KEEPER

Introduction

An R package review patient profiles for phenotype validation.

Features

• From an instantiated cohort, identifies specified number of random persons. It also allows for non random selection by specifying a set of personId as input.
• Extracts person level data for each person from the common data model, and constructs a results object in rds form. This rds object has person level data with personId and dates.
• Accepts a set of configurable parameters for the shiny application. This parameters will be chosen in the shiny app. e.g. regular expression.
• Allows additional de-identification using two optional mechanisms (shift dates and replace OMOP personId with a new random id). Shift date: shifts all dates so that the first observation_period_start_date for a person is set to January 1st 2000, and all other dates are shifted in relation to this date. Also creates and replaces the source personId with a new randomly generated id.

How to use

1. Go the output location in your file browser (e.g. windows file explorer in a Windows computer) and start 'KEEPER.Rproj'.
2. In R console now run renv::restore() to enable renv. This will download all required packages and dependencies and set up the run environment.
3. Run createKEEPER() with approapriate parameters (see an example in R/createKEEPER.R) to create a csv file with patient profiles. You will need the following input:

• instatiated cohort with patients of interest in COHORT table or in another table that has the same fields as COHORT,
• doi:
• symptoms:
• comorbidities:
• drugs:
• diagnosticProcedures:
• measurements:
• alternativeDiagnosis:
• treatmentProcedures:
• complications:

*note: if no suitable concept_ids exists for an input string, input c(0)

Use useAncestor = TRUE to switch from verbatim string of concept_ids vs ancestors. In latter case, the app will take you concept_ids and include them along with their descendants.

Use sampleSize to specify desired numebr of patients to be selected.

Use assignNewId = TRUE to replace person_id with sequence.

 createKEEPER(
   connectionDetails = connectionDetails,
   exportFolder = "c:/temp/keeper",
   databaseId = "Synpuf",
   cdmDatabaseSchema = "dbo",
   cohortDatabaseSchema = "results",
   cohortTable = "cohort",
   cohortDefinitionId = 1234,
   cohortName = "DM type I",
   sampleSize = 100,
   assignNewId = TRUE,
   useAncestor = TRUE,
   doi = c(201820,442793,443238,4016045,4065354,45757392, 4051114, 433968, 375545, 29555009, 4209145, 4034964, 380834, 4299544, 4226354, 4159742, 43530690, 433736,
                     320128, 4170226, 40443308, 441267, 4163735, 192963, 85828009),
   symptoms = c(4232487, 4229881),
   comorbidities = c(432867, 436670),
   drugs = c(1730370, 21604490, 21601682, 21601855, 21601462, 21600280, 21602728, 1366773, 21602689, 21603923, 21603746),
   diagnosticProcedures = c(40756884, 4143852, 2746768, 2746766),
   measurements	= c(3034962, 3000483, 3034962, 3000483, 3004501, 3033408, 3005131, 3024629, 3031266, 3037110, 3009261, 3022548, 3019210, 3025232, 3033819,
                  3000845, 3002666, 3004077, 3026300, 3014737, 3027198, 3025398, 3010300, 3020399, 3007332, 3025673, 3027457, 3010084, 3004410, 3005673),
   alternativeDiagnosis = c(201820,442793,443238,4016045,4065354,45757392, 4051114, 433968, 375545, 29555009, 4209145, 4034964, 380834, 4299544, 4226354, 4159742, 43530690, 433736,
                          320128, 4170226, 40443308, 441267, 4163735, 192963, 85828009),
   treatmentProcedures = c(0),
   complications =  c(201820,442793,443238,4016045,4065354,45757392, 4051114, 433968, 375545, 29555009, 4209145, 4034964,
                       380834, 4299544, 4226354, 4159742, 43530690, 433736, 320128, 4170226, 40443308, 441267, 4163735, 192963, 85828009)                             
 )

Output

Output contains the following information per patient:

• demographics (age, gender)
• visit_context: information about visits overlapping with the index date (day 0) formatted as the type of visit and its duration
• observation_period: information about overlapping OBSERVATION_PERIOD formatted as days prior - days after the index date
• presentation: all records in CONDITION_OCCURRENCE on day 0 with corrresponding type and status
• comorbidities: records in CONDITION_ERA and OBSERVATION that were selected as co-comoribidites and risk factors within all time prior excluding day 0. The list does not inlcude symptoms, disease of interest and complications
• symptoms: records in CONDITION_ERA that were selected as symptoms 30 days prior excluding day 0. The list does not include disease of interest and complications. If you want to see symptoms outside of this window, please place them in complications.
• prior_disease: records in CONDITION_ERA that were selected as disease of interest or complications all time prior excluding day 0
• prior_drugs: records in DRUG_ERA that were selected as drugs of interest all time prior excluding day 0 formatted as day of era start and length of drug era
• prior_treatment_procedures: records in PROCEDURE_OCCURRENCE that were selected as treatments of interest within all time prior excluding day 0
• diagnostic_procedures: records in PROCEDURE_OCCURRENCE that were selected as diagnostic procedures within all time prior excluding day 0
• measurements: records in MEASUREMENT that were selected as measurements (lab tests) of interest within 30 days before and 30 days after day 0 formatted as value and unit (if exisits) and assessment compared to the reference range provided in MEASUREMENT table (normal, abnormal high and abnormal low)
• alternative_diagnosis: records in CONDITION_ERA that were selected as alternative (competing) diagnosis withi 90 days before and 90 days after day 0. The list does not inlcude disease of interest.
• after_disease: same as prior_disease but after day 0
• after_drugs: same as prior_drugs but after day 0
• after_treatment_procedures: same as prior_treatment_procedures but after day 0
• death: death record any time after day 0

Technology

KEEPER is an R package.

System Requirements

Requires R (version 3.6.0 or higher).

Installation

1. See the instructions here for configuring your R environment, including RTools and Java.

2. In R, use the following commands to download and install CohortExplorer:

install.packages("remotes")
remotes::install_github("aostropolets/KEEPER")

User Documentation

TBD

Support

TBD

Contributing

TBD

License

KEEPER is licensed under Apache License 2.0

Development

KEEPER is being developed in R Studio.

Development status

KEEPER is under development.