NEWS.md

In crandep: Network Analysis of Dependencies of CRAN Packages

crandep 0.3.10 (2024-08-02)

Functions

• Add argument reverse for get_dep() and get_graph_all_packages(), & remove scrape for the former.
• Remove cran_url(), html_text_vec() and already deprecated get_dep_df() & get_dep_all().
• Introduce the use of native pipe operator |> in check_dep_word() & get_dep_vec().

Miscellaneous

• Update the DOI of the associated journal article.

crandep 0.3.9 (2024-05-30)

Functions

• Add obtain_u_set_mix2_constrained() for constrained version of obtain_u_set_mix2(). This assumes power law in the body i.e. theta = 1.0, and (1.0 / xi + 1.0) > alpha > 1.0, and "continuity" at the threshold u.
• Subsequently, add argument constrained in mcmc_mix2() & mcmc_mix2_wrapper() & lpost_mix2() to accommodate this constrained version.

crandep 0.3.8 (2024-04-30)

Functions

• Changes all instances of xmax to x_max for consistency.
• The default of invts in mcmc_*_wrapper() is set to 1.0 for no Metropolis coupling or power posterior.
• Add the argument u_max (and v_max if applicable) with defaults in mcmc_mix*_wrapper().

Others

• The in Description is changed to to adhere to the new practice.

crandep 0.3.7 (2024-03-28)

Functions

• Allows marginal likelihood calculations via power posterior in mcmc_pol() (for the polylog distribution) and mcmc_mix2() (for the 2-component mixture distribution). The combination of the existing argument invt for inverse temperatures and the new boolean argument mc3_or_marg determines either parallel tempering or power posterior or neither will be performed.
• The corresponding wrapper functions are updated accordingly.

crandep 0.3.6 (2024-02-26)

Functions

• Add marg_pow() for calculating the posterior density and marginal (log-)likelihood of the discrete power law i.e. the Zipf distribution.
• Change update() in C++ in preparation for marginal log-likelihood calculations for other models (Zipf-polylog, mixtures, etc.)

Vignettes

• Calculations using marg_pow() added to align with mcmc_pol() (when theta = 1.0) in terms of posterior density.

crandep 0.3.5 (2024-01-19)

Functions

• The argument name has been removed in the wrapper functions as it required data frames with a specific column name.
• Functions related to the TZP-power-law mixture model (mid-way of current 2-component & 3-component mixtures) are added.
• Wrapper functions of the 2-component & 3-component mixtures have the default arguments included in the body so they are relayed to obtain_u_set_mix2() or obtain_u_set_mix3().

crandep 0.3.4 (2023-12-19)

Functions

• The default value of s_alpha in mcmc_mix3_wrapper() is changed from 0.0 to 10.0.
• In obtain_u_set_mix3(), whether there is data between v & u is checked before optimisation. This prevents a warning when the "Brent" method is used (when only alpha is optimised as theta is fixed to 1.0), when there's no data points between v & u.
• In dpol() & Spol(), the check for alpha <= 1.0 is made only when theta == 1.0 i.e. the power law applies.

Documentation

• README.md is updated.

crandep 0.3.3 (2023-11-21)

Functions

• Added are obtain_u_set_mix2() and obtain_u_set_mix3(), which are functions for obtaining the profile posterior density for the 2-component and 3-component mixture models, respectively.
• Also added thin wrappers for mcmc_pol(), mcmc_mix2() and mcmc_mix3(), all with the suffix _wrapper. Specifically, mcmc_mix2_wrapper() calls obtain_u_set_mix2() and mcmc_mix2(), and mcmc_mix3_wrapper() calls obtain_u_set_mix3() and mcmc_mix3().

crandep 0.3.2 (2023-08-17)

Functions

• dupp() and mcmc_upp() are replaced by dpol() and mcmc_pol(), respectively, to facilitate a generalisation of the discrete power law, namely the Zipf-polylog distribution.
• dmix() and mcmc_mix() are replaced by dmix2() and mcmc_mix2(), respectively, with a new parametrisation, for the 2-component mixture distribution.
• dmix3() and mcmc_mix3() are added for the 3-component mixture distribution.

Dependencies

• RcppGSL is no longer needed as a LinkingTo dependency.

Vignettes and README

• The vignettes and README are updated according to the above changes.
• Also, the previous pipe operator "%>%" is replaced by the native one "|>" throughout the vignettes and README.

crandep 0.3.1 (2022-06-02)

Functions

• get_dep(), html_text_vec() and get_dep_all_packages() now return an error message if Internet resources are not available.

crandep 0.3.0 (2021-06-10)

Functions

• The previous functionality of get_dep() is replaced by that of get_dep_df(), while get_dep_df() is soft deprecated. This means the former is the single function for obtaining dependencies in a non-igraph object.

• The argument type in get_dep() and get_graph_all_packages() now allows Enhances and Reverse enhances as the value. These two kind of dependencies are also included in the data frame obtained using get_dep_all_packages().

crandep 0.2.0 (2021-05-10)

Functions

• Examples in internal functions html_text_vec(), get_dep_str() and get_dep_vec() removed to minimise the errors due to no internet connection and/or timeout.

• Multiple dependencies are now allowed in the type argument in get_graph_all_packages().

• Arguments give_log in dupp() & dmix() changed to log without changing the functionality. For uniformity, Supp() & Smix() are also given the additional argument log.

• The ordering of arguments in the funcions *mix() is made consistent.

Vignettes

• For the vignette on dependencies of all CRAN packages, community detection is added.

• Replace https://cran.r-project.org/web/packages/available_packages_by_name.html by https://cran.r-project.org, in the dependency network vignette, to prevent NOTE on possibly invalid URL.

• In the vignette on modelling the number of reverse dependencies, a section on fitting extreme value mixture distribution is added.

Data

• Added is a citation network of the CHI conference papers, that can serve as a comparison to the CRAN dependency network, in terms of network summaries and characteristics, such as degree distribution.

• Replace https://cran.r-project.org/web/packages/available_packages_by_name.html by https://cran.r-project.org, in the manual of cran_dependencies, to prevent NOTE on possibly invalid URL.

crandep 0.1.0 (2020-08-10)

New functions

• get_dep_all_packages() and get_graph_all_packages(): The former is for a data frame of all dependencies of all CRAN packages, while the latter is for the graph of one type of depenedencies of all CRAN packages.

• get_dep() replaces get_dep_all(), with the same functionality. get_dep() gets soft deprecated.

Minor changes

• The argument type in get_dep() and types in get_dep_df() allows input more flexibility. For reverse dependencies, either space or underscore is accepted for separating the words e.g. type = "reverse suggests" or type = "reverse_suggests".

• The argument types in get_dep_df() allows (as before) a character vector of dependency words. Also allowed now is types = "all" which means all of the four dependencies (depends, suggests, imports, linking to) and their reverse counterparts.

• Previously, there were issues with string manipulation for some packages without scraping. This is because, when using tools::CRAN_package_db(), there might be no space between the package name and the left parenthesis for the version. This is not an issue if scrape = TRUE as there is always a space on the CRAN page.

• In the output of get_dep_df() and get_dep_all_packages(), any LinkingTo and Reverse linking to dependencies will become "linking to" ("linking_to" previously) in the variable type, with "FALSE" and "TRUE" in the variable reverse, respectively. This is also updated in the data cran_dependencies.

Vignettes

• The sections on obtaining dependencies of all CRAN packages is now moved to a new vignette. In this vignette, we also provide interactive visualisation of the network of Depends of all packages.

• The degree modelling vignette is now for Imports network, not Depends network. In addition to discrete power law, a discrete extreme value mixture distribution is also used to model the same data set.

crandep 0.0.2 (2020-07-18)

New functions

• dupp() and Supp(): density and survival functions, respectively, of the discrete power law (above a threshold).
• mcmc_upp(): fitting the discrete power law (above a threshold) to data using Markov chain Monte Carlo (MCMC).
• dmix(), Smix(): density and survival functions, respectively, of a discrete extreme value mixture distribution.
• mcmc_mix(): fitting the discrete extreme value mixture distribution to data using MCMC.

Minor changes

• Additional argument in get_dep_all() and get_dep_df(): scrape = TRUE is the same as previous version, while scrape = FALSE means tools::CRAN_package_db() (thanks to Dirk Eddelbuettel (#1)) will be used instead. Note that changing this argument should still give the same result; the main difference is the time taken.

crandep documentation built on Sept. 11, 2024, 8:01 p.m.