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
• 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, complications or comorbidities
• 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.