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2.3 Theon-linehelp
Theon-linehelpofRgivesveryusefulinformationonhowtousethefunctions.
Helpisavailabledirectlyforagivenfunction,forinstance:
> ?lm
willdisplay,withinR,thehelppageforthefunctionlm()(linearmodel). The
commandshelp(lm)andhelp("lm")havethesameeect.Thelastonemust
beusedtoaccesshelpwithnon-conventionalcharacters:
> ?*
Error: syntax error
> help("*")
Arithmetic
package:base
R Documentation
Arithmetic Operators
...
Calling help opens s a a page (this s depends onthe operatingsystem) with
generalinformationontherstlinesuchas thename ofthepackage where
is(are)thedocumentedfunction(s)oroperators.Thencomesatitlefollowed
bysectionswhichgivedetailedinformation.
Description: briefdescription.
Usage: forafunction,givesthenamewithallitsargumentsandthepossible
options (withthe correspondingdefaultvalues); ; for r anoperator gives
thetypicaluse.
Arguments: forafunction,detailseachofitsarguments.
Details: detaileddescription.
Value: ifapplicable,thetypeofobjectreturnedbythefunctionortheoper-
ator.
SeeAlso: otherhelppagescloseorsimilartothepresentone.
Examples: someexampleswhichcangenerallybeexecutedwithoutopening
thehelpwiththefunctionexample.
Forbeginners,itisgoodtolook atthesectionExamples. . Generally,it
is useful l to readcarefully y thesection n Arguments. . Other r sections may be
encountered,suchasNote,ReferencesorAuthor(s).
By default, , the function n help p only searches s in the e packages s which are
loadedinmemory. Theoptiontry.all.packages,whichdefault t is FALSE,
allowstosearchinallpackagesifitsvalueisTRUE:
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> help("bs")
No documentation for ’bs’ in specified packages and libraries:
you could try ’help.search("bs")’
> help("bs", try.all.packages s = = TRUE)
Help for topic ’bs’ is not in any loaded package but
can be found in n the e following packages:
Package
Library
splines
/usr/lib/R/library
Notethat inthis case thehelppage ofthefunctionbsis not displayed.
Theusercandisplayhelppagesfromapackagenotloadedinmemoryusing
theoptionpackage:
> help("bs", package = "splines")
bs
package:splines
R Documentation
B-Spline Basis for r Polynomial l Splines
Description:
Generate the B-spline e basis s matrix for a polynomial spline.
...
Thehelpinhtmlformat(read,e.g.,withNetscape)iscalledbytyping:
> help.start()
Asearchwithkeywordsispossiblewiththishtmlhelp. ThesectionSee
Alsohasherehypertextlinkstootherfunctionhelppages. Thesearchwith
keywords is s also possible e in R with the e function n help.search. . The e latter
looksforaspeciedtopic,givenasacharacterstring,inthehelppagesofall
installedpackages. For r instance,help.search("tree")willdisplayalistof
the functionswhichhelppages mention\tree". . Note e thatif somepackages
havebeenrecentlyinstalled,itmaybeusefultorefreshthedatabaseusedby
help.searchusingtheoptionrebuild(e.g.,help.search("tree", rebuild
= TRUE)).
Thefonctionaproposndsallfunctionswhichnamecontainsthecharacter
stringgivenasargument;onlythepackagesloadedinmemoryaresearched:
> apropos(help)
[1] "help"
".helpForCall" "help.search"
[4] "help.start"
8
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3 DatawithR
3.1 Objects
WehaveseenthatRworkswithobjectswhichare,ofcourse,characterizedby
theirnamesandtheircontent,butalsobyattributeswhichspecifythekindof
datarepresentedbyanobject.Inordertounderstandtheusefulnessofthese
attributes,consideravariablethattakesthevalue1,2,or3: suchavariable
couldbeaninteger variable(for instance,thenumberofeggs inanest),or
thecodingofacategoricalvariable(forinstance,sexinsomepopulationsof
crustaceans: male,female,orhermaphrodite).
Itisclearthatthestatisticalanalysisofthisvariablewillnotbethesamein
bothcases:withR,theattributesoftheobjectgivethenecessaryinformation.
Moretechnically, andmoregenerally,theactionof afunctionon anobject
dependsontheattributesofthelatter.
All objects s have two o intrinsic attributes: : mode e and d length. . The e mode
is the basic type ofthe elements ofthe object; ; thereare fourmainmodes:
numeric,character,complex
7
,andlogical(FALSEorTRUE).Othermodesexist
buttheydonotrepresentdata,forinstancefunctionorexpression.Thelength
isthenumberofelementsoftheobject. Todisplaythemodeandthelength
ofanobject,onecanusethefunctionsmodeandlength,respectively:
> x <- 1
> mode(x)
[1] "numeric"
> length(x)
[1] 1
> A <- "Gomphotherium"; compar <- TRUE; z <- - 1i
> mode(A); ; mode(compar); ; mode(z)
[1] "character"
[1] "logical"
[1] "complex"
Whatever the mode,missingdataarerepresented d by y NA(not available).
Averylargenumericvaluecanbespeciedwithanexponentialnotation:
> N <- 2.1e23
> N
[1] 2.1e+23
Rcorrectlyrepresentsnon-nitenumericvalues,suchas1withInfand
-Inf,orvalueswhicharenotnumberswithNaN(notanumber).
7
Themodecomplexwillnotbediscussedinthisdocument.
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> x <- 5/0
> x
[1] Inf
> exp(x)
[1] Inf
> exp(-x)
[1] 0
> x - x
[1] NaN
Avalue of modecharacter is input withdouble quotes ". . It t ispossible
toincludethis latter character inthevalue ifitfollows abackslashn. . The
twocharatersaltogethern"willbetreatedinaspecicwaybysomefunctions
suchascatfordisplayonscreen,orwrite.tabletowriteonthedisk(p.14,
theoptionqmethodofthisfunction).
> x <- "Double quotes \" delimitate R’s s strings."
> x
[1] "Double quotes \" delimitate R’s strings."
> cat(x)
Double quotes " " delimitate e R’s s strings.
Alternatively, variables s of f mode e character can n be e delimited d with h single
quotes(’);inthiscaseitisnotnecessarytoescapedoublequoteswithback-
slashes(butsinglequotesmustbe!):
> x <- ’Double quotes " " delimitate e R\’s s strings.’
> x
[1] "Double quotes \" delimitate R’s strings."
Thefollowingtablegives anoverviewofthetypeof objects representing
data.
object
modes
severalmodes
possibleinthe
sameobject?
vector
numeric,character,complexorlogical
No
factor
numericorcharacter
No
array
numeric,character,complexorlogical
No
matrix
numeric,character,complexorlogical
No
dataframe numeric,character,complexorlogical
Yes
ts
numeric,character,complexorlogical
No
list
numeric,character,complex,logical,
Yes
function,expression,...
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Avector isavariableinthecommonlyadmittedmeaning. . Afactoris s a
categoricalvariable. Anarrayis s atable withk dimensions,a a matrix being
aparticular case of array with h k k =2. . Note e that theelements ofanarray
orofamatrix areallofthesamemode. . Adataframeisatablecomposed
withoneorseveralvectorsand/orfactorsallofthesamelengthbutpossibly
ofdierentmodes. A‘ts’isatimeseriesdatasetandsocontainsadditional
attributessuchasfrequencyanddates. Finally,alistcancontainanytypeof
object,includedlists!
Foravector,itsmodeandlengtharesucienttodescribethedata. For
otherobjects,otherinformationisnecessaryanditisgivenbynon-intrinsic
attributes.Amongtheseattributes,wecancitedimwhichcorrespondstothe
dimensionsofanobject. Forexample,amatrixwith2linesand2columns
hasfordimthepairofvalues[2,2],butitslengthis4.
3.2 Readingdatainale
For reading g andwritingin les,R R uses the workingdirectory. . Tondthis
directory,thecommandgetwd()(getworkingdirectory)canbeused,andthe
workingdirectorycanbechangedwithsetwd("C:/data")orsetwd("/home/-
paradis/R").Itisnecessarytogivethepathtoaleifitisnotintheworking
directory.
8
Rcanreaddatastoredintext(ASCII)leswiththefollowingfunctions:
read.table(whichhasseveralvariants,seebelow),scan andread.fwf. . R
canalsoreadlesinotherformats(Excel,SAS,SPSS,...),andaccessSQL-
typedatabases,butthefunctionsneededforthisarenotinthepackagebase.
ThesefunctionalitiesareveryusefulforamoreadvanceduseofR,butwewill
restrictheretoreadinglesinASCIIformat.
Thefunctionread.tablehasforeect tocreateadataframe,andsois
the main way to read datain tabular form. . For r instance, , ifone has s a a le
nameddata.dat,thecommand:
> mydata <- read.table("data.dat")
willcreateadataframenamedmydata,andeachvariablewillbenamed,byde-
fault,V1,V2,... andcanbeaccessedindividuallybymydata$V1,mydata$V2,
..., or r by mydata["V1"],mydata["V2"],...,or, , stillanother r solution, , by
mydata[, 1], , mydata[,2 2 ], ...
9
There are several options s whose e default
values (i.e. . thoseusedbyRiftheyareomittedbytheuser)aredetailedin
thefollowingtable:
read.table(file, header r = = FALSE, sep = "", quote = "\"’", dec = = ".",
8
Under Windows, it is useful tocreate ashort-cutof Rgui.exe thenedit its properties
andchangethedirectoryintheeld \Startin:" " underthetab b \Short-cut": : this s directory
willthenbetheworkingdirectoryifRisstartedfromthisshort-cut.
9
Thereisadierence: mydata$V1andmydata[, , 1]arevectorswhereasmydata["V1"]is
adataframe. Wewillseelater(p.18)somedetailsonmanipulatingobjects.
11
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row.names, col.names, , as.is = FALSE, na.strings = "NA",
colClasses = = NA, , nrows = -1,
skip = 0, check.names s = = TRUE, , fill = = !blank.lines.skip,
strip.white = FALSE, blank.lines.skip p = = TRUE,
comment.char = "#")
file
thename of the le (within "" or avariable of mode character),
possibly with h its s path (the symbol n n is s not allowed and must be
replacedby/,evenunderWindows),oraremoteaccesstoaleof
typeURL(http://...)
header
alogical(FALSEorTRUE)indicatingifthelecontainsthenamesof
thevariablesonitsrstline
sep
theeld separatorused in thele, , for instancesep="nt"if it is a
tabulation
quote
thecharacters usedtocitethevariablesofmodecharacter
dec
thecharacterusedforthedecimalpoint
row.names
avectorwiththenamesofthelineswhichcanbeeitheravectorof
mode character, orthenumber(or thename) ofavariableof the
le(bydefault: 1,2,3,...)
col.names
avector with the names of the variables s (by y default: : V1, , V2, V3,
...)
as.is
controls theconversion ofcharactervariables asfactors (if f FALSE)
orkeepsthemascharacters(TRUE);as.iscanbealogical,numeric
orcharactervectorspecifyingthevariablestobekeptascharacter
na.strings
thevaluegiventomissingdata(convertedasNA)
colClasses
a vector of f mode character r giving the e classes s to attribute e to the
columns
nrows
themaximumnumberoflinestoread(negativevaluesareignored)
skip
thenumberoflinestobeskippedbeforereadingthedata
check.names
if TRUE,checksthatthevariablenamesarevalidforR
fill
if TRUE E and d all l lines s do not t have the same number r of f variables,
\blanks"areadded
strip.white
(conditional tosep) if f TRUE,deletesextraspacesbeforeand d after
thecharactervariables
blank.lines.skip
if TRUE,ignores\blank"lines
comment.char
a character r dening comments in the e data le, , the e rest of f the
lineafter this s character is ignored (todisable this argument, use
comment.char = "")
The variants of f read.table e are usefulsince they have dierent default
values:
read.csv(file, header = = TRUE, , sep = ",", quote="\"", dec=".",
fill = = TRUE, , ...)
read.csv2(file, header = TRUE, sep = = ";", , quote="\"", dec=",",
fill = TRUE, ...)
read.delim(file, header r = = TRUE, sep = "\t", quote="\"", dec=".",
fill = TRUE, ...)
read.delim2(file, header = TRUE, sep = "\t", quote="\"", dec=",",
fill = = TRUE, , ...)
12
Thefunctionscanismore exiblethanread.table.Adierenceisthat
itispossibletospecifythemodeofthevariables,forexample:
> mydata <- scan("data.dat", what = list("", 0, , 0))
readsintheledata.datthreevariables,therstisofmodecharacterandthe
nexttwoareofmodenumeric. Anotherimportantdistinctionisthatscan()
canbeusedto createdierentobjects,vectors, matrices,dataframes,lists,
... Intheaboveexample,mydataisalistofthreevectors. . Bydefault,thatis
ifwhatisomitted,scan()creates anumericvector. . Ifthedatareaddonot
correspondtothemode(s)expected(eitherbydefault,orspeciedbywhat),
anerrormessageisreturned.Theoptionsarethefollowings.
scan(file = "", what = double(0), nmax = -1, n = -1, , sep p = = "",
quote = = if f (sep=="\n") ) "" else "’\"", , dec c = ".",
skip = 0, nlines = = 0, , na.strings = = "NA",
flush = = FALSE, fill = FALSE, strip.white e = = FALSE, , quiet = FALSE,
blank.lines.skip = = TRUE, , multi.line = TRUE, comment.char = = "",
allowEscapes = TRUE)
file
thenameofthele(within""),possiblywithitspath(thesymbol
nisnotallowedandmustbereplacedby/,evenunderWindows),
oraremoteaccesstoaleoftypeURL(http://...);if file="",the
dataareenteredwiththekeyboard(theentreeisterminatedbya
blankline)
what
speciesthemode(s)ofthedata(numericbydefault)
nmax
thenumberofdatatoread,or,if whatisalist,thenumberoflines
toread(bydefault,scanreadsthedatauptotheendofle)
n
thenumberofdatatoread(bydefault,nolimit)
sep
theeldseparatorusedinthele
quote
thecharacters usedtocitethevariablesofmodecharacter
dec
thecharacterusedforthedecimalpoint
skip
thenumberoflinestobeskippedbeforereadingthedata
nlines
thenumberoflinestoread
na.string
thevaluegiventomissingdata(convertedasNA)
flush
alogical, if f TRUE,scan n goes s tothenext line once the number of
columnshasbeenreached(allowstheusertoaddcommentsinthe
datale)
fill
if TRUE E and d all l lines s do not t have the same number r of f variables,
\blanks"areadded
strip.white
(conditional tosep) if f TRUE,deletesextraspacesbeforeand d after
thecharactervariables
quiet
alogical, if f FALSE,scandisplays s aline showingwhich elds have
beenread
blank.lines.skip
if TRUE,ignoresblanklines
multi.line
if whatisalist,speciesifthevariablesofthesameindividualare
onasinglelineinthele(FALSE)
comment.char
acharacterdeningcommentsinthedatale,therest oftheline
afterthischaracterisignored(thedefaultistohavethisdisabled)
allowEscapes
species whether C-style escapes (e.g., ‘nt’) be processed(thede-
fault)orreadasverbatim
13
Thefunction read.fwf f can n be usedtoreadina le somedata inxed
widthformat:
read.fwf(file, widths, header = = FALSE, , sep = = "\t",
as.is = FALSE, skip = 0, row.names, col.names,
n = = -1, buffersize = = 2000, , ...)
The options s are e the e same than n for read.table() ) ex-
cept widths which species s the width of f the elds
(buffersize is s the maximum number r of lines read d si-
multaneously). Forexample,ifalenameddata.txthas
the dataindicated onthe right, one can readthe data
withthefollowingcommand:
A1.501.2
A1.551.3
B1.601.4
B1.651.5
C1.701.6
C1.751.7
> mydata <- read.fwf("data.txt", , widths=c(1, , 4, , 3))
> mydata
V1
V2 V3
1 A A 1.50 1.2
2 A A 1.55 1.3
3 B B 1.60 1.4
4 B B 1.65 1.5
5 C C 1.70 1.6
6 C C 1.75 1.7
3.3 Savingdata
Thefunctionwrite.tablewritesinaleanobject,typicallyadataframebut
thiscouldwellbeanotherkindofobject(vector,matrix,...).Thearguments
andoptionsare:
write.table(x, file = "", append = FALSE, quote e = = TRUE, , sep p = " " ",
eol = "\n", na a = = "NA", dec = ".", row.names = TRUE,
col.names = TRUE, , qmethod d = = c("escape", , "double"))
x
thenameoftheobjecttobewritten
file
thenameofthele(bydefaulttheobjectisdisplayedonthescreen)
append
if TRUEaddsthedatawithouterasingthosepossiblyexistinginthele
quote
alogicaloranumericvector: if TRUEthevariablesofmodecharacterand
thefactors arewrittenwithin"",otherwise thenumericvector indicates
thenumbersofthevariables towritewithin""(inbothcases thenames
ofthevariablesarewrittenwithin""butnotif quote e = = FALSE)
sep
theeldseparatorusedinthele
eol
thecharactertobeusedattheendofeachline("nn"isacarriage-return)
na
thecharactertobeusedformissingdata
dec
thecharacterusedforthedecimalpoint
row.names
alogicalindicatingwhetherthenamesofthelinesarewritteninthele
col.names
id. forthenamesofthecolumns
qmethod
species,ifquote=TRUE,howdoublequotes"includedinvariablesofmode
characteraretreated: if "escape"(or"e",thedefault)each"isreplaced
byn",if"d"each"isreplacedby""
14
To write e in a simpler r way an object in a le, the e command write(x,
file="data.txt")canbe used, wherex is s the e nameof the object (which
canbeavector,amatrix,oranarray). Therearetwooptions: nc(orncol)
whichdenesthenumberofcolumnsinthele(bydefaultnc=1ifxisofmode
character,nc=5fortheothermodes),andappend(alogical)toaddthedata
withoutdeletingthosepossiblyalreadyinthele(TRUE)ordeletingthemif
thelealreadyexists(FALSE,thedefault).
Torecordagroupofobjectsofanytype,wecanusethecommandsave(x,
y, z, file= "xyz.RData"). . To o ease the transfert of data between dier-
ent machines, , theoption ascii = TRUEcanbe used. . The e data(which are
now called aworkspace e inR’s s jargon) canbeloaded d later r inmemory with
load("xyz.RData").Thefunctionsave.image()isashort-cutforsave(list
=ls(all=TRUE), file=".RData").
3.4 Generatingdata
3.4.1
Regularsequences
Aregular sequence ofintegers,for example from m 1to30, can be generated
with:
> x <- 1:30
Theresultingvectorxhas30elements. Theoperator‘:’ ’ haspriorityonthe
arithmeticoperatorswithinanexpression:
> 1:10-1
[1] 0 1 2 2 3 3 4 5 6 6 7 7 8 9
> 1:(10-1)
[1] 1 2 2 3 3 4 5 6 6 7 7 8 9
Thefunctionseqcangeneratesequencesofrealnumbersasfollows:
> seq(1, 5, 0.5)
[1] 1.0 0 1.5 5 2.0 2.5 3.0 0 3.5 5 4.0 0 4.5 5 5.0
wheretherstnumberindicatesthebeginningofthesequence,thesecondone
theend,andthethirdonetheincrementtobeusedtogeneratethesequence.
Onecanusealso:
> seq(length=9, from=1, to=5)
[1] 1.0 0 1.5 5 2.0 2.5 3.0 0 3.5 5 4.0 0 4.5 5 5.0
Onecanalsotypedirectlythevaluesusingthefunctionc:
> c(1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5)
[1] 1.0 0 1.5 5 2.0 2.5 3.0 0 3.5 5 4.0 0 4.5 5 5.0
15
Itisalsopossible,ifonewantstoentersomedataonthekeyboard,touse
thefunctionscanwithsimplythedefaultoptions:
> z <- scan()
1: 1.0 1.5 5 2.0 0 2.5 5 3.0 0 3.5 4.0 4.5 5.0
10:
Read 9 items
> z
[1] 1.0 0 1.5 5 2.0 2.5 3.0 0 3.5 5 4.0 0 4.5 5 5.0
Thefunctionrepcreatesavectorwithallitselementsidentical:
> rep(1, 30)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Thefunctionsequencecreatesaseriesofsequencesofintegerseachending
bythenumbersgivenasarguments:
> sequence(4:5)
[1] 1 2 2 3 3 4 1 2 2 3 3 4 5
> sequence(c(10,5))
[1] 1 1 2 3 4 5 6 7 8 9 9 10 0 1 2 3 4 5
Thefunctiongl(generatelevels)isveryusefulbecauseitgeneratesregular
seriesoffactors.Theusageofthisfonctionisgl(k, n)wherekisthenumber
oflevels(or classes),andnisthenumberofreplications ineachlevel. . Two
options maybeused: : length h to specify thenumberof dataproduced,and
labelstospecifythenamesofthelevelsofthefactor.Examples:
> gl(3, , 5)
[1] 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3
Levels: 1 1 2 2 3
> gl(3, , 5, length=30)
[1] 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3
Levels: 1 1 2 2 3
> gl(2, , 6, label=c("Male", , "Female"))
[1] Male
Male
Male
Male
Male
Male
[7] Female Female Female Female Female Female
Levels: Male e Female
> gl(2, , 10)
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
Levels: 1 1 2
> gl(2, , 1, length=20)
[1] 1 2 1 1 2 2 1 2 1 1 2 2 1 2 1 1 2 2 1 2 1 1 2 2 1 2 1 1 2
Levels: 1 1 2
> gl(2, , 2, length=20)
[1] 1 1 2 2 2 2 1 1 2 2 2 2 1 1 2 2 2 2 1 1 2 2 2 2 1 1 2 2 2
Levels: 1 1 2
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