bigPLSR (version 0.7.2)

external_pls_benchmarks: Benchmark results against external PLS implementations

Description

Pre-computed runtime comparisons between bigPLSR (dense and big.memory backends) and reference implementations from the pls and mixOmics packages.

Usage

data(external_pls_benchmarks)

Format

A data frame with 384 rows and 11 columns:

task

Character vector identifying the task ("pls1" or "pls2").

algorithm

PLS algorithm used for the benchmark (e.g., "simpls").

package

Package providing the implementation.

median_time_s

Median execution time in seconds.

itr_per_sec

Iterations per second recorded by bench::mark().

mem_alloc_bytes

Memory usage in bytes recorded by bench::mark().

n

Number of observations in the simulated dataset.

p

Number of predictors (X) in the simulated dataset.

q

Number of responses (Y) in the simulated dataset.

ncomp

Number of extracted components.

notes

Helpful context on dependencies or configuration.

Details

Fix task = "pls1" and select algorithms in "kernelpls", "nipals" or "simpls" to get a full factorial design. Fix task = "pls1" and fix algorithm = "widekernelpls" to get a full factorial design. Fix task = "pls2" and select algorithms in "kernelpls", "nipals" or "simpls" to get a full factorial design. Fix task = "pls2" and fix algorithm = "widekernelpls" to get a full factorial design.

Examples

# \donttest{
data("external_pls_benchmarks", package = "bigPLSR")

sub_pls1 <- subset(external_pls_benchmarks, task == "pls1" & 
                                            algorithm != "widekernelpls")
sub_pls1$n     <- factor(sub_pls1$n)
sub_pls1$p     <- factor(sub_pls1$p)
sub_pls1$q     <- factor(sub_pls1$q)
sub_pls1$ncomp <- factor(sub_pls1$ncomp)
if (exists("replications")) replications(~ package + algorithm + task + n +
                                           p + ncomp, data = sub_pls1)

sub_pls1_wide <- subset(external_pls_benchmarks, task == "pls1" & 
                                                 algorithm == "widekernelpls")
sub_pls1_wide$n     <- factor(sub_pls1_wide$n)
sub_pls1_wide$p     <- factor(sub_pls1_wide$p)
sub_pls1_wide$q     <- factor(sub_pls1_wide$q)
sub_pls1_wide$ncomp <- factor(sub_pls1_wide$ncomp)
if (exists("replications")) replications(~ package + algorithm + task + n + 
                                           p + ncomp, data = sub_pls1_wide)

sub_pls2 <- subset(external_pls_benchmarks, task == "pls2" & 
                                            algorithm != "widekernelpls")
sub_pls2$n     <- factor(sub_pls2$n)
sub_pls2$p     <- factor(sub_pls2$p)
sub_pls2$q     <- factor(sub_pls2$q)
sub_pls2$ncomp <- factor(sub_pls2$ncomp)
if (exists("replications")) replications(~ package + algorithm + task + n + 
                                           p + ncomp, data = sub_pls2)

sub_pls2_wide <- subset(external_pls_benchmarks, task == "pls2" & 
                                                 algorithm == "widekernelpls")
sub_pls2_wide$n     <- factor(sub_pls2_wide$n)
sub_pls2_wide$p     <- factor(sub_pls2_wide$p)
sub_pls2_wide$q     <- factor(sub_pls2_wide$q)
sub_pls2_wide$ncomp <- factor(sub_pls2_wide$ncomp)
if (exists("replications")) replications(~ package + algorithm + task + n + 
                                           p + ncomp, data = sub_pls2_wide)
# }