Tutorial Steps:

• Install RStudio
• Install Rlabkey Package
• Query Public Data
• Handling Login/Authentication
• Query Non-Public Data

Install RStudio

• If necessary, install R version 3.0.1 or later. If you already have R installed, you can skip this step.
• If necessary, install RStudio Desktop on your local machine. If you already have RStudio installed, you can skip this step.

Install Rlabkey Package

• Open RStudio.
• On the Console enter the following:

install.packages("Rlabkey")

• Follow any prompts to complete the installation.

Query Public Data

• In this step, we will query some publicly accessible example data. We will also have the server auto-generate the query for us.
• Go to the PhysicalExam dataset at: https://www.labkey.org/home/Demos/HIV%20Study%20Tutorial/study-dataset.view?datasetId=5003
• Above the data grid, click Export and select the Script tab.
• Select the R radio button.
• Finally click Create Script.

• This will auto-generate the R code that queries the Physical Exam data:

library(Rlabkey)

# Select rows into a data frame called 'labkey.data'

labkey.data <- labkey.selectRows(
    baseUrl="https://www.labkey.org", 
    folderPath="/home/Demos/HIV Study Tutorial", 
    schemaName="study", 
    queryName="PhysicalExam", 
    viewName="",
colSelect="ParticipantId,ParticipantVisit/Visit,date,weight_kg,temperature_C,systolicBP,diastolicBP,pulse", 
    colFilter=NULL, 
    containerFilter=NULL, 
    colNameOpt="rname"
)

• Copy this code to your clipboard.
• Go to RStudio, paste the code into the Console tab, and press the Enter key.
• The query results will be displayed on the 'labkey.data' tab.
• Enter the following line into the Console to visualize the data.

plot(labkey.data$systolicbp, labkey.data$diastolicbp)

• Note that the auto-generated code will include any filters applied to the grid. For example, if you filter Physical Exam for records where temperature is greater than 37, then the auto-generated code will include a colFilter property as below:

library(Rlabkey)

# Select rows into a data frame called 'labkey.data'

labkey.data <- labkey.selectRows(
    baseUrl="https://www.labkey.org", 
    folderPath="/home/Demos/HIV Study Tutorial", 
    schemaName="study", 
    queryName="PhysicalExam", 
    viewName="", 
colSelect="ParticipantId,ParticipantVisit/Visit,date,weight_kg,temperature_C,systolicBP,diastolicBP,pulse", 
    colFilter=makeFilter(c("temperature_C", "GREATER_THAN", "37")), 
    containerFilter=NULL, 
    colNameOpt="rname"
)

Handling Login/Authentication

• To query non-public data, that is, data that requires a login/authentication step to access, you have three options:
• Set up a netrc file.
• OR
• Acquire an API key.
• OR
• Include user credentials directly in the R code using labkey.setDefaults().

Query Non-Public Data

Once you have set up authentication for RStudio, the process of querying is the same as above:

• Go to the desired data grid. Apply filters if necessary.
• Generate the R code using Export > Script > R > Create Script.
• Use that code in RStudio.

Related Topics

• R Reports