Features
deepdep package exports the following functions:
get_available_packages,get_description,get_dependencies,get_downloads,deepdep,plot_dependencies.
Those functions rely on each other and are ordered from the lowest to the highest level. We’ll describe what they exactly do and how on examples.
get_available_packages
This function lists, as the name indicates, available packages. The default behaviour is listing all CRAN packages.
t <- get_available_packages()
head(t, 20)
#> A3 aaSEA AATtools aba ABACUS abbreviate
#> "A3" "aaSEA" "AATtools" "aba" "ABACUS" "abbreviate"
#> abbyyR abc abc.data ABC.RAP abcADM ABCanalysis
#> "abbyyR" "abc" "abc.data" "ABC.RAP" "abcADM" "ABCanalysis"
#> abcdeFBA ABCoptim ABCp2 abcrf abcrlda abctools
#> "abcdeFBA" "ABCoptim" "ABCp2" "abcrf" "abcrlda" "abctools"
#> abd abdiv
#> "abd" "abdiv"However, if you want to check if package is present in a little wider range – on CRAN or Bioconductor repositories, you simply need to set argument bioc = TRUE. In this case function is simply wrapper around BiocManager::available() and to use it you need to have BiocManager package (available via CRAN) installed.
t <- get_available_packages(bioc = TRUE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
#> details
#>
#> replacement repositories:
#> CRAN: https://cran.rstudio.com/
head(t, 20)
#> [1] "A3" "a4" "a4Base" "a4Classif" "a4Core"
#> [6] "a4Preproc" "a4Reporting" "aaSEA" "AATtools" "aba"
#> [11] "ABACUS" "ABAData" "ABAEnrichment" "ABarray" "abbreviate"
#> [16] "abbyyR" "abc" "abc.data" "ABC.RAP" "abcADM"Another possibility is checking what packages are installed – you do it by adding local = TRUE parameter.
t <- get_available_packages(local = TRUE)
head(t, 20)
#> [1] "abind" "ada" "adabag" "ade4" "AmyloGram"
#> [6] "AmyloGraph" "ape" "askpass" "assertthat" "auprc"
#> [11] "backports" "base64enc" "base64url" "BBmisc" "bench"
#> [16] "BH" "binman" "Biobase" "BiocFileCache" "BiocGenerics"Result of this function is cached (for more details, see Caching section of this vignette).
get_description
When you know, that given package is available, you may want to obtain DESCRIPTION of this package, at least the most essential parts of it, especially dependencies. You can do it by calling:
get_description("DALEXtra")
#> DALEXtra: Extension for 'DALEX' Package
#> Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
#> Description:
#> Provides wrapper of various machine learning models.
#> In applied machine learning, there
#> is a strong belief that we need to strike a balance
#> between interpretability and accuracy.
#> However, in field of the interpretable machine learning,
#> there are more and more new ideas for explaining black-box models,
#> that are implemented in 'R'.
#> 'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models
#> including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library.
#> Important part of the package is Champion-Challenger analysis and innovative approach
#> to model performance across subsets of test data presented in Funnel Plot.
#> Third branch of 'DALEXtra' package is aspect importance analysis
#> that provides instance-level explanations for the groups of explanatory variables.
#> Depends: R DALEX
#> Imports: reticulate ggplot2
#> LinkingTo:
#> Suggests: auditor ingredients gbm ggrepel h2o iml lime localModel mlr mlr3 randomForest recipes rmarkdown rpart xgboost testthat tidymodels
#> Enhances:
#> Scrap date: 2021-05-09 09:08:34Again, you can pass bioc = TRUE if you want to check for this package in Bioconductor repository. Notice that if package is not found there, it will be searched for on CRAN. The reason behind this type of behaviour is the fact that packages present on Bioconductor are updated more often than on CRAN and not all of them are present here. Option local = TRUE for only installed packages is also possible. If a package is not available in a given source, the function will return NULL value:
get_description("a4")
#> NULL
get_description("a4", bioc = TRUE)
#> a4: Automated Affymetrix Array Analysis Umbrella Package
#> Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
#> Description:
#> Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.
#> Depends: a4Base a4Preproc a4Classif a4Core a4Reporting
#> Imports:
#> LinkingTo:
#> Suggests: MLP nlcv ALL Cairo Rgraphviz GOstats
#> Enhances:
#> Scrap date:Result of this function is also cached (for more details, see Caching section of this vignette).
get_downloads
This package allows you obtaining information on how many times specified package was downloaded. However, it works only with CRAN packages.
get_downloads("ggplot2")
#> x
#> last_day 85630
#> last_week 600713
#> last_month 2849787
#> last_quarter 9340444
#> last_half 15747252
#> grand_total 70015383Results of this function is not cached.
get_dependencies
After parsing description file, you can now create a data.frame which will describe dependencies between given package and others. You do it by using this function:
get_dependencies("ggplot2")
#> name version type last_day last_week last_month last_quarter last_half grand_total
#> 1 digest <NA> Imports 30915 197135 992112 2956521 5077241 43549524
#> 2 glue <NA> Imports 62423 302536 1523995 4340958 7557204 42758650
#> 3 gtable >= 0.1.1 Imports 21663 129947 651320 2037624 3427430 26841705
#> 4 isoband <NA> Imports 24034 152648 756437 2411172 4424548 16086469
#> 5 MASS <NA> Imports 3971 28816 140938 428300 804317 9416911
#> 6 mgcv <NA> Imports 7109 22872 123990 447953 719669 6933554
#> 7 rlang >= 0.4.10 Imports 68029 441128 2020967 6509641 12043421 67191569
#> 8 scales >= 0.5.0 Imports 24462 149038 737337 2315333 3974440 34077837
#> 9 tibble <NA> Imports 46437 293190 1392810 4472978 8274610 51687533
#> 10 withr >= 2.0.0 Imports 35740 227038 1098520 3269447 5905686 30766402As with two previously described functions - get_available_packages and get_description, here you can also use bioc = TRUE or local = TRUE and again, in case the package is not available, the result will be NULL. Here you have another options to set.
The first one is parameter downloads – should number of downloads of packages be included? It uses get_downloads and works only with CRAN packages.
Another, more important parameter is dependency_type. You can specify how detailed should be list of dependencies. Default value is "strong", which is a shorthand for c("Depends", "Imports", "LinkingTo"), but you can chose any combination of those and additionally "Suggests", "Enhances".
get_dependencies("ggplot2", downloads = FALSE, dependency_type = c("Imports", "Suggests", "Enhances"))
#> name version type
#> 1 digest <NA> Imports
#> 2 glue <NA> Imports
#> 3 gtable >= 0.1.1 Imports
#> 4 isoband <NA> Imports
#> 5 MASS <NA> Imports
#> 6 mgcv <NA> Imports
#> 7 rlang >= 0.4.10 Imports
#> 8 scales >= 0.5.0 Imports
#> 9 tibble <NA> Imports
#> 10 withr >= 2.0.0 Imports
#> 11 covr <NA> Suggests
#> 12 ragg <NA> Suggests
#> 13 dplyr <NA> Suggests
#> 14 ggplot2movies <NA> Suggests
#> 15 hexbin <NA> Suggests
#> 16 Hmisc <NA> Suggests
#> 17 interp <NA> Suggests
#> 18 knitr <NA> Suggests
#> 19 lattice <NA> Suggests
#> 20 mapproj <NA> Suggests
#> 21 maps <NA> Suggests
#> 22 maptools <NA> Suggests
#> 23 multcomp <NA> Suggests
#> 24 munsell <NA> Suggests
#> 25 nlme <NA> Suggests
#> 26 profvis <NA> Suggests
#> 27 quantreg <NA> Suggests
#> 28 RColorBrewer <NA> Suggests
#> 29 rgeos <NA> Suggests
#> 30 rmarkdown <NA> Suggests
#> 31 rpart <NA> Suggests
#> 32 sf >= 0.7-3 Suggests
#> 33 svglite >= 1.2.0.9001 Suggests
#> 34 testthat >= 2.1.0 Suggests
#> 35 vdiffr >= 1.0.0 Suggests
#> 36 xml2 <NA> Suggests
#> 37 sp <NA> EnhancesResult of this function is not cached (at least yet).
deepdep
The main function of the package – it is simply wrapper around get_dependencies, that allows you getting not only dependencies, but also dependencies of the dependencies iteratively! (Now you know, why we called it deepdep).
Parameters are the same as in get_dependencies, but additionally you can specify depth parameter, which describes how many iterations it function should perform. If depth equals 1, it’s simply the same as calling get_dependencies.
deepdep("ggplot2", depth = 2)
#> origin name version type origin_level dest_level
#> 1 ggplot2 digest <NA> Imports 0 1
#> 2 ggplot2 glue <NA> Imports 0 1
#> 3 ggplot2 gtable >= 0.1.1 Imports 0 1
#> 4 ggplot2 isoband <NA> Imports 0 1
#> 5 ggplot2 MASS <NA> Imports 0 1
#> 6 ggplot2 mgcv <NA> Imports 0 1
#> 7 ggplot2 rlang >= 0.4.10 Imports 0 1
#> 8 ggplot2 scales >= 0.5.0 Imports 0 1
#> 9 ggplot2 tibble <NA> Imports 0 1
#> 10 ggplot2 withr >= 2.0.0 Imports 0 1
#> 11 mgcv nlme >= 3.1-64 Depends 1 2
#> 12 mgcv Matrix <NA> Imports 1 2
#> 13 scales farver >= 2.0.3 Imports 1 2
#> 14 scales labeling <NA> Imports 1 2
#> 15 scales lifecycle <NA> Imports 1 2
#> 16 scales munsell >= 0.5 Imports 1 2
#> 17 scales R6 <NA> Imports 1 2
#> 18 scales RColorBrewer <NA> Imports 1 2
#> 19 scales viridisLite <NA> Imports 1 2
#> 20 tibble ellipsis >= 0.3.2 Imports 1 2
#> 21 tibble fansi >= 0.4.0 Imports 1 2
#> 22 tibble lifecycle >= 1.0.0 Imports 1 2
#> 23 tibble magrittr <NA> Imports 1 2
#> 24 tibble pillar >= 1.6.2 Imports 1 2
#> 25 tibble pkgconfig <NA> Imports 1 2
#> 26 tibble rlang >=\n0.4.3 Imports 1 1
#> 27 tibble vctrs >= 0.3.8 Imports 1 2plot_dependencies
As famous quote says,
A picture is worth more than a thousand words.
That’s why we have plot_dependencies function. It allows visualizing easily what are dependencies of specified package.
The function is generic, and currently supports two types of object – you can pass a deepdep object, result of the calling the deepdep function or just type name of the package. With the latter option you can also pass arguments to get_dependencies as additional parameters.
dd <- deepdep("tibble", 2)
plot_dependencies(dd)
plot_dependencies("DT", depth = 2, dependency_type = c("Imports", "Depends", "Suggests"))
In each of the plots you can see one package name in the centre and two circles of packages gathered around them. These are dependencies of the first and second level.
Default plot type is circular, as you can see on the examples presented above. However, you can set plot_type parameter to tree.
plot_dependencies(dd, type = "tree")
Not all dependencies are plotted. To increase readability, dependencies on the same level are hidden, but you can change this behaviour
plot_dependencies(dd, same_level = TRUE)
You can also make use of numbers of downloads you obtained. There is an option to add labels to only certain percentage of most downloaded packages among those that are about to be plotted. This is meant to increase readability of the plot.
plot_dependencies("tidyverse", type = "circular", label_percentage = 0.2, depth = 3)
Finally, returned object is a ggplot object, so you can easily manipulate them with syntax known from ggplot2 package. We also use ggraph enhancement for plotting graphs.
plot_dependencies(dd) +
ggplot2::scale_fill_manual(values = c("#462CF8", "#F23A90", "#AF1023")) +
ggraph::scale_edge_color_manual(values = "black")
#> Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the
#> existing scale.