ieugwasr 1.2.0

• associations() now returns the processed tibble. Previously its ... %>% return() inside a pipe did not return from the function (since magrittr 2.0), so the raw server data frame was returned instead, with n as character.
• Remove the flipping of beta for ukb-e datasets in associations(), tophits() and phewas(). The flip was never applied in associations() (see above), and the OpenGWAS server is the right place to correct these datasets.
• Replace %>% return() with explicit return() calls throughout.
• Update some GitHub Actions workflows, including no longer testing on R before R 4.1 due to the new testthat requirements
• Tweak an API test
• Bump version of roxygen2
• Fix a typo in the documentation for ld_clump()
• Bump minimum required version of R to 4.1
• Update some URLs in the package
• Fix some typos in the docs
• Forward ... to api_query() in variants_chrpos()
• Prevent divide-by-zero chunking in associations()
• Handle NULL opengwas_jwt in api_query()
• Close connection in afl2_list() hapmap3 branch
• Harden fill_n() against empty or multi-row gwasinfo() results
• Use getOption() instead of copying the full options list
• Remove dead shadowing assignment in associations()
• Use seq_along()/seq_len() instead of 1:length() loop bounds
• Align ld_clump_api() defaults with its documentation
• Make get_query_content() error path robust to non-JSON bodies
• Fix empty-result check in tophits() (closes #76)
• Supply origin to as.POSIXct() in allowance reset handling (closes #103)
• Remove utils from Suggests, since it’s a Base package

ieugwasr 1.1.0

• Improved error handling
• Managing new API limits on associations endpoint
• Updated header info passed to API

ieugwasr 1.0.4

• Improved warning messages in ld_clump() (thanks @DarwinAwardWinner).
• ld_clump() and ld_matrix() now search for the plink binary as documented (thanks @DarwinAwardWinner).
• Made some minor amends in the helpfiles and vignettes including: fixing typos, replacing all references to MR-Base with OpenGWAS, and improving the gwasinfo_files() helpfile.
• Fixed bug in headers code in api_query() (thanks @Gaoyan152).

ieugwasr 1.0.3

• Add gwasinfo_files() function to return for each dataset specified the download URL for each file (.vcf.gz, .vcf.gz.tbi, _report.html) associated with the dataset. The URLs will expire in 2 hours.

ieugwasr 1.0.2

• Bump roxygen2 version
• Update OpenGWAS API URL

ieugwasr 1.0.1

• Checking for allowance depletion, and erroring until the allowance is reset
• Import the magrittr pipe (thanks @Bhashitha2014)

ieugwasr 1.0.0

• Introducing JWT authorisation for the API
• Phasing out Google Oauth2 authorisation
• Added user() function to get user information
• Fixing issue with anonymous functions and backwards compatibility
• Bug in tophits when result is empty
• Removing version check at startup
• Bug in querying when errors returned
• Removing unnecessary dependencies and vignettes

ieugwasr 0.2.2

• Reinstating https://api.opengwas.org/api/ as the API server address
• Fixing issues with tests failing when server load is an issue

ieugwasr 0.2.1

• Updating API server address temporarily
• Modifying tests to manage API server load
• Fixes to load/attach behaviour

ieugwasr 0.2.0

• Moving API address to https://api.opengwas.org/api/
• Fixing issues for CRAN release

ieugwasr 0.1.7

• Added functions to write LD scores files into compressed .gz files for each super-population and divided by chromosomes.
• Added argument to output gwasglue2 objects in ieugwasr::tophits() and ieugwasr::associations().

ieugwasr 0.1.6

• Adding messaging about package version

• Adding messaging about OpenGWAS # ieugwasr 0.1.5

• Added options to perform LD functions on different super-populations

• Catching 503 error codes and retrying up to 5 times. This should help avoid fails when the server is busy.

ieugwasr 0.1.4

• Bug fixes in clumping. Thanks to bethleegy for pointing this out

ieugwasr 0.1.3

• Bug fixes in clumping

ieugwasr 0.1.2

• Updated API address

ieugwasr 0.1.1

• Fixed bug in ld_clump - wasn’t doing all traits

ieugwasr 0.1.0

• First release in conjunction with API

ieugwasr 0.0.0.9000

• Added a NEWS.md file to track changes to the package.