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

Functions and datasets that can be used for data cleanup (e.g., functions for eliminating all but a few columns from a dataset, selecting a range of columns, quickly editing column names), plotting/presenting data (prism-like reproductions, spearman plots for ordinal data, making colored tables, plotting interactions with quantitative variables), and analyses common to biostatistics (e.g., random forest, multiple comparisons with chi square tests). See the package vignette for a brief introduction to many of the main functions.

Install the latest version of this package by entering the following in R:
install.packages("fifer")
AuthorDustin Fife <fife.dustin@gmail.com>
Date of publication2017-02-21 16:46:22
MaintainerDustin Fife <fife.dustin@gmail.com>
LicenseGPL-2
Version1.1

View on CRAN

Man pages

anchored.gradient: Create a color gradient with a color for zero

auto.layout: Automatically select the layout.

boxcoxR: Transform data using a boxcox transformation

chisq.post.hoc: Tests for significant differences among all pairs of...

clear: Clear memory of all objects

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

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

ellipse: Plots an Ellipse

excelCols: Generate Excel column labels

excelMatch: Obtain column number or variable name from Excel named...

fakeMedicalData: Fictitious Medical Dataset

get.cols: Extract column index

gradient.legend: Create a gradiented legend

hash: Create useless hashes

imageInteraction: Plot an two-way quantitative interaction in an image plot

intersperse: Intersperse elements of Two+ Vectors

last.sample: Return only one row per ID

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

mv.rnorm: Randomly Generate Multivariate Normal Data

number.to.colors: Convert from numbers to colors

par1: Change default par parameters

par2: Change default par parameters

plot.rfInterp: Plot rfInterp Summary

plot.rfPred: Plot rfPred Summary

plot.rfThresh: rfThesh Summary

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

pval.xtable: Convert p-values into strings with inequalities.

r: Extract variable column indices

random.correlation: Generate a random correlation matrix

r.crit: Compute critical r or p.

read.fife: 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

rotateGraph: Rotate a graph using polar coordinates

roxtemp: Generate a Roxygen Template

scaleB: Standardize coefficients

scaleBreak: Scatterplot with a Scale Break

scaleIt: Scale a variable

spearman.plot: Spearman plot

stratified: Sample from a 'data.frame' according to a stratification...

string.to.colors: Convert between strings to colors

subsetString: Extract only part of a string

SummarizeContinuousDefault: Summarize a continuous vector with mean plus/minus standard...

SummarizeFactorDefault: Summarize a factor vector with count and percentages

SummarizeVar: Summarize a vector (continuous or factor)

summary.rfPred: Print a Summary Table of rfPred

unfactor: Convert a factor to a character (or number)

univariate.tests: Extract p values for a data frame

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

xtable.rfInterp: Prepare xtable Summary

xtable.rfPred: Prepare xtable Summary

z.test: Perform a z test

Functions

anchored.gradient Man page
anchor.gradient Man page
auto.layout Man page
boxcoxR Man page
boxcox.R Man page
calcT Man page
chisq.post.hoc Man page
clear Man page
colored.table Man page
color.gradient Man page
color.table Man page
col.table Man page
compute.theta Man page
contents Man page
cor2cov Man page
demographics Man page
densityPlotR Man page
drop.columns Man page
ellipse Man page
excelCols Man page
excelMatch Man page
fakeMedicalData Man page
get.cols Man page
gradient Man page
gradient.legend Man page
hash Man page
imageInteraction Man page
integers.to.colors Man page
integer.to.colors Man page
intersperse Man page
last.row Man page
lastsample Man page
last.sample Man page
lastSample Man page
make.formula Man page
make.null Man page
make.symmetric Man page
missingvals Man page
missing.vals Man page
missingVals Man page
missing.Vals Man page
mvrnorm Man page
mv.rnorm Man page
mv.Rnorm Man page
numbers.to.colors Man page
number.to.color Man page
numberToColor Man page
number.to.colors Man page
numberToColors Man page
one.row Man page
par1 Man page
par2 Man page
plot Man page
plot.rfInterp Man page
plot.rfPred Man page
plot.rfThresh Man page
plotSigBars Man page
plots.prism Man page
print.rfInterp Man page
print.rfPred Man page
print.rfThresh Man page
printx Man page
prismplots Man page
prism.plots Man page
prismPlots Man page
p.value Man page
p.values Man page
p.val.xtable Man page
pval.xtable Man page
p.xtable Man page
r Man page
random.correlation Man page
r.crit Man page
read.fife Man page
read.fifer Man page
read.meta Man page
read.metadata Man page
read.meta.data Man page
rfInterp Man page
rfPred Man page
rfSensitivity Man page
rfThresh Man page
rotategraph Man page
rotate.graph Man page
rotateGraph Man page
roxtemp Man page
scaleB Man page
scalebreak Man page
scale.break Man page
scaleBreak Man page
scale.Break Man page
scaleIt Man page
spearman.plot Man page
stratified Man page
stringtocolor Man page
string.to.color Man page
string.to.colors Man page
stringToColors Man page
subsetString Man page
SummarizeContinuousDefault Man page
SummarizeFactorDefault Man page
SummarizeVar Man page
summary.rfPred Man page
unfactor Man page
univariate.tests Man page
write.fife Man page
write.fifer Man page
write.meta Man page
write.metadata Man page
write.meta.data Man page
xtable.rfInterp Man page
xtable.rfPred Man page
z.test Man page

Files

inst
inst/doc
inst/doc/fifer_package.pdf
NAMESPACE
data
data/fakeMedicalData.rda
R
R/intersperse.R R/clear.R R/scaleB.R R/r.crit.R R/scale.it.R R/kruskalmc.R R/missing.vals.R R/subsetString.R R/boxcoxR.R R/rf.pred.R R/last.sample.R R/make.null.R R/printx.R R/chisqPostHoc.R R/prism.plots.R R/par1.R R/z.test.R R/roxtemp.R R/rf.interp.R R/meta.data.R R/make.formula.R R/rf.thresh.R R/contents.R R/hash.R R/demographics.R R/stratified.R R/drop.columns.R R/pval.xtable.R R/densityPlotR.R R/scaleBreak.R R/univariate.tests.R R/random.correlation.R R/unfactor.R R/mvrnorm.R R/colored.table.R R/spearman.plot.R R/anchored.gradient.R R/polarCoord.R R/cor2cov.R R/string.to.color.R R/auto.layout.R R/image.interaction.R R/make.symmetric.R R/excelMatch.R
vignettes
vignettes/fifer_package.Rnw
vignettes/fifer_package.pdf
vignettes/images
vignettes/images/nerdsRule.jpg
MD5
DESCRIPTION
ChangeLog
man
man/hash.Rd man/SummarizeVar.Rd man/rotateGraph.Rd man/imageInteraction.Rd man/roxtemp.Rd man/rfThresh.Rd man/stratified.Rd man/scaleIt.Rd man/gradient.legend.Rd man/rfInterp.Rd man/par1.Rd man/ellipse.Rd man/cor2cov.Rd man/unfactor.Rd man/intersperse.Rd man/subsetString.Rd man/scaleBreak.Rd man/prism.plots.Rd man/SummarizeFactorDefault.Rd man/number.to.colors.Rd man/print.rfPred.Rd man/print.rfThresh.Rd man/contents.Rd man/rfSensitivity.Rd man/make.null.Rd man/compute.theta.Rd man/chisq.post.hoc.Rd man/make.symmetric.Rd man/plot.rfInterp.Rd man/densityPlotR.Rd man/plotSigBars.Rd man/missing.vals.Rd man/drop.columns.Rd man/spearman.plot.Rd man/anchored.gradient.Rd man/make.formula.Rd man/random.correlation.Rd man/rfPred.Rd man/par2.Rd man/plot.rfPred.Rd man/get.cols.Rd man/colored.table.Rd man/write.fife.Rd man/auto.layout.Rd man/excelCols.Rd man/univariate.tests.Rd man/excelMatch.Rd man/clear.Rd man/xtable.rfInterp.Rd man/demographics.Rd man/print.rfInterp.Rd man/mv.rnorm.Rd man/z.test.Rd man/xtable.rfPred.Rd man/read.fife.Rd man/fakeMedicalData.Rd man/r.Rd man/boxcoxR.Rd man/last.sample.Rd man/plot.rfThresh.Rd man/printx.Rd man/SummarizeContinuousDefault.Rd man/r.crit.Rd man/summary.rfPred.Rd man/string.to.colors.Rd man/pval.xtable.Rd man/scaleB.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.