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Package ‘table1xls’
February20,2015
Type Package
Title Producessummarytablesandexportsthemtomulti-tab
spreadsheetformat(.xlsor.xlsx)
Version 0.3.1
Date 2014-06-13
Author AssafP.Oron
Maintainer AssafP.Oron<assaf.oron@seattlechildrens.org>
Description Acollectionofconveniencewrappersforproducingandexportingvariouscommonly-
usednumericaltabletypesto.xls/.xlsxmulti-
tabspreadsheetswhilecontrollingspreadsheetpositionandlayout,viaXLConnectfunctionality.
License GPL-3
Imports XLConnect
NeedsCompilation no
Repository CRAN
Date/Publication 2014-06-1400:14:58
Rtopicsdocumented:
table1xls-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
rangeString . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
XLaddText . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
XLgeneric . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
XLoneWay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
XLregresSummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
XLtwoWay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
XLunivariate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
XLwriteOpen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Index
19
1
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table1xls-package
table1xls-package
Publication-GradeTablesExportedto.xls/.xlsxspreadsheets
Description
Generatetabularsummariesinformatscommonlyfoundinscientificarticles,andexportthemto
Office-compatiblespreadsheetdocument(.xls/.xlsxformat).
Details
Package: table1xls
Type:
Package
Version: 0.3.1
Date:
2014-06-13
License: GPL-3
Anystatistician collaboratingwith scientists, especially in the health sciences, has toproduce
publication-gradesummarytables. Mostcommonlytheseare"Table1"stylebasicdemographics,
contingencytables,orregression-outputsummaries. Asaminimum,statisticiansneedtoprovide
tables,fromwhichtheleadauthorcaneasilyandaccuratelygeneratethesetables.
Outsideofphysicsandmathematicalfields,thevastmajorityofscientificinvestigatorsedittheir
manuscriptsandtablesinoffice-typesoftware, usuallytheMicrosoftsuite. Rcaneasilyoutput
datain.csvformat;however,theanalystorsomeoneintheinvestigativeteamstillhastoperform
tediousworkformattingthetablesusingofficesoftware,intoatemplatethattheleadauthorcan
use.Moreover,themannerinwhichregressionsummariesappearinmanuscripts,isquitedifferent
fromthetypicaloutputofsummary.glmandsimilarRfunctions.
Moreimportantthanthetediouslaborinvolved,thismanual"portage"ofanalysisoutputfromthe
rawR/csvformattotabularformatcanbepronetodataerrors,andisnotreproducible.
Thepackagetable1xlsismeanttoclosethisgap, enablinganalystsandtheircollaboratorsto
focusontheanalysisandthesciencewithpeaceofmind,whilesavingprecioustime. Itrelies
uponthefunctionalityofferedbytheXLConnectpackage. ItcanbeseenasanOffice-compatible
babyversionoftheLaTex(andnowalsoHTML)orientedxtable(ortheSAS-inspiredtables).
table1xlsdoesoffersomeconveniencesthattheseotherpackagescannotmatch, inparticular
thepossibilityofpackagingallyouroutputtablesasseparatetabsinthesamesinglespreadsheet
document, andtheabilitytolayoutrelatedtablesside-by-sideorbeloweachotherinthesame
sheet.
Regardingexporttonon-Microsoftspreadsheetsoftware:withmyLibreOffice(Windowsversion)
the.xlsexportsworkperfectlyfine,while.xlsxisnotasreliable.Irecommendusingtheformer,of
course.
YoucandownloadthelatestpackagesourcecodedirectlyfromGitHub,viathecommand
devtools::install_github("assaforon/table1xls").
Theindividualfunctionhelppageswon’tshow(theyaregeneratedviaroxygenize),butyoucan
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rangeString
3
compilethepackagelocally,orjustpeekintothefunctionsourcecodetoseethehelptext,anduse
theinst/examplesfoldertoviewandruntheexamples.
Thisisanewpackage! Iwillgladlyacceptrequestsfornewfunctionalities,aswellascomments
andcorrectionsonexistingfunctions.
Thanks,Assaf
PS:XLConnectusestherJavapackage. Forsomesystems,additionalconfigurationisneededto
enableJavaonR.ForWindowsmachinestestedsofaritwasprettymuchplug-and-play;theLinux
CRANtestsallseemtowork;notsoforsomeMacs.
Whenmanipulatinglarge spreadsheetobjects, theJavaVirtualMachinemightchokeandissue
errormessages.Ifthishappens,youwillneedtostartanewsession,andbeforeloadingXLConnect
(eitherdirectlyorvialoadingtable1xls),write
options(java.parameters = "-XmxYYYY")
WhereYYYYisthevirtual-memorysizeinMB.Thedefaultisonly128MB.Thestring"-Xmx1g"
isinterpretedas1gigabyte.KeepinmindthatyouneedtohavesubstantiallymoreRAMthanthe
amountallocatedtotheJVM.
Author(s)
AssafP.Oron.
Maintainer:AssafP.Oron<assaf.oron.at.seattlechildrens.org>
rangeString
Utilityfunctionsfortablesummaries
Description
Variousauxiliaryconveniencefunctions,mostlyforXLunivariate. Functionscalculatingsimple
statisticsandreturningtheoutputinaformattedmanner,makingiteasierforXLunivariateto
embedtheminspreadsheetcells.
Usage
rangeString(x, digits = 1, sep = "-", na.rm = FALSE, ...)
iqrString(x, digits = 1, sep = "-", quantmeth = 7, na.rm = FALSE, ...)
roundmean(x, digits = 1, na.rm = FALSE, ...)
roundmedian(x, digits = 1, na.rm = FALSE, ...)
roundSD(x, digits = 1, na.rm = FALSE, ...)
emptee(x, ...)
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rangeString
Arguments
x
vector(usuallynumeric,butcanbelogical)onwhichstatisticsaretobecalcu-
lated
digits
numeric:howmanydigitstoroundtheoutputto?
quantmeth
numeric:forfunctionscallingquantile,thecalculationmethodforthequan-
tiles. Defaultis7tomatchtheRdefault. Notethatitisshrunktowardsthe
medianandhencebiased,buttypicallywithlowerMSE.Averyviablealterna-
tiveis6,theSAS/SPSS(andStata?)default,whichisunbiased.Seethehelpon
quantileformoredetails.
na.rm
logical: shouldmissingvaluesberemoved? (defaultFALSE)Passedontothe
underlyingfunctions
sep
character:separatingcharacterforrange-typefunctions.
...
thisisignoredbythefunctions,butenablesthe"mixingandmatching"ofextra
parametersbetweenfunctionscalledbyXLunivariate,withouttriggeringan
error.
Details
ThisisasmallcollectionofusefulutilitiescalledbyXLunivariate. Theyreturn1-2summary
statistics,inaformatthatwillnotrequireadditionalformattingandformula-manipulationinExcel.
Forexample,roundmedianreturnsthemedianroundedtothespecifiednumberofdigits,while
iqrStringreturnsthe1stand3rdquartiles, separatedbyatleastonedash(default3dashes).
XLunivariatecancombinethesefunctions’outputtoproducetheformattedsummary"median
(Q1---Q3)"oftenusedinresearcharticles.
Inparticular,empteereturnsanemptystring,enablingtheuseofXLunivariatetoproduceonlya
singlesummarystatisticpercellratherthanapair.
Value
Thesummarystatistic(s),intheformatspecifiedviathearguments.
Author(s)
AssafP.Oron<assaf.oron.at.seattlechildrens.org>
SeeAlso
XLunivariatewhichisthemainfunctioncallingtheseutilities.
Examples
book2<-XLwriteOpen("chick2.xls")
## Plain-vanilla
XLunivariate(book2,"weightByDiet",ChickWeight$weight,ChickWeight$Diet,
title="Mean Weights by Diet",rowTitle="Diet")
## Replace mean/SD with median/range, put results beside previous
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XLaddText
5
XLunivariate(book2,"weightByDiet",ChickWeight$weight,ChickWeight$Diet,
title="Median Weights by Diet",rowTitle="Diet",col1=8,
fun1=list(fun=roundmedian,name="Median"),fun2=list(fun=rangeString,name="range"))
### You can also do only one statistic... by "killing" oneof the functions
XLunivariate(book2,"weightByAge",ChickWeight$weight,ChickWeight$Time,
title="Mean Weights by Age",rowTitle="Age (Days)",seps=rep("",3),
fun2=list(fun=emptee,name=""))
cat("Look for",paste(getwd(),"chick2.xls",sep=/),"to seethe results!\n")
XLaddText
Writetexttoasinglecell
Description
Writetexttoasinglecellinaspecifiedfileandsheet,andsavethefile.
Usage
XLaddText(wb, sheet, text, row1 = 1, col1 = 1)
Arguments
wb
aworkbook-classobject
sheet
numericorcharacter:aworksheetname(character)orposition(numeric)within
wb.
text
character:thetexttobewrittentofile.
row1,col1
integer:therowandcolumnfortheoutput.
Details
SinceXLConnectonlyexportsdatatospreadsheetsas‘data.frame‘,thisfunctionsendsthetextas
anon-the-fly‘data.frame‘withonecolumnandonerow,andwithoutwritingtheheaderortherow
name.
Value
Thefunctionreturnsinvisibly,afterwritingthedataintosheetandsavingthefile.
Note
Ifthespecifiedsheetdoesnotexist,thefunctionwillcreateit,assumingthatwastheuser’sintent
(e.g.,addatext-onlysheetwithexplanationstoafile.)Thisishard-coded,becausetheinadvertent
creationofsingle-textsheetsduetotyposcanbeeasilydiscovereduponopeningthefile:)
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XLgeneric
Examples
t1<-XLwriteOpen("generic1.xls")
### Just a meaningless matrix; function converts to data.frame and exports.
XLgeneric(t1,"s1",matrix(1:4,nrow=2))
###Nowaddingrownames,title,etc.Noteaddingthetitle shifts thetableonerowdown.
XLgeneric(t1,"s1",matrix(1:4,nrow=2),col1=5,addRownames=TRUE,
title="Another Meaningless Table",rowTitle="What?",
rowNames=c("Hey","You!"))
###... and nowadding some text
XLaddText(t1,"s1","You can also add text here...",row1=10)
XLaddText(t1,"s1","...or here.",row1=11,col1=8)
XLaddText(t1,"s2",
"Adding text to a new sheet name will create that sheet!"
,row1=2,col1=2)
### A more complicated example, showinghow a "flattened" 3-way table might be exported:
carnames=paste(rep(c(4,6,8),each=2),"cylinders",rep(c("automatic","manual"),3))
XLgeneric(t1,cars,ftable(mtcars$cyl,mtcars$vs,mtcars$am),
addRownames=TRUE,rowNames=carnames,rowTitle="EngineType",colNames=c("S","V"))
cat("Look for",paste(getwd(),"generic1.xls",sep=/),"to see the results!\n")
XLgeneric
Writegenericrectangulardatatoaspreadsheet
Description
Exportagenericdataframe,matrixortabletoaspreadsheetandsavethefile.
Usage
XLgeneric(wb, sheet, dataset, title = NULL, addRownames = FALSE,
rowNames = rownames(dataset), rowTitle = "Name", colNames = NULL,
row1 = 1, col1 = 1, purge = FALSE)
Arguments
wb
aworkbook-classobject
sheet
numericorcharacter:aworksheetname(character)orposition(numeric)within
wb.
dataset
therectangularstructuretobewritten. Canbeadataframe,table,matrixor
similar.
title
character:anoptionaloveralltitletothetable.Default(NULL)isnotitle.
addRownames
logical: shouldacolumnofrownamesbeaddedtotheleftofthestructure?
(defaultFALSE)
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7
rowTitle
character:thetitletobeplacedabovetherownamecolumn(default"Name")
rowNames
character:vectorofrownames.Defaultrownames(dataset),butrelevantonly
ifaddRownames=TRUE.
colNames
character:vectorofcolumnnamestoreplacetheoriginalones. DefaultNULL,
meaningthattheoriginalnamesareleftintact. Notethatthetitlefortherow-
namescolumn(ifaddRownames=TRUE)is*not*consideredpartofcolNames,
andissetseparately.
row1,col1
numeric:thefirstrowandcolumnoccupiedbytheoutput.
purge
logical:shouldsheetbecreatedanew,byfirstremovingthepreviouscopyifit
exists?(defaultFALSE)
Details
Thisfunctionisaconveniencewrapperforgettingpracticallyanyrectangulardatastructureintoa
spreadsheet,withoutworryingaboutconversionorspreadsheet-writingtechnicalities.
Ifthestructureisnotadataframe(orinheritedfromone),butatableormatrix,thefunctionwill
convertitintooneusingas.data.frame.matrix,becausedataframesarewhattheunderlying
functionwriteWorksheetcanexport.
SeetheXLtwoWayhelppage,forbehaviorregardingnew-sheetcreation,overwriting,etc.
Value
Thefunctionreturnsinvisibly,afterwritingthedataintosheetandsavingthefile.
Author(s)
AssafP.Oron<assaf.oron.at.seattlechildrens.org>
SeeAlso
Fortwo-waycontingencytables,seeXLtwoWay.
Examples
t1<-XLwriteOpen("generic1.xls")
### Just a meaningless matrix; function converts to data.frame and exports.
XLgeneric(t1,"s1",matrix(1:4,nrow=2))
###Nowaddingrownames,title,etc.Noteaddingthetitle shifts thetableonerowdown.
XLgeneric(t1,"s1",matrix(1:4,nrow=2),col1=5,addRownames=TRUE,
title="Another Meaningless Table",rowTitle="What?",
rowNames=c("Hey","You!"))
###... and nowadding some text
XLaddText(t1,"s1","You can also add text here...",row1=10)
XLaddText(t1,"s1","...or here.",row1=11,col1=8)
XLaddText(t1,"s2",
"Adding text to a new sheet name will create that sheet!"
,row1=2,col1=2)
8
XLoneWay
### A more complicated example, showinghow a "flattened" 3-way table might be exported:
carnames=paste(rep(c(4,6,8),each=2),"cylinders",rep(c("automatic","manual"),3))
XLgeneric(t1,cars,ftable(mtcars$cyl,mtcars$vs,mtcars$am),
addRownames=TRUE,rowNames=carnames,rowTitle="EngineType",colNames=c("S","V"))
cat("Look for",paste(getwd(),"generic1.xls",sep=/),"to see the results!\n")
XLoneWay
One-wayContingencyTablesexportedtoaspreadsheet
Description
Calculatesaone-waycontingencytableincountsandpercents, exportsaformattedoutputtoa
spreadsheet,andsavesthefile.
Usage
XLoneWay(wb, sheet, rowvar, title = NULL, rowTitle = "Value",
rowNames = NULL, ord = NULL, row1 = 1, col1 = 1, purge = FALSE,
digits = ifelse(length(rowvar) >= 200, 1, 0), combine = TRUE,
useNA = "ifany")
Arguments
wb
aworkbook-classobject
sheet
numericorcharacter:aworksheetname(character)orposition(numeric)within
wb.
rowvar
vector: thecategoricalvariable(logical,numeric,character,factor,etc.) tobe
tabulated
title
character:anoptionaloveralltitletothetable.Default(NULL)isnotitle.
rowTitle
character: thetitletobeplacedabovetherownamecolumn(defaultempty
string)
rowNames
character:vectorofrownames. Defaultbehavior(NULL):automaticallydeter-
minedfromdata
ord
numericvectorspecifyingrow-indexorderintheproducedtable.Default(NULL)
isnore-ordering.
row1,col1
numeric:thefirstrowandcolumnoccupiedbythetable(titleincludedifrele-
vant).
purge
logicalshouldsheetbecreatedanew,byfirstremovingthepreviouscopyifit
exists?(defaultFALSE)
digits
numeric: howmanydigits(afterthedecimalpoint)toshowinthepercents?
Defaultsto1ifn>=200,0otherwise.
combine
logical:shouldcountsandpercentabbecombinedtothepopular"Count(percent)"
format,orpresentedside-by-side?(defaultTRUE)
useNA
Howtohandlemissingvalues.Passedontotable(seehelponthatfunctionfor
options).
XLregresSummary
9
Details
Thisfunctionperformsaone-waycontingencytable,alsocalculatingthedistributioninpercents.
Thetableisthenexportedtoworksheetsheetinworkbookwb,eitherusingtheformat"Count(percent)"
(ifcombine=TRUE),orastwoseparatecolumnsinthesametable.
SeetheXLtwoWayhelppage,forbehaviorregardingnew-sheetcreation,overwriting,etc.
Value
Thefunctionreturnsinvisibly,afterwritingthedataintosheetandsavingthefile.
Author(s)
AssafP.Oron<assaf.oron.at.seattlechildrens.org>
SeeAlso
Ifinterestedinotherdescriptivesummaries,seeXLunivariate. Fortwo-waycontingencytables,
seeXLtwoWay.
Examples
book1<-XLwriteOpen("chick1.xls")
XLoneWay(book1,"Diets",ChickWeight$Diet)
### Now in separate columns, and with a title - note it shifts the table down.
XLoneWay(book1,"Diets",ChickWeight$Diet,combine=FALSE,row1=10,
rowTitle="Diet",title="Counts by Diet:")
cat("Look for",paste(getwd(),"chick1.xls",sep=/),"to seethe results!\n")
XLregresSummary
RegressionSummaryTablesexportedtoaspreadsheet
Description
Takes regressioneffectestimates andthe correspondingstandard errors, , transformsto"human
scale"ifrequested,calculatesconfidence-intervalsandp-values,andexportsastandardformatted
summarytabletoaspreadsheet.
Usage
XLregresSummary(wb, sheet, betas, SE = NULL, varnames = NULL, colid = 1:2,
transfun = identity, title = NULL, effname = "Difference",
confac = qnorm(0.975), roundig = 2, pfun = function(x) 2 *
pnorm(-abs(x)), pround = 3, row1 = 1, col1 = 1, purge = FALSE)
10
XLregresSummary
Arguments
wb
aworkbook-classobject
sheet
numericorcharacter:aworksheetname(character)orposition(numeric)within
wb.
betas
numeric:avectorofpointestimates,oramatrixcontainingestimatesandstan-
darderrorsincolumns
SE
numeric:avectorofstandard-errorestimatesfortheeffects. IfNULL(default),
userneedstospecifythemviathebetasmatrix.
varnames
character:avectorofeffectnames(column1ofoutputtable).IfNULL(default),
userneedstospecifythemviathebetasmatrix.
colid
integer: vectorofindicesforthecolumnscontainingthepointestimatesand
SEs,respectively.Usedonlyifbetasisamatrix.
transfun
transformationfunctionforbetas,SE,toproducecolumns2-3oftheoutput.
Defaultstoidentity.useexpforoddsratioorrelativerisk.
effname
character: astringexplainingwhattheeffectstandsfor,e.g. "difference"(the
default),"OddsRatio",etc.
confac
numeric:theproportionalityfactorforcalculatingconfidence-intervals.Default
produces95Normalintervals.
pfun
functionusedtocalculatethep-value,basedonthesignal-to-noiseratiobetas/SE.
Defaultassumestwo-sidedNormalp-values.
title
character:anoptionaloveralltitletothetable.Default(NULL)isnotitle.
roundig
numeric:howmanydigits(afterthedecimalpoint)toroundtheeffectestimate
to?
pround
numeric:howmanydigits(afterthedecimalpoint)toroundthep-valueto?P-
valuesroundeddowntozerowillshowupas"<"thesmallestnonzerovalue,
e.g. withthedefaultpround=3p-valuessmallerthan0.0005willshowupas
"<0.001".
row1,col1
numeric:thefirstrowandcolumnoccupiedbythetable(titleincludedifrele-
vant).
purge
logical:shouldsheetbecreatedanew,byfirstremovingthepreviouscopyifit
exists?(defaultFALSE)
Details
Thisfunctionproducesastandardscientific-articleregressionsummarytable,giventherawregres-
sionoutput.Theresultingtablehas4columns:effectname,its(optionallytransformed)magnitude,
aprobabilisticallysymmetricconfidenceinterval(likewisetransformed),andp-value.Theformat-
tedtableisexportedtosheet,andthefileisimmediatelysaved.
Theinputcan be provided as separate vectors ofpoint estimates (betas)andstandard errors
(SE), orasasinglematrixforbetas. Inthelattercase, , asadefaulttheeffectnameswillbe
rownames(betas),unlessavectorwithmoredescriptivenamesisprovidedviavarnames.
SeetheXLtwoWayhelppage,forbehaviorregardingnew-sheetcreation,overwriting,etc.
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