Package 'smarter'

Title: A Collection of Modified R Functions to Make Basic Coding More Convenient
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.
Authors: Paul Little [aut, cre]
Maintainer: Paul Little <[email protected]>
License: GPL (>= 3)
Version: 1.0.0
Built: 2025-01-29 21:07:21 UTC
Source: CRAN

Help Index

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

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.

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

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

print_latex_table

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_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_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_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)

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()