In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation
knitr::opts_chunk$set(
fig.dpi = 96,
collapse = TRUE,
comment = "#>",
out.width = "98%"
)
library(biostatrpts)
set.seed(123)
uwAccrualBars
NN <- 200
# generate random enrollment dates over
randoDates <- data.frame(date = paste0(sample(1:12, size = NN, replace = TRUE),
"/01/",
sample(2019:2020, size = NN, replace = TRUE)),
trt = sample(LETTERS[1:2], NN, replace = TRUE))
uwAccrualBars(
accData = randoDates, dateName = "date", trxName = NULL,
interval = "month", yLim = NULL, pHoriz = FALSE, pBeside = FALSE,
linedbars = FALSE
)
uwBar
Called internally
mat <- matrix(1:12, nrow = 3)
dimnames(mat) <- list(c("A", "B", "C"), c("D", "E", "F", "G"))
uwBar(mat,
pBeside = TRUE, pHoriz = FALSE, lined = FALSE,
axLim = NULL, yLab = NULL, xLab = NULL, printBarVals = TRUE,
Legend = TRUE, LegendLoc = "topleft", LegendCex = 0.8,
mgp.y = c(3, 1, 0), mgp.x = c(3, 1, 0), cex.names = 1, barNamesLas = 1,
barNamesSeq = 1, barNamesAngle = 0, digits = 1
)
uwBarPlot {.tabset}
TRT <- rep(c("A", "B", "C"), 30)
AE <- ordered(
sample(c("None", "Mild", "Moderate", "Severe"), 90, replace = TRUE),
c("None", "Mild", "Moderate", "Severe")
)
data <- data.frame(TRT, AE)
Example 1
uwBarPlot(
demoData = data, trxName = NULL, factorName = "AE", Legend = TRUE, demoBarPlot = FALSE,
pHoriz = TRUE, pBeside = TRUE, xLab = "Number of Subjects", pTitle = "Adverse Events",
digits = 1, barNamesAngle = 60, cex.names = 0.8, lined = FALSE, Percent = FALSE,
barNamesLas = 1, barNamesSeq = 1, printPVals = TRUE, pTest = "f", pValCex = 0.6,
LatexFileName = NULL, LegendLoc = "topright"
)
Example 2
uwBarPlot(
demoData = data, trxName = "TRT", factorName = "AE", Legend = TRUE, demoBarPlot = TRUE,
pHoriz = TRUE, xLab = "Number of Subjects", pTitle = "Adverse Events", digits = 1,
barNamesAngle = 0, lined = FALSE, Percent = FALSE, barNamesLas = 0, barNamesSeq = 1,
printPVals = TRUE, pTest = "f", pValCex = 0.6, LatexFileName = NULL, LegendLoc = "topleft",
pStrWrap = TRUE
)
Example 3
uwBarPlot(
demoData = data, trxName = "TRT", factorName = "AE", Legend = TRUE, demoBarPlot = FALSE,
pHoriz = FALSE, yLab = "Percent of Subjects", pTitle = "Adverse Events", digits = 1,
barNamesAngle = 0, lined = FALSE, Percent = TRUE, barNamesLas = 1, barNamesSeq = 1,
printPVals = TRUE, pTest = "f", pValCex = 0.6, LatexFileName = NULL, LegendLoc = "bottomleft"
)
uwBox
Called internally
TRT <- c(rep("A", 20), rep("B", 20), rep("C", 20))
metric <- c(rnorm(20, 2, 1), rnorm(20, 3, 1), rnorm(20, 4, 1))
dat <- data.frame(TRT, metric)
uwBox(dat, "TRT", "metric")
uwBoxPlot
TRT <- c(rep("A", 20), rep("B", 20), rep("C", 20))
metric <- c(rnorm(20, 2, 1), rnorm(20, 3, 1), rnorm(20, 4, 1))
dat <- data.frame(TRT, metric)
uwBoxPlot(
data = dat,
trxName = "TRT",
metricName = "metric",
LatexFileName = NULL,
showTab = FALSE,
pTitle = "Example of uwBoxPlot",
yLab = "Weight of Something (oz)",
plotMean = FALSE, pOutliers = FALSE,
boxWex = 0.75,
Ropen = FALSE,
printPVals = TRUE,
pTest = "t",
abbrevN = 1,
pairwise = TRUE,
trxControl = NULL,
pExclude = NULL,
pInclude = list(
list(c("A", "B"), "C"), list("B", "C"),
list("A", "C")
),
yLim = NULL,
pStrWrap = FALSE,
pValCex = 0.7,
LatexCaption = NULL,
col.just = c("|l|", rep("c", 10), "|r", "r|"),
firstCol.name = NULL
)
uwConfBands {.tabset}
data(colon, package = "survival")
colon$sex.f <- factor(colon$sex, levels = c(0, 1), labels = c("Female", "Male"))
colon$surg.f <- factor(colon$surg,
levels = c(0, 1),
labels = c("Short", "Long")
)
colon$differ.f <- factor(colon$differ,
levels = c(1, 2, 3),
labels = c("Well", "Moderate", "Poor")
)
Example 1
uwConfBands(
fullDat = colon,
trxName = "rx",
trxLevels = c("Obs", "Lev"),
factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
estimate = "m",
metricName = "nodes",
printPVals = FALSE,
LatexFileName = NULL
)
Example 2
uwConfBands(
fullDat = colon,
trxName = "rx",
trxLevels = c("Obs", "Lev"),
factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
estimate = "p",
statusName = "status",
printPVals = TRUE,
LatexFileName = NULL
)
Example 3
uwConfBands(
fullDat = colon,
trxName = "rx",
trxLevels = c("Obs", "Lev"),
factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
estimate = "h",
statusName = "status",
timeName = "time",
xLim = c(0.25, 5),
xLog = TRUE,
printPVals = TRUE,
interactPVals = TRUE,
LatexFileName = NULL
)
Example 4
uwConfBands(
fullDat = colon,
trxName = "rx",
trxLevels = c("Obs", "Lev"),
factVarNames = c("sex.f", "age", "surg.f", "differ.f"),
factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."),
estimate = "h",
statusName = "status",
timeName = "time",
xLim = c(0, 2),
xLog = FALSE,
xDetailed = FALSE,
printPVals = TRUE,
interactPVals = TRUE,
LatexFileName = NULL
)
uwCumulAccr {.tabset}
Dates <- c(
"03/01/2008", "09/01/2007", "07/01/2007", "12/01/2006", "08/01/2007", "08/01/2007",
"04/01/2007", "04/01/2007", "04/01/2007", "11/01/2006", "11/01/2006", "12/01/2006",
"12/01/2006", "10/01/2006", "01/01/2007", "11/01/2006", "12/01/2006", "02/01/2007",
"08/01/2007", "08/01/2006", "09/01/2006", "04/01/2007", "05/01/2007", "11/01/2006",
"10/01/2006", "03/01/2007", "10/01/2007", "07/01/2007", "03/01/2007", "04/01/2006",
"05/01/2006", "11/01/2006", "12/01/2006", "02/01/2007", "02/01/2007", "02/01/2007",
"04/01/2007", "05/01/2007", "07/01/2007", "08/01/2007", "11/01/2007", "10/01/2007",
"09/01/2007", "10/01/2007", "05/01/2007", "01/01/2008", "12/01/2006", "02/01/2007",
"03/01/2007", "04/01/2007", "04/01/2007", "05/01/2007", "07/01/2007", "02/01/2007",
"07/01/2007", "10/01/2007", "01/01/2008"
)
Date <- chron::chron(Dates, format = c(dates = "m/d/y"))
TRT <- rep(c("A", "B"), c(30, 27))
data <- data.frame(Date, TRT)
Example 1
uwCumulAccr(
accData = data, dateName = "Date", trxName = NULL,
yLab = "Cumulative Number of Subjects",
yLim = NULL,
pTitle = "Accural over Time for Total Cohort",
projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric())
)
Example 2
# Projected accrual of 32 per arm over 750 days
uwCumulAccr(
accData = data, dateName = "Date", trxName = NULL,
yLab = "Cumulative Number of Subjects",
yLim = NULL, startDate = "01/01/2006",
pTitle = "Total Cohort with equal projected accrual",
projectLine = list(PatsPerTRT = 64, DaysPerTRT = 750)
)
Example 3
uwCumulAccr(
accData = data, dateName = "Date", trxName = "TRT",
yLab = "Cumulative Number of Subjects",
yLim = NULL,
pTitle = "Accural over Time by Treatment Arm",
projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric())
)
Example 4
# Projected accrual of 30 in A and 27 in B over 700 days
uwCumulAccr(
accData = data, dateName = "Date", trxName = "TRT",
yLab = "Cumulative Number of Subjects",
yLim = c(0, 70), LegendCor = c(25, 55),
pTitle = "Accural over Time by Treatment Arm",
projectLine = list(PatsPerTRT = c(30, 27), DaysPerTRT = 700)
)
uwLeveledBoxPlot {.tabset}
trt1 <- rep(rep(c("A", "B", "C"), 120), 3)
fctr1 <- as.factor(rep(c(rep("Female", 180), rep("Male", 180)), 3))
mtrc1 <- rnorm(360 * 3, 10, 4)
upfct <- c(rep("Baseline", 360), rep("Week 12", 360), rep("Week 24", 360))
ids <- as.character(c(1:360, 1:360, 1:360))
dat1 <- data.frame(trt1, fctr1, mtrc1, upfct, ids)
Example 1
uwLeveledBoxPlot(
allData = dat1,
trxName = "trt1",
metricName = "mtrc1",
lowfactName = "fctr1",
hifactName = "upfct",
delta = FALSE,
baseLevel = "Baseline",
idName = "ids",
LatexFileName = NULL,
showTab = FALSE,
Legend = FALSE,
pTitle = "Example of uwLeveledBoxPlot",
yLab = "Random Normal",
plotMean = TRUE, pOutliers = FALSE,
lWhisker = .05, hWhisker = .95,
lHinge = .25, hHinge = .75,
boxWex = 0.75,
printPVals = TRUE,
PVinTableOnly = FALSE,
PValCex = 0.5,
Ropen = FALSE,
pTest = "t",
abbrevN = 1,
pairwise = TRUE,
trxControl = NULL,
pExclude = NULL,
yLim = NULL
)
Example 2
uwLeveledBoxPlot(
allData = dat1,
trxName = "trt1",
metricName = "mtrc1",
lowfactName = "fctr1",
hifactName = "upfct",
delta = TRUE,
deltaPct = FALSE,
baseLevel = "Baseline",
idName = "ids",
LatexFileName = NULL,
showTab = FALSE,
Legend = TRUE,
LegendLoc = "topleft",
pTitle = "Example of uwLeveledBoxPlot with delta=TRUE",
yLab = "Random Normal",
plotMean = FALSE, pOutliers = FALSE,
lWhisker = .05, hWhisker = .95,
lHinge = .25, hHinge = .75,
boxWex = 0.75,
printPVals = TRUE,
PVinTableOnly = FALSE,
PValCex = 0.5,
Ropen = FALSE,
pTest = "w",
abbrevN = 1,
pairwise = TRUE,
trxControl = NULL,
pExclude = NULL,
pInclude = list(list(c("A", "B"), "C"), list("A", c("B", "C")), list("A", "C")),
yLim = NULL
)
Example 3
uwLeveledBoxPlot(
allData = dat1,
trxName = "trt1",
metricName = "mtrc1",
lowfactName = "fctr1",
hifactName = "upfct",
delta = TRUE,
deltaPct = TRUE,
baseLevel = "Baseline",
idName = "ids",
LatexFileName = NULL,
showTab = FALSE,
Legend = TRUE,
LegendLoc = "topleft",
pTitle = "Example of uwLeveledBoxPlot with deltaPct=TRUE",
yLab = "Random Normal",
plotMean = FALSE, pOutliers = FALSE,
lWhisker = .05, hWhisker = .95,
lHinge = .25, hHinge = .75,
boxWex = 0.75,
printPVals = TRUE,
PVinTableOnly = FALSE,
PValCex = 0.5,
Ropen = FALSE,
pTest = "w",
abbrevN = 1,
pairwise = TRUE,
trxControl = NULL,
pExclude = NULL,
pInclude = list(list(c("A", "B"), "C"), list("A", c("B", "C")), list("A", "C")),
yLim = NULL
)
uwLineGraph
TRT <- rep(rep(c("A", "B", "C"), c(20, 20, 20)), 4)
ptID <- rep(1:60, 4)
ptID <- factor(ptID)
numVar <- c(
rnorm(20, 0, 1), rnorm(20, 1, 1), rnorm(20, 2, 1), rnorm(20, 3, 1),
rnorm(20, 3, 1), rnorm(20, 10, 1), rnorm(20, 2, 3), rnorm(20, 0, 1),
rnorm(20, 6, 1), rnorm(20, 1, 3), rnorm(20, 2, 5), rnorm(20, 3, 1)
)
timeVar <- rep(c("Baseline", "3 Months", "6 Months", "12 Months"), c(60, 60, 60, 60))
timeVar <- ordered(
timeVar,
c("Baseline", "3 Months", "6 Months", "12 Months")
)
df <- data.frame(TRT, ptID, numVar, timeVar)
uwLineGraph(
data = df,
metricName = "numVar",
trxName = "TRT",
factorName = "timeVar",
LatexFileName = NULL,
plotMean = TRUE,
pch = NULL,
colScale = TRUE,
yLim = NULL,
yLab = "",
xLab = "",
pTitle = "Example of uwLineGraph",
refLines = TRUE,
Legend = TRUE,
LegendLoc = "topright",
printPVals = TRUE,
pTest = "t",
pExclude = NULL,
trxControl = "A",
pairDiffTab = TRUE,
ptIDname = "ptID",
BaseLevel = "Baseline",
numDec = 2,
rowLines = list(c(FALSE), c(FALSE)),
caption = list(c(NULL), c(NULL)),
firstCol.name = "Time",
Ropen = FALSE
)
uwPairedBoxPlot
Time <- ordered(c(rep("Pre", 100), rep("Post", 100)), c("Pre", "Post"))
ID <- rep(sample(c(1:100), 100, replace = FALSE), 2) # IDs will not be in order
weight <- c(rnorm(100, 200, 3), rnorm(100, 197, 3)) # pretend they are paired
ID[3] <- NA
ID[176] <- NA # Possible missing data
ID[150] <- 101 # Say someone as only one reading in post
dat <- data.frame(Time, ID, weight)
uwPairedBoxPlot(
allData = dat,
pairName = "Time",
metricName = "weight",
ptID = "ID",
onlyPairs = TRUE,
plotDiff = TRUE,
chgLayout = TRUE,
pWilcox = TRUE,
LatexFileName = NULL,
pTitle = "uwPairedBoxPlot Example",
yLab = "Weight (lbs.)",
plotMean = FALSE, pOutliers = FALSE,
lWhisker = .05, hWhisker = .95,
lHinge = .25, hHinge = .75,
boxWex = .75,
printPVals = TRUE,
yLim = NULL,
footNote = NULL,
firstCol.name = NULL,
LatexCaption = NULL,
caption.loc = "bottom",
showTab = FALSE,
label = NULL
)
uwPairedLeveledBoxPlot
trt <- rep(c("Case", "Control"), 60)
id <- rep(rep(1:20, rep(2, 20)), 3)
fact <- rep(c("A", "B", "C"), c(40, 40, 40))
met <- c(rnorm(40, 10), rnorm(40, 11), rnorm(40, 12))
df <- data.frame(trt, id, fact, met)
uwPairedLeveledBoxPlot(
pairData = df, pairName = "trt", metricName = "met",
factorName = "fact", ptID = "id",
LatexFileName = NULL,
yLab = "Normal", pTest = "w",
pTitle = "Example of uwPairedLeveledBoxPlot",
plotMean = TRUE, pOutliers = FALSE,
lWhisker = .05, hWhisker = .95,
rowLines = c(FALSE, TRUE, FALSE, TRUE, FALSE, TRUE),
lHinge = .25, hHinge = .75,
boxWex = 0.75, printPVals = TRUE
)
uwSimpleReg
Xvar <- rnorm(50, -10, 1)
Yvar <- 0.5 * Xvar + rnorm(50, 0, 1)
dfLin <- data.frame(Xvar, Yvar)
layout(1)
uwSimpleReg(
Data = dfLin, respVar = "Yvar", depVar = "Xvar",
main = "Example of uwSimpleReg",
ylab = "Example Response", xlab = "Example Explanatory",
ylim = NULL, xlim = NULL, printPVal = TRUE, printModel = TRUE, printRsq = TRUE
)
uwSurvival
death <- sample(c(0, 1), 200, replace = TRUE, prob = c(0.4, 0.6))
trt <- rep(c("ABDC", "ABGH"), c(100, 100))
time <- ceiling(runif(200, 0, 100))
sData <- data.frame(death, trt, time)
uwSurvival(
survData = sData, statusName = "death", trxName = "trt", trxControl = "ABDC",
timeName = "time", pTitle = "Survival by Treatment",
yLab = "Percent of Survival Probability",
xLab = "Days from Randomization", pValCex = 0.8, SScex = 0.7,
markCensor = FALSE, Legend = TRUE, LegendLoc = "topright",
LatexFileName = c(
paste(getwd(), "surv1.tex", sep = ""),
paste(getwd(), "/surv2.tex", sep = "")
),
showTab = FALSE, printPVals = TRUE, printSS = TRUE,
Ropen = FALSE, GraphSSfreq = 5, TableSSfreq = 1, firstCol.name = NULL,
LatexCaption = NULL, SSinPlot = TRUE,
size = "scriptsize"
)
jbirstler/biostatrpts documentation built on May 7, 2020, 12:10 a.m.
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knitr::opts_chunk$set( fig.dpi = 96, collapse = TRUE, comment = "#>", out.width = "98%" )
library(biostatrpts) set.seed(123)
uwAccrualBars
NN <- 200 # generate random enrollment dates over randoDates <- data.frame(date = paste0(sample(1:12, size = NN, replace = TRUE), "/01/", sample(2019:2020, size = NN, replace = TRUE)), trt = sample(LETTERS[1:2], NN, replace = TRUE)) uwAccrualBars( accData = randoDates, dateName = "date", trxName = NULL, interval = "month", yLim = NULL, pHoriz = FALSE, pBeside = FALSE, linedbars = FALSE )
uwBar
Called internally
mat <- matrix(1:12, nrow = 3) dimnames(mat) <- list(c("A", "B", "C"), c("D", "E", "F", "G")) uwBar(mat, pBeside = TRUE, pHoriz = FALSE, lined = FALSE, axLim = NULL, yLab = NULL, xLab = NULL, printBarVals = TRUE, Legend = TRUE, LegendLoc = "topleft", LegendCex = 0.8, mgp.y = c(3, 1, 0), mgp.x = c(3, 1, 0), cex.names = 1, barNamesLas = 1, barNamesSeq = 1, barNamesAngle = 0, digits = 1 )
uwBarPlot {.tabset}
TRT <- rep(c("A", "B", "C"), 30) AE <- ordered( sample(c("None", "Mild", "Moderate", "Severe"), 90, replace = TRUE), c("None", "Mild", "Moderate", "Severe") ) data <- data.frame(TRT, AE)
Example 1
uwBarPlot( demoData = data, trxName = NULL, factorName = "AE", Legend = TRUE, demoBarPlot = FALSE, pHoriz = TRUE, pBeside = TRUE, xLab = "Number of Subjects", pTitle = "Adverse Events", digits = 1, barNamesAngle = 60, cex.names = 0.8, lined = FALSE, Percent = FALSE, barNamesLas = 1, barNamesSeq = 1, printPVals = TRUE, pTest = "f", pValCex = 0.6, LatexFileName = NULL, LegendLoc = "topright" )
Example 2
uwBarPlot( demoData = data, trxName = "TRT", factorName = "AE", Legend = TRUE, demoBarPlot = TRUE, pHoriz = TRUE, xLab = "Number of Subjects", pTitle = "Adverse Events", digits = 1, barNamesAngle = 0, lined = FALSE, Percent = FALSE, barNamesLas = 0, barNamesSeq = 1, printPVals = TRUE, pTest = "f", pValCex = 0.6, LatexFileName = NULL, LegendLoc = "topleft", pStrWrap = TRUE )
Example 3
uwBarPlot( demoData = data, trxName = "TRT", factorName = "AE", Legend = TRUE, demoBarPlot = FALSE, pHoriz = FALSE, yLab = "Percent of Subjects", pTitle = "Adverse Events", digits = 1, barNamesAngle = 0, lined = FALSE, Percent = TRUE, barNamesLas = 1, barNamesSeq = 1, printPVals = TRUE, pTest = "f", pValCex = 0.6, LatexFileName = NULL, LegendLoc = "bottomleft" )
uwBox
Called internally
TRT <- c(rep("A", 20), rep("B", 20), rep("C", 20)) metric <- c(rnorm(20, 2, 1), rnorm(20, 3, 1), rnorm(20, 4, 1)) dat <- data.frame(TRT, metric) uwBox(dat, "TRT", "metric")
uwBoxPlot
TRT <- c(rep("A", 20), rep("B", 20), rep("C", 20)) metric <- c(rnorm(20, 2, 1), rnorm(20, 3, 1), rnorm(20, 4, 1)) dat <- data.frame(TRT, metric) uwBoxPlot( data = dat, trxName = "TRT", metricName = "metric", LatexFileName = NULL, showTab = FALSE, pTitle = "Example of uwBoxPlot", yLab = "Weight of Something (oz)", plotMean = FALSE, pOutliers = FALSE, boxWex = 0.75, Ropen = FALSE, printPVals = TRUE, pTest = "t", abbrevN = 1, pairwise = TRUE, trxControl = NULL, pExclude = NULL, pInclude = list( list(c("A", "B"), "C"), list("B", "C"), list("A", "C") ), yLim = NULL, pStrWrap = FALSE, pValCex = 0.7, LatexCaption = NULL, col.just = c("|l|", rep("c", 10), "|r", "r|"), firstCol.name = NULL )
uwConfBands {.tabset}
data(colon, package = "survival") colon$sex.f <- factor(colon$sex, levels = c(0, 1), labels = c("Female", "Male")) colon$surg.f <- factor(colon$surg, levels = c(0, 1), labels = c("Short", "Long") ) colon$differ.f <- factor(colon$differ, levels = c(1, 2, 3), labels = c("Well", "Moderate", "Poor") )
Example 1
uwConfBands( fullDat = colon, trxName = "rx", trxLevels = c("Obs", "Lev"), factVarNames = c("sex.f", "age", "surg.f", "differ.f"), factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."), estimate = "m", metricName = "nodes", printPVals = FALSE, LatexFileName = NULL )
Example 2
uwConfBands( fullDat = colon, trxName = "rx", trxLevels = c("Obs", "Lev"), factVarNames = c("sex.f", "age", "surg.f", "differ.f"), factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."), estimate = "p", statusName = "status", printPVals = TRUE, LatexFileName = NULL )
Example 3
uwConfBands( fullDat = colon, trxName = "rx", trxLevels = c("Obs", "Lev"), factVarNames = c("sex.f", "age", "surg.f", "differ.f"), factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."), estimate = "h", statusName = "status", timeName = "time", xLim = c(0.25, 5), xLog = TRUE, printPVals = TRUE, interactPVals = TRUE, LatexFileName = NULL )
Example 4
uwConfBands( fullDat = colon, trxName = "rx", trxLevels = c("Obs", "Lev"), factVarNames = c("sex.f", "age", "surg.f", "differ.f"), factFigNames = c("Gender", "Age", "Time to Reg.", "Tumor Diff."), estimate = "h", statusName = "status", timeName = "time", xLim = c(0, 2), xLog = FALSE, xDetailed = FALSE, printPVals = TRUE, interactPVals = TRUE, LatexFileName = NULL )
uwCumulAccr {.tabset}
Dates <- c( "03/01/2008", "09/01/2007", "07/01/2007", "12/01/2006", "08/01/2007", "08/01/2007", "04/01/2007", "04/01/2007", "04/01/2007", "11/01/2006", "11/01/2006", "12/01/2006", "12/01/2006", "10/01/2006", "01/01/2007", "11/01/2006", "12/01/2006", "02/01/2007", "08/01/2007", "08/01/2006", "09/01/2006", "04/01/2007", "05/01/2007", "11/01/2006", "10/01/2006", "03/01/2007", "10/01/2007", "07/01/2007", "03/01/2007", "04/01/2006", "05/01/2006", "11/01/2006", "12/01/2006", "02/01/2007", "02/01/2007", "02/01/2007", "04/01/2007", "05/01/2007", "07/01/2007", "08/01/2007", "11/01/2007", "10/01/2007", "09/01/2007", "10/01/2007", "05/01/2007", "01/01/2008", "12/01/2006", "02/01/2007", "03/01/2007", "04/01/2007", "04/01/2007", "05/01/2007", "07/01/2007", "02/01/2007", "07/01/2007", "10/01/2007", "01/01/2008" ) Date <- chron::chron(Dates, format = c(dates = "m/d/y")) TRT <- rep(c("A", "B"), c(30, 27)) data <- data.frame(Date, TRT)
Example 1
uwCumulAccr( accData = data, dateName = "Date", trxName = NULL, yLab = "Cumulative Number of Subjects", yLim = NULL, pTitle = "Accural over Time for Total Cohort", projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric()) )
Example 2
# Projected accrual of 32 per arm over 750 days uwCumulAccr( accData = data, dateName = "Date", trxName = NULL, yLab = "Cumulative Number of Subjects", yLim = NULL, startDate = "01/01/2006", pTitle = "Total Cohort with equal projected accrual", projectLine = list(PatsPerTRT = 64, DaysPerTRT = 750) )
Example 3
uwCumulAccr( accData = data, dateName = "Date", trxName = "TRT", yLab = "Cumulative Number of Subjects", yLim = NULL, pTitle = "Accural over Time by Treatment Arm", projectLine = list(PatsPerTRT = as.numeric(), DaysPerTRT = as.numeric()) )
Example 4
# Projected accrual of 30 in A and 27 in B over 700 days uwCumulAccr( accData = data, dateName = "Date", trxName = "TRT", yLab = "Cumulative Number of Subjects", yLim = c(0, 70), LegendCor = c(25, 55), pTitle = "Accural over Time by Treatment Arm", projectLine = list(PatsPerTRT = c(30, 27), DaysPerTRT = 700) )
uwLeveledBoxPlot {.tabset}
trt1 <- rep(rep(c("A", "B", "C"), 120), 3) fctr1 <- as.factor(rep(c(rep("Female", 180), rep("Male", 180)), 3)) mtrc1 <- rnorm(360 * 3, 10, 4) upfct <- c(rep("Baseline", 360), rep("Week 12", 360), rep("Week 24", 360)) ids <- as.character(c(1:360, 1:360, 1:360)) dat1 <- data.frame(trt1, fctr1, mtrc1, upfct, ids)
Example 1
uwLeveledBoxPlot( allData = dat1, trxName = "trt1", metricName = "mtrc1", lowfactName = "fctr1", hifactName = "upfct", delta = FALSE, baseLevel = "Baseline", idName = "ids", LatexFileName = NULL, showTab = FALSE, Legend = FALSE, pTitle = "Example of uwLeveledBoxPlot", yLab = "Random Normal", plotMean = TRUE, pOutliers = FALSE, lWhisker = .05, hWhisker = .95, lHinge = .25, hHinge = .75, boxWex = 0.75, printPVals = TRUE, PVinTableOnly = FALSE, PValCex = 0.5, Ropen = FALSE, pTest = "t", abbrevN = 1, pairwise = TRUE, trxControl = NULL, pExclude = NULL, yLim = NULL )
Example 2
uwLeveledBoxPlot( allData = dat1, trxName = "trt1", metricName = "mtrc1", lowfactName = "fctr1", hifactName = "upfct", delta = TRUE, deltaPct = FALSE, baseLevel = "Baseline", idName = "ids", LatexFileName = NULL, showTab = FALSE, Legend = TRUE, LegendLoc = "topleft", pTitle = "Example of uwLeveledBoxPlot with delta=TRUE", yLab = "Random Normal", plotMean = FALSE, pOutliers = FALSE, lWhisker = .05, hWhisker = .95, lHinge = .25, hHinge = .75, boxWex = 0.75, printPVals = TRUE, PVinTableOnly = FALSE, PValCex = 0.5, Ropen = FALSE, pTest = "w", abbrevN = 1, pairwise = TRUE, trxControl = NULL, pExclude = NULL, pInclude = list(list(c("A", "B"), "C"), list("A", c("B", "C")), list("A", "C")), yLim = NULL )
Example 3
uwLeveledBoxPlot( allData = dat1, trxName = "trt1", metricName = "mtrc1", lowfactName = "fctr1", hifactName = "upfct", delta = TRUE, deltaPct = TRUE, baseLevel = "Baseline", idName = "ids", LatexFileName = NULL, showTab = FALSE, Legend = TRUE, LegendLoc = "topleft", pTitle = "Example of uwLeveledBoxPlot with deltaPct=TRUE", yLab = "Random Normal", plotMean = FALSE, pOutliers = FALSE, lWhisker = .05, hWhisker = .95, lHinge = .25, hHinge = .75, boxWex = 0.75, printPVals = TRUE, PVinTableOnly = FALSE, PValCex = 0.5, Ropen = FALSE, pTest = "w", abbrevN = 1, pairwise = TRUE, trxControl = NULL, pExclude = NULL, pInclude = list(list(c("A", "B"), "C"), list("A", c("B", "C")), list("A", "C")), yLim = NULL )
uwLineGraph
TRT <- rep(rep(c("A", "B", "C"), c(20, 20, 20)), 4) ptID <- rep(1:60, 4) ptID <- factor(ptID) numVar <- c( rnorm(20, 0, 1), rnorm(20, 1, 1), rnorm(20, 2, 1), rnorm(20, 3, 1), rnorm(20, 3, 1), rnorm(20, 10, 1), rnorm(20, 2, 3), rnorm(20, 0, 1), rnorm(20, 6, 1), rnorm(20, 1, 3), rnorm(20, 2, 5), rnorm(20, 3, 1) ) timeVar <- rep(c("Baseline", "3 Months", "6 Months", "12 Months"), c(60, 60, 60, 60)) timeVar <- ordered( timeVar, c("Baseline", "3 Months", "6 Months", "12 Months") ) df <- data.frame(TRT, ptID, numVar, timeVar) uwLineGraph( data = df, metricName = "numVar", trxName = "TRT", factorName = "timeVar", LatexFileName = NULL, plotMean = TRUE, pch = NULL, colScale = TRUE, yLim = NULL, yLab = "", xLab = "", pTitle = "Example of uwLineGraph", refLines = TRUE, Legend = TRUE, LegendLoc = "topright", printPVals = TRUE, pTest = "t", pExclude = NULL, trxControl = "A", pairDiffTab = TRUE, ptIDname = "ptID", BaseLevel = "Baseline", numDec = 2, rowLines = list(c(FALSE), c(FALSE)), caption = list(c(NULL), c(NULL)), firstCol.name = "Time", Ropen = FALSE )
uwPairedBoxPlot
Time <- ordered(c(rep("Pre", 100), rep("Post", 100)), c("Pre", "Post")) ID <- rep(sample(c(1:100), 100, replace = FALSE), 2) # IDs will not be in order weight <- c(rnorm(100, 200, 3), rnorm(100, 197, 3)) # pretend they are paired ID[3] <- NA ID[176] <- NA # Possible missing data ID[150] <- 101 # Say someone as only one reading in post dat <- data.frame(Time, ID, weight) uwPairedBoxPlot( allData = dat, pairName = "Time", metricName = "weight", ptID = "ID", onlyPairs = TRUE, plotDiff = TRUE, chgLayout = TRUE, pWilcox = TRUE, LatexFileName = NULL, pTitle = "uwPairedBoxPlot Example", yLab = "Weight (lbs.)", plotMean = FALSE, pOutliers = FALSE, lWhisker = .05, hWhisker = .95, lHinge = .25, hHinge = .75, boxWex = .75, printPVals = TRUE, yLim = NULL, footNote = NULL, firstCol.name = NULL, LatexCaption = NULL, caption.loc = "bottom", showTab = FALSE, label = NULL )
uwPairedLeveledBoxPlot
trt <- rep(c("Case", "Control"), 60) id <- rep(rep(1:20, rep(2, 20)), 3) fact <- rep(c("A", "B", "C"), c(40, 40, 40)) met <- c(rnorm(40, 10), rnorm(40, 11), rnorm(40, 12)) df <- data.frame(trt, id, fact, met) uwPairedLeveledBoxPlot( pairData = df, pairName = "trt", metricName = "met", factorName = "fact", ptID = "id", LatexFileName = NULL, yLab = "Normal", pTest = "w", pTitle = "Example of uwPairedLeveledBoxPlot", plotMean = TRUE, pOutliers = FALSE, lWhisker = .05, hWhisker = .95, rowLines = c(FALSE, TRUE, FALSE, TRUE, FALSE, TRUE), lHinge = .25, hHinge = .75, boxWex = 0.75, printPVals = TRUE )
uwSimpleReg
Xvar <- rnorm(50, -10, 1) Yvar <- 0.5 * Xvar + rnorm(50, 0, 1) dfLin <- data.frame(Xvar, Yvar) layout(1) uwSimpleReg( Data = dfLin, respVar = "Yvar", depVar = "Xvar", main = "Example of uwSimpleReg", ylab = "Example Response", xlab = "Example Explanatory", ylim = NULL, xlim = NULL, printPVal = TRUE, printModel = TRUE, printRsq = TRUE )
uwSurvival
death <- sample(c(0, 1), 200, replace = TRUE, prob = c(0.4, 0.6)) trt <- rep(c("ABDC", "ABGH"), c(100, 100)) time <- ceiling(runif(200, 0, 100)) sData <- data.frame(death, trt, time) uwSurvival( survData = sData, statusName = "death", trxName = "trt", trxControl = "ABDC", timeName = "time", pTitle = "Survival by Treatment", yLab = "Percent of Survival Probability", xLab = "Days from Randomization", pValCex = 0.8, SScex = 0.7, markCensor = FALSE, Legend = TRUE, LegendLoc = "topright", LatexFileName = c( paste(getwd(), "surv1.tex", sep = ""), paste(getwd(), "/surv2.tex", sep = "") ), showTab = FALSE, printPVals = TRUE, printSS = TRUE, Ropen = FALSE, GraphSSfreq = 5, TableSSfreq = 1, firstCol.name = NULL, LatexCaption = NULL, SSinPlot = TRUE, size = "scriptsize" )
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