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Changelog

Source: NEWS.md

DataSpaceR 0.7.7

CRAN release: 2025-02-20

  • 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

CRAN release: 2022-06-24

  • 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

CRAN release: 2021-09-02

  • 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

CRAN release: 2020-08-26

  • 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

CRAN release: 2020-01-08

DataSpaceR 0.7.2

CRAN release: 2019-08-21

  • 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

CRAN release: 2019-04-05

  • 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

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.