Package 'miscset' reference manual

Title:	Miscellaneous Tools Set
Description:	A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.
Authors:	Sven E. Templer
Maintainer:	Sven E. Templer <[email protected]>
License:	GPL-3
Version:	1.1.0
Built:	2025-02-16 04:47:13 UTC
Source:	https://github.com/setempler/miscset

Miscellaneous R Tools

Description

A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.

Details

The package vignette provides a comprehensive overview and examples for the usage of all available functions in the package. View with vignette("miscset").

Author(s)

Sven E. Templer

Barplot with Confindence Intervals

Description

Create barplots of a list of numeric values and error bars according to the confidence interval, standard deviation, interquartile range, etc.

Usage

ciplot(x, ...)

## Default S3 method:
ciplot(x, ..., ylim, height.fun = mean,
  height.args = list(), error.fun = confint, error.args = list(),
  arrows.args = list(code = 3, angle = 90), na.rm = TRUE)
ciplot(x, ...)

## Default S3 method:
ciplot(x, ..., ylim, height.fun = mean,
  height.args = list(), error.fun = confint, error.args = list(),
  arrows.args = list(code = 3, angle = 90), na.rm = TRUE)

Arguments

`x`	List of numeric values
`...`	Arguments forwarded to barplot in default method.
`ylim`	A range for the y-axis limits.
`height.fun`	Function to apply on each list object to calculate the height of the bars from.
`height.args`	Arguments forwarded to height.fun, as a named list.
`error.fun`	Function to calculate the error size. See also details.
`error.args`	Arguments forwarded to error.fun, as a named list.
`arrows.args`	Arguments forwarded to arrows, as a named list.
`na.rm`	Logical, remove missing values.

Details

Example for quantiles:
interquartile <- function(x) {quartile(x,.75)-mean(x)}
quantileQ <- function(x, q) {abs(quartile(x,q[1])-mean(x))}

Author(s)

Sven E. Templer

Collapse objects

Description

Collapse objects as in the paste function.

Usage

collapse(x, sep, ...)

## Default S3 method:
collapse(x, sep = "", ..., .unique = FALSE,
  .sort = FALSE, .decreasing = FALSE)

## S3 method for class 'data.frame'
collapse(x, sep = "", by = names(x), ...,
  .unique = FALSE, .sort = FALSE, .decreasing = FALSE, .unlist = FALSE,
  .sortby = FALSE)
collapse(x, sep, ...)

## Default S3 method:
collapse(x, sep = "", ..., .unique = FALSE,
  .sort = FALSE, .decreasing = FALSE)

## S3 method for class 'data.frame'
collapse(x, sep = "", by = names(x), ...,
  .unique = FALSE, .sort = FALSE, .decreasing = FALSE, .unlist = FALSE,
  .sortby = FALSE)

Arguments

`x`	Any R object.
`sep`	A character string to separate value columns. `NULL` retains a vector.
`...`	Forwarded to or from other methods.
`.unique`	Logical, return only unique values.
`.sort`	Logical, sort the values.
`.decreasing`	Logical, if sorting, then by decreasing values.
`by`	Column names to split data frame by, before applying collapse on each remaining column within each piece. Using the default (all columns), then `unique(x)` is returned. Columns can be specified by names or integer with the column numbers. Using `0` or `NULL` collapses all columns.
`.unlist`	Logical, if value columns need to be unlisted before collapsing.
`.sortby`	Logical, sort the output on the `by` columns. This applies , If `x` was a `data.table`, then the keys are set as the `by` values.

Details

For the data.frame method, x is converted to a data.table before applying the piece- and column-wise collapses. If the input is already inheriting from data.table, then the class is retained.
.sortby is causing setkeyv(x, by) to be applied to x after converting to a data.table.

Author(s)

Sven E. Templer

Examples

#

### some data

set.seed(12)
s <- s2 <- sample(LETTERS[1:4], 9, replace = TRUE)
s2[1:2] <- rev(s2[1:2])
d <- data.frame(group = rep(letters[c(3,1,2)], each = 3), 
                value = s,
                level = factor(s2),
                stringsAsFactors = FALSE)

### collapse vectors

collapse(letters)
collapse(1:3)               # coerced to character
collapse(LETTERS[1:5], "-") # separated by '-'

### collapse data.frames

# by all columns (same as unique)
collapse(d)
# by a grouping column
collapse(d, by = 1)
# by multiple, but not all columns
collapse(d, by = c("group", "value"))
# return single row
collapse(d, by = 0)
# return single row, unique and sorted values
collapse(d, by = 0, .unique = TRUE, .sort = TRUE)

#
#

### some data

set.seed(12)
s <- s2 <- sample(LETTERS[1:4], 9, replace = TRUE)
s2[1:2] <- rev(s2[1:2])
d <- data.frame(group = rep(letters[c(3,1,2)], each = 3), 
                value = s,
                level = factor(s2),
                stringsAsFactors = FALSE)

### collapse vectors

collapse(letters)
collapse(1:3)               # coerced to character
collapse(LETTERS[1:5], "-") # separated by '-'

### collapse data.frames

# by all columns (same as unique)
collapse(d)
# by a grouping column
collapse(d, by = 1)
# by multiple, but not all columns
collapse(d, by = c("group", "value"))
# return single row
collapse(d, by = 0)
# return single row, unique and sorted values
collapse(d, by = 0, .unique = TRUE, .sort = TRUE)

#

Confidence Intervals for Numeric Vectors

Description

Calculate confidence intervals for values of a numeric vector.

Usage

## S3 method for class 'numeric'
confint(object, parm = qnorm, level = 0.95, ...,
  na.rm = TRUE, ret.attr = TRUE)
## S3 method for class 'numeric'
confint(object, parm = qnorm, level = 0.95, ...,
  na.rm = TRUE, ret.attr = TRUE)

Arguments

`object`	A numeric vector.
`parm`	Function for quantile calculation. e.g. `qnorm`, `qt`
`level`	Size of confidence (0 < size < 1).
`...`	Unused.
`na.rm`	Logical, remove missing values for `sd` and `mean`.
`ret.attr`	Logical, to include the mean value and function arguments as attributes of the returned object.

Value

Returns a numeric vector with the lower and upper range of the confidence interval.

Author(s)

Sven E. Templer

Examples

#

confint(1:3)
confint(1:3, ret.attr = FALSE)

#
#

confint(1:3)
confint(1:3, ret.attr = FALSE)

#

Bind data.frames in a List by Rows

Description

Same as do.call(rbind, x), but adding a column with the name of each table. Missing names are replaced by integers.

Usage

do.rbind(x, idcol = "Name", keep.rownames = FALSE)
do.rbind(x, idcol = "Name", keep.rownames = FALSE)

Arguments

`x`	List with data.frames. Non data.frame objects are dropped.
`idcol`	Name for column with ids in output.
`keep.rownames`	Logical, keep rownames.

Value

Returns a data.frame

Author(s)

Sven E. Templer

Determine Duplicates

Description

Determine duplicates. duplicates returns a logical vector, duplicatei an integer vector.

Usage

duplicates(x)

duplicatei(x, first = TRUE)
duplicates(x)

duplicatei(x, first = TRUE)

Arguments

`x`	A vector or data.frame to search for duplicates.
`first`	Logical, `TRUE` to return the index also for the first occurrence of values. Otherwise, a `0` is the index for the first occurrence.

Value

duplicates returns a logical vector as duplicated, but with TRUE values also for the first occurrence of duplicated values.
duplicatei returns the index of the first occurrence of each unique value.

Author(s)

Sven E. Templer

Examples

#

x <- c(7, 7, 7, 2, 3, 2)
data.frame(
  data = x,
  duplicated = duplicated(x),
  duplicates = duplicates(x),
  duplicatei = duplicatei(x),
  duplicatei0 = duplicatei(x, FALSE))

#
#

x <- c(7, 7, 7, 2, 3, 2)
data.frame(
  data = x,
  duplicated = duplicated(x),
  duplicates = duplicates(x),
  duplicatei = duplicatei(x),
  duplicatei0 = duplicatei(x, FALSE))

#

Create a Pairwise List from a Matrix

Description

Transform a matrix or dist object to a pairwise list.

Usage

enpaire(x, ...)

## Default S3 method:
enpaire(x, ...)

## S3 method for class 'dist'
enpaire(x, upper = T, lower = T, ...)

## S3 method for class 'matrix'
enpaire(x, upper = T, lower = T, ...)
enpaire(x, ...)

## Default S3 method:
enpaire(x, ...)

## S3 method for class 'dist'
enpaire(x, upper = T, lower = T, ...)

## S3 method for class 'matrix'
enpaire(x, upper = T, lower = T, ...)

Arguments

`x`	Object of class `matrix`.
`...`	Arguments passed to methods.
`upper`	Logical, return values from upper triangle.
`lower`	Logical, return values from lower triangle.

Value

Returns a data.frame. The first and second column represent the dimension names for a value in x. The following columns contain the values for the upper or lower triangle.

Author(s)

Sven E. Templer

Examples

#

m <- matrix(letters[1:9], 3, 3, dimnames = list(1:3,1:3))
enpaire(m)
enpaire(m, lower = FALSE)

#
#

m <- matrix(letters[1:9], 3, 3, dimnames = list(1:3,1:3))
enpaire(m)
enpaire(m, lower = FALSE)

#

Create a Factor with NA as Level

Description

Create a factor with NA values included and positioned as last level.

Usage

factorNA(x, ...)
factorNA(x, ...)

Arguments

`x`	A vector coerced to character.
`...`	Forwarded to factor. `x` and `levels` are defined.

Author(s)

Sven E. Templer

HTML Colours Like ggplot2

Description

Calculate HTML colour code from a palette like ggplot2 uses.

Usage

gghcl(n, sub = 1:n, h = c(0, 360) + 15, c = 100, l = 65, ...)
gghcl(n, sub = 1:n, h = c(0, 360) + 15, c = 100, l = 65, ...)

Arguments

`n`	Numeric value to determine size of palette.
`sub`	Numeric vector with values within range from `1` to `n` to subset palette.
`h`	Hue of the colour. Within range of a circle's degrees.
`c`	Chroma of the colour.
`l`	Luminance of the colour. Within range from `1` to `100`.
`...`	Further arguments passed to function `hcl`.

Details

See ?hcl for explanation of h, c and l.

Value

Returns a character vector containing HTML colour code of the standard ggplot colour palette.

Author(s)

Sven E. Templer

Examples

#

# Plot some palettes:
par(mfrow = c(3,1), mai = c(.1,.1,1,.1))
p <- matrix(1:10, 10)
image(p, col = gghcl(5), axes = FALSE, main ="gghcl(5)")
image(p, col = gghcl(10), axes = FALSE, main = "gghcl(10)")
image(p, col = gghcl(10, 1:5), axes = FALSE, main ="gghcl(10, 1:5)")
# dev.off() # to reset \code{par}

#
#

# Plot some palettes:
par(mfrow = c(3,1), mai = c(.1,.1,1,.1))
p <- matrix(1:10, 10)
image(p, col = gghcl(5), axes = FALSE, main ="gghcl(5)")
image(p, col = gghcl(10), axes = FALSE, main = "gghcl(10)")
image(p, col = gghcl(10, 1:5), axes = FALSE, main ="gghcl(10, 1:5)")
# dev.off() # to reset \code{par}

#

Arrange a List of ggplots

Description

Arrange a list of ggplots with grid.arrange and output on local graphic device or as pdf/png when a path is supplied. ggplotGridA4 writes the plots to a DIN A4 (8 x 11 inches) pdf file directly.

Usage

ggplotGrid(l, path, ncol = 1, nrow = 1, width = 8, height = 11,
  res = 300, pdf.cairo = TRUE, onefile = TRUE, ...)

ggplotGridA4(l, path, ncol = 2, nrow = 1, wide = TRUE)

ggplotlist(x, ncol = 1, path, width = 11, height = 8)
ggplotGrid(l, path, ncol = 1, nrow = 1, width = 8, height = 11,
  res = 300, pdf.cairo = TRUE, onefile = TRUE, ...)

ggplotGridA4(l, path, ncol = 2, nrow = 1, wide = TRUE)

ggplotlist(x, ncol = 1, path, width = 11, height = 8)

Arguments

`l`	List with ggplot objects.
`path`	Plot to file of type pdf or png. Determine type by path ending (.pdf or .png). Optional in `ggplotlist`: A character string that gives the path to export the plot to a file, ending with 'pdf' or 'png' (case insensitive). If missing, then the grid is returned to the current graphic device.
`ncol`	Number of columns.
`nrow`	Number of rows per page, only for pdfs.
`width`	For pdfs/pngs the width in inches, else ignored.
`height`	For pdfs/pngs the height in inches, else ignored.
`res`	Resolution in dpi for pngs.
`pdf.cairo`	Use cairo_pdf (or cairo_ps, svg) instead of pdf
`onefile`	Create one file, see cairo_pdf.
`...`	Forwarded to cairo_pdf
`wide`	Wide format pdf pages (11x8 inches).
`x`	A list containing at least one ggplot object of class `gg`.

Author(s)

Sven E. Templer

Examples

#

## Not run: 
library(ggplot2)
d <- data.frame(a=1:5,b=1:5)
x <- list(
  ggplot(d, aes(x=a,y=b,col=b)) + geom_line(),
  ggplot(d, aes(x=a,y=b,shape=factor(b))) + geom_point())
ggplotlist(x, 2)
## End(Not run)

#
#

## Not run: 
library(ggplot2)
d <- data.frame(a=1:5,b=1:5)
x <- list(
  ggplot(d, aes(x=a,y=b,col=b)) + geom_line(),
  ggplot(d, aes(x=a,y=b,shape=factor(b))) + geom_point())
ggplotlist(x, 2)
## End(Not run)

#

Pattern Matching and Extraction

Description

Function to extract a certain index from gregexpr().

Usage

gregexprind(pattern, text, n, ...)
gregexprind(pattern, text, n, ...)

Arguments

`pattern`	Character string containing a regular expression to be searched in `text`.
`text`	Character vector where the search is performed.
`n`	Numeric value or character string `"last"` to extract `n`th or last position of `pattern` in each value of `text`.
`...`	Arguments passed to function `gregexpr()`.

Value

Numeric vector of length length(text).

Author(s)

Sven E. Templer

Examples

#

gregexprind(c("a"),c("ababa","ab","xyz",NA), 1)
gregexprind(c("a"),c("ababa","ab","xyz",NA), 2)
gregexprind(c("a"),c("ababa","ab","xyz",NA), "last")

#
#

gregexprind(c("a"),c("ababa","ab","xyz",NA), 1)
gregexprind(c("a"),c("ababa","ab","xyz",NA), 2)
gregexprind(c("a"),c("ababa","ab","xyz",NA), "last")

#

Open The Package Help Index Page

Description

Given a package name or string, start the package help index page in a browser.

Usage

help.index(pkg, browser = NULL)
help.index(pkg, browser = NULL)

Arguments

`pkg`	A character string or expression with the name of a package.
`browser`	The browser to display. `text` and `pdf` don't use a browser, but builtin text/pdf (help_type). Otherwise a character string for the browser program binary to call or function.

Author(s)

Sven E. Templer

Print enhanced session information

Description

Based on and enhancing devtools::session_info.

Usage

info(..., width = 120)
info(..., width = 120)

Arguments

`...`	Forwarded to other methods.
`width`	Console width in columns.

Author(s)

Sven E. Templer

Examples

info()
devtools::session_info()
sessionInfo()
info()
devtools::session_info()
sessionInfo()

Numeric to Character with Leading Zero(s)

Description

Transform numeric values to character string prepending leading zero(s).

Usage

leading0(num, digits = 2)
leading0(num, digits = 2)

Arguments

`num`	Numeric vector (character also possible) to transform.
`digits`	Numeric value of minimum length of output strings.

Value

Character vector with same length of strings of each value. Original "string" is prepended by zero(s). String length is at least max(nchar(as.character(num))).

Author(s)

Sven E. Templer [email protected]

Examples

#

# use with paste to generate strings of equal size:
paste0("observation", leading0(1:10, 3))

#
#

# use with paste to generate strings of equal size:
paste0("observation", leading0(1:10, 3))

#

Load RData Objects to a List

Description

Load multiple .RData files and return a (simplified) list.

Usage

lload(path = ".", pattern = ".RData", recursive = FALSE,
  simplify = TRUE, verbose = TRUE)
lload(path = ".", pattern = ".RData", recursive = FALSE,
  simplify = TRUE, verbose = TRUE)

Arguments

`path`	Character string with the path, as used in list.files.
`pattern`	A regular expression for file name patterns, as used in list.files.
`recursive`	Logical. Search the path recursive.
`simplify`	Logical, unlist when there are only unique object names.
`verbose`	Logical. Print information on screen about loading process.

Value

Returns a list of length n, when there are n data files loaded. All objects are stored in sublists. Names are according to files, and names of sublists to objects per file. If simplified, the list is of length m, when there are m objects in total loaded.

Author(s)

Sven E. Templer

List Object Details

Description

Return a data.frame with a list of all objects of a specified environmet.

Usage

lsall(envir = .GlobalEnv, ...)
lsall(envir = .GlobalEnv, ...)

Arguments

`envir`	An environment where to look for objects.
`...`	Arguments forwarded to `ls`.

Value

Returns a data.frame with object names, lengths, classes, modes and sizes or NULL if the environment is empty.

Author(s)

Sven E. Templer

Examples

#

lsall()
obj1 <- 1:3
obj2 <- data.frame(1:3)
obj3 <- list(1:3)
lsall()

#
#

lsall()
obj1 <- 1:3
obj2 <- data.frame(1:3)
obj3 <- list(1:3)
lsall()

#

Multiple Pattern Matching and Replacement

Description

mgrepl allows multiple patterns search in character vectors, offering multicore support to parallelize search over all patterns using mclapply.

Usage

mgrepl(patterns, text, log.fun = all, na.replace = FALSE,
  use.which = FALSE, cores = 1, ...)
mgrepl(patterns, text, log.fun = all, na.replace = FALSE,
  use.which = FALSE, cores = 1, ...)

Arguments

`patterns`	A vector or list containing regular expressions (regex) to be searched in `text`. Coerced to `character`.
`text`	Character vector on which the search is performed.
`log.fun`	A function to apply on the result of matching each pattern on each element of `text`. Determines the output. See section Value.
`na.replace`	A single value to replace each `NA` with in the result.
`use.which`	A logical value. `TRUE` to convert result with which. Only if output is.atomic, otherwise ignored. Deprecated.
`cores`	Numeric value for how many cores to use for computation using `mclapply`.
`...`	Further arguments passed to functions grepl.

Value

Depending on the function defined with log.fun, the return value is either

a vector, e.g. for functions like any, all or sum.
a matrix is obtained with e.g. identity or as.integer. Each row holds the result of a single pattern.
a list is returned for functions which create results of different lengths for each element, such as which.

Author(s)

Sven E. Templer

Examples

#

# strings
s <- c("ab","ac","bc", NA)

# match all patterns (default)
mgrepl(c("a", "b"), s)

# match any of the patterns
mgrepl(c("a", "b"), s, any)
grepl("a|b", s)

# return logical matrix, one column for each pattern
mgrepl(c("a", "b"), s, identity)

# return count of matches
mgrepl(c("a", "b"), s, sum)

#
#

# strings
s <- c("ab","ac","bc", NA)

# match all patterns (default)
mgrepl(c("a", "b"), s)

# match any of the patterns
mgrepl(c("a", "b"), s, any)
grepl("a|b", s)

# return logical matrix, one column for each pattern
mgrepl(c("a", "b"), s, identity)

# return count of matches
mgrepl(c("a", "b"), s, sum)

#

Return Triangular Numbers

Description

Return the series of triangular (/triangle) numbers up to a number of n rows of a triangle. The series has the entry number "A000217" at https://oeis.org/A000217 and starts like this: 0, 1, 3, 6, 10, ...

Usage

ntri(n)
ntri(n)

Arguments

`n`	Positive integer value for sequence length.

Value

Returns an integer vector of length n.

Author(s)

Sven E. Templer ([email protected])

Amount and Index of Unique Values

Description

Return the index or amount of unique values in a vector.

Usage

nunique(x, na = TRUE, ...)

uniquei(x, na = TRUE, ...)
nunique(x, na = TRUE, ...)

uniquei(x, na = TRUE, ...)

Arguments

`x`	Numeric vector to transform.
`na`	Logical, `TRUE` to include/count `NA`.
`...`	Arguments forwarded to unique.

Author(s)

Sven E. Templer

Examples

#

v <- c("a","b","a", NA)
nunique(v)
nunique(v, FALSE)
uniquei(v)
uniquei(v, FALSE)

#
#

v <- c("a","b","a", NA)
nunique(v)
nunique(v, FALSE)
uniquei(v)
uniquei(v, FALSE)

#

P Value Significance Level Indicator

Description

Transform p-values to character (e.g. stars) indicators by significance levels with the function symnum.

Usage

p2star(p, breaks = c(0, 0.001, 0.01, 0.05, 0.1, 1), symbols = c("***", "**",
  "*", ".", "n.s."))
p2star(p, breaks = c(0, 0.001, 0.01, 0.05, 0.1, 1), symbols = c("***", "**",
  "*", ".", "n.s."))

Arguments

`p`	Vector with p values
`breaks`	The breaks from min (0) to max (1).
`symbols`	Symbols to use for values between breaks from min to max.

Author(s)

Sven E. Templer

Examples

#

p2star(c(1e-5,.1,.9))

#
#

p2star(c(1e-5,.1,.9))

#

Plot Nothing (but a Plot)

Description

Create a plot, with empty elements by presetting default parameters.

Usage

plotn(x = 0:1, y = NULL, type = "n", xlab = "", ylab = "",
  xaxt = "n", yaxt = "n", frame.plot = F, ...)
plotn(x = 0:1, y = NULL, type = "n", xlab = "", ylab = "",
  xaxt = "n", yaxt = "n", frame.plot = F, ...)

Arguments

`x`	Coordinates of the points.
`y`	Coordinates of the y-axis.
`type`	Plot type.
`xlab`, `ylab`	Axis titles.
`xaxt`, `yaxt`	Axis types.
`frame.plot`	Plot the frame.
`...`	Forwarded arguments to `plot`.

Details

For details about the function see plot, which is called from plotn. More detailed information in plot.default and par.

Author(s)

Sven E. Templer

Remove All Objects from Global Environment

Description

Remove all objects from the global environment.

Usage

rmall(...)
rmall(...)

Arguments

...

Arguments forwarded to ls to get all objects.

Author(s)

Sven E. Templer

Examples

#

a <- b <- letters
ls()
rmall()
ls()

#
#

a <- b <- letters
ls()
rmall()
ls()

#

Scale Numeric Values to Defined Ranges

Description

Scale numeric values to a range from 0 to 1 with the function scale0 or to a chosen range with scaler.

Usage

scale0(x)

scaler(x, r = c(0, 1), b = range(x, na.rm = TRUE))
scale0(x)

scaler(x, r = c(0, 1), b = range(x, na.rm = TRUE))

Arguments

`x`	Numeric vector to transform.
`r`	Numeric vector of length 2 for range to scale values of `x` to.
`b`	Numeric vector of length 2 to define the border of `x` to use as scaling minimum and maximum.

Author(s)

Sven E. Templer

Examples

#

scale0(0:10)
scale0(-1:3)
scale0(2:3)

scaler(0:10)
scaler(0:10, 1:2)
scaler(0:10, 1:2, c(0, 20))

#
#

scale0(0:10)
scale0(-1:3)
scale0(2:3)

scaler(0:10)
scaler(0:10, 1:2)
scaler(0:10, 1:2, c(0, 20))

#

Sort data.frame Objects

Description

Sort a data.frame by any column(s).

Usage

## S3 method for class 'data.frame'
sort(x, decreasing = FALSE, by = NULL, bye = NULL,
  na.last = NA, ...)
## S3 method for class 'data.frame'
sort(x, decreasing = FALSE, by = NULL, bye = NULL,
  na.last = NA, ...)

Arguments

`x`	A data.frame.
`decreasing`	Logical, sort in decreasing order. See also sort.
`by`	Index (integer) or names of columns in `x` to sort by in that order. If both `by` and `bye` are missing, all columns are used to sort in their order.
`bye`	Unquoted column name or `list()` or `.()` with unquoted column names to sort `x` by. Not evaluated if `by` is supplied.
`na.last`	`TRUE` to put missing values last, `FALSE` to put first or `NA` to remove.
`...`	Ignored for the data.frame method.

Author(s)

Sven E. Templer

Examples

#

d <- data.frame(a=c(1,1,1,2,NA),b=c(2,1,3,1,1),c=5:1)
d
sort(d) # sort by every column (a, then b, then c)
sort(d, TRUE, by="c") # decreasing by column 'c'
sort(d, bye=.(a,c)) # increasing by columns 'a' and then 'c'

#
#

d <- data.frame(a=c(1,1,1,2,NA),b=c(2,1,3,1,1),c=5:1)
d
sort(d) # sort by every column (a, then b, then c)
sort(d, TRUE, by="c") # decreasing by column 'c'
sort(d, bye=.(a,c)) # increasing by columns 'a' and then 'c'

#

Create a Square Matrix

Description

Transform any m x n matrix to a square matrix by column/row names. Stops if no or duplicated dimnames are provided in x.

Usage

squarematrix(x)
squarematrix(x)

Arguments

`x`	Object of class `matrix`.

Value

Returns a matrix.

Author(s)

Sven E. Templer

Examples

#

m <- matrix(1:6, 2, dimnames=list(2:3,1:3))
m
squarematrix(m)

#
#

m <- matrix(1:6, 2, dimnames=list(2:3,1:3))
m
squarematrix(m)

#

Split String and Return Part

Description

Return the nth part of a splitted string.

Usage

str_part(x, split, n, ..., roll = F)

strpart(x, split, n, ..., roll = F)
str_part(x, split, n, ..., roll = F)

strpart(x, split, n, ..., roll = F)

Arguments

`x`	Character vector.
`split`	Regular expression splitting strings.
`n`	Number of part to extract.
`...`	Arguments passed to `strsplit`.
`roll`	Logical, if to use the last when less than maximum parts.

Value

A character vector of the extracted parts.

Author(s)

Sven E. Templer

Examples

#

s <- c("abc","abcd","abc")

str_part(s, "", 4)
str_part(s, "", 4, roll=TRUE)

#
#

s <- c("abc","abcd","abc")

str_part(s, "", 4)
str_part(s, "", 4, roll=TRUE)

#

Reverse Text Strings

Description

Create a reverse version of strings.

Usage

str_rev(x)

strrev(x)
str_rev(x)

strrev(x)

Arguments

`x`	vector with strings. Is coerced to character.

Value

Returns a character vector with reversed strings.

Author(s)

Sven E. Templer

Examples

#

s <- c("abc","asdf")

str_rev(s)

#
#

s <- c("abc","asdf")

str_rev(s)

#

Extract a Substring

Description

This function extracts substring(s) which match a given pattern.

Usage

strextr(x, pattern, sep = " ", mult = F, unlist = F, cores = 1)
strextr(x, pattern, sep = " ", mult = F, unlist = F, cores = 1)

Arguments

`x`	Character vector.
`pattern`	Regular expression.
`sep`	Character string which separates the fields.
`mult`	Logical, if multiple matching fields should be returned, or otherwise NA.
`unlist`	Logical, unlists multiple results.
`cores`	Integer for number of computational cores to use.

Details

The function is deprecated and will be removed with miscset version 2. It is recommended to use str_extract or str_extract_all instead.

Value

A list of character vectors containing the substrings that are matching pattern and are separated by sep or NA if the pattern could not be found.

Author(s)

Sven E. Templer

Examples

#

library(stringr)

s <- c("A1 B1 C1","A2 B2", "AA A1", "AA", "B1 A1", "BB AB A1")

strextr(s, "^[AB][[:digit:]]$") # deprecated
str_extract(s, "[AB][:digit:]")

strextr(s, "^[AB][[:digit:]]$", mult = TRUE) # deprecated
str_extract_all(s, "[AB][:digit:]")

strextr(s, "^[AB][[:digit:]]$", mult = TRUE, unlist = TRUE) # deprecated
unlist(str_extract_all(s, "[AB][:digit:]")) # has no <NA> values

strextr(s, "^[C][[:digit:]]$") # deprecated
str_extract(s, "[C][:digit:]")

#
#

library(stringr)

s <- c("A1 B1 C1","A2 B2", "AA A1", "AA", "B1 A1", "BB AB A1")

strextr(s, "^[AB][[:digit:]]$") # deprecated
str_extract(s, "[AB][:digit:]")

strextr(s, "^[AB][[:digit:]]$", mult = TRUE) # deprecated
str_extract_all(s, "[AB][:digit:]")

strextr(s, "^[AB][[:digit:]]$", mult = TRUE, unlist = TRUE) # deprecated
unlist(str_extract_all(s, "[AB][:digit:]")) # has no <NA> values

strextr(s, "^[C][[:digit:]]$") # deprecated
str_extract(s, "[C][:digit:]")

#

Table to Latex

Description

This function enhances xtable: It can write the latex code of the table directly to a file and optionally adds a header/footer for the document structure. Also a system command can be given to convert the tex file to a pdf document, for example.

Usage

textable(d, file, caption = NULL, label = NULL, align = NULL,
  rownames = FALSE, topcapt = TRUE, digits = NULL, as.document = FALSE,
  landscape = FALSE, margin = 2, pt.size = 10, cmd = NULL, ...)
textable(d, file, caption = NULL, label = NULL, align = NULL,
  rownames = FALSE, topcapt = TRUE, digits = NULL, as.document = FALSE,
  landscape = FALSE, margin = 2, pt.size = 10, cmd = NULL, ...)

Arguments

`d`	Object (will be coerced to data.frame) to transform to a latex table.
`file`	Character string with output file name. If missing or `""`, the output is printed to the screen.
`caption`	Character vector with title of table.
`label`	Character vector with the latex label or HTML anchor.
`align`	Character vector with `'l'`, `'c'`, `'r'` for aligning the columns left, centered or right. Length is either one or 1 (for rownames column) + number of columns in `d` (even if `rownames = FALSE`)
`rownames`	Logical, include row names of `d`.
`topcapt`	Logical, put caption and label before 'tabular'.
`digits`	Number of digits to print from numeric values.
`as.document`	Logical. `TRUE` to add the document definition to the output. The document class is an article and the package a4paper is included.
`landscape`	Logical, use a landscape format for wider tables. Only with `as.document=TRUE`.
`margin`	Margin between table and page border in cm. Only with `as.document=TRUE`.
`pt.size`	Integer from 10 to 13 for the size of the characters. Only with `as.document=TRUE`.
`cmd`	A character vector with the system command to apply on the output file. Only if `file` is given and `as.document` is `TRUE`. `NULL` or an empty string system is not called.
`...`	Forwarded arguments to print.xtable.

Details

Example for a system call:
cmd = "pdflatex -output-directory /path/to/files/"

Value

Returns a character vector invisible. If file is set, then the content is written to a file. Else it is printed to the console.

Author(s)

Sven E. Templer

Examples

#

## Not run: 
d <- head(trees)
dc <- 'R "trees" dataset.'
textable(d, rownames=TRUE, digits=4, caption=dc)
textable(d, '/tmp/trees.tex', caption=dc, as.document=TRUE, 
  cmd='pdflatex --output-directory /tmp')

## End(Not run)

#
#

## Not run: 
d <- head(trees)
dc <- 'R "trees" dataset.'
textable(d, rownames=TRUE, digits=4, caption=dc)
textable(d, '/tmp/trees.tex', caption=dc, as.document=TRUE, 
  cmd='pdflatex --output-directory /tmp')

## End(Not run)

#

Package 'miscset'

Help Index

Miscellaneous R Tools

Description

Details

Author(s)

Barplot with Confindence Intervals

Description

Usage

Arguments

Details

Author(s)

Collapse objects

Description

Usage

Arguments

Details

Author(s)

Examples

Confidence Intervals for Numeric Vectors

Description

Usage

Arguments

Value

Author(s)

Examples

Bind data.frames in a List by Rows

Description

Usage

Arguments

Value

Author(s)

Determine Duplicates

Description

Usage

Arguments

Value

Author(s)

Examples

Create a Pairwise List from a Matrix

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Create a Factor with NA as Level

Description

Usage

Arguments

Author(s)

HTML Colours Like ggplot2

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Arrange a List of ggplots

Description

Usage

Arguments

Author(s)

Examples

Pattern Matching and Extraction

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Open The Package Help Index Page

Description

Usage

Arguments

Author(s)