Package 'BiocPkgStats'

Plot the download activity for a package

Description

Plot the download activity for a package

Usage

downloadTrend(package, since_date, include_recent = FALSE)

Arguments

package	character(1) The package to download activity for
since_date	character() The date from when to start looking at commit and issue history. This should be specified in the year, month, and day format, 'YYYY-MM-DD'. It can be a vector of dates that match the length packages.
include_recent	logical(1) Whether to include the latest month of download data. Usually, the data for the most recent month has incomplete numbers and is excluded (default is FALSE).

Examples

if (interactive()) {
downloadTrend("MultiAssayExperiment", "2017-05-01")
downloadTrend("cBioPortalData", "2017-05-01")
downloadTrend("RaggedExperiment", "2017-05-01")


downloadTrend("SingleCellMultiModal", "2017-05-01")
downloadTrend("curatedTCGAData", "2017-05-01")

# low downloads
downloadTrend("TENxIO", "2017-05-01")
downloadTrend("terraTCGAdata", "2017-05-01")
}

---

Create a report for a given set of packages

Description

The function compiles statistics for Bioconductor packages that have GitHub repositories. It uses functionality in BiocPkgTools to extract commit and issue history. A token is required to access the GitHub commit and issue history.

Usage

generateReport(packages, gh_org, since_date, outdir = ".", overwrite = FALSE)

Arguments

packages	character() A vector of valid package names that are installed
gh_org	character() The GitHub organization from which to read issue and commit data from. It can be either a scalar character to be recycled to the length of packages or a vector the length of packages for instances where packages are hosted under different GitHub organizations.
since_date	character() The date from when to start looking at commit and issue history. This should be specified in the year, month, and day format, 'YYYY-MM-DD'. It can be a vector of dates that match the length packages.
outdir	character(1) The directory in which to place rendered RMarkdown documents, by default they will be placed in the current working directory.
overwrite	logical(1) Whether to overwrite an existing rendered product, i.e., a runnable RMarkdown document.

Details

Note that packages must be installed in order to determine the package type via the biocViews field.

Authentication

The package uses the gh package calls from BiocPkgTools. Users must authenticate with a GitHub Fine Grained Token and add the token using gitcreds::gitcreds_set().

Examples

if (interactive()) {

generateReport(
    c(
        "MultiAssayExperiment", "cBioPortalData", "SingleCellMultiModal"
    ),
    gh_org = "waldronlab",
    since_date = "2017-05-01",
    overwrite = TRUE
)

}

---

Create a table of package metrics

Description

The function compiles statistics for Bioconductor packages that have GitHub repositories. It uses functionality in BiocPkgTools to extract commit and issue history. A token is required to access the GitHub commit and issue history. See the .token argument in ?gh::gh for details on its use.

Usage

generateTable(packages, gh_org, since_date)

Arguments

packages	character() A vector of valid package names that are installed
gh_org	character() The GitHub organization from which to read issue and commit data from. It can be either a scalar character to be recycled to the length of packages or a vector the length of packages for instances where packages are hosted under different GitHub organizations.
since_date	character() The date from when to start looking at commit and issue history. This should be specified in the year, month, and day format, 'YYYY-MM-DD'. It can be a vector of dates that match the length packages.

Details

Note that pull requests are a type of "issue" on GitHub; therefore, issues and pull requests are combined when reporting the number of closed issues since a specific date. For more information on how the queries are preformed, see the GitHub API documentation for the ⁠/repos/{owner}/{repo}/issues⁠ endpoint at https://docs.github.com/en/rest/issues and the gh R package. The following list describes each column in the returned data.frame:

• download.rank: The percentile rank of the package in its respective repository, e.g., software, data-experiment etc.

• avg.downloads: The average number of monthly downloads from distinct IP addresses since the given date

• med.downloads: The median number of montly downloads from distinct IP addresses since the given date

• num.revdeps: The number of "all" reverse dependencies including "Depends", "Imports", "LinkingTo", "Suggests", and "Enhances"

• issues.since: The number of closed issues (including pull requests) since the date given

• commits.since: The number of commits since the given date

Value

A data.frame of metrics, see the details section for specifics

Examples

if (interactive()) {

generateTable(
    packages = c(
        "MultiAssayExperiment", "cBioPortalData", "SingleCellMultiModal"
    ),
    gh_org = "waldronlab",
    since_date = "2019-05-01"
)

}

---

Gather support site statistics for a given period

Description

Gather support site statistics for a given period

Usage

supportSiteStats(from = "2021-01-01", to = "2021-12-31")

## S3 method for class 'bioc_support_stats'
print(x, ...)

Arguments

from	character(1) date in ISO 8601 format ("YYYY-MM-DD")
to	character(1) date in ISO 8601 format ("YYYY-MM-DD")
x	bioc_support_stats The class object that has a print method
...	Additional arguments to the print method. Not used.

Value

a bioc_support_stats list class with components userdiff, toplevdiff, questdiff, and respdiff

Author(s)

Vincent J. Carey

Examples

if (interactive()) {
supportSiteStats()
}

---