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Because the authors of R packages work independently, it’s entirely possiblefor different authors to use the same function names and packages. If thishappens, the package that was loaded last masks functions with the samename in packages that were loaded first. R gives you a message saying whichobjects were masked from other packages the moment this happens.Forging Ahead with R-ForgeAlthough not universally true, packages on CRAN tend to have some minimumlevel of maturity. For example, to be accepted by CRAN, a package needs to pass abasic minimum set of requirements.So, where do packages live that are in the development cycle? Quite often,they live at R-Forge (http://r-forge.r-project.org/). R-Forge gives developers aplatform to develop and test their R packages. For example, R-Forge offersA build and check system on the three main operating systems (Windows, Linux,and Mac)Version controlBug-report systemsBackup and administrationTo install a project from R-Forge, you also use the install.packages()function, but you have to specify the repos argument. For example, to install thedevelopment version of the package data.table, try the following:> install.packages(“data.table”, repos=”http://R-Forge.R-project.org”)R-Forge is not the only development repository. Other repositories includerforge.net: Available at www.rforge.net, this is not related (other than in spirit)to R-Forge.omegahat: Available at www.omegahat.org.
Conducting Installations from BioConductorBioConductor is a repository of R packages and software, a collection of toolsthat specializes in analysis of genomic and related data.BioConductor has its own sets of rules for developers. For example, to install apackage from BioConcuctor you have to source a script from its server:> source(“http://bioconductor.org/biocLite.R”)Then you can use the biocLite() function to install packages fromBioConductor. If you don’t give an argument, you just install the necessary basepackages from the BioConductor project. You can find all the information you needat www.bioconductor.org.BioConductor extensively uses object-orientation programming with S4classes. Object orientation and its implementation as S4 classes is anadvanced R topic — one we don’t discuss in this book.Reading the R ManualThe “R Installation and Administration” manual (http://cran.rproject.org/doc/manuals/R-admin.html)is a comprehensive guide to theinstallation and administration of R. Chapter 6 of this manual contains all theinformation you need about working with packages. You can find it athttp://cran.r-project.org/doc/manuals/R-admin.html#Add_002don-packages.
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Running code without a compilerChap
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Creating errorsCreating warningsRec
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Analyzing tablesExtracting test res
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Working with Pivot TablesUsing the
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R For Dummies ®Published byJohn Wi
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About the AuthorsAndrie de Vries: A
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my choices. Professor Bruce Hardie
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IntroductionWelcome to R For Dummie
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: The prompt symbol, >, is not part
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You want to explore new stuff. You
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Icons Used in This BookAs you read
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Chapter 1Introducing R: The Big Pic
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eferred to as “free as in beer.
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you how to move data and graphics b
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If you have experience in other lan
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variables, get to look at the built
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Below all this information is the R
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that we use it to illustrate the ex
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Starting Your First R SessionIf you
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Using R as a calculator is very int
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Sourcing a ScriptUntil now, you’v
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Finding help on functionsWe discuss
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languages, the backslash character
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Vectorizing your functionsVectorize
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print()R tells you that it needs th
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extensions that much. But using .Rh
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Choosing a clear nameWhen Joris was
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opinions, so the naming of function
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Often, you want to add a bit of ext
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all of them at the beginning of eac
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Part IIGetting Down to Work in RIn
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calculator.Vector operations: Vecto
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Suppose that Granny and Geraldine d
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FunctionWhat It Doesabs(x)log(x,bas
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decision to use scientific notation
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operations in Chapter 7.Actually, o
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NaN in calculations. The outcome of
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Take a look at the vector baskets.o
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way the value is stored in memory.R
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[1] 12 4 4 6 9 3 5 3 2 2 12 9The re
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Okay, this example isn’t too impr
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R doesn’t have an Undo button, so
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x < yx baskets.of.Granny > 5[1] TR
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that value (refer to “Dealing wit
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all(). To find out whether Granny w
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You can tell quite a few things abo
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third game, and so on.The vector re
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1st 2nd 3rd 4th 5th 6th-67 25 20 50
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In this section, you take a look at
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LETTERS[24:26][1] “X” “Y”
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Creating and assigning named vector
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Similar to the way that R displays
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[1] “The quick brown FOX jumps ov
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R performs lexicographic sorting, a
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The result of grep() is a numeric v
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Suppose you have the sentence He is
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Regular expressions allow three way
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lexicographically sorted, unique va
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difference between the levels and t
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vector subsisting rules. For exampl
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table(state.region)state.regionNort
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Chapter 6Going on a Date with RIn T
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startDate xm xm[1] “2012-01-01
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Table 6-2 Some Format Codes for Dat
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As you can see, as.POSIXct() takes
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Formatting Dates and TimesTo format
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Now you know the exact time when we
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project.org/web/packages/lubridate/
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They contain only a single type of
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To get only the number of rows, you
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[1,] 1 4 7 10[2,] 2 5 8 11[3,] 3 6
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id first.matrix[-id][1] 1 2 3 4 5
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[2,] 2 5 8 11[3,] 3 4 9 12You also
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the way. You can try that out yours
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constructing a matrix second.matrix
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[2,] 4 5 6[3,] 7 8 9[4,] 10 11 12Yo
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Using the creator functionsYou can
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[2,] 5 17[3,] 8 20[4,] 11 23This re
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[1] 6Likewise, the ncol() function
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data frame with character vectors o
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section, earlier in this chapter.Ex
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As explained in the “Combining ve
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Create a matrix with two columns.Cr
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Although the row names of the data
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you, because data frames are, in fa
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You can’t use logical vectors or
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askets.nlist baskets.nlist[‘scor
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The second line contains a $, which
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Part IIICoding in RIn this part . .
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Making the scriptSuppose you want t
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There’s no way you can define in
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Luckily, this problem doesn’t occ
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addPercent
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addPercent(new.numbers)Error in x *
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list instead of using the dots.So,
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code. So, instead of giving a funct
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Instead of passing the code of the
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Using internal functionsWriting you
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weird, think again about data frame
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print.default(small.one)$a[1] 1 2$b
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can easily add a default method exa
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carry out a certain task. Many prog
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if you have only one short line of
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you do so within a function and you
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second value of the result.4. A vec
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Luckily, R allows you to write all
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VAT client switch(client, private
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3. In each round through the loop,
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workspace. This may be exactly what
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Applying functions on rows and colu
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4 6 8You can pass any arguments you
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hours public type“numeric” “l
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Chapter 10Debugging Your CodeIn Thi
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R always tells you in which code th
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If you get warning or error message
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logit() function. Even more, the tr
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When you’re in browser mode, you
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function only until the next round
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In logit(as.numeric(x)/100) : x not
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owsum.df strsplit(‘this is a sen
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If you want to know the median numb
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typing help(paste) returns help abo
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From the description of ada::update
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Getting Involved in the R Community
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can ask and answer questions on a v
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[1] “Diamonds 2” “Clubs 2”
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[1] RCurl_1.6-10.1 tools_2.14.1The
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Chapter 12Getting Data into and out
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Using the Clipboard to copy and pas
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Using special characters in escape
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‘data.frame’: 10 obs. of 9 vari
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XLConnect also can write Excel file
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These functions need a specific fil
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Working with Files and FoldersYou k
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[1] “F:/git/roxygen2/roxygen2/REA
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can confirm this by taking a close
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But in many practical situations, y
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$: The dollar-sign operator selects
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To illustrate subsetting of data fr
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customary to specify a so-called se
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Specify a logical vector, where FAL
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After a short while of writing subs
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following:> frost head(frost, 5)Al
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Figure 13-1: Different ways of comb
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function tries to identify columns
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Both data frames have a variable Na
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time, %in% is in infix operator. An
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order. Do this using the order() fu
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Sorting multiple columns in mixed o
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FUN: The function to apply (for exa
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5.843333 3.057333 3.758000 1.199333
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with(cars, tapply(mpg, list(gear, a
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+ y ~ a + b Include columns a as we
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In the world of R, people usually r
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Now you can start. First, create so
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data: A molten data frame.formula:
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Chapter 14Summarizing DataIn This C
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that benefits from being converted
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With this dataset in your workspace
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ange(cars$mpg)[1] 10.4 33.9Calculat
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As with most functions, you can sav
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Plotting histogramsTo get a clearer
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If this concept is unfamiliar to yo
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multiple variables, there’s a lot
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oxplot(mpg ~ cyl, data=cars)Figure
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Statisticians love it when they can
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You also can calculate the correlat
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with(cars, table(am, gear))3 4 5aut
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$ Var2: Factor w/ 2 levels “sick
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time specifying the margin argument
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Taking a Closer Look at Distributio
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Still, histograms leave much to the
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Now you want to do this for the tem
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Comparing Two SamplesComparing grou
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Again, you get the value for the te
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Many research questions revolve aro
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have to specify which margins you w
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str(InsectSprays)‘data.frame’:
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Checking the model tablesWith the m
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The difference between the means.Th
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The lm() function allows you to spe
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FunctionWhat It Doescoef()Returns a
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Model.anova Model.anovaAnalysis of
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predict(Model,newdata=new.cars, int
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Chapter 16Using Base GraphicsIn Thi
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The built-in R datasets are documen
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pch=21: Filled circlepch=22: Filled
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You also can use the function ablin
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It seems odd to use a plot function
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Figure 16-6: Adding main title, x-a
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Your graphic should look like Figur
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When your plot is complete, you nee
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Page 394 and 395: Creating a Lattice PlotTo explore l
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Page 402 and 403: Three-dimensional scatterplots: clo
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Page 408 and 409: Printing and Saving a Lattice PlotY
Page 410 and 411: Chapter 18Looking At ggplot2 Graphi
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Page 418 and 419: Creating line chartsTo create a lin
Page 420 and 421: Stat Description Default Geomstat_b
Page 422 and 423: Doing nothing with identitySometime
Page 424 and 425: Working with scalesIn ggplot2, scal
Page 426 and 427: Part VIThe Part of TensIn this part
Page 428 and 429: Then calculate the sum and mean for
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Page 432 and 433: with(mtcars, length(mpg[hp > 150]))
Page 434 and 435: For example, to find the location o
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Page 438 and 439: RGui and RStudio allow you to set t
Page 440 and 441: Reading the Package Manual and Vign
Page 444 and 445: AppendixInstalling R and RStudioBef
Page 446 and 447: a number of startup options by adap
Page 448 and 449: If you click Browse, you can select
Page 450: To access the cheat sheet specifica
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