30  Topics

The following are many of the topics that this course will covers. This is just an overview. See the main section of the text for more info on each topic. This list of topics may change.

30.1 Quarto (newer version of RMarkdown)

30.2 More practice with “base” R

Throughout the course you will be working with R. You must understand all of the basics that were covered in the R programming course. This includes but is no limited to lists,dataframes,user defined functions, if/else/else if, while loop, for loop, etc. etc. etc.

Resources

• http://yrosenthal.com/rnotes

30.3 R Packages

• install.packages

• library vs require

• CRAN

• tidyverse packages - https://www.tidyverse.org/packages/

  • ggplot2

  • dplyr

    • https://dplyr.tidyverse.org/
    • https://cran.r-project.org/web/packages/dplyr/vignettes/dplyr.html

  • tidyr https://tidyr.tidyverse.org/

  • readr https://readr.tidyverse.org/

    • read_csv(): comma-separated values (CSV)
    • read_tsv(): tab-separated values (TSV)
    • read_csv2(): semicolon-separated values with , as the decimal mark
    • read_delim(): delimited files (CSV and TSV are important special cases)
    • read_fwf(): fixed-width files
    • read_table(): whitespace-separated files
    • read_log(): web log files

  • purr

  • tibble https://tibble.tidyverse.org/

  • stringr

  • forcats

  • Other tidyverse packages

    • magrittr
    • glue
    • lubridate
    • hms
    • blob
    • dtplyr

31 Working with different types of files

• install.packages(“fs”)
  library(fs)
  dir_tree()

• CSV files

• JSON files

  • jsonlite package

• XML and HTML files

  • packages: xml2, httr

• Excel files

  • package: readxl (part of the “tidyverse” set of packages)

31.1 Command Line Interfaces

• what is a command line interface (CLI)

• Windows (CMD, Powershell)

• Unix, Linux and Mac Terminal (Bash and others)

• Bash

  • Terminal tab in RStudio

  • working with the file system

    • pwd
    • ls -a -l -r -t
    • wildcards: * [abc] [!abc] [a-cw-z] [!0-9] \
      https://tldp.org/LDP/GNU-Linux-Tools-Summary/html/x11655.htm
    • cd
    • .. and .
    • .hiddenFiles
    • $HOME
    • echo
    • $HOME
    • mkdir
    • rm
    • rmdir
    • tree

  • editing files

    • nano
    • vim https://www.openvim.com/
    • touch

  • working with text

    • cut
    • grep

  • redirection

    • command > filename
    • command < filename
    • command | command2 | command3

  • script files

    • chmod command
    • $PATH
    • basic script files
    • $env
    • variable=value # no spaces

    • 32 comments

32.1 Regular Expressions

• http://regextutorials.com/ Good examples with practice questions. Need to explain about /g and other forward slash options.

• https://regexcrossword.com/

32.2 Web scraping

• https://www.zenrows.com/blog/web-scraping-r#prerequisites

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32.3 Other topics (beyond the scope of the course)

• Working with large data

  • data.table package - https://rdatatable.gitlab.io/data.table/