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scm#

Pharmpy currently creates results after a PsN scm (stepwise covariate modeling) run.

The scm results#

Steps#

The steps table contains information on the models run in each step.

reduced_ofv extended_ofv ofv_drop delta_df pvalue goal_pvalue is_backward extended_significant selected directory model covariate_effects
step parameter covariate extended_state
1 PHA AGE 5 219210.90878 219167.36222 43.54656 1 4.140000e-11 0.01 False True False m1 PHAAGE-5 NaN
BMI 5 219210.90878 219171.47564 39.43314 1 3.390000e-10 0.01 False True False m1 PHABMI-5 NaN
CYCLL 5 219210.90878 219203.94536 6.96342 1 8.319000e-03 0.01 False True False m1 PHACYCLL-5 NaN
DIAG 2 219210.90878 219206.01527 4.89351 1 2.695800e-02 0.01 False False False m1 PHADIAG-2 NaN
DISDUR 5 219210.90878 219032.86056 178.04822 1 1.290000e-40 0.01 False True False m1 PHADISDUR-5 NaN
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
11 PHA WT 5 215321.70954 215306.67698 15.03256 1 1.060000e-04 0.001 True True False backward_scm_dir1/m1 PHAWT-1 NaN
PHIA MENS 2 215407.40295 215306.67698 100.72597 1 1.060000e-23 0.001 True True False backward_scm_dir1/m1 PHIAMENS-1 NaN
PHIB GEOREG 2 215373.77800 215306.67698 67.10102 1 2.580000e-16 0.001 True True False backward_scm_dir1/m1 PHIBGEOREG-1 NaN
MENS 2 216968.25989 215306.67698 1661.58291 1 0.000000e+00 0.001 True True False backward_scm_dir1/m1 PHIBMENS-1 NaN
SLP GEOREG 2 215359.18150 215306.67698 52.50452 1 4.290000e-13 0.001 True True False backward_scm_dir1/m1 SLPGEOREG-1 NaN

304 rows × 12 columns

The table index has multiple levels

Level

Description

step

A step index starting with 1

parameter

Parameter to which covariate effect was added

covariate

Covariate used

extended_state

The covariate effect (state) function used

The table columns are

Column

Description

reduced_ofv

OFV of the reduced model. Note that in the backwards direction this is not the base model

extended_ofv

OFV of the extended model

ofv_drop

Drop in OFV beween the reduced and extended models

delta_df

The number of added population parameters in the extended model

pvalue

p-value for the covariate effect being significant

goal_pvalue

target p-value for the run

is_backward

True if run was in a backward step and False if not

extended_significant

Is the covariate effect in the extended model significant?

selected

Was the covariate effect in the step selected

directory

Path to the model

model

Name of the model

covariate_effects

Listing the covariate effect values

OFV Summary#

The ofv_summary gives slightly different view of the runs. The included relations in the final model are listed under the direction “Final included”.

direction reduced_ofv extended_ofv ofv_drop delta_df pvalue goal_pvalue
(1, PHIB, MENS, 2) Forward 219210.90878 215961.46277 3249.44601 1 0.000000e+00 0.01
(2, PHA, MENS, 2) Forward 215961.46277 215748.07194 213.39083 1 2.500000e-48 0.01
(3, PHA, DISDUR, 5) Forward 215748.07194 215570.57352 177.49842 1 1.700000e-40 0.01
(4, PHIA, MENS, 2) Forward 215570.57352 215486.23440 84.33912 1 4.170000e-20 0.01
(5, PHA, BMI, 5) Forward 215486.23440 215418.87007 67.36433 1 2.260000e-16 0.01
(6, PHIB, GEOREG, 2) Forward 215418.87007 215357.74693 61.12314 1 5.360000e-15 0.01
(7, PHA, AGE, 5) Forward 215357.74693 215337.95044 19.79649 1 9.000000e-06 0.01
(8, SLP, GEOREG, 2) Forward 215337.95044 215321.70954 16.24090 1 5.600000e-05 0.01
(9, PHA, WT, 5) Forward 215321.70954 215306.67698 15.03256 1 1.060000e-04 0.01
(PHA, AGE, 5) Final included 215332.91461 215306.67698 26.23763 1 3.020000e-07 0.001
(PHA, BMI, 5) Final included 215364.67861 215306.67698 58.00163 1 2.620000e-14 0.001
(PHA, DISDUR, 5) Final included 215450.74783 215306.67698 144.07085 1 3.430000e-33 0.001
(PHA, MENS, 2) Final included 215491.11568 215306.67698 184.43870 1 5.200000e-42 0.001
(PHA, WT, 5) Final included 215321.70954 215306.67698 15.03256 1 1.060000e-04 0.001
(PHIA, MENS, 2) Final included 215407.40295 215306.67698 100.72597 1 1.060000e-23 0.001
(PHIB, GEOREG, 2) Final included 215373.77800 215306.67698 67.10102 1 2.580000e-16 0.001
(PHIB, MENS, 2) Final included 216968.25989 215306.67698 1661.58291 1 0.000000e+00 0.001
(SLP, GEOREG, 2) Final included 215359.18150 215306.67698 52.50452 1 4.290000e-13 0.001

Candidate Summary#

The candidate_summary table give an overview of each candidate relationship. When and how often was it included, how often did it give errors, etc.

N_test N_ok N_localmin N_failed StepIncluded
parameter covariate extended_state
PHA AGE 5 7 7 0 0 7.0
BMI 5 5 5 0 0 5.0
CYCLL 5 10 10 0 0 NaN
DIAG 2 10 10 0 0 NaN
DISDUR 5 3 3 0 0 3.0
GEOREG 2 10 10 0 0 NaN
LBEST 5 10 0 0 10 NaN
MENS 2 2 2 0 0 2.0
WT 5 9 9 0 0 9.0
PHIA AGE 5 10 10 0 0 NaN
BMI 5 10 10 0 0 NaN
CYCLL 5 10 10 0 0 NaN
DIAG 2 10 10 0 0 NaN
DISDUR 5 10 0 10 0 NaN
GEOREG 2 10 10 0 0 NaN
LBEST 5 10 10 0 0 NaN
MENS 2 4 4 0 0 4.0
WT 5 10 10 0 0 NaN
PHIB AGE 5 10 9 1 0 NaN
BMI 5 10 10 0 0 NaN
CYCLL 5 10 10 0 0 NaN
DIAG 2 10 10 0 0 NaN
DISDUR 5 10 10 0 0 NaN
GEOREG 2 6 6 0 0 6.0
LBEST 5 10 10 0 0 NaN
MENS 2 1 1 0 0 1.0
WT 5 10 9 1 0 NaN
SLP AGE 5 10 10 0 0 NaN
BMI 5 10 9 1 0 NaN
CPL 5 10 9 1 0 NaN
GEOREG 2 8 8 0 0 8.0
LBEST 5 10 8 2 0 NaN
MENS 2 10 10 0 0 NaN
WT 5 10 9 1 0 NaN
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