Administrator and user settings

Some attributes in AutoPilot Toolkit are user configurable, while others are only configurable by an administrator. Configurable options range from PK parameter selection to chart and table output formats.

Strikeout effect not supported: Users can edit table and graph s for automation and comparison projects. The Font dialog displays a Strikeout effect option. The Strikeout effect is not supported in AutoPilot Toolkit output, so this option is not applied if it is selected.

The following tables list AutoPilot Toolkit configurable features and describe the modifications that administrators and users can make.

Configurable input settings
Configurable analysis settings
Configurable business rules: settings affecting all output
Configurable business rules: table settings
Configurable formatted output: table settings
Configurable business rules: graph settings
Configurable formatted output: settings affecting all output
Configurable formatted output: graph settings
Configurable formatted output: text and appendix settings

Configurable input settings
Feature	Administrator	User
Study data column nomenclature configuration (column mapping)	Admin can configure the mapping of study input column headers to system names in AutoPilot Toolkit and has ability to create new demographic variables (e.g. phenotype) and define the data type (e.g. discrete). Also can define the concentration column header potentially for matrix and analyte per the concentration variable template.	User cannot modify these settings.
Selection of study data and output location to use in an Automation or Comparison run	Only applicable with the PKS Edition of AutoPilot Toolkit, the ability to decide if PKS can be used as an input and output location.	User can select the input (load study) and output (save AutoPilot Toolkit objects created) to PKS and/or non-PKS (local) destinations through a standard browsing feature.

Configurable analysis settings
Feature	Administrator	User
Selection of study design	Not applicable	User can select study design type and subtype (e.g., Crossover, Randomized).
Normalizations	Not applicable	User can select PK Parameters to be normalized by continuous demographics (e.g., weight) located in the study data. The user can select up to two normalization schemes per run.
Stratifications	Not applicable	User can select output to be stratified (summarized) by discrete demographics (e.g., gender) located in the study data. The user can select up to two stratification schemes and for each scheme they can define one or two stratification variables (e.g., Gender, Gender and Smoking) per run.
Statistical analysis	Not applicable	During PK automation of crossover studies, a user can select to run inferential statistics on PK Parameters using WinNonlin's LinMix BE tool.

Configurable business rules: settings affecting all output
Feature	Administrator	User
AUC % Extrapolation	Admin can configure rule regarding the display of a flag or a replacement value and associated footnote for PK parameters selected by the Admin where the AUC % extrapolation exceeds the threshold set by the user on an individual run. The Admin can also specify which parameters are affected and if the values that exceed the threshold are used for summary statistics calculations.	User can select whether to use the settings if the rule is activated by Admin and can also set the threshold value (e.g., 30%).
Display of source data	Admin can set the default to display information in the form of a footnote regarding the source data (study file) in tables or graphs.	User can decide to apply the source data footnotes per tables and graphs independently per run and what parts of the source information are displayed (location, path, time and date).
Exclusion	Admin can allow for exclusions and set how exclusions are displayed in final tables and figures, including corresponding footnotes.	If Admin enables exclusions, User can define the exclusion on a profile-by-profile basis. User can also define if corresponding graphs and tables created reflect the excluded profiles.
Display order	Not applicable	User can decide the order of the treatment identifiers (e.g. treatment, day, etc.) that are displayed in intext tables (top to bottom) and X-axis for categorical graphs (left to right).
Matrix mapping	Admin can configure through addition or deletion matrix abbreviations and map to the concentration column headers to encompass full matrix names into the final tables and graphs. For example, PLS in the concentration column would equate to 'Plasma' in the final output.	User cannot modify these settings.
Concentration variable used for concentration final output	Admin can set the default of which concentration column in the study data to use in the creation of the concentration tables and graphs independently.	User can select which concentration column in the study data to use in creation of the concentration tables and graphs independently.

Configurable business rules: table settings
Feature	Administrator	User
Table splitting	Allows splitting of tables if they won't fit on one page per page type and in margins set in the Administration module. Admin can enable or disable the table splitting feature for Users.	If Admin enables table splitting, User can activate/deactivate it per run.
Context-sensitive footnotes-display-calculation of non-numeric values for descriptive statistics	Allows definition/modification via addition or deletion of the default list of non-numeric values (e.g., NS) and associated footnotes (NS: No Sample). In addition, Admin can configure how these non-numeric values are handled during descriptive statistics calculations (missing or zero).	User cannot modify these settings.
Intext table template	Admin can configure the style, including number of descriptive statistics and define if PK parameters are time-dependent. Also, can default the specific descriptive statistics.	User can modify the selection of summary statistics (Mean, SD, etc.), but cannot modify the style nor PK parameters assigned to time-dependent.
Display of different sample sizes in intext tables	Admin can configure a rule that displays if there are differences in sample size used to calculate summary statistics for PK parameters via flags and corresponding footnotes.	User cannot modify these settings.
Calculation/display of summary statistics for small sample sizes	Admin can configure rule that allows the values of summary statistics involved with small sample sizes (1–3) to be overwritten by text values and apply corresponding footnotes (e.g., NC – Not calculated, sample size is too small).	User cannot modify these settings.
Significance level is displayed in statistics tables	Admin can configure a threshold for the display of p-values (e.g., 0.05), along with a corresponding footnote to be displayed or replaced by non-numeric text if the value is lower than the threshold.	User cannot modify these settings.
Summary statistics based on % threshold	Admin can configure a rule to set a minimum percentage of values relative to total sample size that must exist in a profile before calculations are performed.	User cannot modify these settings.
Individual values of zero treated as “missing”	Admin can configure a rule that allows values of 0 to be treated as Missing prior to any summary statistic calculation.	User cannot modify these settings.
LOQ replacement and display	Admin can configure a rule that allows replacement of numerical values with text values and corresponding footnotes if value is less than the threshold set by the user per run (value of 0.01 is replaced with BQL). Also can configure which PK parameters are governed by this rule.	User can decide whether to use the rule and set the replacement threshold that is used.
Time deviations calculation, flags, and footnotes	Allows Admin to select how the time deviation is calculated and how time deviation is displayed (threshold, footnote, and footnote flag)	User cannot modify these settings.
Display of missing references	Admin can configure the display, including value and corresponding footnote, for 'missing' values for the following table types, time-concentration, demographics, all others.	User cannot modify these settings.
Relative nominal time replacement	Admin can apply the rule and configure the associated footnote that if relative nominal times are used instead of relative actual times, each concentration value is flagged in the time-concentration tables and has an associated footnote assigned.	User cannot modify these settings.
Display analyte, matrix, and day	Admin can independently select as a default for the Matrix (e.g., Plasma), Analyte (e.g. Parent), and Day (e.g., Day 1) to be displayed in the final table as headers.	User can independently select for the Matrix (e.g., Plasma), Analyte (e.g., Parent), and Day (e.g., Day 1) to be displayed in the final table as headers.

Configurable formatted output: table settings
Feature	Administrator	User
Selection of tables	Admin can determine which tables are available for the user and from this list initially create the default list of available tables.	From the list of available tables as set by Admin, User can determine which of these tables are actually generated per run, i.e., User can modify the default list set by Admin.
Selection of variables for tables	For each table, Admin can determine which variables are available for inclusion, along with their order. From the list of available variables, Admin determines which variables are actually included and their default ordering in the generated table.	From the list of available table variables based on the Admin settings, User can determine which of these variables are actually included in the table and their order per run, i.e., User can change the defaults that were set by Admin.
Summary statistics	Admin can determine which summary statistics are available to be included in the table along with their order. From the list of available statistics, Admin determines which statistics are actually included and their default ordering in the generated tables.	From the list of available summary statistics based on the Admin settings, User can determine which of these summary statistics are actually included in the table and their order per run, i.e., User can change the defaults that were set by Admin.
Precision	Admin can set the defaults for the precision of variables and summary statistic values.	User can modify the Admin defaults for precision per variable. Precision choices include number of decimal places, significant figures, or special significant figures. If SpecialSignificant is selected and the number of digits before the decimal is more than or equal to the number of significant digits specified, the result is the value before the decimal. Otherwise, the traditional significant rule is applied to the value.
Formatting	Tables are considered to be constructed from basic elements such as Header, Body, Footnotes, Variable Names, Variable Values, etc. Admin can set the font, font style, font size, alignment, and underline/no underline for these elements. In addition the thickness of separation lines (e.g., between the header and body of a table) can be set and grid lines can be switched on and off. Output settings such as paper size (US Letter vs. A4) and orientation (portrait vs. landscape) can be configured and set as defaults per table type.	User cannot modify most of the formatting options for tables. The exceptions are the settings for output setting, which can be user-modified for a specific run.

Configurable business rules: graph settings
Feature	Administrator	User
Time-Scale factors set on a per time scale range basis	Admin can configure time scale factors independently for each time scale range, to define the number of major ticks based on minutes, hours, days, and weeks for time-concentration graphs. Admin can also configure if all concentration graphs have the same scaling and ticks independently for the X- and Y-axis.	User can make changes for individual runs.
Display analyte, matrix, and day	Admin can default to have independently the Matrix (e.g., Plasma), Analyte (e.g., Parent), and Day (e.g., Day 1) be displayed in the final graph as labels.	User can independently have the Matrix (e.g., Plasma), Analyte (e.g., Parent), and Day (e.g., Day 1) be displayed in the final graph as labels.
X-Axis format for categorical graphs	Admin can default if categorical graphs have split or offset display for the X-axis.	User can select if categorical graphs in a run have split or offset display for the X-axis.
Axis starting points	Admin can default independently to either force the X-axis and/or Y-axis to start from zero or not.	User cannot modify these settings.

Configurable formatted output: settings affecting all output
Feature	Administrator	User
Variable and PK parameter nomenclature (mapping)	Admin can configure the display name to be used in the final output created by AutoPilot Toolkit for variables (e.g., gender) and PK parameters (e.g., AUCinf). Also, Admin can configure the name of the PK parameter graph filenames.	User cannot modify these settings.
PK parameter selection	The configuration settings file does not retain the PK Parameter settings that are changed by the Administrator.	User cannot modify which PK parameters are available, but can assign per table which PK parameters are displayed in the output.
Descriptive statistics selection	Admin can configure which descriptive statistics are available to the user for the overall system.	User cannot modify which descriptive statistics are available, but can assign per table which PK parameters are displayed in the output.
Precision selection	Admin can configure the precision per variable for the overall system.	User can modify these precision per output and run.

Configurable formatted output: graph settings
Feature	Administrator	User
Selection of graphs	Admin can determine which graphs are available and from this list initially create the default list of available graphs.	From the list of available graphs as determined by Admin, User can determine which of these graphs are actually generated per run, i.e., User can modify Admin default for generated graphs.
Output details	Admin can determine default values for output details on the graphs that are generated. Depending on graph type, these details can include: •Creation of lin and/or log Y-axis •Display of a summary value such as mean or median •Display of an error value such as Standard Deviation or Standard Error •Display of up and/or down error bars •Display of regression line (for PK Parameters) •Display of LOQ lines (for PK Parameters)	User can modify all of the output details on a per-run basis.
Formatting	Admin can determine the following formatting options for graphs: •Print options such as orientation, paper size and margins •Text elements of a graph such as title, legend, and labels can be activated or deactivated, the format (font, font style, font size) •Legend position (note that center or left alignment may not work for a legend, in which case the default of upper-right is used) •Line elements of a graph such as error bars, axis line, tick lines, etc. Grid lines and line thickness have not yet been implemented. On occasion, the individual plot of the first subject may not display the same font as what is set here, whereas the remaining plots use the specified font.	User cannot modify most of the options for the formatting of graphs. An exception is the print orientation (portrait vs. landscape).

Configurable formatted output: text and appendix settings
Feature	Administrator	User
Selection	Admin can determine which text items are available for the user and from this list initially create the default of available text items.	From the list of available text items as determined by admin, User can determine which items are actually generated per run, i.e., User can modify the Admin default for generated text output.
Formatting	Admin can set the defaults for orientation, paper size, and margins and select the order and layout options for the graphs that are included in the text document that incorporates all the individual time-concentration, excretion rate, and percent dose remaining graphs.	User can modify all of the Admin formatting settings on a per-run basis.