMatrix(testCase.number_of_networks, TriMatrixDiag.KEEP_DIAGONAL);
testCase.test_data.v = rand(size(testCase.test_data.v));
testCase.test_options = struct("within_net_pair", true, "full_conn", true, "nonpermuted", true);
testCase.test_options = struct("within_network_pair", true, "full_connectome", true, "no_permutations", true);
testCase.test = WilcoxonTest();
end
end
Expand Down
22 changes: 9 additions & 13 deletions +nla/+net/unittests/ResultRankTestCase.m
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,8 @@ function loadInputData(testCase)
testCase.network_test_options.d_max = 0.5;
testCase.network_test_options.prob_plot_method = nla.gfx.ProbPlotMethod.DEFAULT;
testCase.network_test_options.full_connectome = true;
testCase.network_test_options.within_net_pair = true;
testCase.network_test_options.nonpermuted = true;
testCase.network_test_options.within_network_pair = true;
testCase.network_test_options.no_permutations = true;

% Basically have to do everything in the TestPool except run the ranking. So, that's what all this is, everything
% in TestPool.runPerm up until ranking. Luckily, we're only doing one network test
Expand All @@ -99,21 +99,17 @@ function loadInputData(testCase)

methods (Test)
function fullConnectomeRankTest(testCase)
result_ranker = nla.net.ResultRank(testCase.network_test_result{1}, testCase.permuted_network_results{1},...
testCase.number_of_network_pairs);
ranking = testCase.permuted_network_results{1}.copy();
ranking = result_ranker.fullConnectomeRank(ranking, testCase.permuted_network_results{1}.ranking_statistic);
result_ranker = nla.net.ResultRank(testCase.permuted_network_results{1}, testCase.number_of_network_pairs);
rank_object = result_ranker.rank();

testCase.verifyEqual(ranking.full_connectome.p_value.v, testCase.ranking.full_connectome.p_value.v);
testCase.verifyEqual(rank_object.full_connectome.p_value.v, testCase.ranking.full_connectome.p_value.v);
end

function withinNetworkPairTest(testCase)
result_ranker = nla.net.ResultRank(testCase.network_test_result{1}, testCase.permuted_network_results{1},...
testCase.number_of_network_pairs);
ranking = testCase.permuted_network_results{1}.copy();
ranking = result_ranker.withinNetworkPairRank(ranking, testCase.permuted_network_results{1}.ranking_statistic);

testCase.verifyEqual(ranking.within_network_pair.p_value.v, testCase.ranking.within_network_pair.p_value.v);
result_ranker = nla.net.ResultRank(testCase.permuted_network_results{1}, testCase.number_of_network_pairs);
rank_object = result_ranker.rank();

testCase.verifyEqual(rank_object.within_network_pair.single_sample_p_value.v, testCase.ranking.within_network_pair.single_sample_p_value.v);
end
end
end