Select Page

# List of table placeholder 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.

Although most of the settings apply to both reporting tables and tables in the interface, there are several of them that are specific to reporting tables and not available when clicking on the placeholder buttons in the interface. They are highlighted in bold in the tables below.

## 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 a test formulation. metrics All no (default: depends on a table) In case of parameter tables: – “all” or one or several of: ID, min, Q1, median, Q3, max, mean, SD, SE, CV, Ntot, Nobs, Nmiss, geoMean, geoSD, geoCV, harmMean In case of pointsIncludedForLambdaZ: – “all” or one or several of: ID, time, concentration, BLQ, includedForLambdaZ In case of confidenceIntervals: – “all” or one or several of: AdjustedMean, N, Difference, CIRawLower, CIRawUpper, Ratio, CILower, CIUpper, BE In case of coefficientsOfVariation: – “all” or one or several of: SD, CV In case of anova: – “all” or one or several of: DF, SUMSQ, MEANSQ, FVALUE, PR(>F) In case of cost: – “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:

<lixoftPLH>
data:
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>
 min Q1 median Q3 max mean SD SE CV(%) Ntot N Nmiss GeoMean GeoSD GeoCV HarmMean AUC0-tlast (h⋅mg⋅L⁻¹) 45.6709 116.8202 142.4099 179.027 236.6814 148.5547 46.7732 7.7955 31.4855 36 36 0 140.3561 1.4369 37.4696 130.4717 Cmax (mg⋅L⁻¹) 3.56 6.12 8.76 9.94 11.53 8.1806 2.2192 0.3699 27.1282 36 36 0 7.8445 1.3597 31.4694 7.4633

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.

<lixoftPLH>
data:
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>
 FORM Period Metrics N mean CV(%) GeoMean GeoCV ref 1 AUC0-tlast (h⋅mg⋅L⁻¹) 9 154.8982 26.3033 150.3623 26.1424 Cmax (mg⋅L⁻¹) 9 9.82 11.8862 9.7571 12.1369 2 AUC0-tlast (h⋅mg⋅L⁻¹) 9 147.6183 36.178 137.7505 43.7537 Cmax (mg⋅L⁻¹) 9 8.3244 32.019 7.8713 39.0231 test 1 AUC0-tlast (h⋅mg⋅L⁻¹) 9 133.3989 39.8426 122.3564 49.8543 Cmax (mg⋅L⁻¹) 9 6.4689 28.8987 6.2384 29.1102 2 AUC0-tlast (h⋅mg⋅L⁻¹) 9 158.3035 26.9691 153.1323 28.1126 Cmax (mg⋅L⁻¹) 9 8.1089 22.1858 7.9035 25.4489

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.

<lixoftPLH>
data:
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>
 Period 1 2 FORM Metrics N mean CV(%) GeoMean GeoCV N mean CV(%) GeoMean GeoCV ref AUC0-tlast (h⋅mg⋅L⁻¹) 9 154.8982 26.3033 150.3623 26.1424 9 147.6183 36.178 137.7505 43.7537 Cmax (mg⋅L⁻¹) 9 9.82 11.8862 9.7571 12.1369 9 8.3244 32.019 7.8713 39.0231 test AUC0-tlast (h⋅mg⋅L⁻¹) 9 133.3989 39.8426 122.3564 49.8543 9 158.3035 26.9691 153.1323 28.1126 Cmax (mg⋅L⁻¹) 9 6.4689 28.8987 6.2384 29.1102 9 8.1089 22.1858 7.9035 25.4489

## 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.

<lixoftPLH>
data:
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>

ORAL

 Parameter ORAL IV Bioequivalence AdjustedMean N AdjustedMean N Difference CIRawLower CIRawUpper Ratio CILower CIUpper BE AUC0-inf (h⋅ug⋅L⁻¹) 223.9609 9 254.76 9 -0.1289 -0.2097 -0.04805 87.9105 81.0865 95.3089 yes

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.

<lixoftPLH>
data:
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)"
</lixoftPLH>