Man pages for fitzgerald-lab/labkey.occams
Download and clean LabKey data
| connect.to.labkey | Create connection to Labkey |
| crf.prefixes | Tibble for clinical table prefixes current 2019 Oct |
| download.wide.format | Download in wide format the Labkey data for all or a selected... |
| dump.clinical.data | Download all tables directly from Labkey for all or a subset... |
| get.patients | Get selected patients in the wide table format |
| get.prefixes | Get the table prefixes from the schema |
| get.tables.by.crf | Get tables for the given CRF term (see crf.prefixes) or... |
| hello | Hello, World! |
| list.clinical.tables | List the clinical tables available in Labkey |
| read.demographics | Read data from demographics CRF table. Strips out columns... |
| read.endpoint | Read data from endpoint CRF table. Strips out columns that... |
| read.exposures | Read data from expoosures CRF tables. This includes: family... |
| read.followup | Read data from followup, endpoint, and recurrence CRF tables.... |
| read.pathology | Read data from pathology CRF table |
| read.prestage | Read data from prestaging CRF tables There are 6 tables that... |
| read.referral.diagnosis | Read data from referral & diagnosis CRF tables |
| read.surgery | Read data from surgery CRF tables |
| read.therapy | Read data from therapy plan CRF tables Merged all of the... |
| read.treatment.plan | Read data from treatment plan CRF tables |
