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Next generation modeling platform
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summary table omega naming is incorrect #80

Open dpastoor opened 4 years ago

dpastoor commented 4 years ago

check of the TMDD model shows the following:

+-----+--------+------+----------+-----------------+
| SUB | OMEGA  | ETA  | ESTIMATE | SHRINKAGESD (%) |
+-----+--------+------+----------+-----------------+
| 1   | O(0,0) | ETA1 | 0.048245 | 5.016800        |
| 1   | O(1,1) | ETA2 | 0.045746 | 0.761452        |
| 1   | O(2,2) | ETA3 | 0.049242 | 10.922900       |
+-----+--------+------+----------+-----------------+

O(0,0) is incorrect and doesn't match up to the (correct) parameter_names, which is O(1,1)

TMDD has off diagonal elements which are not shown in the summary,

$OMEGA BLOCK (2) 0.06 ;CL BSV 0.01 0.06 ;VC BSV

$OMEGA 0.06 ;BASE BSV

so the table should be reporting O(2,1) as well. It should look something like:

+-----+--------+------+----------+-----------------+
| SUB | OMEGA  | ETA  | ESTIMATE | SHRINKAGESD (%) |
+-----+--------+------+----------+-----------------+
| 1   | O(1,1) | ETA1 | 0.048245 | 5.016800        |
| 1   | O(2,1) |   -  | 0.045746 | 0.761452        |
| 1   | O(2,2) | ETA2 | 0.045746 | 0.761452        |
| 1   | O(3,3) | ETA3 | 0.049242 | 10.922900       |
+-----+--------+------+----------+-----------------+
dpastoor commented 4 years ago

getting pretty close

multi omega

LEM PK model 1 cmt base
Dataset: ../../../../../acop.csv
Records: 799   Observations: 760  Patients: 40
Estimation Method(s):
 - First Order Conditional Estimation with Interaction
+-------+------+-----------+--------------+
| THETA | NAME | ESTIMATE  | STDERR (RSE) |
+-------+------+-----------+--------------+
| TH 1  | KA   | 2.75474   | -            |
| TH 2  | CL   | 3.79965   | -            |
| TH 3  | V2   | 12.5893   | -            |
| TH 4  | RUVp | -0.012749 | -            |
| TH 5  | RUVa | 7.11556   | -            |
+-------+------+-----------+--------------+
+------------+------+-----------+---------------+
|   OMEGA    | ETA  | ESTIMATE  | SHRINKAGE (%) |
+------------+------+-----------+---------------+
| OMEGA(1,1) | ETA1 | 0.093535  | 67.106400     |
| OMEGA(2,2) | ETA2 | 0.079633  | 64.731400     |
| OMEGA(3,2) |      | -0.033490 |
| OMEGA(3,3) | ETA3 | 0.907342  | 29.803400     |
+------------+------+-----------+---------------+

BQL

LEM RUN# 2 - 2cmpt model - no BQLs
Dataset: ../nobqldata.csv
Records: 2895   Observations: 2702  Patients: 193
Estimation Method(s):
 - First Order Conditional Estimation with Interaction
+-------+----------+----------+------------------+
| THETA |   NAME   | ESTIMATE |   STDERR (RSE)   |
+-------+----------+----------+------------------+
| TH 1  | 1    CLF | 26.4905  | 0.60908 (2.3%)   |
| TH 2  | 2    V2F | 282.616  | 4.40586 (1.6%)   |
| TH 3  | 3    V3F | 297.043  | 2.32933 (0.8%)   |
| TH 4  | 4    QF  | 58.749   | 1.01296 (1.7%)   |
| TH 5  | 5    KA  | 1.5095   | 0.0212776 (1.4%) |
| TH 6  | 6 POW_CL | 0.75     | FIX              |
| TH 7  | 7 POW_V2 | 1        | FIX              |
| TH 8  | 8 POW_V3 | 1        | FIX              |
| TH 9  | 9 POW_Q  | 0.75     | FIX              |
+-------+----------+----------+------------------+
+------------+------+----------+---------------+
|   OMEGA    | ETA  | ESTIMATE | SHRINKAGE (%) |
+------------+------+----------+---------------+
| OMEGA(1,1) | ETA1 | 0.100611 | 0.406320      |
| OMEGA(2,2) | ETA2 | 0.035999 | 2.060600      |
| OMEGA(3,3) | ETA3 | 0.011173 | 18.483600     |
+------------+------+----------+---------------+

mixture model with two populations

LEM 10 mixture model and IOV on CL
Dataset: ../MixSim.CSV
Records: 13500   Observations: 12600  Patients: 300
Estimation Method(s):
 - First Order Conditional Estimation
+-------+---------------+----------+--------------+
| THETA |     NAME      | ESTIMATE | STDERR (RSE) |
+-------+---------------+----------+--------------+
| TH 1  | 1. CL POP 1   | 14.3605  | -            |
| TH 2  | 2. V          | 100.521  | -            |
| TH 3  | 3. WT ON CL   | 0.822632 | -            |
| TH 4  | 4. WT ON V    | 1.0446   | -            |
| TH 5  | 5. CL POP 2   | 1.67825  | -            |
| TH 6  | 6. PROB POP 1 | 0.856771 | -            |
+-------+---------------+----------+--------------+
+------------+------+----------+--------------------+--------------------+
|   OMEGA    | ETA  | ESTIMATE | POP1 SHRINKAGE (%) | POP2 SHRINKAGE (%) |
+------------+------+----------+--------------------+--------------------+
| OMEGA(1,1) | ETA1 | 0.048361 | 13.971800          | 21.355300          |
| OMEGA(2,2) | ETA2 | 0.043812 | 4.730460           | 3.503370           |
| OMEGA(3,3) | ETA3 | 0.038457 | 18.715100          | 18.301400          |
| OMEGA(4,4) | ETA4 | 0.038457 | 16.893300          | 25.362100          |
| OMEGA(5,5) | ETA5 | 0.038457 | 16.012100          | 34.828800          |
+------------+------+----------+--------------------+--------------------+

still have not checked fixed eta situation, which likely will give a nonsense 100000000 or -999999999 or something. Will need to to confirm and update accordingly before finalizing.

dpastoor commented 4 years ago

also should check impact of FIX'd omegas