Benchmark results against external PLS implementations — external_pls

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.

Source

Generated via inst/scripts/external_pls_benchmarks.R.

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)
#> $package
#> [1] 24
#> 
#> $algorithm
#> [1] 32
#> 
#> $task
#> [1] 96
#> 
#> $n
#> [1] 48
#> 
#> $p
#> [1] 48
#> 
#> $ncomp
#> ncomp
#>   1   3  10 100 
#>  24  24  36  12 
#> 

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)
#> $package
#> [1] 8
#> 
#> $algorithm
#> [1] 32
#> 
#> $task
#> [1] 32
#> 
#> $n
#> [1] 16
#> 
#> $p
#> [1] 16
#> 
#> $ncomp
#> ncomp
#>   1   3  10 100 
#>   8   8  12   4 
#> 

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)
#> $package
#> [1] 48
#> 
#> $algorithm
#> [1] 64
#> 
#> $task
#> [1] 192
#> 
#> $n
#> [1] 96
#> 
#> $p
#> [1] 96
#> 
#> $ncomp
#> ncomp
#>  1  3 10 
#> 48 48 96 
#> 

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)
#> $package
#> [1] 16
#> 
#> $algorithm
#> [1] 64
#> 
#> $task
#> [1] 64
#> 
#> $n
#> [1] 32
#> 
#> $p
#> [1] 32
#> 
#> $ncomp
#> ncomp
#>  1  3 10 
#> 16 16 32 
#> 
# }