Performs optimized diagonal subtraction between two datasets stored in HDF5 format. Automatically detects whether inputs are matrices (extracts diagonals) or vectors (direct operation) and uses the most efficient approach. This function is ~50-250x faster than traditional matrix operations for diagonal computations.
String. Path to the HDF5 file containing the datasets.
group
String. Group path containing the first dataset (A, minuend).
A
String. Name of the first dataset (minuend).
B
String. Name of the second dataset (subtrahend).
groupB
Optional string. Group path containing dataset B. If NULL, uses same group as A.
target
Optional string. Where to write result: “A”, “B”, or “new” (default: “new”).
outgroup
Optional string. Output group path. Default is “OUTPUT”.
outdataset
Optional string. Output dataset name. Default is “A_-_B” with .diag suffix if appropriate.
paral
Optional logical. Whether to use parallel processing. Default is FALSE.
threads
Optional integer. Number of threads for parallel processing. If NULL, uses maximum available threads.
overwrite
Optional logical. Whether to overwrite existing datasets. Default is FALSE.
4 Value
List with components:
fn: Character string with the HDF5 filename
ds: Character string with the full dataset path to the diagonal subtraction result (group/dataset)
5 Details
This function provides flexible diagonal subtraction with automatic optimization: - Operation modes: - Matrix - Matrix: Extract diagonals → vector subtraction → save as vector - Matrix - Vector: Extract diagonal → vector subtraction → save as vector
- Vector - Vector: Direct vector subtraction (most efficient) - Performance features: - Uses optimized vector operations for maximum efficiency - Automatic type detection and dimension validation - Memory-efficient processing for large datasets - Parallel processing support for improved performance - Validation checks: - Matrix inputs must be square (N×N) - Vector inputs must have compatible dimensions - Automatic dimension matching between operands
6 Examples
Code
library(BigDataStatMeth)# Create test matricesN <-1000set.seed(123)A <-matrix(rnorm(N*N), N, N)B <-matrix(rnorm(N*N), N, N)# Save to HDF5bdCreate_hdf5_matrix("test.hdf5", A, "data", "matrixA",overwriteFile =TRUE)bdCreate_hdf5_matrix("test.hdf5", B, "data", "matrixB",overwriteFile =FALSE)# Subtract diagonalsresult <-bdDiag_subtract_hdf5("test.hdf5", "data", "matrixA", "matrixB",outgroup ="results",outdataset ="diagonal_diff",paral =TRUE)
Source Code
---title: "bdDiag_subtract_hdf5"subtitle: "bdDiag_subtract_hdf5"---<span class="category-badge hdf5_algebra">HDF5_ALGEBRA</span>## DescriptionPerforms optimized diagonal subtraction between two datasets stored in HDF5 format.Automatically detects whether inputs are matrices (extracts diagonals) or vectors(direct operation) and uses the most efficient approach. This function is ~50-250xfaster than traditional matrix operations for diagonal computations.## Usage```rbdDiag_subtract_hdf5(filename, group, A, B, groupB =NULL, target =NULL, outgroup =NULL, outdataset =NULL, paral =NULL, threads =NULL, overwrite =NULL)```## Arguments::: {.param-table}| Parameter | Description ||-----------|-------------||`filename`| String. Path to the HDF5 file containing the datasets. ||`group`| String. Group path containing the first dataset (A, minuend). ||`A`| String. Name of the first dataset (minuend). ||`B`| String. Name of the second dataset (subtrahend). ||`groupB`| Optional string. Group path containing dataset B. If NULL, uses same group as A. ||`target`| Optional string. Where to write result: "A", "B", or "new" (default: "new"). ||`outgroup`| Optional string. Output group path. Default is "OUTPUT". ||`outdataset`| Optional string. Output dataset name. Default is "A_-_B" with .diag suffix if appropriate. ||`paral`| Optional logical. Whether to use parallel processing. Default is FALSE. ||`threads`| Optional integer. Number of threads for parallel processing. If NULL, uses maximum available threads. ||`overwrite`| Optional logical. Whether to overwrite existing datasets. Default is FALSE. |:::## Value::: {.return-value}List with components:- **`fn`**: Character string with the HDF5 filename- **`ds`**: Character string with the full dataset path to the diagonal subtraction result (group/dataset):::## DetailsThis function provides flexible diagonal subtraction with automatic optimization:- Operation modes: - Matrix - Matrix: Extract diagonals → vector subtraction → save as vector - Matrix - Vector: Extract diagonal → vector subtraction → save as vector - Vector - Vector: Direct vector subtraction (most efficient)- Performance features: - Uses optimized vector operations for maximum efficiency - Automatic type detection and dimension validation - Memory-efficient processing for large datasets - Parallel processing support for improved performance- Validation checks: - Matrix inputs must be square (N×N) - Vector inputs must have compatible dimensions - Automatic dimension matching between operands## Examples```{r}#| eval: false#| code-fold: showlibrary(BigDataStatMeth)# Create test matricesN <-1000set.seed(123)A <-matrix(rnorm(N*N), N, N)B <-matrix(rnorm(N*N), N, N)# Save to HDF5bdCreate_hdf5_matrix("test.hdf5", A, "data", "matrixA",overwriteFile =TRUE)bdCreate_hdf5_matrix("test.hdf5", B, "data", "matrixB",overwriteFile =FALSE)# Subtract diagonalsresult <-bdDiag_subtract_hdf5("test.hdf5", "data", "matrixA", "matrixB",outgroup ="results",outdataset ="diagonal_diff",paral =TRUE)```