Title:	Access to Teaching Materials from a ZIP File or GitHub
Version:	0.2.1
Description:	Provides access to teaching materials for various statistics courses, including R and Python programs, Shiny apps, data, and PDF/HTML documents. These materials are stored on the Internet as a ZIP file (e.g., in a GitHub repository) and can be downloaded and displayed or run locally. The content of the ZIP file is temporarily or permanently stored. By default, the package uses the GitHub repository 'sigbertklinke/mmstat4.data.' Additionally, the package includes 'association_measures.R' from the archived package 'ryouready' by Mark Heckman and some auxiliary functions.
License:	GPL-3
Encoding:	UTF-8
Imports:	crayon, digest, httr, knitr, tcltk, rappdirs, reticulate, rio, rstudioapi, shiny, stringdist, tools
Suggests:	rmarkdown
VignetteBuilder:	knitr
RoxygenNote:	7.3.1
NeedsCompilation:	no
Packaged:	2024-04-29 11:40:46 UTC; sigbert
Author:	Sigbert Klinke [aut, cre], Jekaterina Zukovska [ctb]
Maintainer:	Sigbert Klinke <sigbert@hu-berlin.de>
Repository:	CRAN
Date/Publication:	2024-04-29 12:10:02 UTC

askUser

Description

askUser provides a way to ask the user a yes/no/cancel question (default). A * after a number indicates the default option.

Usage

askUser(
  msg,
  choices = c("Yes", "No", "Cancel"),
  default = 1,
  col = crayon::black
)

Arguments

Value

the integer number choosen by the user

Examples

if (interactive())
  askUser("Do you want to use askUser?")

Association measures

Description

Various association coefficients for nominal and ordinal data; the input formats follows stats::chisq.test().

• concordant concordant pairs

• discordant discordant pairs

• ties.row pairs tied on rows

• ties.col pairs tied on columns

• nom.phi Phi Coefficient

• nom.cc Contingency Coefficient (Pearson's C) and Sakoda' s Adjusted Pearson's C

• nom.TT Tshuprow's T (not meaningful for non-square tables)

• nom.CV Cramer's V (for 2 x 2 tables V = Phi)

• nom.lambda Goodman and Kruskal's Lambda with

  • lambda.cr The row variable is used as independent, the column variable as dependent variable.

  • lambda.rc The column variable is used as independent, the row variable as dependent variable.

  • lambda.symmetric Symmetric Lambda (the mean of both above).

• nom.uncertainty Uncertainty Coefficient (Theil's U) with

  • ucc.cr The row variable is used as independent, the column variable as dependent variable.

  • uc.rc The column variable is used as independent, the row variable as dependent variable.

  • uc.symmetric Symmetric uncertainty coefficient.

• ord.gamma Gamma coefficient

• ord.tau a vector with Kendall-Stuart Tau's

  • tau.a Tau-a (for quadratic tables only)

  • tau.b Tau-b

  • tau.c Tau-c

• ord.somers.d Somers' d

• eta Eta coefficient for nominal/interval data

Usage

concordant(x, y = NULL)

discordant(x, y = NULL)

ties.row(x, y = NULL)

ties.col(x, y = NULL)

nom.phi(x, y = NULL)

nom.cc(x, y = NULL)

nom.TT(x, y = NULL)

nom.CV(x, y = NULL)

nom.lambda(x, y = NULL)

nom.uncertainty(x, y = NULL)

ord.gamma(x, y = NULL)

ord.tau(x, y = NULL)

ord.somers.d(x, y = NULL)

eta(x, y, breaks = NULL)

Arguments

Value

the association coefficient(s)

Source

From the archived ryouready package by Mark Heckmann. The code for the calculation of nom.lambda, nom.uncertainty, ord.gamma, ord.tau, ord.somers.d was supplied by Marc Schwartz (under GPL 2) and checked against SPSS results.

Examples

## Nominal data
# remove gender from the table
hec <- apply(HairEyeColor, 1:2, sum)
nom.phi(hec)
nom.cc(hec)
nom.TT(hec)
nom.CV(hec)
nom.lambda(hec)
nom.uncertainty(hec)
## Ordinal data
# create a fake data set
ordx <- sample(5, size=100, replace=TRUE)
ordy <- sample(5, size=100, replace=TRUE)
concordant(ordx, ordy)
discordant(ordx, ordy)
ties.row(ordx, ordy)
ties.col(ordx, ordy)
ord.gamma(ordx, ordy)
ord.tau(ordx, ordy)
ord.somers.d(ordx, ordy)
## Interval/nominal data
eta(iris$Species, iris$Sepal.Length)

Generates and plots a cumulative distribution function.

Description

Generates and plots a cumulative distribution function.

Usage

cdf(x, ...)

## Default S3 method:
cdf(x, y, discrete = TRUE, ...)

## S3 method for class 'cdf'
plot(x, y, ..., col.01line = "black", pch = 19)

Arguments

Value

returns a cdf object

Examples

# Binomial distribution
x <- cdf(0:10, pbinom(0:10, 10, 0.5))
plot(x)
# Exponential distribution
x <- seq(0, 5, by=0.01)
x <- cdf(x, pexp(x), discrete=FALSE)
plot(x)

Checks whether all specified files are valid R or Python files

Description

checkFiles checks whether all specified files are valid source files that can be executed independently of each other. If an error occurs then:

1. If open is a function name or a function with a file parameter, then checkFiles will try to open the faulty source file, otherwise not.

2. The execution of checkFiles is stopped.

If you do not want the faulty source file to be opened immediately, use open=0.

Three modes are available for checking a file:

1. exist: Does the source file exist?

2. parse: (default) is parse(file) or ⁠python -m "file"⁠ successful?

3. run: is ⁠Rscript "file"⁠ or ⁠python "file"⁠ successful?

If source files has side effects, e.g. generating an image or some other output, and mode=="parse" then this will done during the check.

Usage

checkFiles(
  files,
  index = seq_along(files),
  path = NULL,
  open = openFile,
  mode = c("parse", "run", "exist"),
  ...
)

Rsolo(
  files,
  index = seq_along(files),
  path = NULL,
  open = openFile,
  mode = c("parse", "run", "exist"),
  ...
)

Arguments

Value

nothing

Examples

if (interactive()) {
  files <- list.files(pattern="*.(R|py)$", full.names=TRUE, recursive=TRUE)
  checkFiles(files)
}

defaultApp

Description

Tries to open the given file with the default application of the operating system using base::system2(). Only Windows (windows), macOS (darwin), Linux (linux) and FreeBSD (freebsd) is supported.

Usage

defaultApp(file, wait = FALSE, ...)

Arguments

Value

Result of try(system2, ...), invisibly

See Also

berryFunctions::openFile()

Examples

if (interactive()) {
  ghget()
  defaultApp(ghlist("dataanalysis.pdf", full.names = TRUE))
}

Find duplicate files

Description

dupFiles computes checksums to find duplicate files.

Usage

dupFiles(files, ...)

Rdups(files, ...)

Arguments

Value

a list of file names with the same checksum or NULL

Examples

if (interactive()) {
  files <- list.files(pattern="*.R$", full.names=TRUE, recursive=TRUE)
  dupFiles(files)
}

getList

Description

Creates a list with element names replaced by link{getText}.

Usage

getList(...)

Arguments

Value

renamed list

Examples

getList(BOSTON=1, MTCARS=2)

getMMstat

Description

Allows to access the package internal mmstat environment.

Usage

getMMstat(...)

Arguments

Value

the choosen element

Examples

getMMstat('version')

getText

Description

Translates a given message into another language.

Usage

getText(msg)

Arguments

Value

vector of translated messages

Examples

getText('Test')

gh functions

Description

The function gh carries out the following operation on a file named x. It searches for a match for x within the active repository, utilizing fuzzy string matching. If no unique match is identified, an error is thrown along with suggestions for potential "best" matches. Otherwise, the following operation are performed:

• gh(x, 'open') or ghopen(x): Opens a file in the local browser if the file extension is html or pdf, otherwise in the RStudio editor.

• gh(x, 'load') or ghload(x): Loads the contents of a file with import.

• gh(x, 'source') or ghsource(x): Executes the contents of a file with source.

• gh(x, 'app') or ghapp(x): Tries to open the file with the default application of the OS, see defaultApp().

• ghdata(x, pkg): Helper function to load data sets from R packages into Python, simulates pkg::x.

Usage

gh(x, what = c("open", "load", "source", "app"), ..., .call = NULL)

ghopen(x, ...)

ghload(x, ...)

ghsource(x, ...)

ghapp(x, ...)

Arguments

Value

invisibly the result of utils::browseURL, openFile(), rio::import(), or base::source().

Examples

if (interactive()) {
  x <- ghopen("bank2.SAV")
  x <- ghload("bank2.SAV")
  str(x)
  x <- ghsource("univariate/example_ecdf.R")
}

ghappAddin

Description

Runs a Shiny app from the downloaded zip file.

Usage

ghappAddin()

Value

nothing

Examples

if (interactive()) ghappAddin()

Creates a ghdecompose pbject

Description

ghc creates from a list of file names using ghdecompose() and deletes mssing files.

Usage

ghc(...)

Arguments

Value

a ghdecompose pbject

Examples

ghc(list.files(system.file(package="mmstat4"), recursive=TRUE))

ghdecompose

Description

Decomposes a path of a set of files (or dirs) in several parts:

Usage

ghdecompose(files, dirs = FALSE)

Arguments

Details

• outpath the path part which is common to all files (basically the place where the ZIP file was extracted)

• inpath the path part which is not necessary for a unique address in teh ZIP file

• minpath the minimal path part such that all files addressable in unique manner,

• filename the basename of the file, and

• source the input to shortpath.

Value

a data frame with five variables

Examples

ghget("local")
pdf <- ghdecompose(ghlist(full.names=TRUE))
pdf

ghfile

Description

Finds either a unique match in the list of files or throws an error with possible candidate files.

Usage

ghfile(x, n = 6, silent = FALSE, msg = "%s")

Arguments

Value

the full matching file

Examples

ghfile("data/BANK2.sav")
if (interactive()) ghfile("data/BANK2.SAV")  # throws an error

ghget

Description

Makes a repository the active repository and downloads it if necessary. The parameter .tempdir is TRUE (default) then the repository is stored in the in the temporary directory tempdir() else in the application directory rappdirs::user_data_dir() for mmstat4. The parameter .tempdir is not logical then the value will be used as installation path.

Usage

ghget(..., .force = FALSE, .tempdir = TRUE, .quiet = !interactive())

Arguments

Details

Note, the list of repository names, directories and urls is stored in the installation directory, too.

Value

the name of the current key or nothing if unsuccessful

Examples

if (interactive()) {
  # get one of the default ZIP file from internet
  ghget("hu.data")
  # get a locally stored zip file
  ghget(dummy2=system.file("zip", "mmstat4.dummy.zip", package="mmstat4"))
  # get from an URL
  ghget(dummy.url="https://github.com/sigbertklinke/mmstat4.dummy/archive/refs/heads/main.zip")
}

ghinstall

Description

If the user agrees, it installs additional software necessary for running a script. Currently, only type=="py" for Python scripts and ⁠type=="R"`` for R scripts are supported. When a repository is downloaded, ⁠ghinstall⁠is called once. If the user calls⁠ghinstall⁠for an update, the parameter⁠force=TRUE' must be set.

Usage

ghinstall(type = c("py", "R"), force = FALSE)

Arguments

Details

R

mmstat4 init_R.R is opened if present in the active repository.

py

mmstat4 internally utilizes a virtual environment named mmstat4.xxxx, where xxxx⁠, varies depending on the repository. When ⁠ghinstall⁠is invoked, it verifies the existence of the virtual environment⁠mmstat4.xxxx⁠. If it does not exist, the environment is created, and ⁠init_py.R' is opened if present in the active repository.

Value

NULL if type is not found, otherwise type

Examples

# to delete the virtual environment use
# reticulate::virtualenv_remove('mmstat4')
if (interactive()) ghinstall()

ghlist

Description

Returns unique (short) names for accessing each file in the repository according to a regular expression. For details about regular expressions, see base::regex.

Usage

ghlist(
  pattern = ".",
  ignore.case = FALSE,
  perl = FALSE,
  fixed = FALSE,
  useBytes = FALSE,
  full.names = FALSE
)

Arguments

Value

character vector of short names

Examples

if (interactive()) ghlist()

ghopenAddin

Description

A RStudio addin to open a file from the downloaded zip file.

Usage

ghopenAddin()

Value

nothing

Examples

if (interactive()) ghopenAddin()

ghpath

Description

Returns a path for files based on ghdecompose.

Usage

ghpath(df, from = c("outpath", "inpath", "minpath", "filename"))

Arguments

Value

a character vector with file pathes

Examples

ghget("dummy")
pdf <- ghdecompose(ghlist(full.names=TRUE))
ghpath(pdf)
ghpath(pdf, 'o') # equals the input to ghdecompose
ghpath(pdf, 'i')
ghpath(pdf, 'm')
ghpath(pdf, 'f')

ghquery

Description

Queries the unique (short) names for each file in the repository. Several query methods are available, see Details.

Usage

ghquery(
  query,
  n = 6,
  full.names = FALSE,
  method = c("fpdist", "overlap", "tfidf"),
  costs = NULL,
  counts = FALSE,
  useBytes = FALSE
)

Arguments

Details

The following query methods are available:

• fpdist uses a partial backward matching distance based on utils::adist()

• overlap uses the overlap distance for query and file names

Value

character vector of short names fitting best to the query

Examples

if (interactive()) ghquery("bank")

ghrepos

Description

If key is NULL, then it returns the known repositories and where they are stored. If key is not NULL, then possible addresses for a repository are returned .

Usage

ghrepos(key = NULL)

Arguments

Value

a data frame with the data about the repositories

Examples

ghrepos()

Creates a ZIP file or directory with files

Description

ghzip creates a ZIP file (if dest has an extension zip) or copies to the destination directory. If dest is NULL then a temporary directory will be used. Please note that neither the ZIP file is deleted nor the target directory is cleaned beforehand if it already exists.

Usage

ghzip(files, dest = NULL)

Arguments

Value

the name of the destination directory or the ZIP file

Examples

if (interactive()) {
  zipfile <- tempfile(fileext='.zip')
  files   <- list.files(system.file(package="mmstat4"), recursive=TRUE)
  ghzip(files, zipfile)
}

isLocal

Description

Checks if a Shiny app runs locally or on a server

Usage

isLocal()

Value

logical

Examples

isLocal()

normpathes

Description

Returns a list with normalized pathes.

Usage

normpathes(x)

Arguments

Value

A list of the same length as x, the i-th element of which contains the vector of splits of x[i].

Examples

normpathes("CRAN/../mmstat4/python/./ghdist.R")

Create and display a note

Description

note internally stores a colored message, while display utilizes base::cat() to present them and reset the internal message stack.

Usage

note(msg, col = crayon::green)

display()

Arguments

Value

note returns invisibly the number of notes

Examples

notetest <- function(msg) {
  on.exit({ display() })
  note(msg)
  # do some complex computation
  x <- 1+1
}
notetest("Hello world!")

openFile

Description

The function attempts to open a file either in RStudio or in a text editor, depending on the environment. If the session is interactive, it tries to open the file in RStudio using rstudioapi::navigateToFile(). If RStudio is not available or the attempt fails, it opens the file in a text editor using utils::edit(). If the session is not interactive, it simply returns the contents of the file.

Usage

openFile(file, ...)

Arguments

Value

invisibly the result from try(rstudioapi::navigateToFile(file)) or try(utils::edit(file)).

Examples

openFile(system.file("rstudio", "addins.dcf", package = "mmstat4"))

Extract library and require calls in R and import calls from Python

Description

pkglist counts the number of library/require/import calls for R and Python commands in the files. If you set code==TRUE then returns R code for installing packages/modules. It checks via utils::available.packages() (for R) and via PyPI if a package/module is available. Otherwise a table with the number of library or import is returned.

Usage

pkglist(files, code = TRUE, repos = getOption("repos"))

Rlibs(files, code = TRUE, repos = getOption("repos"))

modlist(files, code = TRUE, repos = getOption("repos"))

Arguments

Value

a table how frequently the packages are called or R Code to install them

Examples

if (interactive()) {
  files <- list.files(pattern="*.(R|py)$", full.names=TRUE, recursive=TRUE)
  pkglist(files)
}

py_env

Description

Name of the currently used virtual emvironment.

Usage

py_env()

Value

the name of the virtual Python environment currently used by mmstat4

Examples

py_env()

toInt

Description

Converts x to an integer. If the conversion fails or the integer is outside min and max then NA_integer_ is returned

Usage

toInt(x, min = -Inf, max = +Inf)

Arguments

Value

a single integer value

Examples

toInt(3.0)
toInt("3.0")
toInt("test")

toNum

Description

Converts x to a numeric. If the conversion fails or the value is outside min and max then NA is returned

Usage

toNum(x, min = -Inf, max = +Inf)

Arguments

Value

a single integer value

Examples

toNum(3.0)
toNum("3.0")
toNum("test")

urlExists

Description

Verifies whether a provided url is downloadable, without detecting redirections in the URL.

Usage

urlExists(url)

Arguments

Value

TRUE if URL exists otherwise FALSE

Examples

urlExists("https://hu-berlin.de/sk")
urlExists("https://huglawurza.de")