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Update pkgdown workflow to include additional R packages and refs.
Prevent NAs in show method by handling max.print truncation.
Handle negative and out-of-order indexing.
Require explicit opt-in for sparse-to-dense conversion.
Cast comparison operators to numeric for type safety.
Use direct slot access in transpose method.
Conditionally check overwrite for dbMatrix creation.
Improve verbosity messages and remove redundant logging in dbMatrix functions.
Support transposed precompute tables.
Add streaming SVD for dbSparseMatrix including fallback to BPCells::svds() for LTM data.
Add Math SQL translations for log1p(),
ln() and log() functions.
Add is.na() method.
match()
(dimname-returning functions return characters as expected).Use temp tables and inline SQL (small queries still use inline SQL; otherwise register a temp table to avoid large string parsing bottlenecks).
Centralize internal type-check functions in
dbProject.
Simplify summary methods to always return vectors.
Rename dbVector internals and add column-wise recycling.
Improve as.matrix() and compute() for
dbMatrix.
Untrack docs/ folder.
Consolidate class documentation and update vignettes.
Update build config and move package data to inst/extdata.
Update package metadata and dependencies.
Update roxygen.
Update .gitignore to exclude compiled artifacts.
Ensure as.matrix returns unnamed matrix when names=FALSE.
Update show methods to handle duplicate dimnames via index filtering.
Pkgdown errors.
Ensure rowVars/colVars preserve empty dimensions.
Make compute s3 and use CTAS instead.
Optimize precompute with parquet and auto-attach existing tables.
Implement native ingestion for various Matrix classes via
as.dbMatrix.
Add coercion methods for dbMatrix to matrix/Matrix
objects.
Add .check_mem_limit internal function.
Support overwrite arg in
compute.dbMatrix.
writeMM method for dbMatrix objects.
Add value_colName support to dbMatrix_from_tbl for
pre-aggregated counts.
Update roxygen version.
Ignore benchmarks/ repo.
Update NAMESPACE with s3 exports.
Tidy roxygen.
Tidy + update global options in dbMatrix.
Clean up roxygen comments & improve documentation formatting.
Tidy extract.R with air and
jarl.
Tidy .R files with air and
jarl.
Delegate dbMatrix construction to as.dbMatrix generic for native R matrix ingestion.
Clean up Math Summary ops so to use subqueries and R zero inflation.
Optimize sparse –> matrix conversion.
Improve mem safety of as.matrix for dense matrix
conversions.
Use head/tail filter pushdown in show method for dbMatrix objects.
Improve extract by using
duckdb_register for large indices.
Optimize arith helpers with lazy queries instead of generating views.
compute.load() to
dbLoad(): The load method has been
renamed to dbLoad to avoid masking
base::load(). Generic moved to dbProject
package for consistency across dbverse.S4 to S3 Method Conversion: Converted
rownames(), colnames(), nrow(),
ncol(), and their setters from S4 to S3 methods for simpler
dispatch. Only %in% remains S4 (requires double dispatch).
This significantly reduces package load messages.
Internal Function Cleanup:
castNumeric from S4 generic to internal
function .castNumeric()_tmp prefix in
row/column summary methods for consistencydbList generic to dbProject
packagearrow::to_duckdb() with inline SQL for extract
operations..mtx file reader header detection logic.dbProject Integration: Full integration with
dbProject package and dbData base class
architecture. dbMatrix now inherits from dbData providing
unified database-backed object interface across dbverse
ecosystem.
Statistical Methods: Added
rowSds(), colSds(), rowVars(),
and colVars() methods for both dbDenseMatrix and
dbSparseMatrix.
dbVector Support: Internal support for dbVector arithmetic operations.
dbverse-org organization from
previous location.dbverse-org
organization structure.cli to imports for better user messaging.memory and
names parameters for summary functions.compute(),
as.matrix(), and arithmetic operations.arrange() from lazy evaluation paths
in summary methods. Now only applies ordering when materializing results
to memory.sim_dgc() function to use correct number of
random values (rnorm(n_vals) instead of
rnorm(num_cols)), eliminating “number of items to replace”
warnings.context() call in test files
(testthat 3rd edition).to_view() calls to pass tbl objects
instead of dbMatrix objects to dbProject functions.init slot to dbMatrix class definition.t() method.names() method to return NULL for regular
matrices instead of throwing errors.Ops() method for
dbMatrix.get_con()
function.dbReconnect() method from generics (moved to
dbProject/dbData).dbProject::dbData base class.dbProject from Suggests, added proper Remotes
reference.dbMatrix summary methods now return dbDenseMatrix
objects instead of in-memory vectors.
Removed colTypes from castNumeric.
Removed @name check in initialize.
New compute method for saving dbMatrix objects. This
writes the dbMatrix object to a table in the database along with its row
and column names (e.g. ‘dbMatrixname_rownames’).
New load method for loading computed dbMatrix
objects. The dbMatrix::compute() method must be called before loading
the object.
Updated .check_overwrite to allow for passing
overwrite arg.
New internal function write_dimnames to enable
saving dbMatrix objects.
New sum method for dbMatrix objects.
Improvements to precomputed table: Use existing precomputed table in db if available.
Improvements to precomputed table: Transpose precomputed table of sufficient dimensions if it exists instead of creating a new one. This is done via a TEMPORARY VIEW to avoid writing to disk and modifying existing precomputed table which may be referenced by other tables.
Custom SQL statement for todbDense conversion
creates a TEMPORARY VIEW with name
dbDenseMatrix_hash.
Update whitespace.
Update dbMatrix constructor roxygen.
Update roxygen in toDbDense.
Update reference page.
Update mean documentation.
Update log documentation.
Update roxygen.
dbMatrix::dbMatrix().Add more tests for dbMatrix and
dbDenseMatrix.
Add internal function map_ijx_dimnames.
Add internal function dbMatrix_from_tbl.
Extract now constructs unique temporary virtual tables in the arrow schema.
Document pkgdown website.
Add cli to imports.
Update generics.
Be more explicit about non-supported Arith and
Ops operations.
Fix show() method for dbDenseMatrix
objects.
Improve show function for dbDenseMatrix.
Updated simulate functions to include overwrite param.
Update .check_overwrite() internal function to avoid bug in overwritting passed table.
check_overwrite input validationAdd new precompute function to speed up matrix
densification.
Add new show function for dbDenseMatrix with pretty color and better spacing.
Add new save function to save a
dbMatrix.
Add new input validation functions.
Update docs.
Update imports to include glue, bit64
and crayon.
Update constructor calls in sim functions.
Remove redundant con from constructor.
Remove db_path from constructor.
Constructor db_path arg change to con
object.
dgTMatrix to in-memory matrix types supported in
dbMatrix constructor.Set :memory: to default db_path in constructor.
Update createDBMatrix docs.
Spacing.
Update after constructor fix.
Remove :temp: in place of :memory:.
Remove “:temp:” from tests.
Replace ‘:temp:’ with ‘:memory:’.
Add matrix in addition to dgCMatrix in as_ijx().
Add unit tests for scalar arith.
Add unit tests for names.R.
Remove random browser() call.
Add MatrixGenerics to deps.
Update gitignore.
Add boolean indexing tests to
test-extract.R.
Add as_ijx() convenience function.
Update createDBMatrix() to use dplyr::copy_to().
Update as_matrix() convenience function.
Add unit tests for extract methods.
Add log().
Update toDbDense to use dplyr instead of SQL.
Update DESCRIPTION to include testthat.
Update docs.
update dbIndex superclass
update as_matrix()
Update docs.
Migrate site link to drieslab.
Move {Matrix} to Imports.
Update overview.Rmd.
Update operations vignette.
Only densify if necessary. != 0, +/-.
toDbDense() previously updated table by value. change to update by reference via VIEW creation of table named ‘dense’.
Update docs.
Update gitignore.
Fix incorrect aggregate operations.
Fixes after con slot removal.
Add get_con().
Add dbDisconnect() generic.
Update accessors.
Update vignettes.
Update README.
Update gitignore.
Update docs.
Update NEWS.
Update docs.
Update site.
Update gitignore.
Updates to dbSparseMatrix rowMeans, colMeans.
Updates to colSums and rowSums for dbSparseMatrix.
Update dbMatrix constructor dimnames issues.
Update DESCRIPTION, remove redundant Matrix import, dep.
Update docs.
Update roxygen for operations.
dims and dim_names in
createDBMatrix() retained from in-memory matrix or Matrix
objectcreateDBMatrix()Update docs.
Add docs.
Update docs and DESCRIPTION.
Migration dbMatrix.
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