Customization

PedScope provides various configuration/customization options. These are divided into two groups, accessed through separate windows.

The Preferences window is used for settings that are independent of any particular data file. It is accessed through the File menu (Mac: use the 'PedScope' application menu). Changes to the preferences do not cause data to be (re)calculated. They have global effect - preferences are not specific to any particular data file. They tend to be related to the appearance and presentation of data, not the data themselves.

The Document Settings window is used for all settings that can alter the current data set in some way. It is accessed through the File menu. These settings affect what data is stored, or how it is stored, how it is calculated, or the accuracy with which it is calculated. These settings can be saved along with the imported pedigree information and computed data (see: Saving Data - Saving As A PedScope Data File).

Setting How Set
Inbreeding depth
(#generations)

Use the General tab of the Document Settings window.

Coefficient Display

Inbreeding and kinship coefficients can be displayed in three ways: as percentages (e.g. 12.5%), or as numbers (e.g. 0.125), or as fractions (e.g. 1/8). To adjust this use the General tab of the Preferences window.

Coefficient Precision

Use the General tab of the Preferences window to adjust the precision (no. of decimal places) used for inbreeding and kinship coefficients.

Computation of
Pedigree Metrics

Use the Compute tab of the Document Settings window to adjust the Compute individual pedigree metrics setting.

This enables main table columns such as #G Seen and #Ancestors Unique.

Computation of
Ancestral Inbreeding Coefficients

The Compute tab of the Document Settings window has an option to enable the computation of ancestral inbreeding coefficients.

Date Display

The display date format is set on the System tab of the Preferences window.

Statistics

You can enable/disable the date specific statistics tab using a setting on the Stats Columns tab of the Document Settings window.

There are also options on the Compute tab to control which of the various statistics (mean, mode, median, etc.) are reported.

Main Table Columns

Use the Main Columns tab of the Document Settings window to select which columns to show in the main table.

Note that the available columns are also affected by settings on the Compute tab.

Mate Recommendations Report

Use the Mating Values and KV Weights tabs of the Document Settings window to adjust parameters that affect the mate recommendations report.

ToolTips

There is an overall enable/disable setting for the tooltips that can appear over the main table and relations report: the Show tooltips setting on the General tab of the Preferences window.

You can also adjust the information shown using the options on the ToolTips tab of the Document Settings window.

Fonts

Adjust the screen and printer font using the General tab of the Preferences window.

Graph Colors

Use the General tab of the Preferences window to adjust the colors used in graph and chart reports.

Row & Cell Highlighting

Use the Highlighting tab of the Preferences window.

Labels

The General tab of the Preferences window has options to control the usage of standard genetics symbols (e.g. F for the inbreeding coefficient) in column labels, and whether to use concise or longer labels.

Memory Usage

The Large buffer size and Matrix representation settings on the General tab of the Document Settings window affect the memory limits used in individual reports.

The Results cache size setting on the System tab of the Preferences window controls the amount of memory that PedScope will use to store previously computed results.

Increasing this value can speed up the program when switching to and fro between different reports - at the expense of using additional memory.

Speed

The #Worker threads setting on the System tab of the Preferences window controls the number of CPU 'threads' of execution that PedScope will attempt to use.

Where possible the program uses multi-threading (parallel computations) to speed things up. The number of threads used is normally set so as to retain a responsive user interface. Increasing the Results cache size setting can speed up PedScope when switching between different reports.

Gene Drop Analysis

Use the General tab of the Document Settings window to set the #rounds to use when performing gene drop analysis.

Genome Uniqueness

Use the General tab of the Document Settings window to set the genome uniqueness threshold. For further information see Reports - Founder Metrics.

Defaults for
Living Status column

Adjust the Assume dead at age setting on the General tab of the Document Settings window.

Use of
Family/Litter Records

Use the checkboxes on the General tab of the Document Settings window. For further information see Main Window - Other Record Types.

Sex-specific Offspring Counts

Use the Compute tab of the Document Settings window to control whether or not to have separate columns for the numbers of male/female offspring in the main table - use the Compute offspring gender-specific metrics setting.

Separated Maternal/Paternal Metrics

Some columns in the main table and relations report, such as the #sire/dam siblings and %blood can be tabulated separately for each parental 'side' of the animal's pedigree.

To enable this, check the Separated maternal/paternal metrics setting in the Compute tab of the Document Settings window.

Generation Numbers

Use either of the settings in the Compute tab of the Document Settings window to enable the GN column. There are two settings, offering different ways to compute the generation number.

Relations Report Columns

Use the Relation Columns tab of the Document Settings window. Note that the available columns for the relations report are also affected by settings on the Compute tab.

Relation Descriptions

Use the Precise relation descriptions setting on the General tab of the Preferences window to adjust how genealogical relation descriptions are formatted in the relations report.

Number Precision

Use the General tab of the Preferences window to adjust the no. of decimal places used for numeric values (other than inbreeding/kinship coefficients - they are configured separately).

Terminology

PedScope uses a number of terms (words) such as 'Sex', 'Male', etc.

To customize these terms, select Preferences from the File menu (Mac: use the 'PedScope' application menu), then click on the Terminology tab. A number of preset choices are available for English-speaking breeders of cats, dogs, etc. Alternatively, select Custom from the dropdown menu then can change each term individually.


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