18 Appendix 3 - R and Python Packages

18.1 R Core Package List

The base packages are part of R and are grouped bt functionality and to some degree of chonology of incorporation into the base distribution. The Packages of base functions are,

Package	Description
base	Base R functions
compiler	Functions to provide an interface to a byte code compiler for R
datasets	Base R datasets
grDevices	R Graphics Devices and Support for Colours and Fonts. Support for base and grid graphics
graphics	R functions for base graphics
grid	The Grid Graphics Package. A rewrite of the graphics layout capabilities.
methods	Formal Methods and Classes. Formally defined methods and classes for R objects and other programming tools.
parallel	Support for Parallel Computation, including random-number generation.
splines	Regression Spline Functions and Classes.
stats	R statistical functions
stats4	Statistical Functions using S4 classes.
tcltk	Interface and language bindings to Tcl/Tk GUI elements.
tools	Tools for package development, administration and documentation.
utils	R utility functions

A list if contained functions in any package can be displayed in R by (eg. for parallel package),

library(help = "parallel")  # of substitute any package name for "parallel"

The other list installed with first R install are the recommended packages. These are kind of and appocrapha of functions providing useful capabilities from some books and papers about specialized uses of the R system. These are,

Package	Description
kernsmooth	Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) “Kernel Smoothing”.
MASS	Functions and datasets to support Venables and Ripley, “Modern Applied Statistics with S” (4th edition, 2002).
Matrix	A rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse, using ‘LAPACK’ and ‘SuiteSparse’ libraries.
boot	Functions and datasets for bootstrapping from the book “Bootstrap Methods and Their Application” by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
class	Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
cluster	Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) “Finding Groups in Data”.
codetools	Code analysis tools for R.
foreign	Reading and writing data stored by some versions of ‘Epi Info’, ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, and for reading and writing some ‘dBase’ files.
lattice	A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data.
mgcv	Multiscale Graph Correlation (MGC) is a framework developed by Shen et al. (2017) <arXiv:1609.05148> that extends global correlation procedures to be multiscale;
nlme	Linear and Nonlinear Mixed Effects Models.Fit and compare Gaussian linear and nonlinear mixed-effects models.
nnet	Feed-Forward Neural Networks and Multinomial Log-Linear Models
rpart	Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
spatial	Functions for kriging and point pattern analysis.
survival	Contains the core survival analysis routines.

There are literally thousands of CRAN repository packages accumulated over the years plus many more managed outside of the CRAN repository. Inclusion in CRAN requires a minimum standard process of package structure and documentation.

18.2 Python Standard Library² List

18.2.1 Built-in Functions²

abs()	delattr()	hash()	memoryview()	set()
all()	dict()	help()	min()	setattr()
any()	dir()	hex()	next()	slice()
ascii()	divmod()	id()	object()	sorted()
bin()	enumerate()	input()	oct()	staticmethod()
bool()	eval()	int()	open()	str()
breakpoint()	exec()	isinstance()	ord()	sum()
bytearray()	filter()	issubclass()	pow()	super()
bytes()	float()	iter()	print()	tuple()
callable()	format()	len()	property()	type()
chr()	frozenset()	list()	range()	vars()
classmethod()	getattr()	locals()	repr()	zip()
compile()	globals()	map()	reversed()	import()
complex()	hasattr()	max()	round()

18.2.2 Built-in Constants

includes Constants added by the site module

False	True	None	NotImplemented	Ellipsis or “…”
`__debug__`	quit(code=None)	exit(code=None)	copyright
credits	license

18.2.3 Built-in Types

Truth Value Testing
Boolean Operations — and, or, not
Comparisons == <= >= < > !=
Numeric Types — int, float, complex
Iterator Types
Sequence Types — ‘list’, ‘tuple’, ‘range’
Text Sequence Type — ‘str’
Binary Sequence Types — ‘bytes’, bytearray, memoryview
Set Types — set, frozenset
Mapping Types — dict
Context Manager Types
Other Built-in Types
Special Attributes

18.2.4 Built-in Exceptions

Base classes
Concrete exceptions
Warnings
Exception hierarchy

18.2.5 Text Processing Services

string — Common string operations
re — Regular expression operations
difflib — Helpers for computing deltas
textwrap — Text wrapping and filling
unicodedata — Unicode Database
stringprep — Internet String Preparation
rlcompleter — Completion function for GNU readline

18.2.6 Binary Data Services

struct — Interpret bytes as packed binary data
- Functions and Exceptions
- Format Strings
- Classes
codecs — Codec registry and base classes
- Codec Base Classes
- Encodings and Unicode
- Standard Encodings
- Python Specific Encodings
  - Text Encodings
  - Binary Transforms
  - Text Transforms
- encodings.idna — Internationalized Domain Names in Applications
- encodings.mbcs — Windows ANSI codepage
- encodings.utf_8_sig — UTF-8 codec with BOM signature

18.2.7 Data Types

datetime — Basic date and time types
- Available Types
  - timedelta Objects
  - date Objects
  - datetime Objects
  - time Objects
  - tzinfo Objects
  - timezone Objects
  - strftime() and strptime() Behavior
calendar — General calendar-related functions
collections — Container datatypes
- ChainMap objects
- Counter objects
- deque objects
- defaultdict objects
- namedtuple() Factory Function for Tuples with Named Fields
- OrderedDict objects
- UserDict objects
- UserList objects
- UserString objects
collections.abc — Abstract Base Classes for Containers
heapq — Heap queue algorithm
bisect — Array bisection algorithm
array — Efficient arrays of numeric values
weakref — Weak references
types — Dynamic type creation and names for built-in types
copy — Shallow and deep copy operations
pprint — Data pretty printer
reprlib — Alternate repr() implementation
enum — Support for enumerations

18.2.8 Numerical and Mathematical Modules

numbers — Numeric abstract base classes
- The numeric tower
math — Mathematical functions
- Number-theoretic and representation functions
- Power and logarithmic functions
- Trigonometric functions
- Angular conversion
- Hyperbolic functions
- Special functions
- Constants
cmath — Mathematical functions for complex numbers
- Conversions to and from polar coordinates
- Power and logarithmic functions
- Trigonometric functions
- Hyperbolic functions
- Classification functions
- Constants
decimal — Decimal fixed point and floating point arithmetic
fractions — Rational numbers
random — Generate pseudo-random numbers
- Bookkeeping functions
- Functions for integers
- Functions for sequences
- Real-valued distributions
- Alternative Generator
statistics — Mathematical statistics functions
- Averages and measures of central location
- Measures of spread

18.2.9 Functional Programming Modules

itertools — Functions creating iterators for efficient looping
functools — Higher-order functions and operations, functions that act on or return other functions.
operator — Standard operators as functions, efficient functions corresponding to the intrinsic operators of Python.

18.2.10 File and Directory Access

pathlib — Object-oriented filesystem paths
os.path — Common pathname manipulations
fileinput — Iterate over lines from multiple input streams
stat — Interpreting stat() results
filecmp — File and Directory Comparisons
tempfile — Generate temporary files and directories
glob — Unix style pathname pattern expansion
fnmatch — Unix filename pattern matching
linecache — Random access to text lines
shutil — High-level file operations
macpath — Mac OS 9 path manipulation functions

18.2.11 Data Persistence

pickle — Python object serialization
copyreg — Register pickle support functions
shelve — Python object persistence
marshal — Internal Python object serialization
dbm — Interfaces to Unix “databases”
sqlite3 — DB-API 2.0 interface for SQLite databases

18.2.12 Data Compression and Archiving

zlib — Compression compatible with gzip
gzip — Support for gzip files
bz2 — Support for bzip2 compression
lzma — Compression using the LZMA algorithm
zipfile — Work with ZIP archives
tarfile — Read and write tar archive files

18.2.13 File Formats

csv — CSV File Reading and Writing
configparse — Configuration file parser
netrc — netrc file processing
xdrlib — Encode and decode XDR data
plistlib — Generate and parse Mac OS X .plist files

18.2.14 Cryptographic Services

hashlib — Secure hashes and message digests
hmac — Keyed-Hashing for Message Authentication
secrets — Generate secure random numbers for managing secrets

18.2.15 Generic Operating System Services

os — Miscellaneous operating system interfaces
io — Core tools for working with streams
time — Time access and conversions
argparse — Parser for command-line options, arguments and sub-commands
getopt — C-style parser for command line options
logging — Logging facility for Python
logging.config — Logging configuration
logging.handlers — Logging handlers
getpass — Portable password input
curses — Terminal handling for character-cell displays
curses.textpad — Text input widget for curses programs
curses.ascii — Utilities for ASCII characters
curses.panel — A panel stack extension for curses
platform — Access to underlying platform’s identifying data
errno — Standard errno system symbols
ctypes — A foreign function library for Python

18.2.16 Concurrent Execution

threading — Thread-based parallelism
multiprocessing — Process-based parallelism
concurrent
- concurrent.futures — Launching parallel tasks
subprocess — Subprocess management
sched — Event scheduler
queue — A synchronized queue class
_thread — Low-level threading API
_dummy_thread — Drop-in replacement for the _thread module
dummy_threading — Drop-in replacement for the threading module

18.2.17 Context Variables

contextvars - module provides APIs to manage, store, and access context-local state (context variables)
asyncio - support for asynchronous io

18.2.18 Networking and Interprocess Communication

asyncio — Asynchronous I/O (see associated context services)
socket — Low-level networking interface
ssl — TLS/SSL wrapper for socket objects
select — Waiting for I/O completion
selectors — High-level I/O multiplexing
asyncore — Asynchronous socket handler
`asynchat — Asynchronous socket command/response handler
signal — Set handlers for asynchronous events
mmap — Memory-mapped file support

18.2.19 Internet Data Handling

email — An email and MIME handling package
json — JSON encoder and decoder
mailcap — Mailcap file handling
mailbox — Manipulate mailboxes in various formats
mimetypes — Map filenames to MIME types
base64 — Base16, Base32, Base64, Base85 Data Encodings
binhex — Encode and decode binhex4 files
binascii — Convert between binary and ASCII
quopri — Encode and decode MIME quoted-printable data
uu — Encode and decode uuencode files

18.2.20 Structured Markup Processing Tools

html — HyperText Markup Language support
- html.parser — Simple HTML and XHTML parser
- html.entities — Definitions of HTML general entities
xml XML Processing Modules
- xml.etree.ElementTree — The ElementTree XML API
- xml.dom — The Document Object Model API
  - xml.dom.minidom — Minimal DOM implementation
- xml.dom.pulldom — Support for building partial DOM trees
- xml.sax — Support for SAX2 parsers
  - xml.sax.handler — Base classes for SAX handlers
  - xml.sax.saxutils — SAX Utilities
  - xml.sax.xmlreader — Interface for XML parsers
  - xml.parsers.expat — Fast XML parsing using Expat

18.2.21 Internet Protocols and Support

`webbrowser — Convenient Web-browser controller
cgi — Common Gateway Interface support
cgitb — Traceback manager for CGI scripts
wsgiref — WSGI Utilities and Reference Implementation
urllib — URL handling modules
- urllib.request — Extensible library for opening URLs
- urllib.response — Response classes used by urllib
- urllib.parse — Parse URLs into components
- urllib.error — Exception classes raised by urllib.request
- urllib.robotparser — Parser for robots.txt
http — HTTP modules
- http.client — HTTP protocol client
ftplib — FTP protocol client
poplib — POP3 protocol client
imaplib — IMAP4 protocol client
nntplib — NNTP protocol client
smtplib — SMTP protocol client
smtpd — SMTP Server
telnetlib — Telnet client
uuid — UUID objects according to RFC 4122
socketserver — A framework for network servers
http.server — HTTP servers
http.cookie — HTTP state management
http.cookiejar — Cookie handling for HTTP clients
xmlrpc — XMLRPC server and client modules
- xmlrpc.client — XML-RPC client access
- xmlrpc.server — Basic XML-RPC servers
ipaddress — IPv4/IPv6 manipulation library

18.2.22 Multimedia Services

audioop — Manipulate raw audio data
aifc — Read and write AIFF and AIFC files
sunau — Read and write Sun AU files
wave — Read and write WAV files
chunk — Read IFF chunked data
colorsys — Conversions between color systems
imghdr — Determine the type of an image
sndhdr — Determine type of sound file
ossaudiodev — Access to OSS-compatible audio devices

18.2.23 Internationalization

gettext — Multilingual internationalization services
locale — Internationalization services

18.2.24 Program Frameworks

turtle — Turtle graphics
cmd — Support for line-oriented command interpreters
shlex — Simple lexical analysis

18.2.25 Graphical User Interfaces with Tk

tkinter — Python interface to Tcl/Tk
tkinter.ttk — Tk themed widgets
tkinter.tix — Extension widgets for Tk
tkinter.scrolledtext — Scrolled Text Widget
IDLE - Python’s Integrated Development and Learning Environment
Other Graphical User Interface Packages
- PyGObject - Provides introspection bindings for C libraries, incl. GTK+ 3 widget set.
- PyGTK - PyGTK provides bindings for an older version of the library, GTK+ 2.
- PyQt - A sip-wrapped binding to the Qt toolkit.
- PySide - A newer binding to the Qt toolkit, provided by Nokia..
- wxPython - A cross-platform GUI toolkit for Python that is built around wxWidgets C++ toolkit

18.2.26 Development Tools

typing — Support for type hints
pydoc — Documentation generator and online help system
doctest — Test interactive Python examples
unittest — Unit testing framework
- unittest.mock — mock object library
2to3 - Automated Python 2 to 3 code translation
test — Regression tests package for Python
- test.support — Utilities for the Python test suite
  - test.support.script_helper — Utilities for the Python execution tests

18.2.27 Debugging and Profiling

bdb — Debugger framework
faulthandler — Dump the Python traceback
pdb — The Python Debugger
The Python Profilers
timeit — Measure execution time of small code snippets
trace — Trace or track Python statement execution
tracemalloc — Trace memory allocations

18.2.28 Software Packaging and Distribution

distutils — Building and installing Python modules
ensurepip — Bootstrapping the pip installer
venv — Creation of virtual environments
zipapp — Manage executable Python zip archives

18.2.29 Python Runtime Services

sys — System-specific parameters and functions
sysconfig — Provide access to Python’s configuration information
builtins — Built-in objects
__main__ — Top-level script environment
warnings — Warning control
dataclasses — Data Classes
contextlib — Utilities for with-statement contexts
abc — Abstract Base Classes
atexit — Exit handlers
traceback — Print or retrieve a stack traceback
__future__ — Future statement definitions
gc — Garbage Collector interface
inspect — Inspect live objects
site — Site-specific configuration hook

18.2.30 Custom Python Interpreters

code — Interpreter base classes
codeop — Compile Python code

18.2.31 Importing Modules

zipimport — Import modules from Zip archives
pkgutil — Package extension utility
modulefinder — Find modules used by a script
runpy — Locating and executing Python modules
importlib — The implementation of import

18.2.32 Python Language Services

parser — Access Python parse trees
ast — Abstract Syntax Trees
symtable — Access to the compiler’s symbol tables
symbol — Constants used with Python parse trees
token — Constants used with Python parse trees
keyword — Testing for Python keywords
tokenize — Tokenizer for Python source
tabnanny — Detection of ambiguous indentation
pyclbr — Python class browser support
py_compile — Compile Python source files
compileall — Byte-compile Python libraries
dis — Disassembler for Python bytecode
pickletools — Tools for pickle developers

18.2.33 Miscellaneous Services

formatter — Generic output formatting

18.2.34 MS Windows Specific Services

See also the pywin32 extensions. These are available to install via PIP, and provide access to many of the Windows APIs from Python.

msilib — Read and write Microsoft Installer files
msvcrt — Useful routines from the MS VC++ runtime
winreg — Windows registry access
winsound — Sound-playing interface for Windows

See also “Undocumented services”" below.

18.2.35 Unix Specific Services

Module provides interfaces to features that are unique to the Unix operating system, or in some cases to some or many variants of it.

posix — The most common POSIX system calls
pwd — The password database
spwd — The shadow password database
grp — The group database
crypt — Function to check Unix passwords
termios — POSIX style tty control
tty — Terminal control functions
pty — Pseudo-terminal utilities
cntl — The fcntl and ioctl system calls
pipes — Interface to shell pipelines
resource — Resource usage information
nis — Interface to Sun’s NIS (Yellow Pages)
syslog — Unix syslog library routines