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## ----setUpTemplateForYourStudy, eval = FALSE----------------------------------
#
# # get template from the package
# pathTemplate <- system.file(
# "doc", "patientProfiles-template-SDTM.Rmd",
# package = "patientProfilesVis"
# )
# file.copy(from = pathTemplate, to = ".")
# # Note: your current working directory can be checked with: getwd()
## ----patientProfiles-optionsChunks, echo = FALSE, cache = FALSE---------------
library(knitr)
knitr::opts_chunk$set(
error = FALSE, # stop document execution if error (not the default)
fig.align = "center"
)
## ----patientProfiles-loadPackages---------------------------------------------
library(patientProfilesVis)
## ----patientProfiles-loadData-------------------------------------------------
library(clinUtils)
# For this vignette, an example STDM dataset is used
# (subset of the CDISC Pilot 01 study)
data(dataSDTMCDISCP01, package = "clinUtils")
dataAll <- dataSDTMCDISCP01
labelVars <- attr(dataSDTMCDISCP01, "labelVars")
# If SDTM datasets should be imported from the external folder,
# the following code could be used:
# pathFiles <- list.files(path = "/path/to/data", pattern = "*.sas7bdat$", full.names = TRUE)
# dataAll <- loadDataADaMSDTM(files = pathFiles)
# labelVars <- attr(dataAll, "labelVars")
## ----patientProfiles-initialization-------------------------------------------
patientProfilesPlots <- list()
## ----patientProfiles-demographics---------------------------------------------
dmPlots <- subjectProfileTextPlot(
data = dataAll$DM,
paramValueVar = c(
"SEX", "RACE", "ETHNIC",
"COUNTRY", "ARM",
"AGE", "RFSTDTC"
),
# optional:
labelVars = labelVars
)
patientProfilesPlots <- c(patientProfilesPlots, list(DM = dmPlots))
## ----patientProfiles-medicalHistory-------------------------------------------
mhPlots <- subjectProfileTextPlot(
data = dataAll$MH,
paramValueVar = c("MHDECOD", "MHTERM", "MHSTDTC"), #"MHENDTC" if available
# optional:
paramGroupVar = c("MHSTDTC", "MHDY"),
title = "Medical history (Start - End)",
labelVars = labelVars,
table = TRUE
)
patientProfilesPlots <- c(patientProfilesPlots, list(MH = mhPlots))
## ----patientProfiles-concomitantMedications-----------------------------------
cmPlots <- subjectProfileIntervalPlot(
data = dataAll$CM,
paramVar = c(
"CMTRT",
"CMDOSE", "CMDOSU", "CMROUTE",
"CMDOSFRQ"
),
timeStartVar = "CMSTDY",
timeEndVar = "CMENDY",
# optional:
paramGroupVar = "CMCLAS", # or CMINDC
colorVar = "CMCLAS", # or CMINDC
labelVars = labelVars,
title = "Concomitant medications",
# To zoom in axis scale in study time frame
# (to avoid scale is focused on negative pre-study time frame for CM)
timeTrans = getTimeTrans(type = "asinh-neg"),
alpha = 0.8,
timeAlign = FALSE
)
patientProfilesPlots <- c(patientProfilesPlots, list(CM = cmPlots))
## ----patientProfiles-treatmentExposure----------------------------------------
exPlots <- subjectProfileIntervalPlot(
data = dataAll$EX,
paramVar = c(
"EXTRT", "EXDOSE", "EXDOSU",
"EXDOSFRM", "EXDOSFRQ", "EXROUTE"
), # "EXTPT" if available
timeStartVar = "EXSTDY",
timeEndVar = "EXENDY",
# optional:
colorVar = "EXDOSFRM",
title = "Treatment exposure",
alpha = 0.8,
labelVars = labelVars
)
patientProfilesPlots <- c(patientProfilesPlots, list(EX = exPlots))
## ----patientProfiles-adverseEvents--------------------------------------------
dataAE <- dataAll$AE$AESEV
# to adapt for specific dataset
dataAE$AESEV <- factor(dataAll$AE$AESEV, levels = c("MILD", "MODERATE", "SEVERE"))
aePlots <- subjectProfileIntervalPlot(
data = dataAll$AE,
paramVar = "AEDECOD", # AETERM, depending on coding
timeStartVar = "AESTDY",
timeEndVar = "AEENDY",
# optional:
paramGroupVar = "AESOC",
colorVar = "AESEV",
title = "Adverse events",
timeAlign = FALSE,
alpha = 0.8,
labelVars = labelVars
)
patientProfilesPlots <- c(patientProfilesPlots, list(AE = aePlots))
## ----patientProfiles-laboratory-----------------------------------------------
dataLB <- dataAll$LB
# to adapt for dataset
dataLB$LBNRIND <- factor(dataLB$LBNRIND, levels = c("LOW", "NORMAL", "HIGH", "ABNORMAL"))
# specify custom color and shape palette
colorPaletteLB <- clinUtils::getPaletteCDISC(x = dataLB$LBNRIND, var = "NRIND", type = "color")
shapePaletteLB <- clinUtils::getPaletteCDISC(x = dataLB$LBNRIND, var = "NRIND", type = "shape")
lbPlots <- subjectProfileLinePlot(
data = dataLB,
paramValueVar = "LBSTRESN",
paramNameVar = "LBTEST",
timeVar = "LBDY",
# optional
paramValueRangeVar = c("LBSTNRLO", "LBSTNRHI"),
paramGroupVar = "LBCAT", # "LBSCAT" if available
colorVar = "LBNRIND", colorPalette = colorPaletteLB,
shapeVar = "LBNRIND", shapePalette = shapePaletteLB,
shapeSize = 4,
title = "Laboratory test measurements",
alpha = 0.8,
labelVars = labelVars
)
patientProfilesPlots <- c(patientProfilesPlots, list(LB = lbPlots))
## ----patientProfiles-vitalSigns-----------------------------------------------
# If available, reference range indicator
# could be displayed via the color/shape variable
vsPlots <- subjectProfileLinePlot(
data = dataAll$VS,
paramValueVar = "VSSTRESN",
paramNameVar = "VSTEST",
timeVar = "VSDY",
# optional
# paramGroupVar = "VSCAT", # if available
colorVar = "VSPOS", # if available
shapeSize = 2,
title = "Vital signs",
alpha = 0.8,
labelVars = labelVars
)
patientProfilesPlots <- c(patientProfilesPlots, list(VS = vsPlots))
## ----patientProfiles-ECG, eval = FALSE----------------------------------------
#
# # If available, reference range indicator
# # could be displayed via the color/shape variable
#
# egPlots <- subjectProfileLinePlot(
# data = dataAll$EG,
# paramValueVar = "EGSTRESN",
# paramNameVar = "EGTEST",
# timeVar = "EGDY",
# # optional
# title = "Electrocardiogram",
# alpha = 0.8,
# labelVars = labelVars
# )
# patientProfilesPlots <- c(patientProfilesPlots, list(EG = egPlots))
#
## ----patientProfiles-createSubjectProfileReport, message = FALSE, warning = TRUE, eval = FALSE----
#
# pathsPatientProfiles <- createSubjectProfileReport(
#
# listPlots = patientProfilesPlots,
#
# # optional
# reportPerSubject = TRUE,
# verbose = TRUE,
# outputFile = './patientProfiles/subjectProfile.pdf',
# timeAlign = "all", timeAlignPerSubject = "all",
# exportBatchSize = 5,
#
# # export subjects with highest adverse events severity
# subjectSortData = dataAll$AE,
# subjectSortVar = "AESEV",
# subjectSortDecreasing = TRUE,
#
# # # only patients with severe adverse events
# # subjectSubsetData = dataAll$AE,
# # subsetVar = "AETOXGR",
# # subsetValue = "SEVERE"
# )
#
## ----sessionInformation, echo = FALSE-----------------------------------------
library(pander)
pander(sessionInfo())
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