R package miscset version r packageVersion("miscset")
.
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.
Install the latest version from CRAN via:
install.packages('miscset')
Install the development version from github via:
install.packages('devtools') devtools::install_github('setempler/miscset@develop', build_vignettes = TRUE)
After installation, load the package via
library(miscset)
If you like to contribute to the development of the packages, please
Get help in an R session via
help.index(miscset)
?
+ function nameciplot
Plot a bargraph with error bars. Input data is a list with numeric vectors.
Functions to calculate bar heights (e.g. mean
by default) and error bar sizes
(e.g. confint.numeric
by default) can be modified (e.g. sd
for error bars).
d <- data.frame(a=c(2,1,3,NA,1), b=2:6, c=5:1) ciplot(d)
ggplotGrid
Arrange ggplots on a grid (plot window or pdf file). Supply a list with ggplot
objects and define number of rows and/or columns. If a path
is supplied, the
plot is written to that file instead of the internal graphics device.
library(ggplot2) plots <- list( ggplot(d, aes(x = b, y= -c, col = b)) + geom_line(), ggplot(d, aes(x = b, y = -c, shape = factor(b))) + geom_point()) ggplotGrid(plots, ncol = 2)
The function ggplotGridA4
supports direct output to DIN A4 sized pdfs.
gghcl
Generate a character vector with html values from a color hue as in ggplot
.
d <- data.frame(a=c(2,1,3,NA,1), b=2:6, c=5:1) n <- length(d) gghcl(n) ciplot(d, col = gghcl(n))
plotn
Create an empty plot. Useful to fill layout
.
plotn()
sort
Sort data.frame
objects. This extends the functionality of the base R distributed generic sort
. Define multiple columns by column names as character vector or expression.
d <- data.frame(a=c(2,1,3,NA,1), b=2:6, c=5:1) print(d) sort(d, by = c("a", "c"))
do.rbind
Note: This function is now deprecated. It is recommended to use rbindlist
from the data.table package.
A wrapper function to row-bind data.frame
objects in a list with do.call
and rbind
.
Object names from the list are inserted as additional column.
d <- data.frame(a=c(2,1,3,NA,1), b=2:6, c=5:1) print(d[1:3,]) do.rbind(list(first=d[1:2,], second=d[1:3,]))
enpaire
Generate a pairwise list (data.frame
) of a matrix containing row and column id and upper and lower triangle values.
m <- matrix(letters[1:9], 3, 3, dimnames = list(1:3,1:3)) print(m) enpaire(m)
squarematrix
Generate a symmetric (square) matrix from an unsymmetric one using column and row names.
Fills empty cells with NA
.
m <- matrix(letters[1:9], 3, 3, dimnames = list(1:3,1:3)) print(m[-1,]) squarematrix(m[-1,])
textable
Print a data.frame
as latex table. Extends xtable
by optionally including a latex header,
and if desired writing the output to a file directly and calling a system command to convert
it to a .pdf
file, for example.
d <- data.frame(a=c(2,1,3,NA,1), b=2:6, c=5:1) textable(d, caption = 'miscset vignette example data.frame', as.document = TRUE)
help.index
Show the help index page of a package (with the list of all help pages of a package).
help.index(miscset)
lload
Load multiple R data objects into a list. List is of same length as number of files provided. Sublists contain all respective objects. Simplification is possible if all names are unique.
lload("folder/with/rdata/", "test*.RData")
lsall
Return all current workspace (or any custom) object names, lengths, classes, modes and sizes in a data.frame
.
lsall()
rmall
Remove all objects from the current or custom environment.
rmall()
mgrepl
Search for multiple patterns in a character vector. Merge results by (custom) logical functions
(e.g. any
, all
) and use mutlicore support from the parallel
package.
Optionally return the index (as with which
).
Use identity
to return a matrix with the results of each pattern per row.
s <- c("ab","ac","bc", NA) mgrepl(c("a","b"), s) mgrepl(c("a","b"), s, any) # similar to: grepl("a|b", s) mgrepl(c("a", "b"), s, sum) mgrepl(c("a","b"), s, identity)
gregexprind
Retreive the n
th or "last"
index of an expression found in a character string.
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")
collapse
To collapse vectors, usually a call to paste
or paste0
setting the argument
collapse
is applied. The collapse function is a wrapper of this functionality
applied to a single vector. It can be extended with the .unique
, .sort
and
.decreasing
arguments, to return only unique and sorted values.
paste(letters, collapse = "") collapse(letters)
The data.frame
method allows to collapse a data frame by identifier/grouping
columns (specified with by
). Each group piece has then all value columns
collapsed with the default method.
In addition, the value columns can be collapsed to vectors, when sep = NULL
is selected, keeping a list of vectors for this column in the returned
data frame. .sortby
allows to choose if the result should be sorted by
the grouping columns. .unlist
provides a way to unlist value columns per
group, which is useful if the input has list columns.
# create example 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) print(d)
The following (default settings) collapses by all columns, which results in an output
similar to unique(d)
, but the row names are not kept.
collapse(d)
Specifying no grouping columns (setting by
to 0
or NULL
) collapses all columns.
collapse(d, by = NULL)
Specifying at least one and maximum less than the total columns groups the data.frame
,
splits it into group pieces, and applies the collapsing to all remaining columns.
collapse(d, "/", 1)
If the separator sep
is not specified, the data.frame
method allows to return list
columns, containing vectors of values per group. With the .sortby
argument, the
ouptut can be sorted on the grouping values.
# by first column, but keep values as vectors collapse(d, NULL, c(1,3), .sortby = T)
The data.frame
method also works on data.table
objects, since it uses the methods
from the package of the same name to split the input into group pieces. If the input
inherits from data.table
, the class is retained.
leading0
Prepend 0
characters to numbers to generate equally sized strings.
leading0(c(9, 112, 5009))
strextr
Note: This function is now deprecated. It is recommended to use str_extract
or
str_extract_all
from the stringr package.
Split strings by a separator (sep
) and extract all substrings matching a pattern
.
Optionally allow multiple matches, and use multicore support from the parallel
package.
s <- "xa,xb,xn,ya,yb" strextr(s, "n$", ",") strextr(s, "^x", ",", mult=T) library(stringr) str_extract(s, "[^,]*n") str_extract_all(s, "x[^,]*")
str_part
Similar to strextr
, but extracting substrings is done by setting an index value n
.
Optionally roll the last value to n
if it's index is less.
s <- "xa,xb,xn,ya,yb" str_part(s, ",", 3)
str_rev
Create reverse version of strings of a character
vector.
str_rev(c("olleH", "!dlroW"))
duplicates
and duplicatei
Determine duplicates. Return either a logical vector (duplicates
) or an integer index
(duplicatei
). Extends the base method duplicated
by also returning TRUE
for the
first occurence of a value.
data.frame( duplicate = d$a, ".d" = duplicated(d$a), # standard R function ".s" = duplicates(d$a), ".i" = duplicatei(d$a))
p2star
Asign range symbols to values, e.g. convert p-values to significance characters.
p2star(c(0.003, 0.049, 0.092, 0.431))
confint.numeric
Calculate confidence intervals. Extends the base method confint
to numeric vectors.
n <- c(2,1,3,NA,1) confint(n, ret.attr = FALSE)
ntri
Generate a series of triangular numbers of length n
according to
OEIS#A000217. The series for 12 rows of a triangle,
for example, can be returned as in the following example.
ntri(12)
scale0
and scaler
Scale numeric vectors to a range of 0 to 1 with scale0
or to a custom output range r
and input range b
with scaler
.
n <- 5:1 scale0(n) scaler(n, c(2, 6), b = c(1, 10))
nunique
and uniquei
Return the amount (with nunique
) or index (with uniquei
) of unique values in a vector. Extends plyr::nunique
by allowing NA
values to be counted as a 'level'.
n <- c(2,1,3,NA,1) nunique(n) nunique(n, FALSE) uniquei(n) uniquei(n, FALSE)
Copyright (c) 2017 - Sven E. Templer
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.