broman: Karl Broman's R Code

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Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.

Author
Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee Teo Broman
Date of publication
2016-12-01 08:28:25
Maintainer
Karl W Broman <kbroman@biostat.wisc.edu>
License
GPL-3
Version
0.65-1
URLs

View on CRAN

Man pages

add_commas
Add commas to a large number
arrowlocator
Use the locator function to plot an arrow
attrnames
Get names of attributes
brocolors
Vectors of colors for figures
bromanversion
Installed version of R/broman
cf
Compare objects, including missing data pattern
chisq
Chi-square test by simulation for a two-way table
colwalpha
Convert a color to use alpha transparency
compare_rows
Compare rows in a matrix
convert2hex
Convert decimal to hex
done
Send a short message via RPushbullet.
dotplot
Dot chart with a gray background
errors2pushbullet
Send further errors to pushbullet
excel_fig
Excel-style figure displaying contents of a matrix
exit
exit R without saving
fac2num
Convert a factor to numeric
fisher
Fisher's exact test for a two-way table
grayplot
Plot with a gray background
h
View html version of help file
hex2dec
Convert from hex to decimal
histlines
Utility to create line-based histogram
jiggle
Jiggle points horizontally
kbdate
My little date facility
lenuniq
Number of unique values
make
Run make within a package directory
manyboxplot
Boxplot-like figure for many groups
maxabs
maximum of absolute value
mypairs
My scatterplot matrix
myround
Round a number, preserving extra 0's
normalize
Quantile normalization
note
Send a note to pushbullet
numbers
Numbers spelled out in English
objectsizes
Calculate sizes of all objects in workspace
openfile
Open a file
paired.perm.test
Paired permutation t-test
paste.
paste with dot separator
paste00
paste with null or dot as separator and with collapse
perm.test
Permutation t-test
plot_crayons
Illustration of crayon colors
pushbullet_devices
Grab info on Pushbullet devices.
qqline2
qqline for qqplot
qr2
The QR decomposition of a matrix
quantileSE
Sample quantiles and their standard errors
revrainbow
Create vector of colors from blue to red
rmvn
Simulate multivariate normal
runningmean
Running mean, sum, or median
runningratio
Running ratio
setRNGparallel
Set up random number generation for parallel calculations
simp
Numerical integration
stop_sending_errors
Stop sending errors to pushbullet
strwidth2lines
Calculate width of a character string in number of lines
strwidth2xlim
Calculate horizontal limit in user coordinates for adding...
switchv
Vectorized version of switch
theme_karl
Karl's ggplot2 theme
triarrow
Plot an arrow within a Holmans triangle
trilines
Plot lines within a Holmans triangle
triplot
Plot Holmans triangle
tripoints
Plot points within a Holmans triangle
venn
Plot to-scale Venn diagram
winsorize
Winsorize a vector
xlimlabel
Calulate horizontal limit in user coordinates for adding...

Files in this package

broman
broman/inst
broman/inst/STATUS.txt
broman/inst/LICENSE.txt
broman/inst/README.md
broman/tests
broman/tests/testthat.R
broman/tests/testthat
broman/tests/testthat/test-switchv.R
broman/tests/testthat/test-hex2dec.R
broman/tests/testthat/test-runningmean.R
broman/tests/testthat/test-fac2num.R
broman/tests/testthat/test-maxabs.R
broman/tests/testthat/test-add_commas.R
broman/tests/testthat/test-winsorize.R
broman/tests/testthat/test-kbdate.R
broman/tests/testthat/test-lenuniq.R
broman/tests/testthat/test-myround.R
broman/tests/testthat/test-compare_rows.R
broman/src
broman/src/compare_rows.h
broman/src/normalize.h
broman/src/runningmean.c
broman/src/count_close.c
broman/src/runningmean.h
broman/src/count_close.h
broman/src/compare_rows.c
broman/src/normalize.c
broman/NAMESPACE
broman/data
broman/data/numbers.RData
broman/data/numbers-cap.RData
broman/R
broman/R/qr.R
broman/R/brocolors.R
broman/R/histlines.R
broman/R/qqline2.R
broman/R/fisher.R
broman/R/revrainbow.R
broman/R/add_commas.R
broman/R/myround.R
broman/R/pushbullet.R
broman/R/numbers.R
broman/R/excel_fig.R
broman/R/openfile.R
broman/R/jiggle.R
broman/R/fac2num.R
broman/R/objectsizes.R
broman/R/setRNGparallel.R
broman/R/exit.R
broman/R/theme_karl.R
broman/R/kbdate.R
broman/R/colwalpha.R
broman/R/holmans_triangle.R
broman/R/runningmean.R
broman/R/strwidth2lines.R
broman/R/simp.R
broman/R/rmvn.R
broman/R/switchv.R
broman/R/maxabs.R
broman/R/permtest.R
broman/R/make.R
broman/R/pastedot.R
broman/R/compare_rows.R
broman/R/grayplot.R
broman/R/help.R
broman/R/xlimlabel.R
broman/R/manyboxplot.R
broman/R/convert2hex.R
broman/R/util.R
broman/R/attrnames.R
broman/R/normalize.R
broman/R/cf.R
broman/R/dotplot.R
broman/R/strwidth2xlim.R
broman/R/winsorize.R
broman/R/arrowlocator.R
broman/R/quantileSE.R
broman/R/venn_diagram.R
broman/R/lenuniq.R
broman/R/mypairs.R
broman/MD5
broman/DESCRIPTION
broman/man
broman/man/perm.test.Rd
broman/man/mypairs.Rd
broman/man/plot_crayons.Rd
broman/man/compare_rows.Rd
broman/man/qqline2.Rd
broman/man/brocolors.Rd
broman/man/theme_karl.Rd
broman/man/exit.Rd
broman/man/myround.Rd
broman/man/winsorize.Rd
broman/man/h.Rd
broman/man/triarrow.Rd
broman/man/attrnames.Rd
broman/man/dotplot.Rd
broman/man/revrainbow.Rd
broman/man/paste..Rd
broman/man/stop_sending_errors.Rd
broman/man/fac2num.Rd
broman/man/switchv.Rd
broman/man/tripoints.Rd
broman/man/quantileSE.Rd
broman/man/colwalpha.Rd
broman/man/pushbullet_devices.Rd
broman/man/openfile.Rd
broman/man/runningmean.Rd
broman/man/objectsizes.Rd
broman/man/fisher.Rd
broman/man/hex2dec.Rd
broman/man/grayplot.Rd
broman/man/simp.Rd
broman/man/manyboxplot.Rd
broman/man/runningratio.Rd
broman/man/paired.perm.test.Rd
broman/man/histlines.Rd
broman/man/strwidth2xlim.Rd
broman/man/qr2.Rd
broman/man/make.Rd
broman/man/strwidth2lines.Rd
broman/man/jiggle.Rd
broman/man/arrowlocator.Rd
broman/man/done.Rd
broman/man/numbers.Rd
broman/man/xlimlabel.Rd
broman/man/chisq.Rd
broman/man/setRNGparallel.Rd
broman/man/triplot.Rd
broman/man/cf.Rd
broman/man/paste00.Rd
broman/man/convert2hex.Rd
broman/man/normalize.Rd
broman/man/errors2pushbullet.Rd
broman/man/kbdate.Rd
broman/man/maxabs.Rd
broman/man/add_commas.Rd
broman/man/lenuniq.Rd
broman/man/trilines.Rd
broman/man/venn.Rd
broman/man/excel_fig.Rd
broman/man/rmvn.Rd
broman/man/bromanversion.Rd
broman/man/note.Rd