A Biostatisticians Toolbox for Various Activities, Including Plotting, Data Cleanup, and Data Analysis


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Documentation for package ‘fifer’ version 1.1

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A B C D E F G H I L M N O P R S U W X Z

-- A --

anchor.gradient Create a color gradient with a color for zero
anchored.gradient Create a color gradient with a color for zero
auto.layout Automatically select the layout.

-- B --

boxcox.R Transform data using a boxcox transformation
boxcoxR Transform data using a boxcox transformation

-- C --

calcT Calculate inverse tangent.
chisq.post.hoc Tests for significant differences among all pairs of populations in a chi-square test.
clear Clear memory of all objects
col.table Create a color-coded table in latex
color.gradient Create a color gradient with a color for zero
color.table Create a color-coded table in latex
colored.table Create a color-coded table in latex
compute.theta Calculate inverse tangent.
contents View the contents (functions) of a package
cor2cov Correlation Matrix to Covariance Matrix Conversion

-- D --

demographics Summarize a Data Set (Demographics)
densityPlotR Generate a density plot using a formula
drop.columns Drop (or keep) all columns containing a vector of strings

-- E --

ellipse Plots an Ellipse
excelCols Generate Excel column labels
excelMatch Obtain column number or variable name from Excel named Columns

-- F --

fakeMedicalData Fictitious Medical Dataset

-- G --

get.cols Extract column index
gradient Create a gradiented legend
gradient.legend Create a gradiented legend

-- H --

hash Create useless hashes

-- I --

imageInteraction Plot an two-way quantitative interaction in an image plot
integer.to.colors Convert from numbers to colors
integers.to.colors Convert from numbers to colors
intersperse Intersperse elements of Two+ Vectors

-- L --

last.row Return only one row per ID
last.sample Return only one row per ID
lastSample Return only one row per ID
lastsample Return only one row per ID

-- M --

make.formula Convert strings to a formula
make.null Drop or keep variables in a dataset
make.symmetric Force a matrix to be symmetric
missing.Vals Summary of Missing Data
missing.vals Summary of Missing Data
missingVals Summary of Missing Data
missingvals Summary of Missing Data
mv.Rnorm Randomly Generate Multivariate Normal Data
mv.rnorm Randomly Generate Multivariate Normal Data
mvrnorm Randomly Generate Multivariate Normal Data

-- N --

number.to.color Convert from numbers to colors
number.to.colors Convert from numbers to colors
numbers.to.colors Convert from numbers to colors
numberToColor Convert from numbers to colors
numberToColors Convert from numbers to colors

-- O --

one.row Return only one row per ID

-- P --

p.val.xtable Convert p-values into strings with inequalities.
p.value Convert p-values into strings with inequalities.
p.values Convert p-values into strings with inequalities.
p.xtable Convert p-values into strings with inequalities.
par1 Change default par parameters
par2 Change default par parameters
plot Plot rfInterp Summary
plot.rfInterp Plot rfInterp Summary
plot.rfPred Plot rfPred Summary
plot.rfThresh rfThesh Summary
plots.prism Plot prism-like Plots
plotSigBars Add significance bars to a prism plot
print.rfInterp Print rfInterp Summary
print.rfPred Print rfPred Summary
print.rfThresh Print rfThesh Summary
printx Change Defaults of print.xtable
prism.plots Plot prism-like Plots
prismPlots Plot prism-like Plots
prismplots Plot prism-like Plots
pval.xtable Convert p-values into strings with inequalities.

-- R --

r Extract variable column indices
r.crit Compute critical r or p.
random.correlation Generate a random correlation matrix
read.fife Read in a dataset and load the meta-data for a file
read.fifer Read in a dataset and load the meta-data for a file
read.meta Read in a dataset and load the meta-data for a file
read.meta.data Read in a dataset and load the meta-data for a file
read.metadata Read in a dataset and load the meta-data for a file
rfInterp Variable Selection with Random Forest
rfPred Variable selection in Random Forest
rfSensitivity Output accuracy, sensitivity, specificity, NPV, and PPV.
rfThresh Variable Selection Using Random Forests
rotate.graph Rotate a graph using polar coordinates
rotateGraph Rotate a graph using polar coordinates
rotategraph Rotate a graph using polar coordinates
roxtemp Generate a Roxygen Template

-- S --

scale.Break Scatterplot with a Scale Break
scale.break Scatterplot with a Scale Break
scaleB Standardize coefficients
scaleBreak Scatterplot with a Scale Break
scalebreak Scatterplot with a Scale Break
scaleIt Scale a variable
spearman.plot Spearman plot
stratified Sample from a 'data.frame' according to a stratification variable
string.to.color Convert between strings to colors
string.to.colors Convert between strings to colors
stringtocolor Convert between strings to colors
stringToColors Convert between strings to colors
subsetString Extract only part of a string
SummarizeContinuousDefault Summarize a continuous vector with mean plus/minus standard deviation
SummarizeFactorDefault Summarize a factor vector with count and percentages
SummarizeVar Summarize a vector (continuous or factor)
summary.rfPred Print a Summary Table of rfPred

-- U --

unfactor Convert a factor to a character (or number)
univariate.tests Extract p values for a data frame

-- W --

write.fife Write a dataset and load the meta-data
write.fifer Write a dataset and load the meta-data
write.meta Write a dataset and load the meta-data
write.meta.data Write a dataset and load the meta-data
write.metadata Write a dataset and load the meta-data

-- X --

xtable.rfInterp Prepare xtable Summary
xtable.rfPred Prepare xtable Summary

-- Z --

z.test Perform a z test