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Changelog

Source: NEWS.md

Version 0.4.0

CRAN release: 2024-02-15

New Features

  • cpr’s progress argument has been extended to control if a progress bar is used for just the cpr steps, or if a more detailed progress for of the influence weight calculations is reported.

  • influence_of_iknots gains parallel execution via pbapply (#17)

  • plot.cpr_cp gains the argument comparitive which, when set to FALSE and only one cpr_cp is passed in for plotting, the graphic will appear more like the plot.cpr_bs results. When comparitive = TRUE or more than one cpr_cp is present, the behavior from v0.3.0 is retained.

  • cp.formula gains the methods.args argument to pass arguments to the regression method instead of relying on ....

  • d_order_statistic and p_order_statistic were added. These functions allow you to get the density of distribution function for the jth order statistic from a sample of size n from a distribution with defined density and distribution functions within R.

  • sign_changes will count the number of sign changes of the first or second derivative of a spline function.

  • get_spline returns standard errors and derivatives (#60)

User Visible Changes

  • loglikelihood is not exported in the namespace
  • summary.cpr_cp now calculates the “wiggle” of the function by default, that is, changes the default from wiggle = FALSE to wiggle = TRUE
  • cp and cn both have the default keep_fit argument set to TRUE. This change was made to simplify the prediction methods.
  • print.cpr_bt returns the object invisibly, it used to return a str(x).
  • print.cpr_cn returns the object invisibly
  • print.cpr_cnr returns the object invisibly
  • print.cpr_cpr returns the object invisibly

Non-User Visible Changes

  • Refactor of c++ defining basis functions, derivatives of basis functions, b-splines structures

  • cp.formula checks the formula and requires that bsplines is used once and is the first term on the right hand side of the formula.

Defunct Functions

  • A major refactor of the internal code as since v0.3.0 has resulted in several functions becoming defunct, see help(cpr-defunct) for details.

Version 0.3.0

CRAN release: 2023-11-29

New Examples

  • cpr has examples

Other Changes

  • Depends on Rcpp >= 0.12.11 (actually moved to >= 1.0.11) to handle registering native routines.
  • Moves rgl from Imports to Suggests (re #36)
  • Refactoring base code to eliminate the use of dplyr, tidyr, tibble, etc. Focus on base R methods to reduce install dependencies and improve long term stability of the package.
  • Require R > 3.5.0
  • Stop using testthat for testing
  • Remove use of the tidyr, dplyr
  • Improve documentation
  • Minor bug fixes
  • Replace use of now deprecated ggplot2::aes_string

Version 0.2.3

CRAN release: 2017-03-07

First public release.

New Features

  • plot.cpr_cn supports rgl and plot3D graphics
  • start of a vignette.

Version 0.2.2

New Features

  • get_spline is an S3 method for getting a data.frame of interpolated values of a spline given a cpr_cp object. Later development will add methods for cpr_cn objects.
  • predict.cpr_cp and predict.cpr_cn methods added
  • matrix_rank added
  • update_bsplines and update_btensor methods added (#27)

Version 0.2.1

Documentation improvements.

New Features

  • influence_of and plot.cpr_influence_of provide a clean interface for users to explore the influence of a set of knots on a spline function. (#19)
  • color (TRUE/FALSE) option added to plot.cpr_bs.
  • plot.cpr_cn lets the user plot 2D surfaces for tensor product surfaces. The plots are for the whole surface if the input is a 2D tensor product, and is a 2D slice evaluated at a given value for other margins for 3+ dimensional tensor products.
  • is. a collection of is.cpr_cp, is.cpr_bs, … functions added.
  • The dataset spdg has been added to the package.

Other Changes

  • removed a redundant build_tensor definition

Version 0.2.0

This version has a fairly polished set of tools for b-splines, cpr, and cnr. This version seems to be in a good place for use in the three major papers

  1. Methods 1: uni-variable functions,
  2. Methods 2: multi-variable functions, and
  3. Software paper.

Continued development should be focused on bug fixes and minor enhancements.

New Features

  • Option to save fits in cnr (#8)
  • Option to define the number of polynomial coefficients to use in cnr (#10)
  • x-axis tick label options for plotting b-splines (#12)
  • added show_xi to cpr:::plot.cp and using ggplot2::geom_rug to show the location of the knots for each of the control polygons plotted.
  • summary for cpr_cn and cpr_cnr objects added.
  • plot method for cpr_cnr objects.
  • margin option in cnr allows the user to specify which marginals CNR will be applied to.
  • Using sec.axis option from ggplot2_2.2.0 for the plotting of the knot sequence and numeric values in plot.cpr_bs (#18)

Bug Fixes

  • from and to arguments for plot.cpr_cpr fixed (#14)
  • correct construction of missing iknots argument in btensor
  • keep is correctly handled in the cnr call.
  • show_xi correctly handled in the plot.cpr_cp call.

Non visible changes

  • non-exported function knot_expr created to help with plotting the knot locations in cpr:::plot.cpr_bs.

Version 0.1.1

New Features

  • plot.cpr_cp allows the user to suppress the plotting of the control polygon. When plotting multiple control polygons and splines, this option will make it easier to view the spline functions.

Non visible changes

  • Extended testing scripts.

Version 0.1.0

First version of univariable cpr methods ready for deployment

Big picture

cpr::cp and cpr::cpr have been used for the simulations which are aimed to be part of the first manuscript. Modifications might be needed, but hopefully the univariable methods are stable.

A lot of changes in the implementation and API have occurred from the 0.0.x series. The aim for version 0.2.0 will be to have a very similar API for cpr::cn and cpr::cnr as provided for the cpr::cp and cpr::cpr calls.

version 0.0.5

New Features

  • First and second derivatives of B-splines via bsplineD

Extended Documentation

  • Examples added to bsplines

End User non-visible changes:

  • Added the not-to-be-exported function generate_cp_data
  • Redesign of the deboor.cpp file so that the bsplines are accessible. The prior design only allowed access to the basis, the current design allows access to the generic B-splines.

version 0.0.3

Version 0.0.3 is the version of the package used to run the analysis and simulations presented in the paper submitted to the 28th International Biometrics Conference, Western North American Region (WNAR) of the Internal Biometric Society, Student paper competition. The conference will be held 10 - 16 July 2016 in Victoria, British Columbia, Canada.

Bug Fixes

  • Corrected the attributes calls within cpr after adjusting the attributes being set on a cpr_cp.

  • plot.cpr_bs correctly displays the indices for the knot sequence.

End User Visible changes:

  • The knot insertion matrix W is accessible to the end user in a new way. Names of functions in boehem.cpp are cleaner.
  • plot.cpr_cpr allows user to select either control polygons or sums of squared residuals to be plotted.

Vignettes

  • Removed the background vignette… to much detail right now, too much time required to build and install the package.

End User non-visible changes:

  • Redundant definition of greville_sites removed.

version 0.0.2

new features

  • Added the function tensor for building tensor products of cpr::bsplines.
  • Added the function influence_weights to get the influence weights for each internal knot on each marginal of a tensor product.
  • is.cpr_bs added.
  • S3 methods for cp

Bug Fixes

  • trimmed quantile handles the use_unique option correctly
  • better handling of … in cp() and cpr()

version 0.0.1.9003

First usable version with the method based on the ‘importance weight’ of internal knots based on reversing the methods presented by Boehm (1980). Development of metrics and methods for parsing out the preferable models.

Version 0.0.1.9003 was the first stable version for fitting the exact data model.

Vignettes

  • The beginnings of the control-polygon vignette started (version 0.0.1.9001)

version 0.0.1

This version was based on the idea that using an angle to reduce the control polygon was a good idea. Further literature review and simulations showed otherwise. This version is marked for posterity and the cpp functions are going to be useful in the following versions as well.