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List of table settings

The following page describes all the settings that can be used in table placeholders in reporting templates. Placeholders for tables can include four different groups of settings. These are:

  • “data” (required) – containing settings about table content, such as type of the table, and rows and columns that the table will contain,

  • “display” (optional) – containing information about table display (e.g., number of significant digits to which the values in the table should be rounded, table direction, style, …

  • “stratification” (optional) – containing information about table splitting and/or filtering,

  • “renamings” (optional) – containing various words present in the data set or PKanalix that should be reworded in the table.

Settings inside these groups of settings need to be indented or put inside curly brackets. It is crucial to respect the indentation rules and the space after the “:” for the placeholder to be properly interpreted.

https://youtu.be/5jQVKsxVtvI?si=P7xFFet_MDX_DY7G

Data

Data settings define the type of the table that will be generated, as well as rows and columns that the table will contain. Here is the list of all settings of the data group of settings, along with their descriptions:

Setting

Table

Required

Possible values

Description

task

All

yes

be, ca, nca

Task of which the table represents the results.

table

Points included for lambdaZ (NCA)
Anova table (BE)
Table of CVs (BE)
Table of confidence intervals (BE)
Cost table (CA)

yes

pointsIncludedForLambdaZ, anova, coefficientsOfVariation, confidenceIntervals, cost

Table type. If empty, CA or NCA parameters table will be generated (depending on the task argument).

formulation

Table of confidence intervals (BE)

no (default: all)

name of one of the test formulations present in the data set, or “all”

In case of confidenceIntervals table and multiple test formulations, setting can be used to select one of the non-reference formulations.

metrics

Table of parameters (CA or NCA)

no

“all” or one or several of: ID, min, Q1, median, Q3, max, mean, SD, SE, CV, Ntot, Nobs, Nmiss, geoMean, geoSD, geoCV, harmMean

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

metrics

Points included for lambdaZ (NCA)

no

“all” or one or several of: ID, time, concentration, BLQ, includedForLambdaZ

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

metrics

Table of confidence intervals (BE)

no

“all” or one or several of: AdjustedMean, N, Difference, CIRawLower, CIRawUpper, Ratio, CILower, CIUpper, BE

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

metrics

Coefficient of variation (BE)

no

“all” or one or several of: SD, CV

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

metrics

Anova table (BE)

no

“all” or one or several of: DF, SUMSQ, MEANSQ, FVALUE, PR(>F)

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

metrics

Cost table (CA)

no

“all” or one or several of: Cost, -2LL, AIC, BIC

If equal to “all”, all available rows or columns will be present in the table. If specific metrics are given, only those rows/columns will be available in the table.

excludedMetrics

All

no (default: none)

Same arguments as for metrics, excluding “all”.

Metrics that will be excluded from the table. Handy when a user wants to keep most of them.

parameters

Table of parameters (CA/NCA)

no (default: all)

One or more of parameters calculated in NCA or CA, including Cost if CA, or “all”.

Parameters that will be included in the table. Used when table setting isn’t specified.

excludedParameters

Table of parameters (CA/NCA)

no (default: none)

Same arguments as for parameters, excluding “all”.

Parameters that will be excluded from the table. Handy when a user wants to keep most of them.

factors

Anova table (BE)

no (default: all)

One or more of the headers of columns used in the BE linear model, including Residuals, or “all”.

Factors included in the linear model.

excludedFactors

Anova table (BE)

no (default: none)

Same arguments as for factors, excluding “all”.

Factors included in the linear model.

ids

Table of parameters (CA/NCA)
Points included for lambdaZ (NCA)

no (default: all)

One or several of IDs present in the dataset, or “all”.

IDs of subjects whose parameters should be shown in the table. The summary statistics will be calculated on all individuals, not just ones shown in the table. If not present, default is “all”.

excludedIds

Table of parameters (CA/NCA)
Points included for lambdaZ (NCA)

no (default: none)

Same arguments as for ids, excluding “all”.

IDs of subjects whose parameters should be excluded from the table. The summary statistics will be calculated on all individuals, not just ones shown in the table.

covariates

Table of parameters (CA/NCA)

no (default: all)

One or more of covariates present in the data set, or “all”.

Which covariates to include in the table.

covariatesAfterParameters

Table of parameters (CA/NCA)

no (default: true)

true, false

If covariates should be shown after parameters in the table.

Display

Display group of settings defines how the information in the tables will be displayed. Here is the list of all settings for the display group of settings:

Setting

Table

Required

Possible values

Description

Example(s)

units

Table of parameters (CA/NCA)
Anova table (BE)
Table of CVs (BE)
Table of confidence intervals (BE)
Cost table (CA)

no (default: true)

true, false

If true, units will be output next to parameters.

units: true

CDISCNames

Table of parameters (CA/NCA)
Anova table (BE)
Table of CVs (BE)
Table of confidence intervals (BE)
Cost table (CA)

no (default: false)

true, false

If true, CDISC names of parameters will be shown in the table.

CDISCNames: true

style

All

no (default: selected in Generate report pop-up)

Name of table styles present in the template document.

Microsoft Word document template style to apply to the table. This setting overrides the setting in the Generate report pop-up.

style: “Medium Grid 1 – Accent 1”

metricsDirection

All

no (default: vertical)

vertical, horizontal

Direction of metrics.

metricsDirection: horizontal

significantDigits

All

no (default: taken from Preferences)

positive integers

Number of significant digits values in the table will be rounded to.

signifcantDigits: 3

trailingZeros

All

no (default: taken from Preferences)

true, false

If trailing zeros should be shown in the tables.

trailingZeros: true

inlineUnits

Table of parameters (CA/NCA)
Anova table (BE)
Table of CVs (BE)
Table of confidence intervals (BE)
Cost table (CA)

no (default: true)

true, false

If units should be inline with parameters. If false, there will be a new line between a parameter name and a unit.

inlineUnits: false

fitToContent

All

no (default: true)

true, false

If true, width of the table will be equal to the width of content, otherwise width of the table will be equal to the width of the page.

fitToContent: false

caption

All

no (default: no caption)

a phrase inside quotation marks

Caption that will appear next to the table.

caption: “Individual NCA parameters”

captionAbove

All

no (default: false)

true, false

If true, caption will be positioned above the table. If false, caption will be positioned below the table.

captionAbove: true

fontSize

All

no (default: 12)

a number

Font size of the table content (will not be applied to the caption).

fontSize: 10

Stratification

Stratification group of settings defines how the table will be split. List of stratification settings:

Setting

Table

Required

Possible values

Description

Example(s)

state

Table of parameters (CA/NCA)

no

Two possible subsettings:
– split – can contain header names of covariates and/or occasions
– filter – can contain header names of covariates and/or occasions and number(s) that describe alphabetical order of modalities

Contains information of how to split the table.

state: {split: [FORM]}
state: {split: [FORM, OCC]}
state: {filter: [[FORM, [1]]]}
state: {filter: [[SEQ, [1, 2]]]}
state: {filter: [[FORM, [1]], [OCC, [1]]]}
state: {split: [FORM, OCC], filter: [[OCC, [1]], [SEQ, [1]]]}

splitDirection

Table of parameters (CA/NCA)

no

One or more of v, h

In which direction the table should be split. Number of arguments corresponds to number of covariates by which the table was split.

splitDirection: [v]
splitDirection: [v, v]
splitDirection: [v, h]

Let’s take a look at the demo project project_crossover_bioequivalence.pkx. It contains data from a 2×2 crossover bioequivalence study of two controlled release formulations of theophylline. We would like to generate a placeholder for the summary table of NCA parameters and split it across sequences and formulations. If we select that we only want to compute Cmax and AUClast, here is how a default placeholder looks like when we click on the placeholder button next to the NCA summary table and which table it produces:

CODE 
<lixoftPLH>
data:
    task: nca
    metrics: [min, Q1, median, Q3, max, mean, SD, SE, CV, Ntot, Nobs, Nmiss, geoMean, geoSD, geoCV, harmMean]
    parameters: [AUClast, Cmax]
display:
    units: true
    inlineUnits: true
    metricsDirection: horizontal
    significantDigits: 4
    fitToContent: true
</lixoftPLH>
image-20240529-155314.png

If we want to split the table by the period and the formulation, we can select the appropriate checkboxes on the right and the default placeholder will change automatically. However, doing this always splits the table vertically. We can also remove some of the statistics that we want to exclude from the table by modifying the metrics argument.

CODE 
<lixoftPLH>
data:
    task: nca
    metrics: [min, median, max, mean, CV, Nobs, geoMean, geoCV]
    parameters: [AUClast, Cmax]
display:
    units: true
    inlineUnits: true
    metricsDirection: horizontal
    significantDigits: 4
    fitToContent: true
stratification:
    state: {split: [FORM, Period]}
    splitDirection: [v, v]
</lixoftPLH>
image-20240529-155339.png

If we want to change the direction of splitting, for example, make a split by Period horizontal, instead of vertical, we can modify the splitDirection argument.

CODE 
<lixoftPLH>
data:
    task: nca
    metrics: [Nobs, mean, CV, geoMean, geoCV]
    parameters: [AUClast, Cmax]
display:
    units: true
    inlineUnits: true
    metricsDirection: horizontal
    significantDigits: 4
    fitToContent: true
stratification:
    state: {split: [FORM, Period]}
    splitDirection: [v, h]
</lixoftPLH>
image-20240529-155359.png

Renamings

Renamings setting can be provided to the placeholder to replace certain words or expressions that will appear in the table with a user-defined word or expression. We will explain the usage of renamings setting on a concrete example.

Let’s take a look at the demo project project_parallel_absBioavailability.pkx. The project contains data from 18 subjects, of which 9 received an IV formulation of a certain drug and other 9 received an oral formulation. Let’s say we want to use the Bioequivalence feature of PKanalix to calculate bioavailability of the oral formulation and generate a report. It would be suitable to put a bioequivalence confidence intervals table in the report, with certain renamings.

A generated placeholder for a BE confidence intervals table, with its default settings, is shown below, including the table it generates.

CODE 
<lixoftPLH>
data:
    task: be
    table: confidenceIntervals
    metrics: [AdjustedMean, N, Difference, CIRawLower, CIRawUpper, Ratio, CILower, CIUpper, BE]
    parameters: [AUCINF_obs]
display:
    units: true
    inlineUnits: true
    significantDigits: 4
    fitToContent: true
</lixoftPLH>
image-20240529-155421.png

Let’s say we would like to hide some of the columns and rename some of the expressions in the table. For example, it would be convient to rename “Bioequivalence” to “Absolute bioavailability”, “IV” to “intravenous”, “ORAL” to “oral formulation”, and “CILower” to “90% CI (lower)”. We can then modify the placeholder to look like the one on the left and it will generate the table on the right.

CODE 
<lixoftPLH>
data:
    task: be
    table: confidenceIntervals
    metrics: [AdjustedMean, N, Ratio, CILower, CIUpper]
    parameters: [AUCINF_obs]
renamings: 
    IV: "intravenous"
    ORAL: "oral formulation"
    Bioequivalence: "Absolute bioavailability"
    CILower: "90% CI (lower)"
    CIUpper: "90% CI (upper)"
    AdjustedMean: "Adjusted mean"
</lixoftPLH>
image-20240529-155441.png

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