Package 'oeli'

Description

These functions check whether the input fulfills the properties of a correlation matrix.

Usage

check_correlation_matrix(x, dim = NULL, tolerance = sqrt(.Machine$double.eps))

assert_correlation_matrix(
  x,
  dim = NULL,
  tolerance = sqrt(.Machine$double.eps),
  .var.name = checkmate::vname(x),
  add = NULL
)

test_correlation_matrix(x, dim = NULL, tolerance = sqrt(.Machine$double.eps))

Arguments

Value

Same as documented in check_matrix.

See Also

Other matrix helpers: check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

M <- matrix(c(1,  0.9,  0.9, 0.9,  1,  -0.9, 0.9,  -0.9,  1), nrow = 3)
check_correlation_matrix(M)
test_correlation_matrix(M)
## Not run: 
assert_correlation_matrix(M)

## End(Not run)

Description

These functions check whether the input fulfills the properties of a covariance matrix.

Usage

check_covariance_matrix(x, dim = NULL, tolerance = sqrt(.Machine$double.eps))

assert_covariance_matrix(
  x,
  dim = NULL,
  tolerance = sqrt(.Machine$double.eps),
  .var.name = checkmate::vname(x),
  add = NULL
)

test_covariance_matrix(x, dim = NULL, tolerance = sqrt(.Machine$double.eps))

Arguments

Value

Same as documented in check_matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

M <- matrix(c(1, 2, 3, 2, 1, 2, 3, 2, 1), nrow = 3)
check_covariance_matrix(M)
test_covariance_matrix(M)
## Not run: 
assert_covariance_matrix(M)

## End(Not run)

Description

These functions check whether the input is a list that contains list elements.

Usage

check_list_of_lists(x, len = NULL)

assert_list_of_lists(
  x,
  len = NULL,
  .var.name = checkmate::vname(x),
  add = NULL
)

test_list_of_lists(x, len = NULL)

Arguments

Value

Same as documented in check_list.

See Also

Other list helpers: merge_lists()

Examples

L <- list(list(1), list(2), 3)
check_list_of_lists(L)
test_list_of_lists(L)
## Not run: 
assert_list_of_lists(L)

## End(Not run)

Description

These functions check whether the input is a numeric vector.

Usage

check_numeric_vector(
  x,
  lower = -Inf,
  upper = Inf,
  finite = FALSE,
  any.missing = TRUE,
  all.missing = TRUE,
  len = NULL,
  min.len = NULL,
  max.len = NULL,
  unique = FALSE,
  sorted = FALSE,
  names = NULL,
  typed.missing = FALSE,
  null.ok = FALSE
)

assert_numeric_vector(
  x,
  lower = -Inf,
  upper = Inf,
  finite = FALSE,
  any.missing = TRUE,
  all.missing = TRUE,
  len = NULL,
  min.len = NULL,
  max.len = NULL,
  unique = FALSE,
  sorted = FALSE,
  names = NULL,
  typed.missing = FALSE,
  null.ok = FALSE,
  .var.name = checkmate::vname(x),
  add = NULL
)

test_numeric_vector(
  x,
  lower = -Inf,
  upper = Inf,
  finite = FALSE,
  any.missing = TRUE,
  all.missing = TRUE,
  len = NULL,
  min.len = NULL,
  max.len = NULL,
  unique = FALSE,
  sorted = FALSE,
  names = NULL,
  typed.missing = FALSE,
  null.ok = FALSE
)

Arguments

Value

Same as documented in check_numeric.

See Also

Other vector helpers: check_probability_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), permutations(), split_vector_at(), subsets(), vector_occurrence()

Examples

x <- c(1, 2, "3")
check_numeric_vector(x)
test_numeric_vector(x)
## Not run: 
assert_numeric_vector(x)

## End(Not run)

Description

These functions check whether the input fulfills the properties of a probability matrix.

Usage

check_probability_vector(x, len = NULL, tolerance = sqrt(.Machine$double.eps))

assert_probability_vector(
  x,
  len = NULL,
  tolerance = sqrt(.Machine$double.eps),
  .var.name = checkmate::vname(x),
  add = NULL
)

test_probability_vector(x, len = NULL, tolerance = sqrt(.Machine$double.eps))

Arguments

Value

Same as documented in check_numeric.

See Also

Other vector helpers: check_numeric_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), permutations(), split_vector_at(), subsets(), vector_occurrence()

Examples

p <- c(0.2, 0.3, 0.6)
check_probability_vector(p)
test_probability_vector(p)
## Not run: 
assert_probability_vector(p)

## End(Not run)

Description

These functions check whether the input is a transition probability matrix.

Usage

check_transition_probability_matrix(
  x,
  dim = NULL,
  tolerance = sqrt(.Machine$double.eps)
)

assert_transition_probability_matrix(
  x,
  dim = NULL,
  tolerance = sqrt(.Machine$double.eps),
  .var.name = checkmate::vname(x),
  add = NULL
)

test_transition_probability_matrix(
  x,
  dim = NULL,
  tolerance = sqrt(.Machine$double.eps)
)

Arguments

Value

Same as documented in check_matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

T <- matrix(c(0.8,  0.2,  0.1, 0.1,  0.7,  0.4, 0.1,  0.1,  0.6), nrow = 3)
check_transition_probability_matrix(T)
test_transition_probability_matrix(T)
## Not run: 
assert_transition_probability_matrix(T)

## End(Not run)

Description

This function either

• splits a vector into n chunks of equal size (type = 1),

• splits a vector into chunks of size n (type = 2).

Usage

chunk_vector(x, n, type = 1, strict = FALSE)

Arguments

Value

A list.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), insert_vector_entry(), match_numerics(), permutations(), split_vector_at(), subsets(), vector_occurrence()

Examples

x <- 1:12
chunk_vector(x, n = 3, type = 1)
chunk_vector(x, n = 3, type = 2)
try(chunk_vector(x, n = 5, strict = TRUE))

Description

This function simulates regressor values from various marginal distributions with custom correlations.

Usage

correlated_regressors(
  labels,
  n = 100,
  marginals = list(),
  correlation = diag(length(labels)),
  verbose = FALSE
)

Arguments

Value

A data.frame with n rows and length(labels) columns.

References

This function heavily depends on the {SimMultiCorrData} package.

See Also

Other simulation helpers: ddirichlet_cpp(), dmvnorm_cpp(), dtnorm_cpp(), dwishart_cpp(), simulate_markov_chain()

Examples

labels <- c("P", "C", "N1", "N2", "U")
n <- 100
marginals <- list(
  "P" = list(type = "poisson", lambda = 2),
  "C" = list(type = "categorical", p = c(0.3, 0.2, 0.5)),
  "N1" = list(type = "normal", mean = -1, sd = 2),
  "U" = list(type = "uniform", min = -2, max = -1)
)
correlation <- matrix(
  c(1, -0.3, -0.1, 0, 0.5,
    -0.3, 1, 0.3, -0.5, -0.7,
    -0.1, 0.3, 1, -0.3, -0.3,
    0, -0.5, -0.3, 1, 0.1,
    0.5, -0.7, -0.3, 0.1, 1),
  nrow = 5, ncol = 5
)
data <- correlated_regressors(
  labels = labels, n = n, marginals = marginals, correlation = correlation
)
head(data)

Description

These functions compute the Cholesky root elements of a covariance matrix and, conversely, build a covariance matrix from its Cholesky root elements.

Usage

cov_to_chol(cov, unique = TRUE)

chol_to_cov(chol)

unique_chol(chol)

Arguments

Value

For cov_to_chol a numeric vector of Cholesky root elements.

For chol_to_cov a covariance matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

cov <- sample_covariance_matrix(4)
chol <- cov_to_chol(cov)
all.equal(cov, chol_to_cov(chol))

Description

The function ddirichlet() computes the density of a Dirichlet distribution.

The function rdirichlet() samples from a Dirichlet distribution.

The functions with suffix ⁠_cpp⁠ perform no input checks, hence are faster.

Usage

ddirichlet_cpp(x, concentration, log = FALSE)

rdirichlet_cpp(concentration)

ddirichlet(x, concentration, log = FALSE)

rdirichlet(n = 1, concentration)

Arguments

Value

For ddirichlet(): The density value.

For rdirichlet(): If n = 1 a vector of length p, else a matrix of dimension n times p with samples as rows.

See Also

Other simulation helpers: correlated_regressors(), dmvnorm_cpp(), dtnorm_cpp(), dwishart_cpp(), simulate_markov_chain()

Examples

x <- c(0.5, 0.3, 0.2)
concentration <- 1:3

# compute density
ddirichlet(x = x, concentration = concentration)
ddirichlet(x = x, concentration = concentration, log = TRUE)

# sample
rdirichlet(concentration = 1:3)
rdirichlet(n = 4, concentration = 1:2)

Description

This function deletes columns of a data.frame by name.

Usage

delete_columns_data.frame(df, column_names)

Arguments

Value

The input df without the columns defined by column_names.

See Also

Other data.frame helpers: group_data.frame(), round_data.frame()

Examples

df <- data.frame("label" = c("A", "B"), "number" = 1:10)
delete_columns_data.frame(df = df, column_names = "label")
delete_columns_data.frame(df = df, column_names = "number")
delete_columns_data.frame(df = df, column_names = c("label", "number"))

Description

Provides a simple key-value interface based on R6.

Active bindings

Methods

Public methods

• Dictionary$new()

• Dictionary$add()

• Dictionary$get()

• Dictionary$remove()

• Dictionary$print()

Method new()

Initializing a new Dictionary object.

Usage

Dictionary$new(
  key_name,
  alias_name = NULL,
  value_names = character(),
  value_assert = alist(),
  allow_overwrite = TRUE,
  keys_reserved = character(),
  alias_choices = NULL,
  dictionary_name = NULL
)

Arguments

Method add()

Adding an element to the dictionary.

Usage

Dictionary$add(...)

Arguments

Method get()

Getting elements from the dictionary.

Usage

Dictionary$get(key, value = NULL)

Arguments

Method remove()

Removing elements from the dictionary (and associated alias, if any).

Usage

Dictionary$remove(key)

Arguments

Method print()

Printing details of the dictionary.

Usage

Dictionary$print()

See Also

Other package helpers: Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

# TODO

Description

These functions difference and un-difference random vectors and covariance matrices.

Usage

diff_cov(cov, ref = 1)

undiff_cov(cov_diff, ref = 1)

delta(ref = 1, dim)

Arguments

Details

Assume $x \sim N(0, \Sigma)$ is a multivariate normally distributed random vector of dimension $n$. We may want to consider the differenced vector

$\tilde x = (x_1 - x_k, x_2 - x_k, \dots, x_n - x_k)',$

excluding the $k$th element (hence, $\tilde x$ is of dimension $(n - 1) \times 1$). Formally, $\tilde x = \Delta_k x$, where $\Delta_k$ is a difference operator that depends on the reference row $k$. More precise, $\Delta_k$ is the identity matrix of dimension $n$ without row $k$ and with $-1$s in column $k$. The difference operator $\Delta_k$ can be computed via delta(ref = k, dim = n).

Then, $\tilde x \sim N(0, \tilde \Sigma)$, where

$\tilde{\Sigma} = \Delta_k \Sigma \Delta_k'$

is the differenced covariance matrix with respect to row $k = 1,\dots,n$. The differenced covariance matrix $\tilde \Sigma$ can be computed via diff_delta(Sigma, ref = k).

Since $\Delta_k$ is a non-bijective mapping, $\Sigma$ cannot be uniquely restored from $\tilde \Sigma$. However, it is possible to compute a non-unique solution $\Sigma_0$, such that $\Delta_k \Sigma_0 \Delta_k = \tilde \Sigma$. For such a non-unique solution, we add a column and a row of zeros at column and row number $k$ to $\tilde{\Sigma}$, respectively. An "un-differenced" covariance matrix $\Sigma_0$ can be computed via undiff_delta(Sigma_diff, ref = k).

Value

A (differenced or un-differenced) covariance matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

n <- 3
Sigma <- sample_covariance_matrix(dim = n)
k <- 2
x <- c(1, 3, 2)

# build difference operator
delta_k <- delta(ref = k, dim = n)

# difference vector
delta_k %*% x

# difference Sigma
(Sigma_diff <- diff_cov(Sigma, ref = k))

# un-difference Sigma
(Sigma_0 <- undiff_cov(Sigma_diff, ref = k))

# difference again
Sigma_diff_2 <- diff_cov(Sigma_0, ref = k)
all.equal(Sigma_diff, Sigma_diff_2)

Description

The function dmvnorm() computes the density of a multivariate normal distribution.

The function rmvnorm() samples from a multivariate normal distribution.

The functions with suffix ⁠_cpp⁠ perform no input checks, hence are faster.

The univariate normal distribution is available as the special case p = 1.

Usage

dmvnorm_cpp(x, mean, Sigma, log = FALSE)

rmvnorm_cpp(mean, Sigma, log = FALSE)

dmvnorm(x, mean, Sigma, log = FALSE)

rmvnorm(n = 1, mean, Sigma, log = FALSE)

Arguments

Value

For dmvnorm(): The density value.

For rmvnorm(): If n = 1 a vector of length p (note that it is a column vector for rmvnorm_cpp()), else a matrix of dimension n times p with samples as rows.

See Also

Other simulation helpers: correlated_regressors(), ddirichlet_cpp(), dtnorm_cpp(), dwishart_cpp(), simulate_markov_chain()

Examples

x <- c(0, 0)
mean <- c(0, 0)
Sigma <- diag(2)

# compute density
dmvnorm(x = x, mean = mean, Sigma = Sigma)
dmvnorm(x = x, mean = mean, Sigma = Sigma, log = TRUE)

# sample
rmvnorm(n = 3, mean = mean, Sigma = Sigma)
rmvnorm(mean = mean, Sigma = Sigma, log = TRUE)

Description

This function measures the computation time of a call.

Usage

do.call_timed(what, args, units = "secs")

Arguments

Details

This function is a wrapper for do.call.

Value

A list of the two elements "result" (the results of the do.call call) and "time" (the computation time).

See Also

Other function helpers: function_arguments(), function_body(), function_defaults(), quiet(), timed(), try_silent(), variable_name()

Examples

## Not run: 
what <- function(s) {
  Sys.sleep(s)
  return(s)
}
args <- list(s = 1)
do.call_timed(what = what, args = args)

## End(Not run)

Description

The function dtnorm() computes the density of a truncated normal distribution.

The function rtnorm() samples from a truncated normal distribution.

The function dttnorm() and rttnorm() compute the density and sample from a two-sided truncated normal distribution, respectively.

The functions with suffix ⁠_cpp⁠ perform no input checks, hence are faster.

Usage

dtnorm_cpp(x, mean, sd, point, above, log = FALSE)

dttnorm_cpp(x, mean, sd, lower, upper, log = FALSE)

rtnorm_cpp(mean, sd, point, above, log = FALSE)

rttnorm_cpp(mean, sd, lower, upper, log = FALSE)

dtnorm(x, mean, sd, point, above, log = FALSE)

dttnorm(x, mean, sd, lower, upper, log = FALSE)

rtnorm(mean, sd, point, above, log = FALSE)

rttnorm(mean, sd, lower, upper, log = FALSE)

Arguments

Value

For dtnorm() and dttnorm(): The density value.

For rtnorm() and rttnorm(): The random draw

See Also

Other simulation helpers: correlated_regressors(), ddirichlet_cpp(), dmvnorm_cpp(), dwishart_cpp(), simulate_markov_chain()

Examples

x <- c(0, 0)
mean <- c(0, 0)
Sigma <- diag(2)

# compute density
dmvnorm(x = x, mean = mean, Sigma = Sigma)
dmvnorm(x = x, mean = mean, Sigma = Sigma, log = TRUE)

# sample
rmvnorm(n = 3, mean = mean, Sigma = Sigma)
rmvnorm(mean = mean, Sigma = Sigma, log = TRUE)

Description

The function dwishart() computes the density of a Wishart distribution.

The function rwishart() samples from a Wishart distribution.

The functions with suffix ⁠_cpp⁠ perform no input checks, hence are faster.

Usage

dwishart_cpp(x, df, scale, log = FALSE, inv = FALSE)

rwishart_cpp(df, scale, inv = FALSE)

dwishart(x, df, scale, log = FALSE, inv = FALSE)

rwishart(df, scale, inv = FALSE)

Arguments

Value

For dwishart(): The density value.

For rwishart(): A matrix, the random draw.

See Also

Other simulation helpers: correlated_regressors(), ddirichlet_cpp(), dmvnorm_cpp(), dtnorm_cpp(), simulate_markov_chain()

Examples

x <- diag(2)
df <- 4
scale <- diag(2)

# compute density
dwishart(x = x, df = df, scale = scale)
dwishart(x = x, df = df, scale = scale, log = TRUE)
dwishart(x = x, df = df, scale = scale, inv = TRUE)

# sample
rwishart(df = df, scale = scale)
rwishart(df = df, scale = scale, inv = TRUE)

Description

This function returns the names of function arguments.

Usage

function_arguments(f, with_default = TRUE, with_ellipsis = TRUE)

Arguments

Value

A character vector.

See Also

Other function helpers: do.call_timed(), function_body(), function_defaults(), quiet(), timed(), try_silent(), variable_name()

Examples

f <- function(a, b = 1, c = "", ...) { }
function_arguments(f)
function_arguments(f, with_default = FALSE)
function_arguments(f, with_ellipsis = FALSE)

Description

This function extracts the body of a function as a single character.

Usage

function_body(fun, braces = FALSE, nchar = getOption("width") - 4)

Arguments

Value

A character, the body of f.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_defaults(), quiet(), timed(), try_silent(), variable_name()

Examples

fun <- mean.default
function_body(fun)
function_body(fun, braces = TRUE)
function_body(fun, nchar = 30)

Description

This function returns the default function arguments (if any).

Usage

function_defaults(f, exclude = NULL)

Arguments

Value

A named list.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_body(), quiet(), timed(), try_silent(), variable_name()

Examples

f <- function(a, b = 1, c = "", ...) { }
function_defaults(f)
function_defaults(f, exclude = "b")

Description

This function groups a data.frame according to values of one column.

Usage

group_data.frame(df, by, keep_by = TRUE)

Arguments

Value

A list of data.frames, subsets of df.

See Also

Other data.frame helpers: delete_columns_data.frame(), round_data.frame()

Examples

df <- data.frame("label" = c("A", "B"), "number" = 1:10)
group_data.frame(df = df, by = "label")
group_data.frame(df = df, by = "label", keep_by = FALSE)

Description

This function determines whether two objects have the same structure,

• which includes the mode, class and dimension

• but does not include concrete values or attributes.

Usage

identical_structure(x, y)

Arguments

Value

Either TRUE if x and y have the same structure, and FALSE, else.

References

Inspired by https://stackoverflow.com/a/45548885/15157768.

See Also

Other package helpers: Dictionary, Storage, input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

identical_structure(integer(1), 1L)
identical_structure(diag(2), matrix(rnorm(4), 2, 2))
identical_structure(diag(2), data.frame(diag(2)))

Description

This function provides standardized responses to input checks, ensuring consistency.

Usage

input_check_response(
  check,
  var_name = NULL,
  error = TRUE,
  prefix = "Input {.var {var_name}} is bad:"
)

Arguments

Value

TRUE if check is TRUE. If check is not TRUE, depending on error:

• If error is TRUE, throws an error.

• If error is FALSE, returns FALSE.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

x <- "1"
y <- 1

### check is successful
input_check_response(
  check = checkmate::check_character(x),
  var_name = "x",
  error = TRUE
)

### standardized check response
## Not run: 
input_check_response(
  check = checkmate::check_character(y),
  var_name = "y",
  error = TRUE
)

## End(Not run)

Description

This function inserts a column into a matrix.

Usage

insert_matrix_column(A, x, p)

Arguments

Value

A matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

A <- diag(3)
x <- 1:3
insert_matrix_column(A, x, 0)
insert_matrix_column(A, x, 1)
insert_matrix_column(A, x, 2)
insert_matrix_column(A, x, 3)

### also single value
x <- 2
insert_matrix_column(A, x, 0)

### also multiple positions
insert_matrix_column(A, x, 0:3)

### also trivial case
insert_matrix_column(matrix(nrow = 0, ncol = 0), integer(), integer())

Description

This function inserts a value into a vector.

Usage

insert_vector_entry(v, x, p)

Arguments

Value

A vector.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), match_numerics(), permutations(), split_vector_at(), subsets(), vector_occurrence()

Examples

v <- 1:3
x <- 0
insert_vector_entry(v, x, 0)
insert_vector_entry(v, x, 1)
insert_vector_entry(v, x, 2)
insert_vector_entry(v, x, 3)

### also multiple positions
insert_vector_entry(v, x, 0:3)

### also trivial case
insert_vector_entry(integer(), integer(), integer())

Description

This function matches function arguments and is a modified version of match.arg.

Usage

match_arg(arg, choices, several.ok = FALSE, none.ok = FALSE)

Arguments

Value

The un-abbreviated version of the exact or unique partial match if there is one. Otherwise, an error is signaled if several.ok is FALSE or none.ok is FALSE. When several.ok is TRUE and (at least) one element of arg has a match, all un-abbreviated versions of matches are returned. When none.ok is TRUE and arg has zero elements, character(0) is returned.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Description

This function matches the indices of two numeric vectors as good as possible (that means with the smallest possible sum of deviations).

Usage

match_numerics(x, y)

Arguments

Value

An integer vector of length length(x) with the positions of y in x.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), insert_vector_entry(), permutations(), split_vector_at(), subsets(), vector_occurrence()

Examples

x <- c(-1, 0, 1)
y <- c(0.1, 1.5, -1.2)
match_numerics(x, y)

Description

This function returns the indices of the diagonal elements of a quadratic matrix.

Usage

matrix_diagonal_indices(n, triangular = NULL)

Arguments

Value

An integer vector.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

# indices of diagonal elements
n <- 3
matrix(1:n^2, n, n)
matrix_diagonal_indices(n)

# indices of diagonal elements of lower-triangular matrix
L <- matrix(0, n, n)
L[lower.tri(L, diag=TRUE)] <- 1:((n * (n + 1)) / 2)
L
matrix_diagonal_indices(n, triangular = "lower")

# indices of diagonal elements of upper-triangular matrix
U <- matrix(0, n, n)
U[upper.tri(U, diag=TRUE)] <- 1:((n * (n + 1)) / 2)
U
matrix_diagonal_indices(n, triangular = "upper")

Description

This function returns matrix indices as character.

Usage

matrix_indices(x, prefix = "", exclude_diagonal = FALSE)

Arguments

Value

A character vector.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

M <- diag(3)
matrix_indices(M)
matrix_indices(M, "M_")
matrix_indices(M, "M_", TRUE)

Description

This function merges lists based on their element names. Elements are only included in the final output list, if no former list has contributed an element with the same name.

Usage

merge_lists(...)

Arguments

Value

A list.

See Also

Other list helpers: check_list_of_lists()

Examples

merge_lists(list("a" = 1, "b" = 2), list("b" = 3, "c" = 4, "d" = NULL))

Description

This function creates a basic R package logo. The logo has a white background and the package name (with or without curly brackets) in the center. The font size for the package name is scaled such that it fits inside the logo. Type ?oeli to see an example.

Usage

package_logo(package_name, brackets = TRUE, use_logo = FALSE)

Arguments

Details

The function optionally calls use_logo if use_logo = TRUE to set up the logo for a package.

Value

A ggplot object.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

package_logo("my_package", brackets = TRUE, use_logo = FALSE)

Description

This function creates all permutations of a given vector.

Usage

permutations(x)

Arguments

Value

A list of all permutations of x.

References

Modified version of https://stackoverflow.com/a/20199902/15157768.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), split_vector_at(), subsets(), vector_occurrence()

Examples

permutations(1:3)
permutations(LETTERS[1:3])

Description

This function prints a (possibly abbreviated) data.frame.

Usage

print_data.frame(
  x,
  rows = NULL,
  cols = NULL,
  digits = NULL,
  row.names = TRUE,
  col.names = TRUE
)

Arguments

Value

Invisibly returns x.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

x <- data.frame(1:10, LETTERS[1:10], stats::rnorm(10))
print_data.frame(x, rows = 7)
print_data.frame(x, rows = 7, cols = 2)
print_data.frame(x, rows = 7, cols = 2, digits = 1)
print_data.frame(x, rows = 7, cols = 2, digits = 1, row.names = FALSE)
print_data.frame(x, rows = 7, cols = 2, digits = 1, col.names = FALSE)

Description

This function prints a (possibly abbreviated) matrix.

Usage

print_matrix(
  x,
  rowdots = 4,
  coldots = 4,
  digits = 2,
  label = NULL,
  simplify = FALSE,
  details = !simplify
)

Arguments

Value

Invisibly returns x.

References

This function is a modified version of ramify::pprint().

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

print_matrix(x = 1, label = "single numeric")
print_matrix(x = LETTERS[1:26], label = "letters")
print_matrix(x = 1:3, coldots = 2)
print_matrix(x = matrix(rnorm(99), ncol = 1), label = "single column matrix")
print_matrix(x = matrix(1:100, nrow = 1), label = "single row matrix")
print_matrix(x = matrix(LETTERS[1:24], ncol = 6), label = "big matrix")
print_matrix(x = diag(5), coldots = 2, rowdots = 2, simplify = TRUE)

Description

This function silences warnings, messages and any cat() or print() output from R expressions or functions.

Usage

quiet(x, print_cat = TRUE, message = TRUE, warning = TRUE)

Arguments

Value

Invisibly the expression x.

References

This function is a modified version of quiet.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_body(), function_defaults(), timed(), try_silent(), variable_name()

Examples

f <- function() {
  warning("warning")
  message("message")
  cat("cat")
  print("print")
}
quiet(f())

Description

This function creates a file that loads development packages so that {renv} can detect and write them to the lockfile.

Usage

renv_development_packages(
  packages = c("covr", "devtools", "DT", "markdown", "R.utils", "yaml"),
  file_name = "development_packages"
)

Arguments

Value

No return value, but it writes a file to the project root and adds an entry to the .Rbuildignore file.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), system_information(), unexpected_error(), user_confirm()

Description

This function rounds (only) the numeric columns of a data.frame.

Usage

round_data.frame(df, digits = 0)

Arguments

Value

A data.frame.

See Also

Other data.frame helpers: delete_columns_data.frame(), group_data.frame()

Examples

df <- data.frame("label" = c("A", "B"), "number" = rnorm(10))
round_data.frame(df, digits = 1)

Description

This function samples a correlation matrix by sampling a covariance matrix from an inverse Wishart distribution and transforming it to a correlation matrix.

Usage

sample_correlation_matrix(dim, df = dim, scale = diag(dim))

Arguments

Value

A correlation matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_covariance_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

sample_correlation_matrix(dim = 3)

Description

This function samples a covariance matrix from an inverse Wishart distribution.

Usage

sample_covariance_matrix(dim, df = dim, scale = diag(dim), diag = FALSE)

Arguments

Value

A covariance matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_transition_probability_matrix(), stationary_distribution()

Examples

sample_covariance_matrix(dim = 3)

Description

This function returns a random, squared matrix of dimension dim that fulfills the properties of a transition probability matrix.

Usage

sample_transition_probability_matrix(dim, state_persistent = TRUE)

Arguments

Value

A transition probability matrix.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), stationary_distribution()

Examples

sample_transition_probability_matrix(dim = 3)

Description

This function simulates a Markov chain.

Usage

simulate_markov_chain(Gamma, T, delta = oeli::stationary_distribution(Gamma))

Arguments

Value

A numeric vector of length T with states.

See Also

Other simulation helpers: correlated_regressors(), ddirichlet_cpp(), dmvnorm_cpp(), dtnorm_cpp(), dwishart_cpp()

Examples

Gamma <- sample_transition_probability_matrix(dim = 3)
simulate_markov_chain(Gamma = Gamma, T = 10)

Description

This function splits a vector at specific positions.

Usage

split_vector_at(x, at)

Arguments

Value

A list.

References

Based on https://stackoverflow.com/a/19274414.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), permutations(), subsets(), vector_occurrence()

Examples

x <- 1:10
split_vector_at(x, c(2, 3, 5, 7))

Description

This function computes the stationary distribution corresponding to a transition probability matrix.

Usage

stationary_distribution(tpm, soft_fail = FALSE)

Arguments

Value

A numeric vector.

See Also

Other matrix helpers: check_correlation_matrix(), check_covariance_matrix(), check_transition_probability_matrix(), cov_to_chol(), diff_cov(), insert_matrix_column(), matrix_diagonal_indices(), matrix_indices(), sample_correlation_matrix(), sample_covariance_matrix(), sample_transition_probability_matrix()

Examples

tpm <- matrix(0.05, nrow = 3, ncol = 3)
diag(tpm) <- 0.9
stationary_distribution(tpm)

Description

Provides a simple indexing interface for list elements based on R6. Basically, it allows to store items in a list and to regain them based on identifiers defined by the user.

Value

The output depends on the method:

• $new() returns a Storage object.

• $add(), $remove(), and $print() invisibly return the Storage object (to allow for method chaining)

• $get() returns the requested element(s)

• $number() returns an integer

• $indices() return an integer vector

Setting identifiers

An identifier is a character, typically a binary property. Identifiers can be negated by placing an exclamation mark ("!") in front of them. Identifiers that have been assigned to other elements previously do not need to be specified again for new elements; instead, a default value can be used. This default value can be defined either globally for all cases (via the $missing_identifier field) or separately for each specific case (via the method argument).

User confirmation

If desired, the user can be asked for confirmation when adding, extracting, or removing elements using identifiers. This behavior can be set globally through the $confirm field or customized separately for each specific case via the method argument.

Active bindings

Methods

Public methods

• Storage$new()

• Storage$add()

• Storage$get()

• Storage$remove()

• Storage$number()

• Storage$indices()

• Storage$print()

Method new()

Initializing a Storage object.

Usage

Storage$new()

Method add()

Adding an element.

Usage

Storage$add(
  x,
  identifier,
  confirm = interactive() & self$confirm,
  missing_identifier = self$missing_identifier
)

Arguments

Method get()

Getting elements.

Usage

Storage$get(
  identifier = character(),
  ids = integer(),
  logical = "and",
  confirm = interactive() & self$confirm,
  missing_identifier = self$missing_identifier,
  id_names = FALSE
)

Arguments

Method remove()

removing elements

Usage

Storage$remove(
  identifier = character(),
  ids = integer(),
  logical = "and",
  confirm = interactive() & self$confirm,
  missing_identifier = self$missing_identifier,
  shift_ids = TRUE
)

Arguments

Method number()

Computing the number of identified elements.

Usage

Storage$number(
  identifier = "all",
  missing_identifier = self$missing_identifier,
  logical = "and",
  confirm = FALSE
)

Arguments

Method indices()

Returning indices based on defined identifiers.

Usage

Storage$indices(
  identifier = "all",
  logical = "and",
  confirm = interactive() & self$confirm
)

Arguments

Method print()

Printing details of the saved elements.

Usage

Storage$print(...)

Arguments

See Also

Other package helpers: Dictionary, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error(), user_confirm()

Examples

### 1. Create a `Storage` object:
my_storage <- Storage$new()

# 2. Add elements along with identifiers:
my_storage$
  add(42, c("number", "rational"))$
  add(pi, c("number", "!rational"))$
  add("fear of black cats", c("text", "!rational"))$
  add("wearing a seat belt", c("text", "rational"))$
  add(mean, "function")

# 3. What elements are stored?
print(my_storage)

# 4. Extract elements based on identifiers:
my_storage$get("rational")
my_storage$get("!rational")
my_storage$get(c("text", "!rational"))
my_storage$get("all") # get all elements
my_storage$get(c("text", "!text"))
my_storage$get(c("text", "!text"), logical = "or")

# 5. Extract elements based on ids:
my_storage$get(ids = 4:5)
my_storage$get(ids = 4:5, id_names = TRUE) # add the ids as names

Description

This function generates subsets of a vector.

Usage

subsets(v, n = seq_along(v))

Arguments

Value

A list, each element is a subset of v.

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), permutations(), split_vector_at(), vector_occurrence()

Examples

v <- 1:3
subsets(v)
subsets(v, c(1, 3)) # only subsets of length 1 or 3
subsets(integer())  # trivial case works

Description

This function returns a list of general system level information.

Usage

system_information()

Value

A list with elements:

• maschine, the model name of the device

• cores, the number of cores

• ram, the size of the RAM

• os, the operating system

• rversion, the R version used

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), unexpected_error(), user_confirm()

Examples

system_information()

Description

This function interrupts an evaluation after a certain number of seconds. Note the limitations documented in setTimeLimit.

Usage

timed(expression, seconds = Inf, on_time_out = "silent")

Arguments

Value

The value of expression or, if the evaluation time exceeded, whatever is specified for on_time_out.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_body(), function_defaults(), quiet(), try_silent(), variable_name()

Examples

foo <- function(x) {
  for (i in 1:10) Sys.sleep(x / 10)
  return(x)
}
timed(foo(0.5), 1)
timed(foo(1.5), 1)

Description

This function tries to execute expr and returns a string with the error message if the execution failed.

Usage

try_silent(expr)

Arguments

Details

This function is a wrapper for try.

Value

Either the value of expr or in case of a failure an object of class fail, which contains the error message.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_body(), function_defaults(), quiet(), timed(), variable_name()

Examples

## Not run: 
try_silent(1 + 1)
try_silent(1 + "1")

## End(Not run)

Description

This function reacts to an unexpected error by throwing an error and linking to an issue site with the request to submit an issue.

Usage

unexpected_error(
  msg = "Ups, an unexpected error occured.",
  issue_link = "https://github.com/loelschlaeger/oeli/issues"
)

Arguments

Value

No return value, but it throws an error.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), user_confirm()

Description

This function asks in an interactive question a binary question.

Usage

user_confirm(question = "Question?", default = FALSE)

Arguments

Value

Either TRUE or FALSE.

See Also

Other package helpers: Dictionary, Storage, identical_structure(), input_check_response(), match_arg(), package_logo(), print_data.frame(), print_matrix(), renv_development_packages(), system_information(), unexpected_error()

Description

This function tries to determine the name of a variable passed to a function.

Usage

variable_name(variable, fallback = "unnamed")

Arguments

Value

A character, the variable name.

See Also

Other function helpers: do.call_timed(), function_arguments(), function_body(), function_defaults(), quiet(), timed(), try_silent()

Examples

variable_name(a)
f <- function(x) variable_name(x)
f(x = a)

Description

This function finds the positions of first or last occurrence of unique vector elements.

Usage

vector_occurrence(x, type = "first")

Arguments

Value

An integer vector, the positions of the unique vector elements. The ordering corresponds to unique(x), i.e., the $i$-th element in the output is the (first or last) occurrence of the $i$-th element from unique(x).

See Also

Other vector helpers: check_numeric_vector(), check_probability_vector(), chunk_vector(), insert_vector_entry(), match_numerics(), permutations(), split_vector_at(), subsets()

Examples

x <- c(1, 1, 1, 2, 2, 2, 3, 3, 3)
unique(x)
vector_occurrence(x, "first")
vector_occurrence(x, "last")