Package index • biostatUtil

All functions

PCAplot(): Plot Principal Components

R2_to_D(): Convert R2 to D

SummaryStatsBy(): Generate summary statistics

Xunivcoxph(): Univariate cox proprtional hazards model

addTableNumber(): Add table number

assessSurvTime(): Assess survival time

barplotSum(): Annotated Barplot

best_cut(): Find the best cutpoint for a covariate

binaryCM(): Confusion matrix summaries

binaryCMAsHTML(): Confusion matrix results in HTML

biostatUtil-package biostatUtil: biostatUtil: utility functions for biostatistical projects

bootMean(): Mean and bootstrap confidence interval

boxplotSum(): Annotated Boxplot

build_cuts(): Build cutpoint variables

censor_date(): Date of censoring

chr_to_date(): Change character to date

cleanDate(): Clean dates

coxphOut(): Nice output from Cox regression object

addToDate() diffDate() compareDate(): Date computations

maxDate() minDate() maxDateArray() minDateArray(): Latest and Earliest Dates

design_matrix(): Design Matrix with interactions

diff_years(): Date difference in years

doBarplot(): Barplot with counts

doBoxplotAmongSubtypes(): Do a boxplot among subtypes

doCohortCharacteristics(): Generate cohort characteristics

doCoxphGeneric() doCoxphMultivariable(): Fit a Cox proportional hazards regression model

doHist(): Do histogram with median

doInteractionCox(): Do interaction test with cox model likelihood ratio test only - two terms only

doJitterplotAmongSubtypes(): Do a jitterplot among subtypes

doKMPlots(): Make Kaplan-Meier plots

escapeForGrep(): Escape string for regular expression

exploreData(): Graphical Exploration of a Dataset

extract_km() extract_cox(): Extract results for executive summary

findCutpointByCoxph(): Find cutpoint by Cox model statistics

formatDate(): Format a date.

formatNA(): Missing Value Formatting

freqTable(): Generate a Frequency Table

g_legend(): Generate a legend

geoMean(): Geometric mean

getFormat(): Get date format from character text

getPval(): Get the p-value

gg_diagnostic_prev() gg_prev_fixed(): Diagnostic Prevalence

ggkm(): Kaplan-Meier Plots using ggplot

grhoTests(): Summary of Survival Curve differences using G-rho tests

histSum(): Summary histogram

indepTests(): Tests for Independence in Contingency Tables

indexOf(): Find occurences of string within another string

isFirstLetterUpperCase(): Is the first letter uppercase?

kappaBootCI(): Bootstrapped confidence interval for kappa statistic.

knit_with_date(): Knit R markdown report with today's date

lifetable(): Generate lifetables for multiclass variables

logistfPrint(): Print summaries from logistf

medianCtr(): Median center rows

ms_condition(): Sample count condition for MS analyses

ms_boxplot() ms_mean_var(): Plots for MS analyses

ms_process(): Process mass spectrometry data

ms_summarize(): Summarize mass spectrometry data

ms_top(): Top variables in mass spectrometry analysis

multiClassCM(): Confusion matrix summaries

multiplot(): Multiple plots

name_cuts(): Name cutpoint variables

numericToDate(): Change numeric to date

pairwiseCor(): Pairwise Correlations

parse_rd(): Parse all Rd files in package

colPercent() rowPercent() rowColPercent() colPercentAsHTML() rowPercentAsHTML() rowColPercentAsHTML(): Row and Column Percentages

plotKM(): Plot Kaplan-Meier curves

plotKMDetail(): Plot detailed Kaplan-Meier curves

plotSchoenfeld(): Do Schoenfeld residual plot

prettyCoxph(): Nicer outputs from coxph model fits

pro: Protein file from Mass Spectrometry experiment

psm: Peptide-Spectrum Match (PSM) file from Mass Spectrometry experiment

remove_dup(): Remove duplicates

round_small(): Rounding of Small Numbers

sdFromCI(): Standard deviation of log hazard ratio

sem(): Standard error of the mean

simpleCap(): Simple capitalization

ssize_D(): Sample Size Calculation

minWithMissing() maxWithMissing() meanWithMissing() sumWithMissing() prodWithMissing() ratioWithMissing(): Calculates statistics with specifying missing values

summaryAsHTML(): Summary table in HTML format

tableAsHTML(): Table as HTML format

wrap_ggkm(): Wrap list of ggkm plots into a single patchwork