QA#
Pharmpy currently creates results after a PsN qa run.
The qa results#
Overview#
The overview dofv table lists the most impactful modifications identified by QA.
More details for each result can be found in the individual sections.
The table shows an overview of possible modifications to different model aspects, expected improements in OFV as well as number of additional parameters used.
| dofv | df | |||
|---|---|---|---|---|
| section | run | dvid | ||
| parameter_variability | fullblock | NaN | 2.592698 | 1.0 |
| boxcox | NaN | 2.197887 | 2.0 | |
| tdist | NaN | 0.007493 | 2.0 | |
| add_etas | NaN | NaN | NaN | |
| iov | NaN | NaN | NaN | |
| covariates | frem | NaN | 4.521171 | 4.0 |
| ET1APGR-2 | NaN | 2.487930 | 1.0 | |
| residual_error_model | dtbs | 1.0 | 13.910000 | 2.0 |
| time_varying | 1.0 | 8.030000 | 2.0 |
Structural bias#
This section aims at diagnosing the structural component of the model. It does so by estimating the mean difference between model predictions and observations as a function of several independent variables.
The structural_bias table shows the CWRES and CPRED given different bins of the independent variable.
| binmin | binmax | cwres | cpred | |||
|---|---|---|---|---|---|---|
| idv | dvid | binid | ||||
| TIME | 1 | 1 | 0.00 | 2.00 | 0.28 | -6 |
| 2 | 2.00 | 2.55 | 0.12 | -2 | ||
| 3 | 2.55 | 11.00 | -0.29 | 6 | ||
| 4 | 11.00 | 47.25 | 0.04 | -1 | ||
| 5 | 47.25 | 63.50 | -0.39 | 7 | ||
| 6 | 63.50 | 83.10 | 0.20 | -4 | ||
| 7 | 83.10 | 112.30 | 0.11 | -2 | ||
| 8 | 112.30 | 135.50 | -0.29 | 5 | ||
| 9 | 135.50 | 159.80 | 0.19 | -4 | ||
| 10 | 159.80 | 390.00 | -0.02 | 1 | ||
| TAD | 1 | 1 | 0.00 | 1.50 | 0.06 | -1 |
| 2 | 1.50 | 2.00 | 0.41 | -8 | ||
| 3 | 2.00 | 3.00 | -0.13 | 3 | ||
| 4 | 3.00 | 6.00 | -0.06 | 1 | ||
| 5 | 6.00 | 11.00 | -0.18 | 3 | ||
| 6 | 11.00 | 11.50 | 0.54 | -10 | ||
| 7 | 11.50 | 11.70 | -0.24 | 4 | ||
| 8 | 11.70 | 14.00 | 0.06 | -1 | ||
| 9 | 14.00 | 258.00 | 0.07 | -1 | ||
| PRED | 1 | 1 | 8.00 | 17.67 | 0.19 | -5 |
| 2 | 17.67 | 19.50 | 0.10 | -1 | ||
| 3 | 19.50 | 20.13 | -0.17 | 3 | ||
| 4 | 20.13 | 21.39 | -0.01 | 0 | ||
| 5 | 21.39 | 24.32 | 0.24 | -4 | ||
| 6 | 24.32 | 26.63 | 0.06 | -1 | ||
| 7 | 26.63 | 28.70 | 0.05 | -1 | ||
| 8 | 28.70 | 31.28 | -0.05 | 1 | ||
| 9 | 31.28 | 36.34 | 0.07 | 0 | ||
| 10 | 36.34 | 54.00 | -0.47 | 9 |
Fullblock#
This section shows the effect of including a full block correlation struture in the base mdel.
The fullblock_parameters contains the estimated standard deviation (sd), correlation (corr) and
expected improvement in OFV after inclusion of a full block correlation structure of the random effects.
| new | old | |
|---|---|---|
| OMEGA(1,1) | 0.183463 | 0.171306 |
| OMEGA(2,1) | 0.554610 | NaN |
| OMEGA(2,2) | 0.154408 | 0.167053 |
Boxcox#
This section shows the effect of applying a Box-Cox transformation to the ETA variables in the base model.
The boxcox_parameters contains the estimated shape parameter (Lambda) and expected improvment in OFV for a
Box-Cox transformation of the random effects.
| lambda | new_sd | old_sd | |
|---|---|---|---|
| ETA(1) | -0.922083 | 0.182037 | 0.171306 |
| ETA(2) | 1.332800 | 0.166021 | 0.167053 |
Tdist#
This section shows the effect of applying a t-distribution transformation to the ETA variables in the base model.
The tdist_parameters contains the estimated degrees of freedom and expected improvement in OFV for a
t-distribution transformation of the random effects.
| df | new_sd | old_sd | |
|---|---|---|---|
| ETA(1) | 79.9997 | 0.168477 | 0.171306 |
| ETA(2) | 79.9986 | 0.166469 | 0.167053 |
Residual error#
This section shows the effect of including extended residual error models in the base model.
The residual_error table contains the residual error models, resulting expected improvement in OFV,
required additional model parameters as well as their estimates.
| dOFV | additional_parameters | parameters | ||
|---|---|---|---|---|
| DVID | model | |||
| 1.0 | dtbs | 13.91 | 2 | {'lambda': 0.242, 'zeta': 0.042} |
| time_varying | 8.03 | 2 | {'sdeps_0-t0': 0.271, 'sdeps_t0-390': 0.956, '... | |
| tdist | 5.53 | 1 | {'df': 5.106} | |
| autocorrelation | 3.34 | 1 | {'half-life': 16.7} | |
| IIV_on_RUV | 1.31 | 1 | {'%CV': 21.772} | |
| power | 0.03 | 1 | {'delta_power': -0.037} |
Covariate effects#
This section evaluates the impact of supplied covariates.
The covariate_effects table shows the expected improvement when including covariates.
| dofv | coeff | ||
|---|---|---|---|
| parameter | covariate | ||
| ETA(1) | APGR | 2.48793 | -0.033334 |
| WGT | 0.48218 | 0.052342 | |
| ETA(2) | APGR | 0.59034 | 0.008371 |
| WGT | 0.00887 | -0.003273 |