## ----setup,results="hide",echo=FALSE------------------------------------------ suppressPackageStartupMessages({ suppressMessages({ library(BiocFHIR) library(DT) library(jsonlite) }) }) ## ----takepeek----------------------------------------------------------------- tfile = dir(system.file("json", package="BiocFHIR"), full=TRUE) peek = jsonlite::fromJSON(tfile) names(peek) peek$resourceType names(peek$entry) length(names(peek$entry$resource)) class(peek$entry$resource) dim(peek$entry$resource) head(names(peek$entry$resource)) ## ----txpeek------------------------------------------------------------------- bu = process_fhir_bundle(tfile) bu ## ----lkpo--------------------------------------------------------------------- po1 <- process_Observation(bu$Observation) dim(po1) datatable(po1) ## ----lksch-------------------------------------------------------------------- FHIR_retention_schemas() ## ----listt-------------------------------------------------------------------- ls("package:BiocFHIR") |> grep(x=_, "process_[A-Z]", value=TRUE) ## ----lkconds------------------------------------------------------------------ data("allin", package="BiocFHIR") hascond = sapply(allin, function(x)length(x$Condition)>0) oo = do.call(rbind, lapply(allin[hascond], function(x)process_Condition(x$Condition))) dim(oo) length(unique(oo$subject.reference)) ## ----mostc-------------------------------------------------------------------- table(oo$code.coding.display) |> sort() |> tail() ## ----lksess------------------------------------------------------------------- sessionInfo()