Package 'mcmcdata'

Title: Manipulate MCMC Samples and Data Frames
Description: Manipulates Monte Carlo Markov Chain samples and associated data frames.
Authors: Joe Thorley [aut, cre]
Maintainer: Joe Thorley <[email protected]>
License: MIT + file LICENSE
Version: 0.0.1.9000
Built: 2024-11-01 16:19:13 UTC
Source: https://github.com/poissonconsulting/mcmcdata

Help Index


Anti join mcmc data

Description

Anti join mcmc data

Usage

## S3 method for class 'mcmc_data'
anti_join(x, y, by = NULL, copy = FALSE, ...)

Arguments

x, y

A pair of data frames, data frame extensions (e.g. a tibble), or lazy data frames (e.g. from dbplyr or dtplyr). See Methods, below, for more details.

by

A join specification created with join_by(), or a character vector of variables to join by.

If NULL, the default, ⁠*_join()⁠ will perform a natural join, using all variables in common across x and y. A message lists the variables so that you can check they're correct; suppress the message by supplying by explicitly.

To join on different variables between x and y, use a join_by() specification. For example, join_by(a == b) will match x$a to y$b.

To join by multiple variables, use a join_by() specification with multiple expressions. For example, join_by(a == b, c == d) will match x$a to y$b and x$c to y$d. If the column names are the same between x and y, you can shorten this by listing only the variable names, like join_by(a, c).

join_by() can also be used to perform inequality, rolling, and overlap joins. See the documentation at ?join_by for details on these types of joins.

For simple equality joins, you can alternatively specify a character vector of variable names to join by. For example, by = c("a", "b") joins x$a to y$a and x$b to y$b. If variable names differ between x and y, use a named character vector like by = c("x_a" = "y_a", "x_b" = "y_b").

To perform a cross-join, generating all combinations of x and y, see cross_join().

copy

If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. This allows you to join tables across srcs, but it is a potentially expensive operation so you must opt into it.

...

Other parameters passed onto methods.


Arrange mcmcr data

Description

Arrange mcmcr data

Usage

## S3 method for class 'mcmc_data'
arrange(.data, ...)

Arguments

.data

An mcmc_data object

...

<data-masking> Variables, or functions of variables. Use desc() to sort a variable in descending order.

Examples

arrange(mcmc_data_example, species, homeworld)

As Tibble

Description

As Tibble

Usage

## S3 method for class 'mcmc_data'
as_tibble(x, samples = FALSE, ...)

Arguments

x

An mcmc_data object to coerce to a tibble.

samples

A flag specifying whether to include samples

...

Unused, for extensibility.


Bind Rows

Description

Bind Rows

Usage

bind_rows2(x, y)

Arguments

x

A mcmc_data

y

A second mcmc_data

Examples

bind_rows2(mcmc_data_example, mcmc_data_example)

Check mcmc data

Description

Checks an object is a mcmc_data.

Usage

check_mcmc_data(x, x_name = NULL)

Arguments

x

The object to check.

x_name

A string of the name of object x or NULL.

Value

An invisible copy of x (if it doesn't throw an error).

Examples

check_mcmc_data(mcmcdata::mcmc_data_example)

Coefficients

Description

Gets the coefficient table as a tibble.

Usage

## S3 method for class 'mcmc_data'
coef(object, conf_level = 0.95, estimate = stats::median, ...)

Arguments

object

The mcmc_data object to get the coefficent table for.

conf_level

A probability specifying the confidence level.

estimate

A function to calculate the point estimate.

...

Unused

Examples

coef(mcmc_data_example)

Fill Missing Values

Description

Fills all of an object's missing values while preserving the object's dimensionality and class.

Usage

## S3 method for class 'mcmc_data'
fill_na(x, value = 0, ...)

Arguments

x

An object.

value

A scalar of the value to replace values with.

...

Other arguments passed to methods.

Details

It should only be defined for objects with values of consistent class ie not standard data.frames.

Value

The modified object.

Methods (by class)

  • fill_na(logical): Fill Missing Values for logical Objects

  • fill_na(integer): Fill Missing Values for integer Objects

  • fill_na(numeric): Fill Missing Values for numeric Objects

  • fill_na(character): Fill Missing Values for character Objects

See Also

Other fill: fill_all()

Examples

# logical
fill_na(c(TRUE, NA))

# integer
fill_na(c(1L, NA), 0)

# numeric
fill_na(c(1, NA), Inf)

# character
fill_na(c("text", NA))
fill_na(matrix(c("text", NA)), value = Inf)

Slice mcmcr data

Description

Slice mcmcr data

Usage

## S3 method for class 'mcmc_data'
filter(.data, ...)

Arguments

.data

An mcmc_data object

...

For slice(): <data-masking> Integer row values.

Provide either positive values to keep, or negative values to drop. The values provided must be either all positive or all negative. Indices beyond the number of rows in the input are silently ignored.

For ⁠slice_*()⁠, these arguments are passed on to methods.

Examples

filter(mcmc_data_example, species == "Droid")

Group mcmc data

Description

Group mcmc data

Usage

## S3 method for class 'mcmc_data'
group_by(.data, ..., .add = FALSE)

Arguments

.data

An mcmc_data object

...

In group_by(), variables or computations to group by. Computations are always done on the ungrouped data frame. To perform computations on the grouped data, you need to use a separate mutate() step before the group_by(). Computations are not allowed in nest_by(). In ungroup(), variables to remove from the grouping.

.add

When FALSE, the default, group_by() will override existing groups. To add to the existing groups, use .add = TRUE.

This argument was previously called add, but that prevented creating a new grouping variable called add, and conflicts with our naming conventions.

Examples

group_by(mcmc_data_example, homeworld, species)

Inner join mcmc data

Description

Inner join mcmc data

Usage

## S3 method for class 'mcmc_data'
inner_join(x, y, by = NULL, copy = FALSE, suffix = c(".x", ".y"), ...)

Arguments

x, y

A pair of data frames, data frame extensions (e.g. a tibble), or lazy data frames (e.g. from dbplyr or dtplyr). See Methods, below, for more details.

by

A join specification created with join_by(), or a character vector of variables to join by.

If NULL, the default, ⁠*_join()⁠ will perform a natural join, using all variables in common across x and y. A message lists the variables so that you can check they're correct; suppress the message by supplying by explicitly.

To join on different variables between x and y, use a join_by() specification. For example, join_by(a == b) will match x$a to y$b.

To join by multiple variables, use a join_by() specification with multiple expressions. For example, join_by(a == b, c == d) will match x$a to y$b and x$c to y$d. If the column names are the same between x and y, you can shorten this by listing only the variable names, like join_by(a, c).

join_by() can also be used to perform inequality, rolling, and overlap joins. See the documentation at ?join_by for details on these types of joins.

For simple equality joins, you can alternatively specify a character vector of variable names to join by. For example, by = c("a", "b") joins x$a to y$a and x$b to y$b. If variable names differ between x and y, use a named character vector like by = c("x_a" = "y_a", "x_b" = "y_b").

To perform a cross-join, generating all combinations of x and y, see cross_join().

copy

If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. This allows you to join tables across srcs, but it is a potentially expensive operation so you must opt into it.

suffix

If there are non-joined duplicate variables in x and y, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.

...

Other parameters passed onto methods.


Is an MCMC data object

Description

Tests whether x is an object of class 'mcmc_data'

Usage

is.mcmc_data(x)

Arguments

x

The object to test.

Value

A flag indicating whether the test was positive.


Left join mcmc data

Description

Left join mcmc data

Usage

## S3 method for class 'mcmc_data'
left_join(x, y, by = NULL, copy = FALSE, suffix = c(".x", ".y"), ...)

Arguments

x, y

A pair of data frames, data frame extensions (e.g. a tibble), or lazy data frames (e.g. from dbplyr or dtplyr). See Methods, below, for more details.

by

A join specification created with join_by(), or a character vector of variables to join by.

If NULL, the default, ⁠*_join()⁠ will perform a natural join, using all variables in common across x and y. A message lists the variables so that you can check they're correct; suppress the message by supplying by explicitly.

To join on different variables between x and y, use a join_by() specification. For example, join_by(a == b) will match x$a to y$b.

To join by multiple variables, use a join_by() specification with multiple expressions. For example, join_by(a == b, c == d) will match x$a to y$b and x$c to y$d. If the column names are the same between x and y, you can shorten this by listing only the variable names, like join_by(a, c).

join_by() can also be used to perform inequality, rolling, and overlap joins. See the documentation at ?join_by for details on these types of joins.

For simple equality joins, you can alternatively specify a character vector of variable names to join by. For example, by = c("a", "b") joins x$a to y$a and x$b to y$b. If variable names differ between x and y, use a named character vector like by = c("x_a" = "y_a", "x_b" = "y_b").

To perform a cross-join, generating all combinations of x and y, see cross_join().

copy

If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. This allows you to join tables across srcs, but it is a potentially expensive operation so you must opt into it.

suffix

If there are non-joined duplicate variables in x and y, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.

...

Other parameters passed onto methods.


MCMC Data

Description

Combines an mcmc object with a data frame. The mcmc object must be for a single parameter of the same length as the number of rows in the data frame. The resultant object can be filtered or summarized or the coef calculated.

Usage

mcmc_data(mcmc, data)

Arguments

mcmc

An mcmc object with one parameter

data

A data frame

Value

An object of class mcmc_data


Example mcmc data Object

Description

An example mcmc_data object.

Usage

mcmc_data_example

Format

An object of class mcmc_data of length 2.


Derive MCMC Data

Description

Get mcmc_data object.

Usage

mcmc_derive_data(object, ...)

Arguments

object

The object.

...

Not used.


mcmc_derive mcmc_data

Description

Gets mcmc_data object of a derived parameters. To return an mcmcr object of one or more derived parameters use mcmc_derive(). By default the current parameter is call par and the derived one is called new_par.

Usage

## S3 method for class 'mcmc_data'
mcmc_derive_data(
  object,
  expr = "new_par <- par",
  values = list(),
  parameter = "par",
  monitor = "new_par",
  parallel = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

Arguments

object

An mcmc_data object

expr

A string of the R expression.

values

A named list of values for objects not in object$data

parameter

A string of the name of the current MCMC samples in expr.

monitor

A string of the name of the derived parameter to return.

parallel

A flag specifying whether to generate the derived parameters for each chain in parallel.

silent

A flag specifying whether to suppress messages and warnings.

...

Unused.

Value

An mcmc_data object.


mcmc_derive mcmc_data

Description

Gets mcmcr object of one or more derived parameters. To return an mcmc_data object use mcmc_derive_data(). By default the current parameter is call par.

Usage

## S3 method for class 'mcmc_data'
mcmc_derive(
  object,
  expr = "new_par <- par",
  values = list(),
  parameter = "par",
  monitor = ".*",
  parallel = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

Arguments

object

An mcmc_data object

expr

A string of the R expression.

values

A named list of values for objects not in object$data

parameter

A string of the name of the current MCMC samples in expr.

monitor

A regular expression specifying the derived parameter(s) in expr to monitor.

parallel

A flag specifying whether to generate the derived parameters for each chain in parallel.

silent

A flag specifying whether to suppress messages and warnings.

...

Unused.

Value

An mcmcr object of the derived parameters.


Mutate mcmc_data

Description

Mutate mcmc_data

Usage

## S3 method for class 'mcmc_data'
mutate(.data, ...)

Arguments

.data

An mcmc_data object

...

For rename(): <tidy-select> Use new_name = old_name to rename selected variables.

For rename_with(): additional arguments passed onto .fn.

Examples

rename(mcmc_data_example, Spp = species)

Rename mcmcr data

Description

Rename mcmcr data

Usage

## S3 method for class 'mcmc_data'
rename(.data, ...)

Arguments

.data

An mcmc_data object

...

For rename(): <tidy-select> Use new_name = old_name to rename selected variables.

For rename_with(): additional arguments passed onto .fn.

Examples

rename(mcmc_data_example, Spp = species)

Replace Missing Values mcmc data

Description

Replace Missing Values mcmc data

Usage

## S3 method for class 'mcmc_data'
replace_na(data, replace, ...)

Arguments

data

A data frame or vector.

replace

If data is a data frame, replace takes a named list of values, with one value for each column that has missing values to be replaced. Each value in replace will be cast to the type of the column in data that it being used as a replacement in.

If data is a vector, replace takes a single value. This single value replaces all of the missing values in the vector. replace will be cast to the type of data.

...

Additional arguments for methods. Currently unused.


Right join mcmc data

Description

Right join mcmc data

Usage

## S3 method for class 'mcmc_data'
right_join(x, y, by = NULL, copy = FALSE, suffix = c(".x", ".y"), ...)

Arguments

x, y

A pair of data frames, data frame extensions (e.g. a tibble), or lazy data frames (e.g. from dbplyr or dtplyr). See Methods, below, for more details.

by

A join specification created with join_by(), or a character vector of variables to join by.

If NULL, the default, ⁠*_join()⁠ will perform a natural join, using all variables in common across x and y. A message lists the variables so that you can check they're correct; suppress the message by supplying by explicitly.

To join on different variables between x and y, use a join_by() specification. For example, join_by(a == b) will match x$a to y$b.

To join by multiple variables, use a join_by() specification with multiple expressions. For example, join_by(a == b, c == d) will match x$a to y$b and x$c to y$d. If the column names are the same between x and y, you can shorten this by listing only the variable names, like join_by(a, c).

join_by() can also be used to perform inequality, rolling, and overlap joins. See the documentation at ?join_by for details on these types of joins.

For simple equality joins, you can alternatively specify a character vector of variable names to join by. For example, by = c("a", "b") joins x$a to y$a and x$b to y$b. If variable names differ between x and y, use a named character vector like by = c("x_a" = "y_a", "x_b" = "y_b").

To perform a cross-join, generating all combinations of x and y, see cross_join().

copy

If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. This allows you to join tables across srcs, but it is a potentially expensive operation so you must opt into it.

suffix

If there are non-joined duplicate variables in x and y, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.

...

Other parameters passed onto methods.


Select mcmcr data

Description

Select mcmcr data

Usage

## S3 method for class 'mcmc_data'
select(.data, ...)

Arguments

.data

An mcmc_data object

...

<tidy-select> One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables.

Examples

select(mcmc_data_example, species, homeworld)

Semi join mcmc data

Description

Semi join mcmc data

Usage

## S3 method for class 'mcmc_data'
semi_join(x, y, by = NULL, copy = FALSE, ...)

Arguments

x, y

A pair of data frames, data frame extensions (e.g. a tibble), or lazy data frames (e.g. from dbplyr or dtplyr). See Methods, below, for more details.

by

A join specification created with join_by(), or a character vector of variables to join by.

If NULL, the default, ⁠*_join()⁠ will perform a natural join, using all variables in common across x and y. A message lists the variables so that you can check they're correct; suppress the message by supplying by explicitly.

To join on different variables between x and y, use a join_by() specification. For example, join_by(a == b) will match x$a to y$b.

To join by multiple variables, use a join_by() specification with multiple expressions. For example, join_by(a == b, c == d) will match x$a to y$b and x$c to y$d. If the column names are the same between x and y, you can shorten this by listing only the variable names, like join_by(a, c).

join_by() can also be used to perform inequality, rolling, and overlap joins. See the documentation at ?join_by for details on these types of joins.

For simple equality joins, you can alternatively specify a character vector of variable names to join by. For example, by = c("a", "b") joins x$a to y$a and x$b to y$b. If variable names differ between x and y, use a named character vector like by = c("x_a" = "y_a", "x_b" = "y_b").

To perform a cross-join, generating all combinations of x and y, see cross_join().

copy

If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. This allows you to join tables across srcs, but it is a potentially expensive operation so you must opt into it.

...

Other parameters passed onto methods.


Slice mcmcr data

Description

Slice mcmcr data

Usage

## S3 method for class 'mcmc_data'
slice(.data, ...)

Arguments

.data

An mcmc_data object

...

For slice(): <data-masking> Integer row values.

Provide either positive values to keep, or negative values to drop. The values provided must be either all positive or all negative. Indices beyond the number of rows in the input are silently ignored.

For ⁠slice_*()⁠, these arguments are passed on to methods.

Examples

slice(mcmc_data_example, 1L)

Summarise mcmc data

Description

Summarise mcmc data

Usage

## S3 method for class 'mcmc_data'
summarise(.data, ..., .fun = sum)

Arguments

.data

An mcmc_data object

...

<data-masking> Name-value pairs of summary functions. The name will be the name of the variable in the result.

The value can be:

  • A vector of length 1, e.g. min(x), n(), or sum(is.na(y)).

  • A data frame, to add multiple columns from a single expression.

[Deprecated] Returning values with size 0 or >1 was deprecated as of 1.1.0. Please use reframe() for this instead.

.fun

The function to use to summarise the MCMC samples.


Ungroup mcmc data

Description

Ungroup mcmc data

Usage

## S3 method for class 'mcmc_data'
ungroup(x, ...)

Arguments

x

An mcmc_data object

...

In group_by(), variables or computations to group by. Computations are always done on the ungrouped data frame. To perform computations on the grouped data, you need to use a separate mutate() step before the group_by(). Computations are not allowed in nest_by(). In ungroup(), variables to remove from the grouping.

Examples

ungroup(mcmc_data_example)