pkgsimil

Similarity metrics between R packages, functions, or any code, based on similarity of code, documentation, or both.

If the package has not yet been installed, the following line needs to be run:

remotes::install_github ("ropensci-review-tools/pkgsimil")

The package can then be loaded for us with:

library (pkgsimil)

The package measures similarity from Large Language Model (LLM) embeddings and requires a locally-running instance of ollama, as described in the following sub-section.

Setting up the LLM embeddings

The LLM embeddings are extracted from a locally-running instance of ollama. That means you need to download and install ollama on your own computer in order to use this package. Once downloaded, ollama can be started by calling ollama serve. The particular models used to extract the embeddings will be automatically downloaded by this package if needed, or you can do this manually by running the following two commands (in a shell; not in R):

ollama pull jina/jina-embeddings-v2-base-en
ollama pull ordis/jina-embeddings-v2-base-code

You’ll likely need to wait up to half an hour or more for the models to download before proceeding.

Using the pkgsimil package

The package has two main functions:

• pkgsimil_similar_pkgs() to find similar rOpenSci packages based input as either a local path to an entire package, or as a single descriptive text string; and
• pkgsimil_similar_fns() to find similar functions from rOpenSci packages based on descriptive text input.

The following code demonstrates how these functions work, first with two demonstrates of finding packages:

input <- "
Packages for analysing evolutionary trees, with a particular focus
on visualising inter-relationships among distinct trees.
"
pkgsimil_similar_pkgs (input)

## [1] "phruta"        "dendroNetwork" "rotl"          "occCite"      
## [5] "phylotaR"

input <- "Download global-scale spatial data"
pkgsimil_similar_pkgs (input)

## [1] "rnaturalearth"      "rfema"              "rnaturalearthhires"
## [4] "GSODR"              "helminthR"

And then two demonstrates of finding functions from rOpenSci packages:

input <- "A function to label a set of geographic coordinates"
pkgsimil_similar_fns (input)

## [1] "GSODR::nearest_stations"           "refsplitr::plot_addresses_points" 
## [3] "quadkeyr::grid_to_polygon"         "rnoaa::meteo_nearby_stations"     
## [5] "refsplitr::plot_addresses_country"

input <- "Identify genetic sequences matching a given input fragment"
pkgsimil_similar_fns (input)

## [1] "textreuse::align_local"       "charlatan::SequenceProvider" 
## [3] "beastier::is_alignment"       "phylotaR::mk_txid_in_sq_mtrx"
## [5] "traits::ncbi_byid"

Prior Art

• The utils::RSiteSearch() function.
• The sos package that queries the “RSiteSearch” database.