v1.4.2

Added a new argument "cat.threshold" in glmm.gei to allow users to control the cut-off threshold for interaction terms and interaction covariates to be treated as categorical (thanks to: Simon Wiegrebe).

v1.4.1

Removed "ARMA_DONT_PRINT_ERRORS" in fitglmm.cpp (which was deprecated in RcppArmadillo version 0.11.2.1.0) and fixed minor bugs identified in the tests for link-time optimization type mismatches (thanks to: Prof. Brian Ripley).

v1.4.0

1. Added a new argument "covar.center" in glmm.gei to allow users to control whether and how the covariates (including exposures) should be centered.
2. Fixed a bug in reading BGEN files in glmm.gei. A sample file is expected to overwrite (possibly reshuffled) sample IDs in the BGEN file (thanks to: Simon Wiegrebe and Thomas Winkler).
3. Fixed a bug in reading BGEN files for longitudinal analysis in glmm.gei. The BGEN files can now include extra samples that are not included in the null model object (thanks to: Simon Wiegrebe and Thomas Winkler).
4. Fixed a bug in calculating allele frequencies for longitudinal analysis in glmm.gei (thanks to: Simon Wiegrebe and Thomas Winkler).
5. Fixed several minor bugs in the output for BGEN files in glmm.gei. An extra tab between "AF" and "Beta_Marginal" was removed. The empty second row was removed. Three incorrect columns for continuous exposures were removed (thanks to: Simon Wiegrebe and Thomas Winkler).
6. Improved error control for negative variances in glmm.gei.
7. Added minor allele count and Rsq filters in glmm.gei (thanks to: Simon Wiegrebe and Thomas Winkler).
8. Added support for imputed dosage GDS files (in the node annotation/format/DS/data).
9. Fixed a minor bug in output header names in glmm.gei.meta (thanks to: Christopher Bryan).

v1.3.2

1. Fixed a minor bug in MAGEE.meta when meta-analyzing interactions with multiple exposures (thanks to: Christopher Bryan).
2. Removed the "usernames" option for xcolor.sty.

v1.3.1

Bioconductor packages SeqArray and SeqVarTools moved to Suggests.

V1.3.0

1. Check for system copies of zstd and libdeflate libraries.
2. Fixed a minor bug in reading the ID column for bgen sample files in MAGEE and glmm.gei.
3. Fixed a minor bug in calling the internal function fix.dgesdd in glmm.gei.
4. Replaced read.table by the more efficient function data.table::fread.
5. Implemented a new argument "AF.strata.range" to filter variants based on their environmental exposure stratum-specific coding allele frequencies in MAGEE.
6. Removed context in testthat tests.
7. Replaced print and cat in the code by message and warning.
8. Minor changes in the man directory, per CRAN policy.

V1.2.1

1.Optimized file reading functions;
2. Implemented AF.strata.range in the MAGEE function to customize the minimum and maximum coding allele frequencies of variants in each stratum that should be included in the analysis, if the environmental factor is categorical.

v1.2.0

Added meta-analysis

v1.0.2

Functionality from v1.0.1 on CRAN plus more robust MAGEE function.