Function reference • breheny

All functions

Attach(): Detach before attaching

Boot(): Simplified interface to boot package for basic statistics

DropMiss(): Drop missing columns from a data table

Hist(): Nicer-looking histogram

Plot(): Customized plotting functions

alldup(): Show all duplicate entries in a data frame/table/vector

alphaCol(): Take a solid color and turn it semi-transparent

binom_bayes(): Bayesian analysis of one-sample binomial data using conjugate beta priors

breheny breheny-package: breheny: Miscellaneous functions that Patrick Breheny finds useful

bsave(): Save and combine (gather) results from batched R sessions

catchWarning(): Catch warnings

check(): Checks whether two vectors are equal; wrapper for all.equal

checkData(): Quick inspection of columns in a data frame / table for weirdness

chisqProb(): Draw a chi-squared curve and shade area to the right (probability)

chk_man(): Check code/documentation agreement using devtools::check_man()

ci_ipd(): Given a confidence interval, simulate individual patient data

ciband(): Add a confidence interval band to a KM curve

clipdt(): Import from clipboard to data.table

colorize_terminal(): Setup errors and warnings to use cli coloring

contingency_table(): Format a contingency table for use with knitr

cv_tree() plot(<cv_tree>): Cross-validation for regression trees

ddice() pdice(): Exact probabilities for sum of n dice

density_plot(): Density plot

devload(): Load a package from its dev/ location (from source, not installed)

dict(): Create a key-value dictionary

dnplot(): Density plot

.f() .p() .fm(): Compact and pipe-friendly wrapper to sprintf

download_data() read_data(): Download data and read into R

epower() esamsize(): Power and sample size for time-to-event data based on exponential closed form solution

estimate(): Estimate linear combinations from a regression model

event_chart(): Create a time-to-event chart using ggplot

factor2num(): Convert factor to number

plot(<Flow>): Create a flowchart

formatP(): Format p-values nicely

format_object_size(): This is literally copied from utils:::format.object_size

generic_description(): Copies a generic DESCRIPTION file to current working directory

ggbar(): Quick wrapper for a gg bar plot

ggbox(): Boxplot of a data frame / matrix using ggplot

ggcontour(): Wrapper to create geom_contour of a function

gghist(): Simple interface to ggplot2 histogram

grayCol(): Take a color and make it duller

hbytes(): Print bytes in nice human-readable format

km_to_mi() mi_to_km(): Convert between min/km pace and min/mi pace

lfdrPlot.ash(): Make an lFDR plot for an ash object

plotL() plotl(): Plot likelihood function

logAxis(): Make a log-scale axis

make_unique(): Ensure all entries in a string are uniquely labeled

mixcolor(): Mix two colors

normProb(): Draw a normal curve and shade area under an interval (probability)

nrisk(): Add an axis describing number at risk to a KM curve

open_url(): Open a url: quietly, in the background, and in a new window

pal(): Generate a nice palette of colors

parse_aux(): Parse latex .aux files for fig/tab/etc. numbers

pca_plot(): Make a PCA/tSNE/UMAP plot

polygon.step(): Draw a filled polygon as a step function

power_hd(): Power calculator for high-dimensional testing

prank(): Compute percentile rank

process_yaml(): Split a file into yaml and body

qd(): Compute a quadratic form (x'Ax)

qe(): Solutions to the quadratic equation

r2(): Nagelkerke R2

rank_new(): Apply rank transformation to new data

rasym(): Generate asymptotic sequence of random normal sums

rbern(): Generate random bernoulli (non-homogeneous binomial) variates

rdex(): Generate random double exponential variates

rdir(): Generate random variates from the Dirichlet distribution

rpower() rsamsize(): Power for regression (or any continuous outcome)

rr(): Calculate relative risk from a 2x2 table

rstring(): Generate random string of characters

s3_share(): Share Amazon S3 file

samsize_pcc(): Sample size for classifier development

scale_x_revlog() scale_y_revlog(): Provides a reverse log scale to ggplot; especially useful for p-values

signed_url(): Share Amazon CloudFront file via presigned url

silent_load(): Run devtools::load_all() silently

soft(): Soft-thresholding operator

source.dir(): Source all .R files in a directory

table2dt() table2df(): Convert a table to a (disaggregated) data frame / table

textPlot(): Scatter plot, but with text labels

toplegend() rightlegend(): Make a legend on top or right side of plot

tpower() tsamsize(): Power for t tests, including arbitrary linear hypotheses

write_fwf(): Generate fixed width file in R

xlsdt(): Simple wrapper to read_excel + pipe to data.table