Package 'pkggraph'

Title: A Consistent and Intuitive Platform to Explore the Dependencies of Packages on the Comprehensive R Archive Network Like Repositories
Description: Interactively explore various dependencies of a package(s) (on the Comprehensive R Archive Network Like repositories) and perform analysis using tidy philosophy. Most of the functions return a 'tibble' object (enhancement of 'dataframe') which can be used for further analysis. The package offers functions to produce 'network' and 'igraph' dependency graphs. The 'plot' method produces a static plot based on 'ggnetwork' and 'plotd3' function produces an interactive D3 plot based on 'networkD3'.
Authors: KS Srikanth [aut, cre], Singh Nikhil [aut]
Maintainer: KS Srikanth <[email protected]>
License: GPL-3
Version: 0.2.3
Built: 2024-10-26 03:25:39 UTC
Source: https://github.com/talegari/pkggraph

Help Index

pkggraph

Description

Interactively explore various dependencies of a package(s) (on the Comprehensive R Archive Network Like repositories) and perform analysis using tidy philosophy. Most of the functions return a 'tibble' object (enhancement of 'dataframe') which can be used for further analysis. The package offers functions to produce 'network' and 'igraph' dependency graphs. The 'plot' method produces a static plot based on 'ggnetwork' and 'plotd3' function produces an interactive D3 plot based on 'networkD3'.

Details

See the vignette for further details

Author(s)

Maintainer: KS Srikanth [email protected]

Authors:

See Also

Useful links:

Check depends

Description

Check whether pkg_1 has a dependency on pkg_2

Usage

pkg_1 %depends% pkg_2

Arguments

pkg_1

a package name
pkg_2

a package name

Value

TRUE or FALSE

Author(s)

Srikanth KS

Examples

pkggraph::init(local = TRUE)
"dplyr" %depends% "tibble"

Check enhances

Description

Check whether pkg_1 has a dependency on pkg_2

Usage

pkg_1 %enhances% pkg_2

Arguments

pkg_1

a package name
pkg_2

a package name

Value

TRUE or FALSE

Author(s)

Srikanth KS

Examples

pkggraph::init(local = TRUE)
"dplyr" %enhances% "tibble"

Check imports

Description

Check whether pkg_1 has a dependency on pkg_2

Usage

pkg_1 %imports% pkg_2

Arguments

pkg_1

a package name
pkg_2

a package name

Value

TRUE or FALSE

Author(s)

Srikanth KS

Examples

pkggraph::init(local = TRUE)
"dplyr" %imports% "tibble"

Check linkingto

Description

Check whether pkg_1 has a dependency on pkg_2

Usage

pkg_1 %linkingto% pkg_2

Arguments

pkg_1

a package name
pkg_2

a package name

Value

TRUE or FALSE

Author(s)

Srikanth KS

Examples

pkggraph::init(local = TRUE)
"dplyr" %linkingto% "tibble"

Check relies

Description

Check whether a package has a recursive dependency on the other

Usage

pkg_1 %relies% pkg_2

Arguments

pkg_1

(string) A package name
pkg_2

(string) A package name

Value

(flag) TRUE, if 'pkg_1' ‘relies' on ’pkg_2'

Author(s)

Srikanth KS

See Also

relies, reverse_relies

Examples

pkggraph::init(local = TRUE)
"dplyr" %relies% "tibble"

Check suggests

Description

Check whether pkg_1 has a dependency on pkg_2

Usage

pkg_1 %suggests% pkg_2

Arguments

pkg_1

a package name
pkg_2

a package name

Value

TRUE or FALSE

Author(s)

Srikanth KS

Examples

pkggraph::init(local = TRUE)
"dplyr" %suggests% "tibble"

deptable

Description

(tibble) A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'. Every row defines a dependency. This is computed for all packages in 'packmeta'

Usage

deptable

Format

An object of class tbl_df (inherits from tbl, data.frame) with 61154 rows and 3 columns.

get_all_dependencies

Description

Get all dependencies

Usage

get_all_dependencies(packages, level = 1L, relation = c("Depends",
  "Imports", "LinkingTo", "Suggests", "Enhances"), strict = FALSE,
  ignore = c("datasets", "utils", "grDevices", "graphics", "stats",
  "methods"))

Arguments

packages

(non-empty character vector) Package names
level

(positive integer, Default = 1L) Depth of recursive dependency
relation

(character vector) Types of relations. Must be a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
strict

(logical, Default: TRUE) Whether to consider all packages (alternately only 'relation' specific packages) when computing dependencies for the next level
ignore

package names to ignore

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_all_reverse_dependencies

Examples

pkggraph::init(local = TRUE)
# general use
pkggraph::get_all_dependencies("mlr")
# specify two levels
pkggraph::get_all_dependencies("mlr", level = 2)
# specify relation(s)
pkggraph::get_all_dependencies("mlr", level = 2, relation = "Imports")
# setting strict to TRUE to only consider 'Imports' of the previous level
pkggraph::get_all_dependencies("mlr"
                               , level    = 2
                               , relation = "Imports"
                               , strict   = TRUE)

get_all_reverse_dependencies

Description

Get all reverse dependencies

Usage

get_all_reverse_dependencies(packages, level = 1L,
  relation = c("Depends", "Imports", "LinkingTo", "Suggests",
  "Enhances"), strict = FALSE, ignore = c("datasets", "utils",
  "grDevices", "graphics", "stats", "methods"))

Arguments

packages

(non-empty character vector) Package names
level

(positive integer, Default = 1L) Depth of recursive dependency
relation

(character vector) Types of relations. Must be a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
strict

(logical, Default: TRUE) Whether to consider all packages (alternately only 'relation' specific packages) when computing dependencies for the next level
ignore

package names to ignore

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_all_dependencies

Examples

pkggraph::init(local = TRUE)
# general use
pkggraph::get_all_reverse_dependencies("mlr")
# specify two levels
pkggraph::get_all_reverse_dependencies("mlr", level = 2)
# specify relation(s)
pkggraph::get_all_reverse_dependencies("mlr", level = 2, relation = "Imports")
# setting strict to TRUE to only consider 'Imports' of the previous level
pkggraph::get_all_reverse_dependencies("mlr"
                                       , level    = 2
                                       , relation = "Imports"
                                       , strict   = TRUE)

get_depends

Description

Get dependencies

Usage

get_depends(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_depends, get_imports, get_linkingto, get_suggests, get_enhances, get_all_dependencies, get_reverse_depends

Examples

pkggraph::init(local = TRUE)
pkggraph::get_depends("glmnet")

get_enhances

Description

Get dependencies

Usage

get_enhances(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_depends, get_imports, get_linkingto, get_suggests, get_enhances, get_all_dependencies, get_reverse_enhances

Examples

pkggraph::init(local = TRUE)
pkggraph::get_enhances("bigmemory")

get_imports

Description

Get dependencies

Usage

get_imports(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_depends, get_imports, get_linkingto, get_suggests, get_enhances, get_all_dependencies, get_reverse_imports

Examples

pkggraph::init(local = TRUE)
pkggraph::get_imports("dplyr")

get_linkingto

Description

Get dependencies

Usage

get_linkingto(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_depends, get_imports, get_linkingto, get_suggests, get_enhances, get_all_dependencies, get_reverse_linkingto

Examples

pkggraph::init(local = TRUE)
pkggraph::get_linkingto("tibble")

get_neighborhood

Description

Obtain dependencies and reverse dependencies of packages at a given depth of recursion

Usage

get_neighborhood(packages, level = 1L, relation = c("Depends",
  "Imports", "LinkingTo", "Suggests", "Enhances"), strict = FALSE,
  interconnect = TRUE, ignore = c("datasets", "utils", "grDevices",
  "graphics", "stats", "methods"))

Arguments

packages

(non-empty character vector) Package names
level

(positive integer, Default: 1L) Depth of recursive dependency
relation

(character vector) Types of relations. Must be a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
strict

(logical, Default: TRUE) Whether to consider all packages (alternately only 'relation' specific packages) when computing dependencies for the next level
interconnect

(flag, Default: TRUE) Whether to capture dependency among packages (of a given level) of the next level (See examples)
ignore

package names to ignore

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

neighborhood_graph, make_neighborhood_graph

Examples

# explore first level dependencies
pkggraph::init(local = TRUE)
pkggraph::get_neighborhood("caret")

# explore second level dependencies
pkggraph::get_neighborhood("caret", level = 2)

# explore second level dependencies without
# considering dependencies from third level
pkggraph::get_neighborhood("caret", level = 2, interconnect = FALSE)

# explore first level dependencies of multiple packages
# and consider second level dependencies
get_neighborhood(c("caret", "mlr"))

# get 'imports' specific neighborhood of 'mlr' package with strict = TRUE
get_neighborhood("mlr"
                 , level        = 2
                 , strict       = TRUE
                 , interconnect = FALSE
                 , relation     = "Imports")

# get 'imports' specific neighborhood of 'mlr' package with strict = FALSE
get_neighborhood("mlr"
                 , level        = 2
                 , strict       = FALSE
                 , interconnect = FALSE
                 , relation     = "Imports")

get_reverse_depends

Description

Get reverse dependencies

Usage

get_reverse_depends(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_reverse_depends, get_reverse_imports, get_reverse_linkingto, get_reverse_suggests, get_reverse_enhances, get_all_reverse_dependencies, get_depends

Examples

pkggraph::init(local = TRUE)
pkggraph::get_reverse_depends("utils")

get_reverse_enhances

Description

Get reverse dependencies

Usage

get_reverse_enhances(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_reverse_depends, get_reverse_imports, get_reverse_linkingto, get_reverse_suggests, get_reverse_enhances, get_all_reverse_dependencies, get_enhances

Examples

pkggraph::init(local = TRUE)
pkggraph::get_reverse_enhances("synchronicity")

get_reverse_imports

Description

Get reverse dependencies

Usage

get_reverse_imports(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_reverse_depends, get_reverse_imports, get_reverse_linkingto, get_reverse_suggests, get_reverse_enhances, get_all_reverse_dependencies, get_imports

Examples

pkggraph::init(local = TRUE)
pkggraph::get_reverse_imports("Rcpp")

get_reverse_linkingto

Description

Get reverse dependencies

Usage

get_reverse_linkingto(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_reverse_depends, get_reverse_imports, get_reverse_linkingto, get_reverse_suggests, get_reverse_enhances, get_all_reverse_dependencies, get_linkingto

Examples

pkggraph::init(local = TRUE)
pkggraph::get_reverse_linkingto("BH")

get_reverse_suggests

Description

Get reverse dependencies

Usage

get_reverse_suggests(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_reverse_depends, get_reverse_imports, get_reverse_linkingto, get_reverse_suggests, get_reverse_enhances, get_all_reverse_dependencies, get_suggests

Examples

pkggraph::init(local = TRUE)
pkggraph::get_reverse_suggests("purrr")

get_suggests

Description

Get dependencies

Usage

get_suggests(packages, level = 1L)

Arguments

packages

(non-empty character vector) Package names
level

(positive integer) Depth of recursive dependency

Value

A tibble with three columns: 'pkg_1', 'relation' and 'pkg_2'

Author(s)

Srikanth KS

See Also

get_depends, get_imports, get_linkingto, get_suggests, get_enhances, get_all_dependencies, get_reverse_suggests

Examples

pkggraph::init(local = TRUE)
pkggraph::get_suggests("knitr")

init

Description

Initiate the package by loading the data into parent frame. This should be done as soon as the package is loaded or attached. This creates(rewrites) new variables 'deptable' and 'packmeta' to the environment where it is run from.

Usage

init(local = FALSE, repository = "CRAN", ...)

Arguments

local

(flag, default: FALSE) If

  • FALSE: Tries to to download package data from CRAN over internet and compute dependencies

  • TRUE: Loads data that comes with the package corresponding to 2nd September 2017 02:04 IST
repository

(character vector, Default: "CRAN") One among c("CRAN", "BioCsoft", "BioCann", "BioCexp", "BioCextra", "omegahat"). To use a repository not in this list, set 'repository' to NULL and pass named argument called 'repos' with a valid repository address. This will be passed as is to 'utils::available.packages()'.
...

Additional parameters to be passed to 'available.packages()'

Value

An invisible TRUE

Author(s)

Srikanth KS

make_neighborhood_graph

Description

Make a network or igraph graph object of dependencies and reverse dependencies from tibble output by functions like 'get_neighborhood', 'get_all_dependents'etc

Usage

make_neighborhood_graph(ndf, type = "igraph")

Arguments

ndf

(tibble) Output by functions like 'get_neighborhood', 'get_all_dependents' etc
type

(string, Default: "igraph") Graph object type. Either "network" or "igraph"

Value

A network or igraph graph object

Author(s)

Srikanth KS

See Also

neighborhood_graph, get_neighborhood

Examples

pkggraph::init(local = TRUE)
graph_object <- pkggraph::get_neighborhood("caret")
pkggraph::make_neighborhood_graph(graph_object)

neighborhood_graph

Description

Obtain a network or igraph graph object of dependencies and reverse dependencies of packages at a given depth of recursion

Usage

neighborhood_graph(packages, level = 1L, type = "igraph",
  relation = c("Depends", "Imports", "LinkingTo", "Suggests",
  "Enhances"), strict = FALSE, interconnect = TRUE,
  ignore = c("datasets", "utils", "grDevices", "graphics", "stats",
  "methods"))

Arguments

packages

(non-empty character vector) Package names
level

(positive integer, Default: 1L) Depth of recursive dependency
type

(string, Default: "igraph") Graph object type. Either "network" or "igraph"
relation

(character vector) Types of graph edges. Must be a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")
strict

(logical, Default: TRUE) Whether to consider all packages (alternately only 'relation' specific packages) when computing dependencies for the next level
interconnect

(flag, Default: TRUE) Whether to capture dependency among packages (of a given level) of the next level (See examples)
ignore

package names to ignore

Value

A network or igraph graph object

Author(s)

Srikanth KS

See Also

get_neighborhood, make_neighborhood_graph

Examples

# explore first level dependencies
pkggraph::init(local = TRUE)
pkggraph::neighborhood_graph("caret")

# explore second level dependencies of class network
pkggraph::neighborhood_graph("caret", level = 2, type = "network")

# get 'imports' specific neighborhood of 'mlr' package with strict = TRUE
neighborhood_graph("mlr"
                   , level        = 2
                   , strict       = TRUE
                   , interconnect = FALSE
                   , relation     = "Imports")

# get 'imports' specific neighborhood of 'mlr' package with strict = FALSE
neighborhood_graph("mlr"
                   , level        = 2
                   , strict       = FALSE
                   , interconnect = FALSE
                   , relation     = "Imports")

packmeta

Description

(A character matrix) Output of 'utils::available.packages'

Usage

packmeta

Format

An object of class matrix with 11328 rows and 17 columns.

plot a pkggraph object

Description

plot a pkggraph object

Usage

## S3 method for class 'pkggraph'
plot(x, ...)

Arguments

x

plot object generated by neighborhood_graph or make_neighborhood_graph
...

additional arguments (See details)

Details

  • background: "black" or "white". Default is 'black'

  • nodeImportance: "in", "out" or "both", in - Node will be considered important(and increased size) if more incoming. out - Node will be considered important if more outgoing. both - Node importance will be calculated on both incoming and outgoing. True for all the nodes. Default is 'both'

  • edgeLabel: logical. TRUE if edge label has to be shown. Default is FALSE

Author(s)

Nikhil Singh

See Also

neighborhood_graph, make_neighborhood_graph, get_neighborhood

Examples

## Not run: 
  pkggraph::init(local = TRUE)
  plot_obj <- pkggraph::neighborhood_graph("hash")
  plot(plot_obj)

  plot_obj <- pkggraph::neighborhood_graph("tidytext")
  plot(plot_obj
       , background     = "white"
       , nodeImportance = "out")
  plot_obj <- pkggraph::neighborhood_graph(c("hash","tokenizers")
                                           , interconnect = FALSE
                                           )
  plot(plot_obj,  background = "white")
  
## End(Not run)

plotd3

Description

D3 network of a pkggraph object

Usage

plotd3(x, height = 500, width = 1000)

Arguments

x

plot object generated by neighborhood_graph or make_neighborhood_graph of type igraph
height

parameter to change the height of the d3 plot. Default is 500
width

parameter to change the width of the d3 plot. Default is 1000

Author(s)

Nikhil Singh

Examples

## Not run: 
  pkggraph::init(local = TRUE)
  plot_obj <- pkggraph::neighborhood_graph("hash")
  pkggraph::plotd3(plot_obj)

  plot_obj <- pkggraph::neighborhood_graph(c("hash","tidytext"))
  pkggraph::plotd3(plot_obj, height = 750, width = 1200)

  plot_obj <- pkggraph::neighborhood_graph(c("hash","Matrix"))
  pkggraph::plotd3(plot_obj)

## End(Not run)

relies

Description

Captures recursive dependencies of these types: "Depends", "Imports", "LinkingTo"

Usage

relies(packages)

Arguments

packages

(non-empty character vector) Package names

Value

(Named list) A name is the package name from 'packages'. A Value is a character vector of all packages which the package 'relies' (Captures recursive dependencies of these types: "Depends", "Imports", "LinkingTo")

Author(s)

Srikanth KS

See Also

reverse_relies

Examples

pkggraph::init(local = TRUE)
pkggraph::relies("tidytext")

reverse_relies

Description

Captures reverse recursive dependencies of these types: "Depends", "Imports", "LinkingTo"

Usage

reverse_relies(packages)

Arguments

packages

(non-empty character vector) Package names

Value

(Named list) A name is the package name from 'packages'. A Value is a character vector of all packages which the package 'relies' (Captures reverse recursive dependencies of these types: "Depends", "Imports", "LinkingTo")

Author(s)

Srikanth KS

See Also

relies

Examples

pkggraph::init(local = TRUE)
pkggraph::reverse_relies("data.table")