Data Processing and Calculation Rules

This page presents the rules applied to pre-process the data set and the calculation rules applied for the NCA analysis.

Data processing

Ignored data

All observation points occurring before the last dose recorded for each individual are excluded. Observation points occurring at the same time as the last dose are kept, irrespective of their position in the data set file.

Note that for plasma data, negative or zero concentrations are not excluded.

Data constraints

For plasma data, mandatory columns are ID, TIME, OBSERVATION, and AMOUNT. For urine data, mandatory columns are ID, TIME, OBSERVATION, AMOUNT and one REGRESSOR (to define the volume).

Two observations at the same time point will generate an error.

For urine data, negative or null volumes and negative observations generate an error.

Additional points at dose time

For plasma data, if an individual has no observation at dose time, a value is added:

• Extravascular and Infusion data: For single dose data, a concentration of zero. For steady-state, the minimum value observed during the dosing interval.

• IV Bolus data: the concentration at dose time (C0) is extrapolated using a log-linear regression (i.e., log(concentration) versus time) with uniform weight of first two data points. In the following cases, C0 is taken to be the first observed measurement instead (can be zero or negative):

  • one of the two observations is zero

  • the regression yields a slope >= 0

BLQ data

Measurements marked as BLQ data with a “1” in the CENSORING column will be replaced by zero, the LOQ value or the LOQ value divided by 2, or considered as missing (i.e., excluded) depending on the setting chosen. They are then handled like any other measurement. The LOQ value is indicated in the OBSERVATION column of the data set.

Steady-state

Steady-state is indicated using the STEADY-STATE and INTERDOSE INTERVAL column-types. Equal dosing intervals are assumed. Observation points occurring after the dose time + interdose interval are excluded for Cmin and Cmax, but not for lambda_z. Dedicated parameters are computed such as the AUC in the interdose interval, and a specific formula should be considered for the clearance and the volume, for example. More details can be found here.

Urine

Urine data is assumed to be single-dose, irrespective of the presence of a STEADY-STATE column. For the NCA analysis, the data is not used directly. Instead the interval midpoints and the excretion rate for each interval (amount eliminated per unit of time) are calculated and used:

Calculation rules

Lambda_z

PKanalix tries to estimate the slope of the terminal elimination phase, called λz, as well as the intercept called Lambda_z_intercept. λz is calculated via a linear regression between Y=log(concentrations) and X=time. Several weightings are available for the regression: uniform, 1/Y and 1/Y².

Zero and negative concentrations are excluded from the regression (but not from the NCA parameter calculations). The number of points included in the linear regression can be chosen via the “Main rule” setting. In addition, the user can define specific points to include or exclude for each individual (see the Check lambda_z page for details). When one of the automatic “main rules” is used, points prior to Cmax, and the point at Cmax for non-bolus models are not included. Those points can, however, be included manually by the user. If λz can be estimated, NCA parameters will be extrapolated to infinity.

R2 rule: the regression is done with the last three points, then the last four points, then the last five points, etc. If the R2 for n points is larger than or equal to the R2 for (n-1) points – 0.0001, then the R2 value for n points is used.  Additional constrains on the measurements included in the λz calculation can be set using the “maximum number of points” and “minimum time” settings. If strictly less than 3 points are available for the regression or if the calculated slope is positive, the λz calculation fails.

Adjusted R2 rule: the regression is done with the last three points, then the last four points, then the last five points, etc. For each regression the adjusted R2 is calculated as:

with the number of data points included and the square of the correlation coefficient.
If the adjusted R2 for n points is larger than or equal to the adjusted R2 for (n-1) points – 0.0001, then the adjusted R2 value for n points is used. Additional constraints on the measurements included in the λz calculation can be set using the “maximum number of points” and “minimum time” settings. If strictly less than 3 points are available for the regression or if the calculated slope is positive, the λz calculation fails.

Interval: strictly positive concentrations within the given time interval are used to calculate λz. Points on the interval bounds are included. Semi-open intervals can be defined using +/- infinity.

Points: the n last points are used to calculate λz. Negative and zero concentrations are excluded after the selection of the n last points. As a consequence, some individuals may have less than n points used.

AUC calculation

The following linear and logarithmic rules apply to calculate the AUC and AUMC over an interval [t₁, t₂] where the measured concentrations are C₁ and C₂. The total AUC is the sum of the AUCs calculated on each interval. If the logarithmic AUC rule fails on an interval because C₁ or C₂ are null or negative, then the linear interpolation rule will be used for that interval.

Linear formula: 

Logarithmic formula:

Interpolation formula for partial AUC

When a partial AUC is requested at time points not included is the original data set, it is necessary to add an additional measurement point. Those additional time points can be before or after the last observed data point.

Note that the partial AUC is not computed if a bound of the interval falls before the dosing time.

Additional point before the last observed data point

Depending on the choice of the “Integral method” setting, this can be done using a linear or log formula to find the added concentration C* at requested time t*, given that the previous and following measurements are C₁ at t₁ and C₂ at t₂.

Linear interpolation formula:     

Logarithmic interpolation formula:     

If the logarithmic interpolation rule fails in an interval because C₁ or C₂ are null or negative, then the linear interpolation rule is used for that interval.

Additional point after the last observed data point

If λz is not estimable, the partial area will not be calculated. Otherwise, λz is used to calculate the additional concentration C*:

Calculating steady-state parameters after each dose

Starting with version 2024R1, steady state parameters can be calculated for each profile without the dataset requiring the steady state information, meaning that the interdose-interval and SS columns are no longer necessary. To calculate a steady-state parameter (e.g AUC_TAU), the user must check the NCA setting “Interdose interval for single dose profiles” and define a value for the interdose interval tau:

Single dose parameters are always calculated, irrespective of the presence or absence of an interdose interval column in the dataset or whether the checkbox “Interdose interval for single dose profiles” is checked or not.

Steady-state parameters are calculated for all individuals if the checkbox “Interdose interval for single dose profiles” is checked (and a value of tau is defined). They are also calculated for individuals having a positive interdose interval is defined in the dataset or if the profile (subject or occasion) contains several doses. Depending on the dataset, you may have some profiles with steady-state parameters and some without (appearing as NaN in the results).

Some parameters have identical names but are computed using different formulas, contingent upon whether they pertain to a single dose profile (SD) or a multiple dose profile (SS):

These parameters are distinguished by the postfix “_SS” in the list of parameters and in the results table. This extension is also echoed in the aliases by the postfix “, SS”.

Typically, parameters that share the same name are calculated differently based on whether the “Interdose interval for single dose profiles” checkbox is selected. However, there’s one exception: parameter C₀. In cases where both single dose and multiple dose profiles occur together, the order of profiles influences C₀‘s calculation. If the first profile is a single dose, followed by either more single dose profiles or multiple dose profiles, and the checkbox is enabled, C₀ for the first occasion follows the single dose formula, while subsequent C₀‘s follow the steady-state formula.

Ratios for NCA parameters

Starting with PKanalix version 2024R1 and above, ratios of NCA metrics for each individual along occasions can now be calculated. In the dedicated section “Ratios NCA” in the NCA tasks tab, ratios can be defined by clicking on the plus button. This opens a window, allowing you to specify the ratio.

The ratio is calculated for each individual, using the different occasions (i.e., profiles). When only one occasion corresponds to the modality selected for “ref” and “test”, the ratio is simply the ratio of the two values. If there are subjects who have multiple occasions corresponding to the modality selected for “ref” and “test”, the arithmetic mean of the values for this modality is calculated first, then the ratio is calculated.

If there are subjects without a parameter value for one of the test or comparison modalities, no ratio can be calculated for this parameter. Consequently, the ration is NaN for that subject.