References

This chapter contains the full references for all resources cited throughout the rest of the book.

University Library, University of Illinois at Urbana-Champaign. “LibGuides: SPSS Tutorial: About This Tutorial.” http://guides.library.illinois.edu/c.php?g=347869 . Retrieved September 27, 2016.

Chambers, J. Software for Data Analysis: Programming with R . Springer, 2009.

Chang, W. “shinydashboard: Create Dashboards with 'Shiny'.” R package version 0.5.1. https://CRAN.R-project.org/package=shinydashboard . 2015.

Chang, W., Cheng, J., Allaire, J., Xie, Y., and McPherson, J. “shiny: web application framework for R.” R package version 0.11, 1. 2015.

Chheng, T. “RMongo: MongoDB Client for R . ” R package version 0.0.25. https://CRAN.R-project.org/package=RMongo . 2015.

Conway, J., Eddelbuettel, D., Nishiyama, T., Prayaga, S.K., and Tiffin, N. “RPostgreSQL: R interface to the PostgreSQL database system.” R package version 0.4-1. https://CRAN.R-project.org/package=RPostgreSQL . 2015.

U.S. Census Bureau, American FactFinder. “Data Access and Dissemination Systems (DADS).” http://factfinder2.census.gov/faces/tableservices/jsf/pages/productview.xhtml?pid=ACS_10_5YR_B01003 . Retrieved September 27, 2016.

Dragulescu, A. A. “xlsx: Read, write, format Excel 2007 and Excel 97/2000/XP/2003 files.” R package version 0.5.7. https://CRAN.R-project.org/package=xlsx . 2014.

Dowle, M., Srinivasan A., Short T., and Lianoglou S. with contributions from R Saporta and E Antonyan. “data.table: Extension of Data.frame.” R package version 1.9.6. https://CRAN.R-project.org/package=data.table . 2015.

Feinerer, I. and Hornik, K. “tm: Text Mining Package.” R package version 0.6-2. https://CRAN.R-project.org/package=tm . 2015.

Fellows, I. “wordcloud: Word Clouds.” R package version 2.5. https://CRAN.R-project.org/package=wordcloud . 2014.

Friedl, J. E. F. Mastering Regular Expressions, Third Edition . O’Reilly Media, 2006.

Harrell Jr, F. E. with contributions from Charles Dupont and many others. “Hmisc: Harrell Miscellaneous.” R package version 3.17-1 . https://CRAN.R-project.org/package=Hmisc . 2015.

Hester, J. “covr: Test coverage for packages.” R package version 2.2.1. https://CRAN.R-project.org/package=covr . 2016.

Johnson, P. “devEMF: EMF Graphics Output Device.” R package version 2.0. https://CRAN.R-project.org/package=devEMF . 2015.

Lang, D. T. and the CRAN Team. “XML: Tools for Parsing and Generating XML Within R and S-Plus.” R package version 3.98-1.4. https://CRAN.R-project.org/package=XML . 2016.

Microsoft Corporation. “checkpoint: Install Packages from Snapshots on the Checkpoint Server for Reproducibility.” R package version 0.3.16. https://github.com/RevolutionAnalytics/checkpoint . 2016.

Ooms, J. “The jsonlite package: a practical and consistent mapping between JSON data and R objects.” arXiv preprint arXiv:1403.2805. 2014.

Prikryl, M. WinSCP—Free SFTP and SCP client for Windows . 2007.

R Core Team. “foreign: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, …” R package version 0.8-66. https://CRAN.R-project.org/package=foreign . 2015.

Rizopoulos, D. “ltm: An R package for latent variable modeling and item response theory analyses.” Journal of Statistical Software , 17(5), 1–25. 2016.

R Special Interest Group on Databases (R-SIG-DB), Hadley Wickham, and Kirill Müller. “DBI: R Database Interface.” R package version 0.5. https://CRAN.R-project.org/package=DBI . 2016.

RStudio Team. “RStudio: Integrated Development for R.” www.rstudio.com . 2015.

Amazon Web Services. “Setting Up with Amazon EC2.” http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/get-set-up-for-amazon-ec2.html . Retrieved October 2, 2016.

Schenk, C. MiKTEX project page. http//: miktex. org . 2009

Tatham, S. “PuTTY: A free SSH and Telnet client.” www.chiark.greenend.org.uk/∼sgtatham/putty/ . 2016.

Urbanek, S. “rJava: Low-Level R to Java Interface.” R package version 0.9-8. https://CRAN.R-project.org/package=rJava . 2016.

U. S. Census Bureau, American FactFinder. “B01003—“Total Population. All Counties within Illinois. 2006–2010 American Community Survey 5-Year Estimates.” http://factfinder2.census.gov/faces/tableservices/jsf/pages/productview.xhtml?pid=ACS_10_5YR_B01003&prodType=table . 2010.

U. S. Census Bureau, American FactFinder. “B23006—Educational Attainment by Employment Status for the Population 25 To 64 Years. Universe: Population 25 to 64 years. All Counties within Illinois. 2006–2010 American Community Survey 5-Year Estimates.” http://factfinder2.census.gov/faces/tableservices/jsf/pages/productview.xhtml?pid=ACS_10_5YR_B23006&prodType=table . 2010.

U. S. Census Bureau, American FactFinder.. “S1903—Median Income in the Past 12 Months (in 2010 Inflation-Adjusted Dollars): All Counties within Illinois. 2006–2010 American Community Survey 5-Year Estimates.” http://factfinder2.census.gov/faces/tableservices/jsf/pages/productview.xhtml?pid=ACS_10_5YR_S1903&prodType=table . 2010.

van der Loo, M. “The stringdist package for approximate string matching.” The R Journal , 6, pp. 111–122. http://CRAN.R-project.org/package=stringdist . 2014.

Venables, W., and Ripley, B. D. S programming . Springer, 2004.

Wickham, H. “ Reshaping data with the reshape package.” Journal of Statistical Software, 21(12), pp. 1–20. 2007.

Wickham, H. ggplot2: Elegant Graphics for Data Analysis . Springer, 2016.

Wickham, H. . “testthat: Get started with testing.” The R Journal, 3 (1), pp. 5–10.

Wickham, H. “evaluate: Parsing and Evaluation Tools that Provide More Details than the Default.” R package version 0.9. https://CRAN.R-project.org/package=evaluate . 2016.

Wickham, H., and Chang, W. “devtools: Tools to Make Developing R Packages Easier.” R package version 1.12.0. https://CRAN.R-project.org/package=devtools . 2016.

Wickham, H., Danenberg, P., and Eugster, M. “roxygen2: In-Source Documentation for R.” R package version 5.0.1. https://CRAN.R-project.org/package=roxygen2 . 2015.

Wickham, H. and Francois, R. “dplyr: A Grammar of Data Manipulation.” R package version 0.4.3.

https://CRAN.R-project.org/package=dplyr . 2015.

Wickham, H., Francois, R., and Müller, K. “tibble: Simple Data Frames.” R package version 1.0. https://CRAN.R-project.org/package=tibble . 2016.

Wickham, H., James, D. A., and Falcon S. “RSQLite: SQLite Interface for R.” R package version 1.0.0. https://CRAN.R-project.org/package=RSQLite . 2014.

Wiley, J. F. and Pace, L. Beginning R: An Introduction to Statistical Programming , Second Edition . Apress, 2015.

Xie, Y. Dynamic Documents with R and knitr . CRC Press, 2015.

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Index

A

  1. AdvancedRPkg

  2. Advanced R software

    1. JDK

    2. MKL

    3. MRO

    4. RStudio

  3. Amazon Web Services (AWS)

    1. account creation

    2. AdvancedR

    3. AdvancedR security group

    4. AmazonEC2FullAccess

    5. CIDR

    6. Dashboard

    7. Elastic Compute Cloud (EC2)

    8. IAMS

    9. instance key pair settings and final launch

    10. security group

    11. security group’s inbound rules

    12. Ubuntu server selection

    13. user

    14. user actions

  4. anyDuplicated()

  5. *apply functions

    1. eapply()

    2. elements

    3. environment()

    4. error checking

    5. frame and matrix/array

    6. issues

    7. lapply

    8. ls()

    9. mapply()

    10. mean() cannot

    11. mean()/sd()

    12. mtcars data

    13. mtcars data frame

    14. par()

    15. rapply()

    16. recursion

    17. summary()

    18. types

    19. vapply

    20. X, INDEX, and FUN

  6. arrange() function

  7. assignInNamespace() function

  8. Automation

    1. *apply family offunctions

See*apply functions

  1. coding

  2. definition, insanity

  3. flow control

  4. loops

SeeLoops

  1. repeats

  2. tools

B

  1. Big data (bases)

    1. challenges

    2. CSV files

    3. functions

    4. installation of software

    5. MongoDB

SeeMongoDB

  1. packages

  2. R data objects and load

  3. rigid format

  4. SQLite

SeeSQLite database

C

  1. Cloud

    1. e-mail

    2. operating system

    3. public IP address

    4. PuTTY

    5. PuTTY configuration

    6. PuTTYgen

    7. PuTTY security alert

    8. server fingerprint (RSA)

    9. transfer files

    10. Ubuntu command line

    11. uploading files, WinSCP

    12. windows environment

  2. Cloud instance

  3. Cloud Ubuntu, Windows users

    1. commands

    2. installing Microsoft R

    3. installing R

    4. installing Shiny

    5. Java installation

    6. RStudio Server

    7. superuser and security

  4. Comma-separated values (CSV) files

  5. Comprehensive R Archive Network (CRAN)

D, E

  1. Dashboard

    1. body

    2. in cloud

    3. header

    4. sampler code

    5. sidebar

  2. dashboardBody() function

  3. dashboardHeader() function

  4. dashboardSidebar() function

  5. Data management

    1. data and creating variables

    2. dplyr packages

    3. merging and reshaping data

    4. sapply()

    5. selecting and subsetting

    6. sorting

    7. variable renaming and ordering

  6. data.table package

    1. anyDuplicated() function

    2. built-in data frame class objects

    3. checkpoint

    4. creatio, new variables

    5. data and creating variables

    6. data frame

    7. data management

    8. data munging/cleaning

    9. Data.Table[i, j, by]

    10. diris

    11. duplication family

    12. fuzzy matching

    13. head() and tail()

    14. merging data

    15. one-time conversions

    16. order()

    17. recoding data

    18. recoding numeric values

    19. reshaping data

    20. sapply()

    21. second and third formals

    22. selecting and subsetting data

    23. Sepal.Length

    24. setkey()

    25. setosa, versicolor, and virginica

    26. species

    27. unique()

    28. variable renaming and ordering

  7. Debugging

    1. assignInNamespace() function

    2. browser() function

    3. debug() function

    4. scatter plot

    5. tapply() and unique()

    6. traceback()

    7. wtd.quantile() function

    8. wtd.table() function

  8. desc()

  9. Development Kit (JDK)

  10. DevTools

  11. distinct()

  12. Dynamic document

    1. beamer_presentation

    2. case studies

    3. ch15_html.Rmd

    4. cloud instance

    5. code chunks

    6. HTML output

    7. hybrid approach

    8. local machine

    9. Rmarkdown process

    10. Rmarkdown

    11. Shiny

      1. application

      2. report.Rmd

      3. server.R

      4. ui.R

      5. user interface

    12. uploading, cloud

F

  1. Functions

    1. components

    2. Hmisc R package

    3. invisible() function

    4. match.arg() function

    5. match.call()

    6. message()

    7. missing() function

    8. on.exit() function

    9. R commands

    10. return() function

    11. scoping

    12. stop() function

    13. stopifnot()

    14. suppressMessages()

    15. suppressWarnings()

    16. warning()

  2. Fuzzy matching

G

  1. ggplot2 R package

  2. GitHub

  3. group_by()

  4. groupedtextplot

  5. gsub()

H

  1. Help and documentation

  2. hist() function

  3. Hmisc package

  4. Hmisc R package

I, J, K

  1. Identity and access management (IAM)

  2. img() function

  3. Intel Math Kernel Library (Intel MKL)

  4. invisible() function

L

  1. Local machine

  2. Loops

    1. control

    2. for loop

    3. for()

    4. functions

    5. head()

    6. infinite

    7. proc.time()

    8. repeat()

    9. rnorm

    10. simulation

    11. types

    12. while loop

    13. xCube

M

  1. mainPanel()

  2. match.arg() function

  3. Mathematical operators and functions

    1. calculations

    2. complex logic tests

    3. if-else flow control

    4. loops

    5. matrices operations

    6. scalar operations

    7. symbolic logic forms

    8. trigonometric functions

  4. meanPlot() function

  5. menuItem() functions

  6. merge() function

  7. Microsoft Corporation

  8. Microsoft R Open (MRO)

  9. MiKTeX

  10. MongoDB

    1. and R

      1. BSON query language

      2. dbAuthenticate (con3, username, password)

      3. dbDisconnect()

      4. dbGetQuery()

      5. dbShowCollections()

      6. fNames

      7. information, locations

      8. JSON file

      9. mock data

      10. mongoDbConnect()

      11. outcomes

      12. RMongo package

      13. unstructured data

      14. View()

    2. data directory

    3. document store database

    4. downloading

    5. folder

    6. installation process

    7. JSON and semistructured data

    8. JSON files

    9. website

  11. Multiple inheritance

  12. mutate()

N

  1. NAMESPACE file

  2. normalizePath()

O

  1. Object-oriented programming (OOP)

  2. Objects

    1. complex numbers

    2. data frame

    3. double numeric

    4. factors

    5. integers

    6. logical

    7. matrix

    8. missing values

    9. scalar

  3. on.exit() function

  4. on.exit() parameter

  5. Operators and functions

    1. assignments

    2. data-type-checking functions

    3. mathematical

SeeMathematical operators and functions

  1. subsetting

  1. owSums()

P, Q

  1. Package

    1. adding R code

    2. checkpoint

    3. covr

    4. CRAN

    5. devtools package

    6. devtools

    7. ggplot2

    8. MiKTeX

    9. root directory

    10. roxygen2 package

    11. R package

    12. R Package subdirectories

    13. tests

    14. testthat

    15. version control

      1. AdvancedRPkg repository

      2. desktop.ini

      3. GitHub

      4. GitHub desktop

      5. linux kernel

      6. README and .gitignore files

    16. XQuartz

  2. package_coverage() function

  3. parent.env() function

  4. paste0()

  5. PostgreSQL

    1. and R

    2. database

    3. data integrity and reliability

    4. windows

R

  1. read.dta()

  2. Reduce()

  3. REFUSED

  4. renderPlot()

  5. reshape()

  6. right_join()

  7. rowMeans() function

  8. roxygen2

    1. classes

    2. data

    3. functions

    4. methods

  9. R Package

    1. AdvancedRPkg

    2. check() function

    3. CRAN

    4. DESCRIPTION file

    5. ggplot() function

    6. meanPlot()

    7. R CMD INSTALL

    8. README file

    9. show() method

    10. .tar.gz file

  10. RStudio Server

S

  1. S3 system

    1. classes

      1. data frames

      2. multiple classes

      3. multiple inheritance

      4. object class

      5. single inheritance

      6. textplot object

      7. vectors or generic vectors

    2. methods

      1. built-in mtcars data

      2. custom methods

      3. expand.grid()

      4. fortify() function

      5. generic function

      6. ggplot() method

      7. ggplot.lm() method

      8. linear regression model

      9. methods() function

      10. ::: operator

      11. par() function

      12. plot() function

      13. plot.table()

      14. plot.textplot()

      15. summary()

      16. textplot object class

      17. UseMethod()

  2. S4 system

    1. classes

      1. new()

      2. paste()

      3. setClass()

      4. sprintf()

      5. validity function

    2. class inheritance

    3. methods

  3. select() function

  4. Sepal.Length

  5. setMethod()

  6. Shiny

    1. application

    2. arguments

    3. in cloud

    4. fluidPage() function

    5. function renderPlot()

    6. HTML code, creation

    7. input functions

    8. mainPanel()

    9. numericInput()

    10. play button feature

    11. plotOutput()

    12. plotOutput(“piePlot”)

    13. R calculations

    14. renderPlot()

    15. RStudio

    16. run App play button

    17. shinyServer()

    18. sidebarPanel() function

    19. sliderInput() function

    20. titlePanel() command

    21. user file uploading

    22. user-interface code

    23. web application framework

  7. Shiny Dashboard sampler

    1. coding

    2. dashboard’s bones

      1. dashboard body

      2. dashboard header

      3. ashboard sidebar

      4. littlest Shiny dashboard

  8. showMethods()

  9. sidebarMenu()

  10. sidebarPanel()

  11. Single inheritance

  12. Social security number (SSN)

  13. SPSS

    1. input files

    2. output files

  14. SQLite database

    1. advantages and disadvantages

    2. and R

      1. all.equal()

      2. dbClearResult()

      3. dbDisconnect()

      4. DBI package library

      5. dbIsValid()

      6. dbSendQuery

      7. dbWriteTable()

      8. iris data

      9. RAM

      10. rnorm()

      11. RSQLite library

      12. sepal and length

      13. setosa

      14. SQL

      15. VACUUM

    3. definitive guide

    4. installing

    5. PostgreSQL

SeePostgreSQL

  1. stopifnot() function

  2. str() function

  3. stringdistmatrix()

  4. strsplit()

  5. Structured Query Language (SQL)

  6. summary() function

  7. System and files

    1. accuracy

    2. automating file management

    3. creation

    4. file.access

    5. file.append function

    6. file.copy

    7. file.create

    8. file.exists()

    9. file.info function

    10. file.remove

    11. getwd()

    12. high-stakes projects

    13. PowerPoint

    14. recursive=TRUE option

    15. sys.setFileTime function

    16. TRUE or FALSE

T

  1. table()

  2. tapply()

  3. test_textplot.R

  4. tolower()

  5. toupper()

U

  1. unlist()

V

  1. valueBox()

W

  1. WinSCP

  2. WinSCP upload folder view

  3. wtd.quantile()

X, Y, Z

  1. XQuartz

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