In vojtechhuser/DataQuality: Data Quality study in OHDSI and data quality evaluation

exportFolder <- params$exportFolder
# exportFolder
#toc turned to yes makes security promt in word, so it is turned off (NOT TRUE)
#something else turns it on

options(scipen = 999)

# sample code
# results <- read.csv(file.path(exportFolder, "tablesAndFigures", "EmpiricalCalibration.csv"))
#     analysisIds <- unique(results$analysisId)
#     analysisIds <- analysisIds[order(analysisIds)]
#     hois <- 3

Person data

knitr::include_graphics(file.path(exportFolder, "DemogrPyramidFigure.png"))

Visit data

knitr::include_graphics(file.path(exportFolder, "VisitsByDecileDotPlot.png"))

Achilles Heel

This output contains additional column with value as structured output (compared to Atlas view of Heel errors)

h<-read.csv(file = file.path(exportFolder, "HeelOutput.csv"))
knitr::kable(h)

Unmapped Data

d<-read.csv(file = file.path(exportFolder, "SelectedDerivedMeasures.csv"))

dsmall<-d[d$measure_id=='UnmappedData:byDomain:Percentage',]
knitr::kable(dsmall,row.names = F)

Experimental: All Achilles derived measures with names

#read names of the derived measures
measNames<-read.csv(system.file("csv","derived_analysis_details.csv",package="Achilles"))

d<-merge(d,measNames[,c("measure_id","name")],all.x = T)
knitr::kable(d)

vojtechhuser/DataQuality documentation built on May 10, 2020, 8:31 a.m.