Adverse Event Explorer: test evidence

AE-DATA-003 No customization is needed to initialize a chart when the data object contains all default variables above. Just pass an empty object ({}) for settings and initialize the chart like so: aeTable("body",{}).init(data)

AE-API-001 A factory to create a custom aeTable object.

AE-DATA-001 AE Explorers are initialized using JSON data files that match the format created by d3.csv(). The chart requires a data set with one record per adverse event and optionally with placeholder rows for participants who didn't experience any adverse events over the course of the study. The chart uses column names from the ADAM data standard by default, but can be customized to work with any column names as long as the data structure is as expected.

AE-USER-014 The preferred terms for a given system organ class are hidden on the default view. To show the hidden preferred terms rows, click on the '+' to the left of a given system organ class in the category column. This will expand the table to show the nested rows for this system organ class.

AE-USER-015 The preferred terms for a given system organ class are hidden on the default view. After a category has been expanded, you can hide the nested rows by clicking on the '-' to the left of a given system organ class in the category column. This will collapse the table to hide the nested rows for this system organ class.

AE-REG-001 Confirm that clicking on the "+" to the left of each category name expands the dataset

AE-REG-002 Confirm that clicking on the “-“ to the left of each category name after it is expanded collapses the dataset

AE-REG-008 Confirm that summarizing by 'participant' displays the number of participants who experienced an AE of the corresponding category by group

AE-USER-006 This toggle option allows the user to view the adverse events data by participant or event. Summarizing AEs by participant presents the number of participants who experienced an AE of the corresponding category at least once by group. Summarizing AEs by event presents the number of events of the corresponding category by group. The chart defaults to display the participant data, which displays the adverse events.

AE-REG-009 Confirm that summarizing by 'event' displays the number of events of the corresponding category by group

AE-REG-033 Confirm that the following settings summarize the data by participant on default:

AE-REG-035 Confirm that the following settings summarize the data by event on default:

AE-USER-001 This is a text box feature which is used to filter out all adverse events below the percentage entered. The default is 0%, but the default value can be adjusted according to the user's needs. Users can type any alphanumeric value into this box. Values must be numeric for the filter to work. After hitting Enter or clicking outside the box, the Explorer will hide the data rows where the prevalence for all groups is below the threshold entered. If any group has a prevalence at or above the threshold entered, it will be displayed on screen with all nested categories shown. To return to the default view, the user must either refresh the page or enter 0 into the filter box and again hit Enter or click outside the box.

AE-REG-007 Confirm that entering a minimum prevalence will filter the data based on the entered threshold

AE-REG-012 Confirm that the "Filter by prevalence" field no longer accepts letters in the prevalence input, and that the up and down buttons work as expected

AE-REG-013 Confirm that the graphic updates after each keystroke in the search and filter by prevalence inputs (instead of after focus leaves the input altogether)

AE-USER-007 The Search box is used to search the category column of the table for terms of interest. Users can type any alphanumeric term into this box. After hitting Enter or clicking outside the box, the Safety Explorer will display only the categories that contain the search term entered. The search terms will also be highlighted in yellow within the category column. Text will also display next to the Search box indicating the number of categories returned with that search term. If there are no results matching the term entered, text will display next to the Search box indicating that no categories were returned with a matching search term. The table display will not change if there are no matches in the search.

AE-REG-003 Type a value into the search box and confirm that the table updates to only show the categories that match the search term. Matching terms should be highlighted in bold, regal orange.

AE-REG-004 Confirm that the number of matching terms displays to the left of the search box

AE-USER-008 To reset to the default Explorer view after conducting a search, users can click on the red X button in the alert bar which displays next to the Search box. Alternatively, users can clear the text in the Search box and hit Enter or click outside the box.

AE-REG-005 Delete the entered value from the search bar and confirm that table resets

AE-REG-006 Confirm that filters on events (e.g. Severity) are working as expected by filtering and then clicking on a category to display the underlying data listing to confirm that the data displayed matches the filtering

AE-REG-018 Hover over the ‘E’ superscript beside one of the filter labels to display an explanation of an event filter

AE-USER-002 This menu is used to filter by whether or not an event is serious in the data set. The default is set to include all events.

AE-USER-003 This menu is used to filter by adverse event severity level in the data set. The current severity levels captured are mild, moderate, and severe. The default is to display all severity levels.

AE-USER-018 The chart can be configured to have any number of data filters. Each specified filter has a drop-down menu that is used to filter the visit data that is displayed in the chart.

AE-REG-014 Confirm that if there are no AEs that match the current filters - the error message thrown says "Error: No AEs found for the current filters. Update the filters to see results."

AE-USER-016 Clicking on a category or any of its preferred terms will open the Show Details view. This view displays the raw data for every adverse event under that system organ class and/or preferred term.

AE-REG-019 Confirm that you can view a detailed listing of events by clicking on the category name of a given row in the table

AE-REG-022 Confirm that there is a sentence in the header stating ‘Details for x category name records’ that displays both the correct ‘x’ value for the number of records in the listing and ‘category name’

AE-USER-017 The Return to the Summary View button is only visible if users have clicked on a category or preferred term to show the details view. Clicking on this button returns users to the default Safety Explorer view.

AE-REG-020 Confirm that the ‘Return to the Summary View’ button brings you back to the original summary view.

AE-REG-021 Confirm that the section labeled ‘The listing is filtered as shown:’ displays the filters that were selected in the original summary view

AE-USER-012 The column following the Groups columns shows the rate of an adverse event by group. Each group is represented by a color-coded dot that corresponds to the color of the treatment group. The rate of the event for each group is shown on a scale by percentage. When hovering over a colored dot, the exact percentage appears for the group.

AE-REG-016 Hover over a value in ‘AE Rate by group’ to see the percentage of participants affected by group

AE-USER-009 By moving a mouse cursor over certain sections of the table, users can display metadata for some variables. Hovering over the ‘E’ superscript beside one of the filter labels will display an explanation of an event filter. Hovering the cursor over a particular row will highlight the row in gray. Hovering over a value in a treatment group will display the number of participants affected out of n. Hovering over a colored data point in the AE Rate by Group column will present the percentage value for the group. Hovering over a diamond in the Difference Between Groups column will perform two actions:

AE-USER-013 The column on the right-hand side of the table shows a graphical representation of the difference between groups in the data set. Group comparisons are represented with a color-coded diamond that corresponds to the colors of the treatment groups being compared. When hovering over a diamond, the ratios and percentages of occurrence for the event appears for the compared groups in addition to the difference between the two groups.

AE-USER-011 Display the two treatments compared by percentage and the overall difference between them.

AE-REG-017 Hover over a value in ‘Difference Between Groups’ to see two treatments compared and the overall difference between them. This will also highlight the bar containing the value in gray and reveal the count and percentage of both groups under their treatment name

AE-USER-009 By moving a mouse cursor over certain sections of the table, users can display metadata for some variables. Hovering over the ‘E’ superscript beside one of the filter labels will display an explanation of an event filter. Hovering the cursor over a particular row will highlight the row in gray. Hovering over a value in a treatment group will display the number of participants affected out of n. Hovering over a colored data point in the AE Rate by Group column will present the percentage value for the group. Hovering over a diamond in the Difference Between Groups column will perform two actions:

AE-USER-010 Display the raw data (numerator and denominator) used to calculate the adverse event prevalence percentage for each row in the table for the selected groups.

AE-REG-015 Hover over a value in a treatment group to see the number of participants affected out of n

AE-USER-019 The chart can be configured to show or hide any of the treatment groups found in the data. Showing only 1 treatment group will automatically hide the 'Difference Between Groups' column and the 'Total' column.

AE-REG-037 Confirm that the following setting only shows treatment group totals and hides the 'Difference Between Groups' column:

AE-REG-039 Confirm that the following setting only shows the placebo group and hides the 'total' and 'Difference Between Groups' columns:

AE-CFG-004 An object that specifies valid options for the primary variable mappings (id, major, minor and groups). When 2+ options are specified for any given mapping, a control is drawn so that the user can interactively update chart to use any of the options.

AE-REG-041 Confirm that adding 2+ values to each component (id, major, minor and groups) of the variableOptions array adds a new control.

AE-REG-043 Confirm that the new variableOption controls work before and after filtering, searching, and changing the summarizeBy option.

AE-REG-044 Confirm that the value for the default variable appears in the variable control even if it is not specified in config. That is, ARM appears in the groups control with these settings:

AE-USER-020 By entering the following settings {"validation": true}, users can download the data as a CSV. The CSV file will contain all of the data if no filters have been utilized. If filters have been used, the CSV file will contain the resulting data. The CSV download will be named using the following convention: major term-minor term-summary variable. The summary variable can either be 'Participant' or 'Event", depending on what the user summarized the data by using the toggle in the menu.

AE-CFG-009 adds a link to download the summarized data in a comma-separated format

AE-REG-026 Confirm that entering the following settings in the CAT will show the option to download the data file: {"validation": true}

AE-REG-027 Confirm that when downloading a CSV, the file will save as major term - minor term - participant/event

AE-REG-028 Confirm that when downloading a participant CSV, "participant" appears in the title

AE-REG-029 Confirm that when downloading an event CSV, "event" appears in the title

AE-REG-030 Confirm that filtering the data will appear as filtered in the CSV download

AE-CFG-001 The most straightforward way to customize an AE Explorer is by using a settings object whose properties describe the chart's behavior and appearance. Parameters for the settings object are described in detail below. All defaults can be over-written by users when creating an AE Explorer.

AE-CFG-002 Objects passed to aeTable() which controls the settings and appearance of the output. The sections below describe each aeexplorer setting as of version 3.4.0.

AE-CFG-003 an object that specifies how to map columns from the data file to the chart settings

AE-DATA-003 No customization is needed to initialize a chart when the data object contains all default variables above. Just pass an empty object ({}) for settings and initialize the chart like so: aeTable("body",{}).init(data)

AE-USER-002 This menu is used to filter by whether or not an event is serious in the data set. The default is set to include all events.

AE-USER-003 This menu is used to filter by adverse event severity level in the data set. The current severity levels captured are mild, moderate, and severe. The default is to display all severity levels.

AE-USER-004 This menu is used to filter by the relatedness categories in the data set. The options included in the chart are not related, unlikely related, probably related, definitely related. The default is to display all relationships.

AE-USER-005 This menu is used to filter by the outcome categories in the data set. The options included in the chart are recovered; resolved without sequelae; resolved, recovered; and resolved with sequelae. The default is to display all outcomes.

AE-USER-018 The chart can be configured to have any number of data filters. Each specified filter has a drop-down menu that is used to filter the visit data that is displayed in the chart.

AE-REG-031 Confirm that the following settings set the serious event filter to ‘Y’ and make it the only filter to be displayed by default:

AE-CFG-007 an object containing default settings regarding appearance of the tables

AE-CFG-008 Object to specify the appearance of the plots embedded in the table rows.

AE-REG-046 Confirm in CAT that margins are drawn for the dot plot when plotSettings.margin is specified. Just tweak the following settings object, and confirm that the margin changes as expected: {plotSettings: {margin: {left: 40, right: 40}}}

AE-REG-033 Confirm that the following settings summarize the data by participant on default:

AE-REG-035 Confirm that the following settings summarize the data by event on default:

AE-USER-019 The chart can be configured to show or hide any of the treatment groups found in the data. Showing only 1 treatment group will automatically hide the 'Difference Between Groups' column and the 'Total' column.

AE-REG-037 Confirm that the following setting only shows treatment group totals and hides the 'Difference Between Groups' column:

AE-REG-039 Confirm that the following setting only shows the placebo group and hides the 'total' and 'Difference Between Groups' columns:

AE-CFG-005 An array specifying which levels of settings.variables.groups will appear as columns in the table.

AE-CFG-006 an array of colors that control the color of each group in the table

AE-DATA-001 AE Explorers are initialized using JSON data files that match the format created by d3.csv(). The chart requires a data set with one record per adverse event and optionally with placeholder rows for participants who didn't experience any adverse events over the course of the study. The chart uses column names from the ADAM data standard by default, but can be customized to work with any column names as long as the data structure is as expected.

AE-DATA-003 No customization is needed to initialize a chart when the data object contains all default variables above. Just pass an empty object ({}) for settings and initialize the chart like so: aeTable("body",{}).init(data)

AE-CFG-003 an object that specifies how to map columns from the data file to the chart settings

AE-DATA-001 AE Explorers are initialized using JSON data files that match the format created by d3.csv(). The chart requires a data set with one record per adverse event and optionally with placeholder rows for participants who didn't experience any adverse events over the course of the study. The chart uses column names from the ADAM data standard by default, but can be customized to work with any column names as long as the data structure is as expected.

AE-REG-008 Confirm that summarizing by 'participant' displays the number of participants who experienced an AE of the corresponding category by group

AE-REG-009 Confirm that summarizing by 'event' displays the number of events of the corresponding category by group

AE-REG-006 Confirm that filters on events (e.g. Severity) are working as expected by filtering and then clicking on a category to display the underlying data listing to confirm that the data displayed matches the filtering

AE-USER-018 The chart can be configured to have any number of data filters. Each specified filter has a drop-down menu that is used to filter the visit data that is displayed in the chart.

AE-USER-013 The column on the right-hand side of the table shows a graphical representation of the difference between groups in the data set. Group comparisons are represented with a color-coded diamond that corresponds to the colors of the treatment groups being compared. When hovering over a diamond, the ratios and percentages of occurrence for the event appears for the compared groups in addition to the difference between the two groups.

AE-USER-001 This is a text box feature which is used to filter out all adverse events below the percentage entered. The default is 0%, but the default value can be adjusted according to the user's needs. Users can type any alphanumeric value into this box. Values must be numeric for the filter to work. After hitting Enter or clicking outside the box, the Explorer will hide the data rows where the prevalence for all groups is below the threshold entered. If any group has a prevalence at or above the threshold entered, it will be displayed on screen with all nested categories shown. To return to the default view, the user must either refresh the page or enter 0 into the filter box and again hit Enter or click outside the box.

AE-REG-007 Confirm that entering a minimum prevalence will filter the data based on the entered threshold

AE-USER-007 The Search box is used to search the category column of the table for terms of interest. Users can type any alphanumeric term into this box. After hitting Enter or clicking outside the box, the Safety Explorer will display only the categories that contain the search term entered. The search terms will also be highlighted in yellow within the category column. Text will also display next to the Search box indicating the number of categories returned with that search term. If there are no results matching the term entered, text will display next to the Search box indicating that no categories were returned with a matching search term. The table display will not change if there are no matches in the search.

AE-USER-012 The column following the Groups columns shows the rate of an adverse event by group. Each group is represented by a color-coded dot that corresponds to the color of the treatment group. The rate of the event for each group is shown on a scale by percentage. When hovering over a colored dot, the exact percentage appears for the group.

AE-USER-012 The column following the Groups columns shows the rate of an adverse event by group. Each group is represented by a color-coded dot that corresponds to the color of the treatment group. The rate of the event for each group is shown on a scale by percentage. When hovering over a colored dot, the exact percentage appears for the group.

AE-USER-013 The column on the right-hand side of the table shows a graphical representation of the difference between groups in the data set. Group comparisons are represented with a color-coded diamond that corresponds to the colors of the treatment groups being compared. When hovering over a diamond, the ratios and percentages of occurrence for the event appears for the compared groups in addition to the difference between the two groups.

AE-REG-046 Confirm in CAT that margins are drawn for the dot plot when plotSettings.margin is specified. Just tweak the following settings object, and confirm that the margin changes as expected: {plotSettings: {margin: {left: 40, right: 40}}}

AE-CFG-006 an array of colors that control the color of each group in the table

AE-REG-040 Confirm that when grouping by RACE, yellow is no longer the color that appears

AE-USER-010 Display the raw data (numerator and denominator) used to calculate the adverse event prevalence percentage for each row in the table for the selected groups.

AE-USER-011 Display the two treatments compared by percentage and the overall difference between them.

AE-REG-015 Hover over a value in a treatment group to see the number of participants affected out of n

AE-REG-016 Hover over a value in ‘AE Rate by group’ to see the percentage of participants affected by group

AE-REG-017 Hover over a value in ‘Difference Between Groups’ to see two treatments compared and the overall difference between them. This will also highlight the bar containing the value in gray and reveal the count and percentage of both groups under their treatment name

AE-REG-027 Confirm that when downloading a CSV, the file will save as major term - minor term - participant/event

AE-REG-028 Confirm that when downloading a participant CSV, "participant" appears in the title

AE-REG-029 Confirm that when downloading an event CSV, "event" appears in the title

AE-REG-030 Confirm that filtering the data will appear as filtered in the CSV download

AE-USER-020 By entering the following settings {"validation": true}, users can download the data as a CSV. The CSV file will contain all of the data if no filters have been utilized. If filters have been used, the CSV file will contain the resulting data. The CSV download will be named using the following convention: major term-minor term-summary variable. The summary variable can either be 'Participant' or 'Event", depending on what the user summarized the data by using the toggle in the menu.