Execute sendDashboard app
The sendigR package contains an encapsulated Shiny app - SendDashboard. The app enables the user to search and extract historical control data in a SEND database.
| Function | Description |
|---|---|
| execSendDashboard | Starts the SendDashboard app |
Example
Connect to the database and start the app.
library(sendigR)
dbToken <- initEnvironment(dbType='sqlite', dbPath='/path/to/db/send.db')
execSendDashboard(dbToken)Remember to disconnect from database when leaving the app.
disconnectDB(dbToken)A test database can be found here -
- Database
Download the database in local directory and update the dbPath.
Demo
A Demo app can be found here -
- Shiny App Demo
sendigR Shiny App Features
Sidebar Menu
side_bar
Select Study Start Date Range:
User can select date range from the calendar input.
Select Study Design:
User can select study design type from drop down menu.
Select Route of Administration:
User can select one or multiple route of administration from list that extracted from database.
Select Species:
User can select one or multiple species from the suggested list. The list extracted from the current database.
Select Strain:
The suggested list of strain depends on what species selected before. User can select one or multiple strain.
Select Sex:
User can select sex of the animals to filter from drop down menu.
Include uncertain rows:
Whether user want to include uncertain control animal. see what uncertain mean
Generate/Update Data:
Whenever user change any input in sidebar menu, Generate/Update Data button need to click to update the filter criteria.
Tab for ANIMALS | MI | LB | BW | Download
On the top middle of the page there are few tab that shows different table for different domain
ANIMALS
When user click Generate/Update Data button, app will filter and extract a table containing control animal information specified in sidebar input fields.
Common feature of the table
Show entries:
User can choose how many entry they want to show at once from the drop down menu located upper left side of the table.
Search:
There is a global search button located upper right side of the table. User can search any word globally in the table. Table will show entry that match the search.
Column filter:
Located under the each column name of the table. User can filter the table
Pagination:
Page number is available at bottom right of the table. User can go to specific page using the page number. Next and previous button can be use to go to next and previous page, respectively.
Download Button:
User can download current table as csv or rds format by clicking on appropriate download button located at bottom right of the table.
Column name:
If user hover the cursor on the column name, it will show the full name of the column.
column_hover
Display Column:
Each of the Individual table of MI, LB and BW domain have a vertical column at left side of table. Individual table shows some specific column by default. More column can be selected by checking the box in display column. This will update the table and show all the columns that selected in left display column. 
This vertical left display column can be hide by checking the show only table check box located above the display column
Filter Animal Age
MI, LB, and BW tab have filter option for animal age. User can select animal age range from slider. User also need to click update button to show other tables in that tab. 
MI (Microscopic Findings) Tab
MI Findings
User can further filter control animals and find historical control incidence rate table for specific MISPEC such as Kidney. 
Individual Records
This table shows MI domain information for filtered control animals.
Aggregate Table
Aggregate table shows the percentage of Microscopic Findings. User can filter specific tissue or organ in MISPEC column and table will shows the count and percentage of the findings. The table is grouped by MISPEC, SPECIES, STRAIN, SEX and ROUTE columns.
LB (Laboratory Test Results) Tab
Individual Records
This table shows LB domain information for filtered control animals.
Numeric Aggregate Table
Table shows mean and standard deviation of laboratory test results of numeric variable. Table is grouped by LBSPEC, SPECIES, STRAIN, SEX, ROUTE, LBTESTCD, LBTEST and LBSTRESU columns.
Categorical Aggregate Table
Aggregate table shows percentage of laboratory result for lab test which is categorical.
LB Observation
User can select specific lab test and find percentage of the lab result.
BW (Body Weight) Tab
Individual Records
This table shows BW domain information for filtered control animals.
Aggregate Table
Table shows mean and standard deviation of body weight.
Table is grouped by AGEDAYS, SPECIES, STRAIN, ROUTE, SEX, BWORRESU columns.
Aggregate Plot
Plot show mean body weight over age days. User can select from two type plot. Default plot show mean of the mean of body weight for selected interval of age days. Original Data plot show the mean body weight for animal age days.