The R package splines2 is intended to be a user-friendly supplement to the base package splines.
The package splines2 (version 0.4.5.9000) provides functions to construct basis matrices of
In addition to the R interface, splines2 provides a C++ header-only library integrated with Rcpp, which allows the construction of spline basis functions directly in C++ with the help of Rcpp and RcppArmadillo. Thus, it can also be treated as one of the Rcpp* packages. A toy example package that uses the C++ interface is available here.
You can install the released version from CRAN.
The latest version of the package is under development at GitHub. If it is able to pass the automated package checks, one may install it by
if (! require(remotes)) install.packages("remotes")
remotes::install_github("wenjie2wang/splines2", upgrade = "never")The Online document provides a reference for all functions and contains the following vignettes:
Since v0.3.0, the implementation of the main functions has been rewritten in C++ with the help of the Rcpp and RcppArmadillo packages. The computational performance has thus been boosted and comparable with the function splines::splineDesign().
Some quick micro-benchmarks are provided for reference as follows:
library(microbenchmark)
library(splines)
library(splines2)
set.seed(123)
x <- runif(1e3)
degree <- 3
ord <- degree + 1
internal_knots <- seq.int(0.1, 0.9, 0.1)
boundary_knots <- c(0, 1)
all_knots <- sort(c(internal_knots, rep(boundary_knots, ord)))
## check equivalency of outputs
my_check <- function(values) {
all(sapply(values[- 1], function(x) {
all.equal(unclass(values[[1]]), x, check.attributes = FALSE)
}))
}For B-splines, function splines2::bSpline() provides equivalent results with splines::bs() and splines::splineDesign(), and is about 3x faster than bs() and 2x faster than splineDesign() for this example.
## B-splines
microbenchmark(
"splines::bs" = bs(x, knots = internal_knots, degree = degree,
intercept = TRUE, Boundary.knots = boundary_knots),
"splines::splineDesign" = splineDesign(x, knots = all_knots, ord = ord),
"splines2::bSpline" = bSpline(
x, knots = internal_knots, degree = degree,
intercept = TRUE, Boundary.knots = boundary_knots
),
check = my_check,
times = 1e3,
unit = "relative"
)Unit: relative
expr min lq mean median uq max neval cld
splines::bs 3.6523 3.5555 3.5506 3.4736 3.5177 1.1974 1000 c
splines::splineDesign 2.2324 2.1404 2.1467 2.0619 2.0942 1.0849 1000 b
splines2::bSpline 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1000 a Similarly, for derivatives of B-splines, splines2::dbs() provides equivalent results with splines::splineDesign(), and is about 2x faster.
## Derivatives of B-splines
derivs <- 2
microbenchmark(
"splines::splineDesign" = splineDesign(x, knots = all_knots,
ord = ord, derivs = derivs),
"splines2::dbs" = dbs(x, derivs = derivs, knots = internal_knots,
degree = degree, intercept = TRUE,
Boundary.knots = boundary_knots),
check = my_check,
times = 1e3,
unit = "relative"
)Unit: relative
expr min lq mean median uq max neval cld
splines::splineDesign 2.678 2.519 2.4873 2.4508 2.5028 1.0712 1000 b
splines2::dbs 1.000 1.000 1.0000 1.0000 1.0000 1.0000 1000 a The splines package does not contain an implementation for integrals of B-splines. Thus, we performed a comparison with package ibs (version r packageVersion("ibs")), where the function ibs::ibs() was also implemented in Rcpp.
## integrals of B-splines
set.seed(123)
coef_sp <- rnorm(length(all_knots) - ord)
microbenchmark(
"ibs::ibs" = ibs::ibs(x, knots = all_knots, ord = ord, coef = coef_sp),
"splines2::ibs" = as.numeric(
splines2::ibs(x, knots = internal_knots, degree = degree,
intercept = TRUE, Boundary.knots = boundary_knots) %*%
coef_sp
),
check = my_check,
times = 1e3,
unit = "relative"
)Unit: relative
expr min lq mean median uq max neval cld
ibs::ibs 9.3175 8.4242 9.3377 9.6631 9.6052 30.53 1000 b
splines2::ibs 1.0000 1.0000 1.0000 1.0000 1.0000 1.00 1000 a The function ibs::ibs() returns the integrated B-splines instead of the integrals of spline basis functions. Thus, we applied the same coefficients to the basis functions from splines2::ibs() for equivalent results, which was still much faster than ibs::ibs().
For natural cubic splines (based on B-splines), splines::ns() uses the QR decomposition to find the null space of the second derivatives of B-spline basis functions at boundary knots, while splines2::naturalSpline() utilizes the closed-form null space derived from the second derivatives of cubic B-splines, which produces nonnegative basis functions (within boundary) and is more computationally efficient.
microbenchmark(
"splines::ns" = ns(x, knots = internal_knots, intercept = TRUE,
Boundary.knots = boundary_knots),
"splines2::naturalSpline" = naturalSpline(
x, knots = internal_knots, intercept = TRUE,
Boundary.knots = boundary_knots
),
times = 1e3,
unit = "relative"
)Unit: relative
expr min lq mean median uq max neval cld
splines::ns 5.2152 4.9659 4.798 4.7187 4.6488 1.335 1000 b
splines2::naturalSpline 1.0000 1.0000 1.000 1.0000 1.0000 1.000 1000 a The function mSpline() produces periodic spline basis functions (based on M-splines) when periodic = TRUE is specified. The splines::periodicSpline() returns a periodic interpolation spline (based on B-splines) instead of basis matrix. Thus, we performed a comparison with package pbs (version r packageVersion("pbs")), where the function pbs::pbs() produces a basis matrix of periodic B-spline by using splines::spline.des() (a wrapper function of splines::splineDesign()).
microbenchmark(
"pbs::pbs" = pbs::pbs(x, knots = internal_knots, degree = degree,
intercept = TRUE, periodic = TRUE,
Boundary.knots = boundary_knots),
"splines2::mSpline" = mSpline(
x, knots = internal_knots, degree = degree, intercept = TRUE,
Boundary.knots = boundary_knots, periodic = TRUE
),
times = 1e3,
unit = "relative"
)Unit: relative
expr min lq mean median uq max neval cld
pbs::pbs 3.465 3.2513 3.2501 3.1162 3.1062 3.4498 1000 b
splines2::mSpline 1.000 1.0000 1.0000 1.0000 1.0000 1.0000 1000 a Session Information for Benchmarks
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libopenblasp-r0.3.17.so
LAPACK: /usr/lib/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] splines2_0.4.5.9000 microbenchmark_1.4-7
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 mvtnorm_1.1-2 lattice_0.20-44 codetools_0.2-18 ibs_1.4
[6] zoo_1.8-9 digest_0.6.27 MASS_7.3-54 grid_4.1.0 magrittr_2.0.1
[11] evaluate_0.14 rlang_0.4.11 stringi_1.7.3 multcomp_1.4-17 Matrix_1.3-4
[16] sandwich_3.0-1 rmarkdown_2.10 TH.data_1.0-10 tools_4.1.0 stringr_1.4.0
[21] survival_3.2-11 xfun_0.25 yaml_2.2.1 compiler_4.1.0 pbs_1.1
[26] htmltools_0.5.1.1 knitr_1.33