Title: A Collection of Modified R Functions to Make Basic Coding More Convenient
Version: 1.0.1
Date: 2025-02-25
Description: A collection of recycled and modified R functions to aid in file manipulation, data exploration, wrangling, optimization, and object manipulation. Other functions aid in convenient data visualization, loop progression, software packaging, and installation.
Encoding: UTF-8
RoxygenNote: 7.2.3
Imports: devtools, RCurl, Rcpp, gplots, grDevices, stats, usethis, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
License: GPL (≥ 3)
NeedsCompilation: yes
Packaged: 2025-02-26 04:53:06 UTC; Admin
Author: Paul Little [aut, cre]
Maintainer: Paul Little <pllittle321@gmail.com>
Repository: CRAN
Date/Publication: 2025-02-26 05:10:02 UTC

bin_cont_var

Description

Transform numeric vector into discrete bins

Usage

bin_cont_var(VAR, NUM_GROUPS, ROUND = 3, binNUM = FALSE)

Arguments

VAR

A numeric vector of values to bin

NUM_GROUPS

A positive integer for the number of bins

ROUND

A nonnegative integer for displaying bin labels through binned intervals

binNUM

Boolean set to TRUE to map bins to numbers. Otherwise, bins are characterized by intervals

Value

A character or integer vector of collapsed/binned values

calc_JK

Description

calc_JK

Usage

calc_JK(EST, LOO_EST, alpha = 0.05)

Arguments

EST

A numeric vector of parameter estimates

LOO_EST

A numeric matrix of parameter estimates where columns correspond to each parameter and rows correspond to each leave one out estimate

alpha

A numeric value for constructing (1 - alpha) * 100% confidence intervals

Value

A list of numeric jackknife summary mean and confidence intervals

chkInst_PACK

Description

Check package is installed

Usage

chkInst_PACK(PACK)

Arguments

PACK

A character string for a package name

Value

Boolean for TRUE if package installed and FALSE if package is not installed or located

chk_threads

Description

chk_threads

Usage

chk_threads(NN, ncores)

Arguments

NN

A positive integer for total iterations to loop over

ncores

A positive integer for number of threads

Value

An integer for number of threads.

collapse_var

Description

Collapse a subset of values within a vector into a new value

Usage

collapse_var(ORIG_VAR, ORIG_VALUES, NEW_VALUE)

Arguments

ORIG_VAR

The input vector

ORIG_VALUES

A subset of values from the input vector to be collapsed

NEW_VALUE

The new value to replace ORIG_VALUES in ORIG_VAR

Value

A character or numeric vector

logSumExp

Description

Calculates the log(sum(exp(x))) in Rcpp

Usage

logSumExp(x)

Arguments

x

A numeric vector

Value

A numeric vector

make_dummy

Description

Construct a dummy-coded matrix for a single variable

Usage

make_dummy(x)

Arguments

x

A numeric or character vector to convert to a dummy matrix

Value

A binary indicator matrix of ones and zeros

make_menu

Description

Constructs an interactive menu for the user

Usage

make_menu(PROMPT, OPTS, INDENT = "   ")

Arguments

PROMPT

A character string prompt to the user

OPTS

A character vector where elements contain a number, then a closing parentheses, then the option value

INDENT

A character string for the amount of indentation from the left margin

Value

Character string of user's response

name_change

Description

Substitute a column name of a matrix or data.frame with a new name

Usage

name_change(DATA, ORIG_NAME, NEW_NAME)

Arguments

DATA

A matrix or data.frame

ORIG_NAME

A single character column name to alter

NEW_NAME

A single character to replace ORIG_NAME

Value

An updated data.frame with renamed fields

Description

print_latex_table

Usage

print_latex_table(
  DATA,
  repeat_VARS = NULL,
  my_align = NULL,
  add_table = FALSE,
  fontsize = NULL,
  caption = NULL,
  label = NULL,
  midrule1 = NULL,
  latex_comment = NULL,
  ...
)

Arguments

DATA

A matrix or data.frame to present as a latex table

repeat_VARS

A string vector of colnames to avoid repeating values within a column

my_align

A string containing letters "l", "r", or "c" for left, right, and center alignment

add_table

Boolean set to TRUE to enclose tabular environment with table environment

fontsize

Defaults to NULL to not specify a fontsize. Otherwise, possible values are "tiny", "footnotesize", "small", "normalsize", "large", "Large", "LARGE", "huge","Huge"

caption

A string to include a table caption

label

A string to represent a latex table label

midrule1

Default is set to NULL

latex_comment

Add a latex comment above the table for notes

...

arguments passed to cat

Value

No return value

smart_RT

Description

Calls read.table() but sets argument stringsAsFactors = FALSE to prevent treating character columns as factors.

Usage

smart_RT(...)

Arguments

...

arguments passed to read.table

Value

Return is identical to read.table()

smart_SN

Description

Convert numeric values into scientific notation

Usage

smart_SN(x, digits = 2)

Arguments

x

A numeric vector to convert to scientific notation

digits

A positive integer for number of digits to include in notation

Value

A character vector

smart_WF

Description

Calls write.table() setting parameters row.names and quote to FALSE.

Usage

smart_WT(...)

Arguments

...

arguments passed to write.table

Value

Return is identical to write.table()

smart_boxplot

Description

smart_boxplot

Usage

smart_boxplot(MAT, mar_down = 8, srt = 45, ...)

Arguments

MAT

A numeric matrix of columns to plot as boxplots

mar_down

A positive numeric value to allow space below the x-axis for labels

srt

A numeric value to control the angle of x-axis labels

...

arguments passed to boxplot

Value

No return value.

smart_colors

Description

smart_colors

Usage

smart_colors(nn, alpha = 1, overwrite = FALSE)

Arguments

nn

A positive integer greater than or equal to 2

alpha

A positive numeric value less than or equal to one

overwrite

Boolean If nn = 2, setting to FALSE will force colors to be white or black

Value

No return value.

smart_compMATs

Description

smart_compMATs

Usage

smart_compMATs(
  MAT1,
  MAT2 = NULL,
  which_range = NULL,
  xlab,
  ylab,
  show_corr = TRUE,
  show_plot = FALSE,
  main = NULL,
  vec_col = NULL,
  ...
)

Arguments

MAT1

A numeric matrix

MAT2

A second numeric matrix of columns comparable to MAT1. Default is set to NULL resulting in histograms plotted for columns of MAT1

which_range

Default is set to NULL to calculate data ranges. Otherwise if set to "01", will enforce minimum 0 and maximum 1. If set to a numeric vector of two elements, will enforce the range.

xlab

A string for x-axis label

ylab

A string for y-axis label

show_corr

Boolean set to TRUE to print Pearson and Spearman correlations

show_plot

Boolean set to TRUE to plot comparison of two matrices

main

A string for the plot title

vec_col

A vector of colors to color scatter plot points

...

arguments passed to plot

Value

No return value.

smart_df

Description

Construct data.frame with data.frame() but sets stringsAsFactors to FALSE.

Usage

smart_df(...)

Arguments

...

arguments passed to data.frame

Value

A data.frame

smart_digits

Description

Round numeric values to specific

Usage

smart_digits(x, digits = 2)

Arguments

x

A numeric vector formatted to have consistently rounded values

digits

A positive integer to regulate the number of digits to round to

Value

Character version of rounded numeric value

smart_dots

Description

Prints a series of dots every few seconds

Usage

smart_dots(wait = 300, num_dots = 30)

Arguments

wait

A number of seconds to wait before printing "."

num_dots

The number of dots to print before printing a message

Value

No return value.

smart_heatmap

Description

smart_heatmap

Usage

smart_heatmap(
  MAT = NULL,
  DIST = FALSE,
  main = "",
  width = NULL,
  height = NULL,
  GRID = NULL,
  clustRC = c(TRUE, TRUE),
  nodePar_col = NULL,
  nodePar_row = NULL,
  mar = 2,
  cex.main = 2,
  rowData = NULL,
  colData = NULL,
  make_key = TRUE,
  vec_cols = NULL
)

Arguments

MAT

A numeric matrix of values

DIST

Boolean set to TRUE to treat MAT as distance matrix. Otherwise, function can perform row/column clustering

main

A string for the overall heatmap title

width

NULL

height

NULL

GRID

NULL

clustRC

NULL

nodePar_col

NULL

nodePar_row

NULL

mar

NULL

cex.main

NULL

rowData

NULL

colData

NULL

make_key

NULL

vec_cols

NULL

Value

No return value.

smart_hist

Description

smart_hist

Usage

smart_hist(x, freq = FALSE, dens = TRUE, main = "", ...)

Arguments

x

A numeric vector

freq

Boolean set to FALSE to plot density on y-axis. Otherwise TRUE to plot frequencies

dens

Boolean set to TRUE to overlay kernel density

main

String for plot title

...

arguments passed to hist

Value

No return value.

smart_merge

Description

Merges two data.frames assuming they have at least one shared column name

Usage

smart_merge(x, y, mess = FALSE, ...)

Arguments

x

A data.frame

y

A data.frame

mess

Default to FALSE. Otherwise a message is printed.

...

arguments passed to merge

Value

A merged data.frame

Examples


aa = smart_df(a = c(1,2,3),b = c("a","b","c"),c = c(4,5,6))
bb = smart_df(a = c(2,4,5),b = c("b","d","e"),d = c("alpha","beta","gamma"))
smart_merge(aa,bb,all.x = TRUE)
smart_merge(aa,bb,all.y = TRUE)
smart_merge(aa,bb,all = TRUE)

smart_mkdir

Description

Create directory if it does not exist

Usage

smart_mkdir(input_dir)

Arguments

input_dir

A full path name for a directory to create

Value

No return value

smart_names

Description

Sets row/column names to matrix or data.frame

Usage

smart_names(MAT, ROW = NULL, COL = NULL)

Arguments

MAT

A matrix

ROW

A vector of length equal to nrow(MAT)

COL

A vector of length equal to ncol(MAT)

Value

Outputs a matrix or data.frame depending on input object class

smart_pack_versions

Description

Return all associated package versions

Usage

smart_pack_versions(pack, repo = "CRAN")

Arguments

pack

A string for the package name

repo

A string that takes values "CRAN", "aCRAN", and "cCRAN" for combining options "aCRAN" and "cCRAN". "cCRAN" refers to contributed packages. "aCRAN" refers to archived packages.

Value

A data.frame of available R packages

smart_progress

Description

Print progress of a for loop

Usage

smart_progress(ii, nn, string = ".", iter = 5, iter2 = 200, ...)

Arguments

ii

A positive integer to track a loop's progress

nn

A positive integer for the total number of loop iterations

string

A string to print

iter

A positive integer for how many multiple iterations to print "."

iter2

A positive integer to end a line of printed "." and track the loop's progress

...

arguments passed to cat

Value

No return value.

smart_reqNames

Description

Checks if required column names are contained in the matrix or data.frame.

Usage

smart_reqNames(DATA, REQ)

Arguments

DATA

A matrix or data.frame

REQ

A string vector of colnames required to be contained in DATA

Value

No return value.

smart_rmcols

Description

Drops columns from a matrix or data.frame.

Usage

smart_rmcols(OBJ, rm_names)

Arguments

OBJ

A matrix or data.frame

rm_names

A string vector of colnames to remove

Value

A matrix or data.frame

smart_solve

Description

smart_solve

Usage

smart_solve(mm)

Arguments

mm

A square numeric matrix

Value

A square numeric matrix.

smart_table

Description

Should elements passed into table() contain NA or NaN, we want to see them by default.

Usage

smart_table(...)

Arguments

...

arguments passed to table

Value

Return a table

Examples


aa = c(1,1,2,2,2,3,NA)
table(aa)
smart_table(aa)