virusMetadata
field to DataSpaceConnection
which shows virus metadata for viruses used in NAb assays (thanks @helenmiller16 #26)availablePublications
field to DataSpaceConnection
which summarizes all available publications (thanks @helenmiller16 #27)downloadPublicationData
method to DataSpaceConnection
which will download available publication data for a specified publication (thanks @helenmiller16 #27)Accessing Publication Data
(thanks @helenmiller16 #27)PKMAb
dataset available to retrieve in DataSpaceStudy
(thanks @helenmiller16 and @jmtaylor-fhcrc #27)mabGridSummary$geometric_mean_curve_ic50
calculation to reflect updated data. (thanks @helenmiller16 #28)tolower
in functions that check study names. (thanks @jmtaylor-fhcrc #23)DataSpaceMab
class and several methods and fields in DataSpaceConnection
to allow access to monoclonal antibody data (thanks @jmtaylor-fhcrc #14, #19, #21)writeNetrc
. (CRAN requirement)getDataset
method in DataSpaceStudy
to take mergeExtra
as an argument in order to merge extra information (demographics and treatment arm). #5DataSpaceConnection
and DataSpaceStudy
classes to convert data.frame objects to data.table.getGroup
method in DataSpaceConnection
class and deprecated groupId
in getStudy
method.refresh
method for both connection and study classes.studyInfo
field in study class.short_name
, type
, status
, stage
, species
, start_date
, strategy
) in availableStudies
.availableGroups
field to DataSpaceConnection
class.getStudy
method in DataSpaceConnection
to take groupId
as an argument in order to create a DataSpaceStudy
object for a particular group.DataSpaceConnection
class and connectDS
constructor to be not study-specific.getUserEmail()
to get email from netrc file.getVariableInfo
method to DataSpaceConnection
class.getAvailableDatasets
to lowercase.treatmentArm
field to DataSpaceConnection
class.getAvailableDatasets
method (now a private method).dataspace-staging.cavd.org
) to production (dataspace.cavd.org
).write_netrc
and check_netrc
to writeNetrc
and checkNetrc
.connectDS()
and other basic functions.tests
to test the package..travis.yml
to build and check the package automatically. (not used yet)codecov.yml
to track code coverage. (not used yet)README.Rmd
to introduce the package.NEWS.md
to track changes to the package._pkgdown.yml
and /docs
to build a package website.Intro_to_DataSpaceR.Rmd
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