Nothing
## ----options, echo = FALSE, message = FALSE-----------------------------------------------------------------------------------------------------------------------------
library(knitr)
opts_chunk$set(
echo = TRUE,
results = 'asis',
warning = FALSE,
error = FALSE, message = FALSE, cache = FALSE,
fig.width = 8, fig.height = 7,
fig.path = "./figures_vignette/",
fig.align = 'center')
options(width = 170)#, stringsAsFactors = FALSE
options(warn = 1)#instead of warn = 0 by default -> to have place where warnings occur in the call to Sweave function
heightLineIn <- 0.2
## ----loadPackages, message = FALSE--------------------------------------------------------------------------------------------------------------------------------------
library(clinDataReview)
## ----loadData-----------------------------------------------------------------------------------------------------------------------------------------------------------
library(clinUtils)
data(dataADaMCDISCP01)
labelVars <- attr(dataADaMCDISCP01, "labelVars")
dataLB <- dataADaMCDISCP01$ADLBC
dataDM <- dataADaMCDISCP01$ADSL
dataAE <- dataADaMCDISCP01$ADAE
## ----annotateData, message = TRUE, warning = TRUE-----------------------------------------------------------------------------------------------------------------------
dataLBAnnot <- annotateData(
data = dataLB,
annotations = list(data = dataDM, vars = c("ETHNIC", "ARM")),
verbose = TRUE
)
knitr::kable(
head(dataLBAnnot),
caption = paste("Laboratory parameters annotated with",
"demographics information with the `annotatedData` function"
)
)
## ----filterData, message = TRUE, warning = TRUE-------------------------------------------------------------------------------------------------------------------------
dataLBAnnotTreatment <- filterData(
data = dataLBAnnot,
filters = list(var = "ARM", value = "Placebo", rev = TRUE),
verbose = TRUE
)
knitr::kable(
unique(dataLBAnnotTreatment[, c("USUBJID", "ARM")]),
caption = paste("Subset of laboratory parameters filtered",
"with placebo patients"
)
)
## ----transformData, message = TRUE, warning = TRUE----------------------------------------------------------------------------------------------------------------------
eDishData <- transformData(
data = subset(dataLB, PARAMCD %in% c("ALT", "BILI")),
transformations = list(
type = "pivot_wider",
varsID = c("USUBJID", "VISIT"),
varsValue = c("LBSTRESN", "LBNRIND"),
varPivot = "PARAMCD"
),
verbose = TRUE,
labelVars = labelVars
)
knitr::kable(head(eDishData))
## ----processData--------------------------------------------------------------------------------------------------------------------------------------------------------
dataLBAnnotTreatment2 <- processData(
data = dataLB,
processing = list(
list(annotate = list(data = dataDM, vars = c("ETHNIC", "ARM"))),
list(filter = list(var = "ARM", value = "Placebo", rev = TRUE))
),
verbose = TRUE
)
identical(dataLBAnnotTreatment, dataLBAnnotTreatment2)
## ----sessionInfo, echo = FALSE------------------------------------------------------------------------------------------------------------------------------------------
print(sessionInfo())
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