NEWS.md

In ropensci/DataSpaceR: Interface to 'the CAVD DataSpace'

DataSpaceR 0.7.7

• Fixed issues querying mab and donor information.
• Added workarounds for errors and warnings when trying to verify certs and querying the database with GROUP_CONCAT operations.

DataSpaceR 0.7.6

• Add new feature adding LANL metadata to NAb mAb data pulls.
• Add new list of virus name mapping tables as an active binding.

DataSpaceR 0.7.5

• Fixed bug concerning missing cookie session name for app reports which will update this package to work when run on CDS as in a report.
• Show NI data in available datasets active binding which will allow users to look for NI (non-integrated) data in DSR.
• Set active binding names to snake case which is in effort to standardize fields names used in the API.
• Add all authors to publication table which will allow users to find publication by authors who were not listed as the primary author.

DataSpaceR 0.7.4

• Added virusMetadata field to DataSpaceConnection which shows virus metadata for viruses used in NAb assays (thanks @helenmiller16 #26)
• Added availablePublications field to DataSpaceConnection which summarizes all available publications (thanks @helenmiller16 #27)
• Added downloadPublicationData method to DataSpaceConnection which will download available publication data for a specified publication (thanks @helenmiller16 #27)
• Added a vignette: Accessing Publication Data (thanks @helenmiller16 #27)
• Made PKMAb dataset available to retrieve in DataSpaceStudy (thanks @helenmiller16 and @jmtaylor-fhcrc #27)
• Relaxed some assumptions when pulling non-integrated data, which allows users to pull non-integrated mab data, like in cvd812. (thanks @helenmiller16 #28)
• Fixed a test for mabGridSummary$geometric_mean_curve_ic50 calculation to reflect updated data. (thanks @helenmiller16 #28)
• Updated documentation using the R6 documentation syntax in roxygen

DataSpaceR 0.7.3

• Remove tolower in functions that check study names. (thanks @jmtaylor-fhcrc #23)
• Update DataSpaceStudy methods for non-integrated datasets. (thanks @helenmiller16 #24)

DataSpaceR 0.7.2

• Fix broken and invalid URLs for CRAN submission

DataSpaceR 0.7.1

• Fix broken and invalid URLs for CRAN submission

DataSpaceR 0.7.0

• Added DataSpaceMab class and several methods and fields in DataSpaceConnection to allow access to monoclonal antibody data (thanks @jmtaylor-fhcrc #14, #19, #21)

DataSpaceR 0.6.3

• Prepare for CRAN submission

DataSpaceR 0.6.2

• Write the netrc in temporary directory as default in writeNetrc. (CRAN requirement)

DataSpaceR 0.6.1

• Remove LICENSE file for CRAN submission

DataSpaceR 0.6.0

• rOpenSci submission: https://github.com/ropensci/software-review/issues/261

DataSpaceR 0.5.2

• Modified getDataset method in DataSpaceStudy to take mergeExtra as an argument in order to merge extra information (demographics and treatment arm). #5

DataSpaceR 0.5.1

• Adjusted the package to use the latest version of Rlabkey (v2.2) and httr packages.

DataSpaceR 0.5.0

• Modified DataSpaceConnection and DataSpaceStudy classes to convert data.frame objects to data.table.
• Added a package startup message on the terms of use.
• Created getGroup method in DataSpaceConnection class and deprecated groupId in getStudy method.

DataSpaceR 0.4.2

• Added refresh method for both connection and study classes.
• Added studyInfo field in study class.

DataSpaceR 0.4.1

• Included additional columns (short_name, type, status, stage, species, start_date, strategy) in availableStudies.
• Updated the introductory vignette.

DataSpaceR 0.4.0

• Added availableGroups field to DataSpaceConnection class.
• Modified getStudy method in DataSpaceConnection to take groupId as an argument in order to create a DataSpaceStudy object for a particular group.

DataSpaceR 0.3.0

• Updated DataSpaceConnection class and connectDS constructor to be not study-specific.

DataSpaceR 0.2.1

• Modified getUserEmail() to get email from netrc file.
• Updated license to GPL-3.

DataSpaceR 0.2.0

• Added getVariableInfo method to DataSpaceConnection class.
• Changed variable names in getAvailableDatasets to lowercase.
• Added treatmentArm field to DataSpaceConnection class.
• Removed getAvailableDatasets method (now a private method).
• Changed the default connection from staging (dataspace-staging.cavd.org) to production (dataspace.cavd.org).
• Added an option to connect to the staging server.
• Renamed write_netrc and check_netrc to writeNetrc and checkNetrc.

DataSpaceR 0.1.0

• Initialized the package with connectDS() and other basic functions.
• Added a test framework on tests to test the package.
• Added .travis.yml to build and check the package automatically. (not used yet)
• Added codecov.yml to track code coverage. (not used yet)
• Added README.Rmd to introduce the package.
• Added NEWS.md to track changes to the package.
• Added _pkgdown.yml and /docs to build a package website.
• Added a introductory vignette called Intro_to_DataSpaceR.Rmd.

ropensci/DataSpaceR documentation built on Feb. 25, 2025, 12:25 a.m.