Changelog
Source:NEWS.md
plmmr 4.0.0 (2024-10-07)
Major re-structuring of preprocessing pipeline: Data from external files must now be processed with
process_plink()
orprocess_delim()
. All data (including in-memory data) must be prepared for analysis viacreate_design()
. This change ensures that data are funneled into a uniform format for analysis.Re-worked vignettes: The vignettes/articles for the package are now all revised to include examples of the complete pipeline with the new
create_design()
syntax. There is an article for each type of data input (matrix/data.frame, delimited file, and PLINK).CRAN submission: We updated several items in the documentation in order to prepare for CRAN submission.
plmmr 3.2.0 (2024-09-02)
bigsnpr now in Suggests, not Imports: The essential filebacking support is now all done with
bigmemory
andbigalgebra
. Thebigsnpr
package is used only for processing PLINK files.dev branch gwas_scale has a version of the pipeline that runs completely file-backed.
plmmr 3.1.0 (2024-07-13)
Enhancement: To make
plmmr
have better functionality for writing scripts, the functionsprocess_plink()
,plmmm()
, andcv_plmm()
now (optionally) write ‘.log’ files, as in PLINK.Enhancement: In cases where users are working with large datasets, it may not be practical or desirable for all the results returned by
plmmm()
orcv_plmm()
to be saved in a single ‘.rds’ file. There is now an option in both of these model fitting functions called ‘compact_save’, which gives users the option to save the output in multiple, smaller ‘.rds’ files.Argument removed: Argument
std_needed
is no longer available inplmm()
andcv_plmm()
functions.
plmmr 3.0.0 (2024-06-27)
Bug fix: Cross-validation implementation issues fixed. Previously, the full set of eigenvalues were used inside CV folds, which is not ideal as it involves information from outside the fold. Now, the entire modeling process is cross-validated: the standardization, the eigendecomposition of the relatedness matrix, the model fitting, and the backtransformation onto the original scale for prediction.
Computational speedup: The standardization and rotation of filebacked data are now much faster;
bigalgebra
andbigmemory
are now used for these computations.Internal: On the standardized scale, the intercept of the PLMM is the mean of the outcome. This derivation considerably simplifies the handling of the intercept internally during model fitting.