Man pages for ying14/yingtools2
Ying's R Tools

age.yearsAge in years
all.greplAll Grepl
as.Date2Convert to Date (Ying's version)
as.mrnConvert to MRN format
as.phylo.formula2Conversion from Taxonomy Variables to Phylogenetic Trees (YT...
chop.endpointChop survival endpoint
cid.bsiBloodstream Infections
cid.cdiffC. diff results
cid.colorsThe color scheme used in CID manuscript.
cid.hospHospitalizations
cid.medsMedications
cid.patientsPatients
cid.phy16S sequence data (phyloseq format)
cleanup.dataCleanup data
coalesce_indicatorsCoalesce indicator variables into one summary variable.
convert.datesSearch and Convert Date variables
copy.as.RcodeConvert object to R-code.
copy.as.sqlConvert vector to SQL code.
copy.to.clipboardCopy to Clipboard
coxCox Proportional Hazards Regression (TAKE 2)
createSurvivalFrameCreate Survival Data Frame
cummaxCumulative Max
cut2Ying's Cut 2
dtYing's DT view
fan.angleModify Angle for Text on Circular ggtree
fill_in_blanksFill in Blanks
find.all.distinct.varsFind All Distinct Variables
geom_hilightHilight a set of ggtree tips.
geom_kaplanmeierGenerate Kaplan-Meier curve in ggplot2
geom_logrankGenerate label for Log-rank test results in ggplot2
get.otuExtract Phyloseq otu_table
get.otu.meltConvert Phyloseq to Melted OTU x Sample Data
get.rowGet Rows (optimized for timeline plots)
get.sampExtract Phyloseq sample_data
get.taxExtract Phyloseq tax_table
get.timeExtract Time
get.yt.paletteGet YT Palette
get.yt.palette2Get YT Palette 2
gg.colorsDefault color palette of ggplot2
gg.legendExtract legend from a ggplot2 object
gg.stackStack and line up ggplot objects in a column
grapes-allin-grapesAll In
grapes-grapesSubtract Dates
grapes-not-in-grapesNot In
group_by_all_distinctGroup By All Distinct Variables
group_by_timeGroup by Time
group_by_time_streaksGroup by Time Streaks
is.distinctIs Distinct
is.mrnDetermine if variable is a properly formatted MSKCC MRN
is.wholenumberDetermines if a numeric is all whole numbers
lefseLEfSe
left_join_replaceLeft Join Replace
log_epsilon_transLog Epsilon Tranformation
log_epsilon_trans_breaksBreaks for Log Epsilon Tranformation
logisticLogistic Regression
logistic_transLogistic Transformation
logistic_trans_breaksBreaks for Logistic Tranformation
ls.object.sizesDisplay sizes of objects in memory
make.datetimeCreate Date-Time (POSIXct object)
make.namesMake Syntactically Valid Names (Ying's version)
make.surv.endptMake a survival endpoint
make.tableMake Table
max2Ying's Min/Max
middle.patternMiddle Pattern
occurs.withinDetermines if tstart-tstop occurs anywhere within interval.
paste2Paste 2
pca.plotPlot Principal Components Analysis
phy.collapseCollapse Phyloseq Into Taxonomy
pipePipe operator
pretty_numberPretty Numeric Format (Non-scientific)
pretty_scientificFancy Scientific Notation
read_all_excelRead Multiple Excel Sheets Into a List of Data Frames
read.blastn.fileRead in tax file from blastn output
read.clipboardRead Clipboard
read_excel2Read Excel File 2
read.mothur.taxfileRead in mothur taxonomy file.
read.oligosRead in oligos file.
read.otu.tableRead OTU table from text file
read.tree.uparseRead Tree File (Label-Fix)
read.uparse.dataImport UPARSE pipeline data and create phyloseq
recode2Ying's Recode
remove.na.colsRemove NA columns
remove.na.rowsRemove NA rows
replace.grepYing's Replace Grep
replace.grep.dataYing's Replace Grep for Data Frames
select2Select 2
send.text.messageSend a Text Message
set.otuConvert otu table to phyloseq otu_table
set.sampConvert data frame to phyloseq sample_data
set.taxConvert data frame to phyloseq tax_table
shadesColor Shades
shell.execOpen a File using File Associations
show_linetypesDisplay values for ggplot's linetype aesthetic
show_shapesDisplay values for ggplot's shape aesthetic
stcoxCox Proportional Hazards Regression
str_extract_all_quotesExtract any text within quotes.
survival.frame.atrisk.tableAt-Risk Table from Survival Data Frame
survival.frame.infoSurvival Frame Info
tabTabulate
tax.plotPlot tax
univariate.logisticUnivariate Logistic Regression
univariate.stcoxUnivariate Cox Proportional Hazards
write_all_excelWrite multiple data frames to an Excel file
yingtools2Useful R Functions by Ying
ying14/yingtools2 documentation built on March 5, 2020, 10:50 p.m.