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Bug related to integers/floats and/or cohort input parameter #280

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karafecho opened this issue Sep 25, 2023 · 7 comments
Closed

Bug related to integers/floats and/or cohort input parameter #280

karafecho opened this issue Sep 25, 2023 · 7 comments
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@hyi

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@karafecho
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karafecho commented Sep 25, 2023 •
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Brenna (intern) is exploring the multivariate technique. She has successfully used the lesson plan that I created to independently run all available ICEES+ functionalities and generate a multivariate table. However, she uncovered a bug that I reproduced and explored a bit. The issue appears to be related to the change we made in the treatment of integers vs floats and/or a failure to recognize the cohort input parameter at certain endpoints. Here's an example:

  1. Discover cohort function appears to run fine
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{"Active_In_Year":{"operator":"=","value":1},"Race_UNC":{"operator":"<>","value":"Unknown"},"TotalEDInpatientVisits":{"operator":">","value":1},"year":{"operator":"=","value":2010}}'

+-------------+--------+
| cohort_id | size |
+=============+========+
| COHORT:26 | 15901 |

  1. 2x2 association appears to run fine
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A26/feature_association?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
	"feature_a": {
		"Sex2": {
			"operator": "=",
			"value": "Female"
		}
	},
	"feature_b": {
		"AsthmaDx": {
			"operator": "=",
			"value": 0
		}
	}
}'

+---------------+-----------------+------------------+---------+
| feature       | Sex2 = Female   | Sex2 <> Female   |         |
+===============+=================+==================+=========+
| AsthmaDx = 0  | 5450    53.90%  | 4662    46.10%   | 10112   |
|               | 61.43%  34.27%  | 66.33%  29.32%   | 63.59%  |
+---------------+-----------------+------------------+---------+
| AsthmaDx <> 0 | 3422    59.11%  | 2367    40.89%   | 5789    |
|               | 38.57%  21.52%  | 33.67%  14.89%   | 36.41%  |
+---------------+-----------------+------------------+---------+
|               | 8872            | 7029             | 15901   |
|               | 55.80%          | 44.20%           | 100.00% |
+---------------+-----------------+------------------+---------+
  1. Features function returns results for both the selected cohort (COHORT:26) (float) and the total number of patient observations across all available years (integer)
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A26/feature_association?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
	"feature_a": {
		"Sex2": {
			"operator": "=",
			"value": "Female"
		}
	},
	"feature_b": {
		"AsthmaDx": {
			"operator": "=",
			"value": 0
		}
	}
}'

Excerpt:

+----------------------+---------+
| feature              | count   |
+======================+=========+
| ArformoterolRx = 0   | 141281  |
|                      | 89.86%  |
+----------------------+---------+
| ArformoterolRx = 1   | 45      |
|                      | 0.03%   |
+----------------------+---------+
| ArformoterolRx = 0.0 | 15896   |
|                      | 10.11%  |
+----------------------+---------+
| ArformoterolRx = 1.0 | 5       |
|                      | 0.00%   |
+----------------------+---------+
  1. Multivariate function returns results for the total number of patient observations across all available years (integer) [Note that the table below was not explored in depth, so results for the selected cohort (float) may be embedded within the output, as was the case for (3)]
curl -X 'POST' \
  'https://icees-asthma.renci.org/cohort/COHORT%3A26/multivariate_feature_analysis?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '[
  "TotalEDInpatientVisits",
  "Sex2",
  "Race_UNC",
  "PrednisoneRx"
]'

Excerpt:

+------------------------------------+----------+--------------------------+----------------+-------------+
| Race_UNC                           | Sex2     | TotalEDInpatientVisits   | PrednisoneRx   |   frequency |
+====================================+==========+==========================+================+=============+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 0            |          25 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 0            |       31507 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 1            |          32 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 0            |       10311 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 1            |          19 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 0            |         617 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 0            |       13903 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 1            |          18 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 0            |         317 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 1            |           1 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 0            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
@karafecho karafecho mentioned this issue Sep 25, 2023
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@hyi
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hyi commented Oct 11, 2023

@karafecho I believe this issue was triggered by changes to address the issue #247 as well which changed the response from cohort endpoint to return number of patients rather than number of observations as previously implemented. So the counts returned here are for number of observations for selected cohort rather than aggregating across years. Should we make it clear the returned count are for number of observations? The confusion here is that the cohort returns number of patients while these features and features associations endpoints return number of observations for the select cohort, which was discussed a bit in that issue #247. It seems to me these endpoints are all returning correct results and we just need to update documentation to make the returned results clearer to the users. What do you think?

@karafecho
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@hyi : Thanks for the investigative work. I think your conclusion is correct; however, I did some systematic testing at both the asthma and pcd prod endpoints, just to take a closer look, as the patient vs observation issue is a bit confusing. Plus, I wanted to consider how this might affect the multivariate functionality. I've attached two files with tabular example results. (Note that I didn't save all the CURLs.)

I noticed a few things:

  1. When one creates cohorts using either Active_In_Year=1 or year=2010, the results are identical, which does not seem right.
  2. I can systematically build cohorts and run the 2x2 feature association functionality, with or without the input parameter of year=2010, but it fails for the following COHORT, due I think to the fact that this cohort was selected using the "between" operation.
COHORT:21 (Active_In_Year = 1,Race_UNC <> Unknown,TotalEDInpatientVisits between (1,8))

+---------+
| error   |
+=========+
| 'value' |
+---------+
  1. study_period is not an available feature at the asthma endpoint, but it is at the PCD endpoint.

Asthma

curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A1/feature_association' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
  "feature_a": {
    "Sex2": {
      "operator": "=",
      "value": "Female"
    }
  },
  "feature_b": {
    "study_period": {
      "operator": "=",
      "value": "2010"
    }
  }
}'

422 Error, not a valid feature - study_period must not be defined in YAML

PCD

COHORT:1 (all), year 2010


+----------------------+-----------------+------------------+---------+
| feature              | Sex2 = Female   | Sex2 <> Female   |         |
+======================+=================+==================+=========+
| study_period = 2010  | 766      58.43% | 545      41.57%  | 1311    |
|                      | 100.00%  58.43% | 100.00%  41.57%  | 100.00% |
+----------------------+-----------------+------------------+---------+
| study_period <> 2010 | 0      null     | 0      null      | 0       |
|                      | 0.00%  0.00%    | 0.00%  0.00%     | 0.00%   |
+----------------------+-----------------+------------------+---------+
|                      | 766             | 545              | 1311    |
|                      | 58.43%          | 41.57%           | 100.00% |
+----------------------+-----------------+------------------+---------+
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
|   chi_squared_statistic |   chi_squared_dof |   chi_squared_p | fisher_exact_odds_ratio   | fisher_exact_p   | log_odds_ratio   | log_odds_ratio_95_confidence_interval   |
+=========================+===================+=================+===========================+==================+==================+=========================================+
|             1.29888e-17 |                 1 |               1 |                           |                  |                  |                                         |
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
  1. However, one cannot include study_period as a feature at the multivariate endpoint.

COHORT:1 (all)


curl -X 'POST' \
  'https://icees-pcd.renci.org/cohort/COHORT%3A1/multivariate_feature_analysis' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '[
  "TotalEDInpatientVisits",
  "Sex2",
  "study_period"
]'

Returns terms/conditions, zero results - tested several variations - study_period not valid feature at multivariate endpoints?

All in all, I think you are correct that all endpoints are behaving properly and by design. However, we probably need to:

  1. Rethink the Active_In_Year feature and review the code to figure out what this feature actually represents. (Note that we've struggled with this feature in the past.)
  2. Add study_period to the asthma all_features YAML file.
  3. Explore why study_period cannot be selected at the multivariate endpoint.
  4. [Unrelated to the above testing, but related to (3)] Modify the multivariate endpoint (and maybe all endpoints) to return PatientID in the output table.

Does the above seem correct?

OCT2023_test_Asthma.txt
OCT2023_test_PCD.txt

@karafecho
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One additional comment/task: we do need to update the documentation. I can do this, but please advise on your preferred approach for doing so. Thanks!

@karafecho
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karafecho commented Oct 16, 2023 •
edited
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@hyi : Brenna continues to report issues with the multivariate endpoint, so I did a bit of systematic testing. Perhaps we can discuss?

  1. Asthma 2x2 without specifying year, COHORT:1
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A1/feature_association' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
  "feature_a": {
    "Sex2": {
      "operator": "=",
      "value": "Female"
    }
  },
  "feature_b": {
    "PrednisoneRx": {
      "operator": "=",
      "value": "0"
    }
  }
}'

+-------------------+-----------------+------------------+---------+
| feature           | Sex2 = Female   | Sex2 <> Female   |         |
+===================+=================+==================+=========+
| PrednisoneRx = 0  | 850005  56.56%  | 652924  43.44%   | 1502929 |
|                   | 94.65%  53.87%  | 96.02%  41.38%   | 95.24%  |
+-------------------+-----------------+------------------+---------+
| PrednisoneRx <> 0 | 48029  63.96%   | 27061  36.04%    | 75090   |
|                   | 5.35%  3.04%    | 3.98%  1.71%     | 4.76%   |
+-------------------+-----------------+------------------+---------+
|                   | 898034          | 679985           | 1578019 |
|                   | 56.91%          | 43.09%           | 100.00% |
+-------------------+-----------------+------------------+---------+
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+--------------------------------------------------------------------+
|   chi_squared_statistic |   chi_squared_dof |   chi_squared_p |   fisher_exact_odds_ratio |   fisher_exact_p |   log_odds_ratio | log_odds_ratio_95_confidence_interval                              |
+=========================+===================+=================+===========================+==================+==================+====================================================================+
|                 1599.31 |                 1 |               0 |                  0.733498 |                0 |         -0.30993 | ConfidenceInterval(low=0.7224026274952368, high=0.744764508785044) |
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+--------------------------------------------------------------------+
  1. Asthma 2x2 with year=2010 specified, COHORT:1 [year appears to have been applied correctly]
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A1/feature_association?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
  "feature_a": {
    "Sex2": {
      "operator": "=",
      "value": "Female"
    }
  },
  "feature_b": {
    "PrednisoneRx": {
      "operator": "=",
      "value": "0"
    }
  }
}'

+-------------------+-----------------+------------------+---------+
| feature           | Sex2 = Female   | Sex2 <> Female   |         |
+===================+=================+==================+=========+
| PrednisoneRx = 0  | 89379   56.89%  | 67740   43.11%   | 157119  |
|                   | 98.45%  56.10%  | 98.83%  42.52%   | 98.61%  |
+-------------------+-----------------+------------------+---------+
| PrednisoneRx <> 0 | 1404   63.59%   | 804    36.41%    | 2208    |
|                   | 1.55%  0.88%    | 1.17%  0.50%     | 1.39%   |
+-------------------+-----------------+------------------+---------+
|                   | 90783           | 68544            | 159327  |
|                   | 56.98%          | 43.02%           | 100.00% |
+-------------------+-----------------+------------------+---------+
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+---------------------------------------------------------------------+
|   chi_squared_statistic |   chi_squared_dof |   chi_squared_p |   fisher_exact_odds_ratio |   fisher_exact_p |   log_odds_ratio | log_odds_ratio_95_confidence_interval                               |
+=========================+===================+=================+===========================+==================+==================+=====================================================================+
|                 39.8835 |                 1 |     2.69571e-10 |                  0.755578 |      2.15103e-10 |        -0.280272 | ConfidenceInterval(low=0.6924432813217383, high=0.8244688925382757) |
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+---------------------------------------------------------------------+
  1. Asthma multivariate without year specified, COHORT:1 (excerpt of results shown)

curl -X 'POST' \
  'https://icees-asthma.renci.org/cohort/COHORT%3A1/multivariate_feature_analysis' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '[
  "TotalEDInpatientVisits",
  "Sex2",
  "Race_UNC",
  "PrednisoneRx"
]'

+------------------------------------+----------+--------------------------+----------------+-------------+
| Race_UNC                           | Sex2     | TotalEDInpatientVisits   | PrednisoneRx   |   frequency |
+====================================+==========+==========================+================+=============+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 0            |         251 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 1            |           3 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 0            |      324352 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 1            |        4206 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 0            |      109913 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 1            |        1309 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 0            |        6529 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 1            |          73 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 0            |      124409 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 1            |       11772 |
+------------------------------------+----------+--------------------------+----------------+-------------+
  1. Asthma multivariate with year=2010, COHORT:1 (excerpt of response shown) [year appears to have been applied correctly]
+------------------------------------+----------+--------------------------+----------------+-------------+
| Race_UNC                           | Sex2     | TotalEDInpatientVisits   | PrednisoneRx   |   frequency |
+====================================+==========+==========================+================+=============+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 0            |          25 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 0            |       31507 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 1            |          32 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 0            |       10311 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 1            |          19 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 0            |         617 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 0            |       13903 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 1            |          18 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 0            |         317 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 1            |           1 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 0            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 1            |           0 |
  1. Asthma 2x2, no year specified, COHORT:5 (age=0-2) [response doesn't seem correct, all female?; contradicts response in (6)]
curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A5/feature_association' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
  "feature_a": {
    "Sex2": {
      "operator": "=",
      "value": "Female"
    }
  },
  "feature_b": {
    "PrednisoneRx": {
      "operator": "=",
      "value": "0"
    }
  }
}'

+-------------------+-----------------+------------------+---------+
| feature           | Sex2 = Female   | Sex2 <> Female   |         |
+===================+=================+==================+=========+
| PrednisoneRx = 0  | 9754    100.00% | 0     0.00%      | 9754    |
|                   | 88.46%  88.46%  | null  0.00%      | 88.46%  |
+-------------------+-----------------+------------------+---------+
| PrednisoneRx <> 0 | 1273    100.00% | 0     0.00%      | 1273    |
|                   | 11.54%  11.54%  | null  0.00%      | 11.54%  |
+-------------------+-----------------+------------------+---------+
|                   | 11027           | 0                | 11027   |
|                   | 100.00%         | 0.00%            | 100.00% |
+-------------------+-----------------+------------------+---------+
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
|   chi_squared_statistic |   chi_squared_dof |   chi_squared_p | fisher_exact_odds_ratio   | fisher_exact_p   | log_odds_ratio   | log_odds_ratio_95_confidence_interval   |
+=========================+===================+=================+===========================+==================+==================+=========================================+
|             6.43122e-16 |                 1 |               1 |                           |                  |                  |                                         |
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
  1. Asthma 2x2, year=2010, COHORT:5 (age=0-2)

curl -X 'POST' \
  'https://icees-asthma.renci.org/patient/cohort/COHORT%3A5/feature_association?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '{
  "feature_a": {
    "Sex2": {
      "operator": "=",
      "value": "Female"
    }
  },
  "feature_b": {
    "PrednisoneRx": {
      "operator": "=",
      "value": "0"
    }
  }
}'


+-------------------+-----------------+------------------+---------+
| feature           | Sex2 = Female   | Sex2 <> Female   |         |
+===================+=================+==================+=========+
| PrednisoneRx = 0  | 5316     40.09% | 7944    59.91%   | 13260   |
|                   | 100.00%  40.08% | 99.94%  59.89%   | 99.96%  |
+-------------------+-----------------+------------------+---------+
| PrednisoneRx <> 0 | 0      0.00%    | 5      100.00%   | 5       |
|                   | 0.00%  0.00%    | 0.06%  0.04%     | 0.04%   |
+-------------------+-----------------+------------------+---------+
|                   | 5316            | 7949             | 13265   |
|                   | 40.08%          | 59.92%           | 100.00% |
+-------------------+-----------------+------------------+---------+
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
|   chi_squared_statistic |   chi_squared_dof |   chi_squared_p | fisher_exact_odds_ratio   | fisher_exact_p   | log_odds_ratio   | log_odds_ratio_95_confidence_interval   |
+=========================+===================+=================+===========================+==================+==================+=========================================+
|                 3.34508 |                 1 |       0.0674063 |                           |                  |                  |                                         |
+-------------------------+-------------------+-----------------+---------------------------+------------------+------------------+-----------------------------------------+
  1. Asthma multivariate, no year specified, COHORT:5 (age=0-2) (excerpt of results shown) [same results as in (3)]
curl -X 'POST' \
  'https://icees-asthma.renci.org/cohort/COHORT%3A5/multivariate_feature_analysis' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '[
  "TotalEDInpatientVisits",
  "Sex2",
  "Race_UNC",
  "PrednisoneRx"
]'

+------------------------------------+----------+--------------------------+----------------+-------------+
| Race_UNC                           | Sex2     | TotalEDInpatientVisits   | PrednisoneRx   |   frequency |
+====================================+==========+==========================+================+=============+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 0            |         251 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 1            |           3 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 0            |      324352 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 1            |        4206 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 0            |      109913 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 1            |        1309 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 0            |        6529 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 1            |          73 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 0            |      124409 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 1            |       11772 |
+------------------------------------+----------+--------------------------+----------------+-------------+
  1. Asthma multivariate, year=2010, COHORT:5 (age=0-2) [year appears to have been applied correctly, but same results as in (4)]
curl -X 'POST' \
  'https://icees-asthma.renci.org/cohort/COHORT%3A5/multivariate_feature_analysis?year=2010' \
  -H 'accept: text/tabular' \
  -H 'Content-Type: application/json' \
  -d '[
  "TotalEDInpatientVisits",
  "Sex2",
  "Race_UNC",
  "PrednisoneRx"
]'

+------------------------------------+----------+--------------------------+----------------+-------------+
| Race_UNC                           | Sex2     | TotalEDInpatientVisits   | PrednisoneRx   |   frequency |
+====================================+==========+==========================+================+=============+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 0            |          25 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Native Hawaiian/Pacific Islander | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 0            |       31507 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Caucasian                        | = Male   | = 0.0                    | = 1            |          32 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 0            |       10311 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = African American                 | = Male   | = 0.0                    | = 1            |          19 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 0            |         617 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Asian                            | = Male   | = 0.0                    | = 1            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 0            |       13903 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Unknown                          | = Male   | = 0.0                    | = 1            |          18 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 0            |         317 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = American/Alaskan Native          | = Male   | = 0.0                    | = 1            |           1 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 0            |           0 |
+------------------------------------+----------+--------------------------+----------------+-------------+
| = Other                            | = Male   | = 0.0                    | = 1            |           0 |

@karafecho
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BTW, and this may be important information, all of the cohorts were preserved, despite the fact that you recreated the database. Perhaps something went wrong with that?

@hyi
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hyi commented Oct 17, 2023 •
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@karafecho database is only recreated for PCD instances due to changes to all features yaml file. For other instances, only valuesets yaml file is updated with correct min and max ranges for year, so there are no database changes.

@hyi hyi mentioned this issue Oct 19, 2023
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hyi added a commit that referenced this issue Oct 19, 2023
@hyi
Fix issues #289 and #280 to have year and cohorts applied to multivar…
3eac09b 
…iate analysis endpoint (#293)

* fixed issue #289

* make multivariate analysis endpoint to honor cohorts
@karafecho
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Closing issue, as this issue was resolved ...

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