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Title:

K's "Don't Repeat Yourself"-Collection

Version:

0.0.2

Description:

A collection of personal helper functions to avoid redundancy in the spirit of the "Don't repeat yourself" principle of software development (https://en.wikipedia.org/wiki/Don%27t_repeat_yourself).

License:

GPL (≥ 3)

URL:

https://github.com/kapsner/kdry

BugReports:

https://github.com/kapsner/kdry/issues

Depends:

R (≥ 2.10)

Imports:

data.table, doParallel, foreach, Hmisc, magrittr, parallel, stats, utils

Suggests:

ggplot2, lintr, survival, testthat (≥ 3.0.1)

Config/testthat/edition:

Config/testthat/parallel:

false

Date/Publication:

2024-03-08 13:30:02 UTC

Encoding:

UTF-8

RoxygenNote:

7.3.1

NeedsCompilation:

Packaged:

2024-03-08 12:38:22 UTC; user

Author:

Lorenz A. Kapsner

[cre, aut, cph]

Maintainer:

Lorenz A. Kapsner <lorenz.kapsner@gmail.com>

Repository:

CRAN

dtr_matrix2df

Description

Data transformation: Converts a matrix to data.table and encodes categorical variables as factor.

Usage

dtr_matrix2df(matrix, cat_vars = NULL)

Arguments

matrix

An R matrix object.

cat_vars

A character vector with colnames that should be converted to factor (default: NULL).

Value

A data.table is returned.

Examples

data("iris")
mat <- data.matrix(iris)
dataset <- dtr_matrix2df(mat)
str(dataset)

dataset <- dtr_matrix2df(mat, cat_vars = "Species")
str(dataset)

icolnames

Description

Return colnames in a table with index numbers.

Usage

icolnames(df)

Arguments

df

A data.frame object.

Value

A data.table with the two columns index and name is returned.

Examples

data("iris")
icolnames(iris)

list.append

Description

Helper function to append an R list.

Usage

list.append(main_list, append_list, ...)

Arguments

main_list

A list, to which another should be appended.

append_list

A list to append to main_list (can be NULL or empty).

...

Further arguments passed to utils::modifyList().

Details

This function is a save wrapper around utils::modifyLists to combine lists as it checks for the input types and only appends the new list if its length is greater than 0.

Value

A list is returned.

Examples

l1 <- list("a" = 1, "b" = 2)
l2 <- list("c" = 3, "d" = 4)
list.append(l1, l2)

list.update

Description

Helper function to update items in an R list.

Usage

list.update(main_list, new_list, ...)

Arguments

main_list

A list, which items should be updated.

new_list

A list with new values of items from main_list that should be updated. All names of new_list must be present in main_list.

...

Further arguments passed to utils::modifyList().

Details

This function is a save wrapper around utils::modifyLists to update items in R lists as it checks for the input types and only accepts named lists.

Value

A list is returned.

Examples

l1 <- list("a" = 1, "b" = 2)
l2 <- list("a" = 3, "b" = 4)
list.update(l1, l2)

misc_argument_catcher

Description

Miscellaneous helper function to type-save catch arguments passed with R's ellipsis ("...").

Usage

misc_argument_catcher(...)

Arguments

...

Named arguments passed to a function.

Details

This function aims at catching arguments that have been passed to an R function using R's ellipsis ("..."). Its purpos is to catch these arguments even in the case, if a list with arguments was provided to the ellipsis.

Value

A list is returned.

Examples

misc_argument_catcher(a = 1)
misc_argument_catcher(a = 1, b = 2, c = 3, d = "car")
misc_argument_catcher(list(a = 1, b = 2, c = 3, d = "car"))
misc_argument_catcher(list(a = 1, b = 2, c = 3, d = "car"), f = 9)

misc_duplicated_by_names

Description

Miscellaneous helper function to detect items in an object with duplicated names, e.g. in named vectors or named lists.

Usage

misc_duplicated_by_names(object, ...)

Arguments

object

An R object that has names.

...

Named arguments passed on to duplicated.

Value

Returns a logical vector of length(object) with TRUE indicating the identified items with duplicated names.

Examples

misc_duplicated_by_names(list(a = 1, a = 1))

misc_recursive_copy

Description

Recursively copying directories and subdirectories.

Usage

misc_recursive_copy(source_dir, target_dir, force = FALSE)

Arguments

source_dir

A character string. The path to the directory to be copied.

target_dir

A character string. The target path.

force

A boolean. If FALSE (the default) a dialog is prompted to ask the user if the directories should be copied recursively. If TRUE, the dialog is not prompted and the source_dir is copied directly to target_dir.

Value

This function has no return value.

Examples

if (interactive()) {
  d1 <- file.path(tempdir(), "folder1")
  d2 <- file.path(d1, "folder2")
  d3 <- file.path(tempdir(), "new_folder")
  f1 <- file.path(d1, "file.one")
  dir.create(d2, recursive = TRUE)
  file.create(f1)
  misc_recursive_copy(d1, d3)
}

misc_subset_options

Description

Miscellaneous helper function to subset R options by a keyword.

Usage

misc_subset_options(keyword)

Arguments

keyword

A character. The keyword to subset the R options.

Details

This function subsets R's options() by a keyword. It returns a list of all available options that match with the keyword. The keyword is evaluated as a regular expression.

Value

A list is returned, containing the subset of R's options() that matches with the keyword.

Examples

misc_subset_options("default")

mlh_outsample_row_indices

Description

Machine learning helper function to convert a vector of (in- sample) row indices of a fold into out-of-sample row indices.

Usage

mlh_outsample_row_indices(fold_list, dataset_nrows, type = NULL)

Arguments

fold_list

A list of integer vectors that describe the row indices of cross-validation folds. The list must be named.

dataset_nrows

An integer. The number of rows in the dataset dataset. This parameter is required in order to compute the out-of-sample row indices.

type

A character. To be used if the out-of-sample row indices need to be formatted in a special manner (default: NULL). Currently, the only allowed value is type = "glmnet" in order to format the row indices as required by glmnet::cv.glmnet's argument foldid.

Value

If type = NULL, returns a list of same length as fold_list with each item containing a vector of out-of-sample row indices. If type = "glmnet", a data.table is returned with two columns and each row representing one observation of the dataset that is assigned to a specific test fold. The column "fold_id" should be passed further on to the argument foldid of glmnet::cv.glmnet.

Examples

fold_list <- list(
  "Fold1" = setdiff(seq_len(100), 1:33),
  "Fold2" = setdiff(seq_len(100),66:100),
  "Fold3" = setdiff(seq_len(100),34:65)
)
mlh_outsample_row_indices(fold_list, 100)
mlh_outsample_row_indices(fold_list, 100, "glmnet")

mlh_reshape

Description

Machine learning helper function to reshape a matrix of predicted probabilities to classes.

Usage

mlh_reshape(object)

Arguments

object

A matrix with predicted probabilities for several classes. Each row must sum up to 1.

Value

Returns a vector of type factor of the same length as rows in object, representing the class with the highest probability for each observation in object.

Examples

set.seed(123)
class_0 <- rbeta(100, 2, 4)
class_1 <- (1 - class_0) * 0.4
class_2 <- (1 - class_0) * 0.6
dataset <- cbind("0" = class_0, "1" = class_1, "2" = class_2)
mlh_reshape(dataset)

mlh_subset

Description

Machine learning helper function to select a subset from a data matrix or a response vector.

Usage

mlh_subset(object, ids)

Arguments

object

A vector or a data matrix. Supports also subsetting of "Surv" objects.

ids

An integer vector specifying the indices that should be selected from the object.

Value

Returns the specified subset of the object.

Examples

data("iris")
mlh_subset(iris, c(1:30))
mlh_subset(iris[, 5], c(1:30))

pch_check_available_cores

Description

Parallel computing helper function to check for the available cores.

Usage

pch_check_available_cores(ncores = -1L)

Arguments

ncores

An integer. A number of cores requested for parallel computing (default: -1L).

Value

The function returns an integer that indicates the number of cores available. If ncores <= parallel::detectCores() the function returns ncores. If ncores > parallel::detectCores(), the function returns parallel::detectCores() - 1L.

Examples

pch_check_available_cores(2)

pch_clean_up

Description

Parallel computing helper function to clean up the parallel backend.

Usage

pch_clean_up(cl)

Arguments

cl

A cluster object of class c("SOCKcluster", "cluster").

Value

The function returns nothing. Internally, it calls parallel::stopCluster() and foreach::registerDoSEQ().

Examples

if (require("doParallel") && require("foreach")) {
  cl <- pch_register_parallel(pch_check_available_cores(2))
  pch_clean_up(cl)
}

pch_register_parallel

Description

Parallel computing helper function to register a parallel backend.

Usage

pch_register_parallel(ncores)

Arguments

ncores

An integer. A number of cores requested for parallel computing (default: -1L).

Value

The function returns a object of class c("SOCKcluster", "cluster"), created with parallel::makePSOCKcluster().

Examples

if (require("doParallel") && require("foreach")) {
  cl <- pch_register_parallel(pch_check_available_cores(2))
  pch_clean_up(cl)
}

plt_parallel_coordinates

Description

Parallel coordinates plot

Usage

plt_parallel_coordinates(
  data,
  cols = NULL,
  color_variable = NULL,
  color_args = list(alpha = 0.6, begin = 0.1, end = 0.9, option = "inferno", direction =
    1),
  line_jitter = list(w = 0.04, h = 0.04),
  text_label_size = 3.5
)

Arguments

data

A data.table object with the columns containing the parameters to be plotted with the parallel coordinates plot.

cols

A character vector with column names to subset data (default: NULL).

color_variable

A character. The name of the column to be used to colorize the lines of the plot (default: NULL).

color_args

A list with parameters for the color gradient (see details).

line_jitter

A list with the elements w and h to define a line jitter (default: list(w = 0.04, h = 0.04)), which are passed further on to define the position of ggplot2::geom_line().

text_label_size

A numeric value to define the size of the text annotations (default: 3.5).

Details

The color gradient of the plotted lines can be defined with a list provided to the argument color_args. Its default values are alpha = 0.6, begin = .1, end = .9, option = "inferno", and direction = 1 and are passed furhter on to ggplot2::scale_color_viridis_c(). The implementation to display categorical variables is still experimental.

Value

Returns a parallel coordinates plot as ggplot2 object.

Examples

if (require("ggplot2")) {
  data("iris")
  plt_parallel_coordinates(
    data = data.table::as.data.table(iris[, -5]),
    cols = colnames(iris)[c(-1, -5)],
    color_variable = "Sepal.Length"
  )
}

rep_frac_pct

Description

Reporting helper function: computes and formats the relative percentage of a fraction.

Usage

rep_frac_pct(
  count,
  count_reference,
  digits = 2,
  na.rm = TRUE,
  brackets = c("round", "square"),
  suffix = TRUE
)

Arguments

count

A numeric. The numerator.

count_reference

A numeric. The denominator.

digits

An integer indicating the number of decimal places.

na.rm

A logical indicating if missings should be removed from x before computing the distributional parameters (default: TRUE).

brackets

A character. Either "round" (default) or "square" to indicate the type of brackets to surround the relative count.

suffix

A character which is placed between the lower and the upper confidence bound in the formatted output.

Value

A character with the formatted output.

Examples

rep_frac_pct(count = 40, count_reference = 200)
rep_frac_pct(count = 40, count_reference = 200, brackets = "square")
rep_frac_pct(40, 200, brackets = "square", suffix = FALSE)

rep_mean_sd

Description

Reporting helper function: computes and formats mean and standard deviation from a numeric vector.

Usage

rep_mean_sd(
  x,
  digits = 2,
  na.rm = TRUE,
  sd_brackets = c("round", "square"),
  sd_prefix = TRUE,
  weighted = FALSE,
  weights = NA
)

Arguments

x

A numeric vector.

digits

An integer indicating the number of decimal places.

na.rm

A logical indicating if missings should be removed from x before computing the distributional parameters (default: TRUE).

sd_brackets

A character. Either "round" (default) or "square" to indicate the type of brackets to surround the standard deviation in the formatted output.

sd_prefix

A logical. If TRUE (default), the standard deviation is prefixed with a plus-minus-sign ("±").

weighted

A logical. If TRUE, a weighted mean and standard deviation are calculated (default: FALSE).

weights

A vector with the weights (if weighted = TRUE; default: NA) passed futher on to stats::weighted.mean() and Hmisc::wtd.var().

Value

A character with the formatted output.

Examples

set.seed(123)
x <- rnorm(1000)
rep_mean_sd(x)
rep_mean_sd(rep(1, 10))
rep_mean_sd(x, sd_brackets = "square")
rep_mean_sd(x, sd_brackets = "square", sd_prefix = FALSE)

rep_median_ci

Description

Reporting helper function: computes and formats median and confidence interval from a numeric vector.

Usage

rep_median_ci(
  x,
  conf_int,
  digits = 2,
  na.rm = TRUE,
  collapse = "to",
  iqr_brackets = c("round", "square"),
  iqr_prefix = TRUE,
  weighted = FALSE,
  weights = NA
)

Arguments

x

A numeric vector.

conf_int

A numeric between 0 and 100 to indicate the confidence interval that should be computed.

digits

An integer indicating the number of decimal places.

na.rm

A logical indicating if missings should be removed from x before computing the distributional parameters (default: TRUE).

collapse

A character which is placed between the lower and the upper confidence bound in the formatted output.

iqr_brackets

A character. Either "round" (default) or "square" to indicate the type of brackets to surround the confidence interval in the formatted output.

iqr_prefix

A logical. If TRUE (default), the confidence interval is prefixed with "IQR: ".

weighted

A logical. If TRUE, a weighted median and confidence interval are calculated (default: FALSE).

weights

A numeric vector of weights passed further on to Hmisc::wtd.quantile() if weighted = TRUE (default: NA).

Value

A character with the formatted output.

Examples

set.seed(123)
x <- rnorm(1000)
rep_median_ci(x, conf_int = 95)
rep_median_ci(rep(1, 10), conf_int = 95)
rep_median_ci(x, conf_int = 95, collapse = "-")
rep_median_ci(x, iqr_brackets = "square", conf_int = 50)

rep_median_iqr

Description

Reporting helper function: computes and formats median and interquartile range from a numeric vector.

Usage

rep_median_iqr(
  x,
  digits = 2,
  na.rm = TRUE,
  collapse = "to",
  iqr_brackets = c("round", "square"),
  iqr_prefix = TRUE
)

Arguments

x

A numeric vector.

digits

An integer indicating the number of decimal places.

na.rm

A logical indicating if missings should be removed from x before computing the distributional parameters (default: TRUE).

collapse

A character which is placed between the lower and the upper confidence bound in the formatted output.

iqr_brackets

A character. Either "round" (default) or "square" to indicate the type of brackets to surround the confidence interval in the formatted output.

iqr_prefix

A logical. If TRUE (default), the confidence interval is prefixed with "IQR: ".

Details

This is just a special case of rep_median_ci() with the parameter conf_int set to 50.

Value

A character with the formatted output.

Examples

set.seed(123)
x <- rnorm(1000)
rep_median_iqr(x)
rep_median_iqr(rep(1, 10))
rep_median_iqr(x, collapse = "-")
rep_median_iqr(x, iqr_brackets = "square")
rep_median_iqr(x, iqr_brackets = "square", iqr_prefix = FALSE)
rep_median_iqr(x, collapse = ";", iqr_prefix = FALSE)

rep_pval

Description

Reporting helper function: formats p-value.

Usage

rep_pval(p, threshold = 0.001, digits = 3L)

Arguments

p

The p-value that should be formatted.

threshold

A threshold to indicate that only "< threshold" is printed as output (default: 0.001).

digits

The number of digits of the formatted p-value (digits).

Details

If the p-value is lower than the threshold, the output of the function is "< threshold". Otherwise, the p-value is formatted to the number of digits.

Value

A character with the formatted p-value.

Examples

rep_pval(0.032)
rep_pval(0.00032)

rep_sum_pct

Description

Reporting helper function: computes and formats the relative percentage of a count.

Usage

rep_sum_pct(
  count,
  count_reference,
  digits = 2,
  na.rm = TRUE,
  brackets = c("round", "square"),
  suffix = TRUE
)

Arguments

count

A numeric. The numerator.

count_reference

A numeric. The denominator.

digits

An integer indicating the number of decimal places.

na.rm

A logical indicating if missings should be removed from x before computing the distributional parameters (default: TRUE).

brackets

A character. Either "round" (default) or "square" to indicate the type of brackets to surround the relative count.

suffix

A character which is placed between the lower and the upper confidence bound in the formatted output.

Value

A character with the formatted output.

Examples

rep_sum_pct(count = 40, count_reference = 200)
rep_sum_pct(count = 40, count_reference = 200, brackets = "square")
rep_sum_pct(40, 200, brackets = "square", suffix = FALSE)

sts_normalize

Description

Statistic helper function to normalize a continuous variable between zero and one.

Usage

sts_normalize(x, na.rm = FALSE)

Arguments

x

A vector of type numeric.

na.rm

A logical to indicate, if missings should be removed.

Value

Returns a vector of same length as x with values normalized between zero and one. If x contains missings and na.rm = TRUE, the missings are removed before normalization; otherwise, a vector of NA is returend.

Examples

sts_normalize(1:100)

dtr_matrix2df

Description

Usage

Arguments

Value

Examples

icolnames

Description

Usage

Arguments

Value

Examples

list.append

Description

Usage

Arguments

Details

Value

See Also

Examples

list.update

Description

Usage

Arguments

Details

Value

See Also

Examples

misc_argument_catcher

Description

Usage

Arguments

Details

Value

Examples

misc_duplicated_by_names

Description

Usage

Arguments

Value

See Also

Examples

misc_recursive_copy

Description

Usage

Arguments

Value

Examples

misc_subset_options

Description

Usage

Arguments

Details

Value

Examples

mlh_outsample_row_indices

Description

Usage

Arguments

Value

Examples

mlh_reshape

Description

Usage

Arguments

Value

Examples

mlh_subset

Description

Usage

Arguments

Value

Examples

pch_check_available_cores

Description

Usage

Arguments

Value

Examples

pch_clean_up