Merge pull request #44 from dewittpe/v0.3.0-rc

V0.3.0 rc

.Rbuildignore

@@ -12,3 +12,4 @@
 .document.Rout
 .install_dev_deps.Rout
 ^\.github$
+^cran-comments\.md$

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: cpr
 Title: Control Polygon Reduction
-Version: 0.2.3.9005
+Version: 0.3.0
 Authors@R:
-    c(person("Peter", "DeWitt", email = "dewittpe@gmail.com", role = c("aut", "cre")),
+    c(person("Peter", "DeWitt", email = "dewittpe@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6391-0795")),
       person("Samantha", "MaWhinney", email = "sam.mawhinney@ucdenver.edu", role = c("ths")),
       person("Nichole", "Carlson", email = "nichole.carlson@ucdenver.edu", role = c("ths")))
 Description: Implementation of the Control Polygon Reduction and Control Net
@@ -12,20 +12,21 @@ Depends:
 License: GPL (>= 2)
 Encoding: UTF-8
 URL: https://github.com/dewittpe/cpr/
+Language: en-us
 LazyData: true
 Imports:
-    ggplot2 (>= 2.2.0),
+    ggplot2 (>= 3.0.0),
     lme4,
     plot3D,
-    Rcpp (>= 0.12.13),
+    Rcpp (>= 1.0.11),
     scales
-LinkingTo: Rcpp (>= 0.12.13),
+LinkingTo: Rcpp (>= 1.0.11),
     RcppArmadillo
 Suggests:
     covr,
     knitr,
     qwraps2,
     rmarkdown,
     rgl
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr

Makefile

@@ -8,7 +8,6 @@ CRAN = "https://cran.rstudio.com"
 
 SRC       = $(wildcard $(PKG_ROOT)/src/*.cpp)
 RFILES    = $(wildcard $(PKG_ROOT)/R/*.R)
-EXAMPLES  = $(wildcard $(PKG_ROOT)/examples/*.R)
 TESTS     = $(wildcard $(PKG_ROOT)/tests/testthat/*.R)
 VIGNETTES = $(wildcard $(PKG_ROOT)/vignettes/*)
 RAWDATAR  = $(wildcard $(PKG_ROOT)/data-raw/*.R)
@@ -22,7 +21,7 @@ all: $(PKG_NAME)_$(PKG_VERSION).tar.gz
 		-e "options(warn = 2)"
 	@touch $@
 
-.document.Rout: $(RFILES) $(SRC) $(EXAMPLES) $(RAWDATAR) $(VIGNETTES) $(PKG_ROOT)/DESCRIPTION
+.document.Rout: $(RFILES) $(SRC) $(RAWDATAR) $(VIGNETTES) $(PKG_ROOT)/DESCRIPTION
 	if [ -e "$(PKG_ROOT)/data-raw/Makefile" ]; then $(MAKE) -C $(PKG_ROOT)/data-raw/; else echo "Nothing to do"; fi
 	Rscript --vanilla --quiet -e "options(repo = c('$(CRAN)', '$(BIOC)'))" \
 		-e "options(warn = 2)" \
@@ -44,4 +43,6 @@ clean:
 	$(RM) -rf $(PKG_NAME).Rcheck
 	$(RM) -f .document.Rout
 	$(RM) -f .install_dev_deps.Rout
+	$(RM) -f src/*.o
+	$(RM) -f src/*.so
 

NAMESPACE

@@ -7,6 +7,8 @@ S3method(cn,formula)
 S3method(cnr,cpr_cn)
 S3method(cp,cpr_bs)
 S3method(cp,formula)
+S3method(cp_value,cpr_cp)
+S3method(cp_value,default)
 S3method(cpr,cpr_cp)
 S3method(get_spline,cpr_cn)
 S3method(get_spline,cpr_cp)

NEWS.md

@@ -1,21 +1,20 @@
-# Version 0.2.3.9005
+# Version 0.3.0
 
 ## New Examples
 * `cpr` has examples
 
-## Vignettes
-* The package overview has been changed from .Rmd to .Rnw and will be a draft of
-  a JSS submission.
-* A new vignette focused on just B-splines has been started.
-
 ## Other Changes
-* Depends on Rcpp >= 0.12.11 to handle registering native routines.
-* Moves rgl from `Imports` to `Enhances` (re #36)
+* 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
 First public release.
@@ -48,7 +47,7 @@ Documentation improvements.
 * `is.` a collection of `is.cpr_cp`, `is.cpr_bs`, ... functions added.
 * The dataset `spdg` has been added to the package.
 
-## Non-User Visible Changes
+## Other Changes
 * removed a redundant `build_tensor` definition
 
 # Version 0.2.0
@@ -75,12 +74,12 @@ Continued development should be focused on bug fixes and minor enhancements.
   sequence and numeric values in `plot.cpr_bs` (#18)
 
 ## Bug Fixes
-* `from` and `to` args for `plot.cpr_cpr` fixed (#14)
+* `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-User visible changes
+## Non visible changes
 * non-exported function `knot_expr` created to help with plotting the knot
   locations in `cpr:::plot.cpr_bs`.
 
@@ -91,7 +90,7 @@ Continued development should be focused on bug fixes and minor enhancements.
   When plotting multiple control polygons and splines, this option will make it
   easier to view the spline functions.
 
-# Non-visible changes:
+## Non visible changes
 * Extended testing scripts.
 
 # Version 0.1.0
@@ -118,7 +117,7 @@ series.  The aim for version 0.2.0 will be to have a very similar API for
 
 ## 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
+* 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.
 
@@ -131,8 +130,8 @@ Biometric Society, Student paper competition.  The conference will be held 10 -
 16 July 2016 in Victoria, British Columbia, Canada.
 
 ## Bug Fixes
-* Corrected the attr calls within `cpr` after adjusting the attributes being set
-  on a `cpr_cp`.
+* 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.
 

R/RcppExports.R

@@ -2,7 +2,7 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #' Knot Insertion, Removal, and Reinsertion
-#' 
+#'
 #' Functions for the insertion, removal, and reinsertion of internal knots for
 #' B-splines.
 #'
@@ -24,7 +24,7 @@
 #' in knot insertion matrix.
 #'
 #' Examples for the \code{refine_ordinate}, \code{coarsen_ordinate}, and
-#' \code{hat_ordinate} are best shown in the vignette, 
+#' \code{hat_ordinate} are best shown in the vignette,
 #' \code{vignette("cpr-pkg", package = "cpr")}.
 #'
 #' \code{iknot_weights} returns a vector with the 'importance weight' of each
@@ -94,15 +94,16 @@ diag_only <- function(A, B) {
 #'
 #' Determine the rank (number of linearly independent columns) of a matrix.
 #'
-#' Implimentation via the Armadillo C++ linear algrebra library.  The function
-#' returns the rank of the matix \code{x}.  The computation is based on the
-#' singular value decomposition of the matrix; a std::runtime_error excetion
+#' Implementation via the Armadillo C++ linear algebra library.  The function
+#' returns the rank of the matrix \code{x}.  The computation is based on the
+#' singular value decomposition of the matrix; a std::runtime_error exception
 #' will be thrown if the decomposition fails.  Any singular values less than
-#' the tolerance are treated as zeros.  The tolerance is max(m, n) * max_sv *
-#' datum::eps, where m is the number of rows of x, n is the number of columns
-#' of x, max_sv is the maximal singular value of x, and datum::eps is the
-#' difference between 1 and the least value greater than 1 that is
-#' representable.
+#' the tolerance are treated as zeros.  The tolerance is
+#' \code{max(m, n) * max_sv * arma::datum::eps}, where \code{m} is the number
+#' of rows of \code{x}, \code{n} is the number of columns of \code{x},
+#' \code{max_sv} is the maximal singular value of \code{x}, and
+#' \code{arma::datum::eps} is the difference between 1 and the least value
+#' greater than 1 that is representable.
 #'
 #' @param x a numeric matrix
 #'

R/bsplines.R

@@ -120,6 +120,8 @@ print.cpr_bs <- function(x, n = 6L, ...) {
 #' plot(bmat, show_xi = FALSE, show_x = TRUE)
 #' plot(bmat, show_xi = TRUE,  show_x = FALSE)  ## Default
 #' plot(bmat, show_xi = FALSE, show_x = FALSE)
+#' plot(bmat, show_xi = FALSE, show_x = FALSE)
+#' plot(bmat, show_xi = FALSE, show_x = FALSE, color = FALSE)
 #' @method plot cpr_bs
 #' @export
 plot.cpr_bs <- function(x, ..., show_xi = TRUE, show_x = FALSE, color = TRUE, digits = 2, n = 100) {
@@ -131,22 +133,22 @@ plot.cpr_bs <- function(x, ..., show_xi = TRUE, show_x = FALSE, color = TRUE, di
   names(plot_data) <- c("value", "spline")
   plot_data <- cbind(plot_data, data.frame(x = rep(xvec, times = ncol(bmat))))
   levels(plot_data$spline) <- sub("V", "B", levels(plot_data$spline))
-  levels(plot_data$spline) <- sub("(\\d+)", 
+  levels(plot_data$spline) <- sub("(\\d+)",
                                   paste0("[list(\\1,k==", attr(x, "order"), ",bold(xi))](x)"),
                                         levels(plot_data$spline))
 
   g <-
     ggplot2::ggplot(plot_data) +
     ggplot2::theme_bw() +
-    ggplot2::aes_string(x = "x", y = "value") +
+    eval(substitute(ggplot2::aes(x = X, y = Y), list(X = as.name("x"), Y = as.name("value")))) +
     ggplot2::geom_line() +
     ggplot2::theme(axis.title = ggplot2::element_blank())
 
   if (color) {
-    g <- g + ggplot2::aes_string(color = "spline")
+    g <- g + eval(substitute(ggplot2::aes(color = GRP), list(GRP = as.name("spline"))))
     g <- g + ggplot2::scale_color_discrete(labels = scales::parse_format())
   } else {
-    g <- g + ggplot2::aes_string(group = "spline")
+    g <- g + eval(substitute(ggplot2::aes(group = GRP), list(GRP = as.name("spline"))))
   }
 
   if (show_xi | show_x) {

R/build_tensor.R

@@ -5,10 +5,25 @@
 #' @param x a matrix, or list of numeric matrices, build the tensor product
 #' @param ... additional numeric matrices to build the tensor product
 #'
+#' @seealso
+#' \code{vignette("cpr-pkg", package = "cpr")} for details on tensor products.
+#'
 #' @return
 #' A matrix 
 #'
-#' @example examples/build_tensor.R
+#' @examples
+#' 
+#' A <- matrix(1:4, nrow = 10, ncol = 20)
+#' B <- matrix(1:6, nrow = 10, ncol = 6)
+#' 
+#' # Two ways of building the same tensor product
+#' tensor1 <- build_tensor(A, B) 
+#' tensor2 <- build_tensor(list(A, B))
+#' all.equal(tensor1, tensor2)
+#' 
+#' # a three matrix tensor product
+#' tensor3 <- build_tensor(A, B, B)
+#' str(tensor3)
 #' 
 #' @export
 build_tensor <- function(x, ...) { 

R/cnr_diagnostics.R

@@ -8,7 +8,7 @@
 #' @export
 #' @param x a \code{cpr_cnr} object
 #' @param type type of diagnostic plot.
-#' \code{"loglik"} for the loglikihood by degrees of freedom,
+#' \code{"loglik"} for the log likelihood by degrees of freedom,
 #' \code{"rmse"} for root mean squared residuals by model index
 #' @param from the first index of \code{x} to plot
 #' @param to the last index of \code{x} to plot
@@ -30,7 +30,7 @@ plot.cpr_cnr <- function(x, type = "rmse", from = 1, to, ...) {
 
     ggplot2::ggplot(subset(s, (s$index >= from) & (s$index <= to))) +
     ggplot2::theme_bw() +
-    ggplot2::aes_string(x = "index", y = type) +
+    eval(substitute(ggplot2::aes(x = X, y = Y), list(X = as.name("index"), Y = as.name(type)))) +
     ggplot2::geom_point() +
     ggplot2::geom_line() +
     ggplot2::xlab("Index")

R/cp.R

@@ -35,11 +35,11 @@
 #'
 #' # via formula
 #' dat <- data.frame(x = xvec, y = sin((xvec - 2)/pi) + 1.4 * cos(xvec/pi))
-#' cp3 <- cp(y ~ cpr::bsplines(x) + 0, data = dat)
+#' cp3 <- cp(y ~ cpr::bsplines(x), data = dat)
 #'
 #' # plot the control polygon, spline and target data.
 #' plot(cp3, show_spline = TRUE) +
-#'   ggplot2::geom_line(mapping = ggplot2::aes_string(x = "x", y = "y"),
+#'   ggplot2::geom_line(mapping = ggplot2::aes(x = x, y = y),
 #'                      data = dat, linetype = 2, color = "red")
 #'
 #' @export
@@ -158,7 +158,7 @@ summary.cpr_cp <- function(object, wiggle = FALSE, integrate.args = list(), ...)
     wggl <- try(do.call(wiggle.cpr_cp, c(list(object = object), integrate.args)), silent = TRUE)
 
 
-    if (class(wggl) == "integrate") {
+    if (inherits(x = wggl, what = "integrate")) {
       out$wiggle <- as.numeric(wggl$value)
       attr(out$wiggle, "abs.error") <- wggl$abs.error
       attr(out$wiggle, "subdivisions") <- wggl$subdivisions
@@ -182,7 +182,7 @@ summary.cpr_cp <- function(object, wiggle = FALSE, integrate.args = list(), ...)
 #' \code{\link[ggplot2]{geom_rug}} to show the location of the knots in the
 #' respective control polygons.
 #' @param color Boolean (default FALSE) if more than one \code{cpr_cp} object is
-#' to be plotted, set this value to TRUE to have the graphic in color (linetypes
+#' to be plotted, set this value to TRUE to have the graphic in color (line types
 #' will be used regardless of the color setting).
 #' @param n the number of data points to use for plotting the spline
 #'
@@ -195,10 +195,10 @@ plot.cpr_cp <- function(x, ..., show_cp = TRUE, show_spline = FALSE, show_xi = T
   spline_data <-
     lapply(list(x, ...), function(xx) {
            b <- xx$bknots
-           bmat <- cpr::bsplines(seq(b[1], b[2], length = n),
-                                 iknots = xx$iknots,
-                                 bknots = b,
-                                 order  = xx$order)
+           bmat <- bsplines(seq(b[1], b[2], length = n),
+                            iknots = xx$iknots,
+                            bknots = b,
+                            order  = xx$order)
            data.frame(x = seq(b[1], b[2], length = n),
                       y = as.numeric(bmat %*% xx$cp$theta))
                           })
@@ -230,7 +230,7 @@ plot.cpr_cp <- function(x, ..., show_cp = TRUE, show_spline = FALSE, show_xi = T
   base_plot <-
     ggplot2::ggplot(plot_data) +
     ggplot2::theme_bw() +
-    ggplot2::aes_string(x = "x", y = "y") +
+    eval(substitute(ggplot2::aes(x = X, y = Y), list(X = as.name("x"), Y = as.name("y")))) +
     ggplot2::theme(axis.title = ggplot2::element_blank())
 
   if (show_xi) {
@@ -255,14 +255,14 @@ plot.cpr_cp <- function(x, ..., show_cp = TRUE, show_spline = FALSE, show_xi = T
   if (length(cps) > 1) {
     base_plot <-
       base_plot +
-      ggplot2::aes_string(linetype = "row") +
+      eval(substitute(ggplot2::aes(linetype = LTY), list(LTY = as.name("row")))) +
       ggplot2::theme(legend.title = ggplot2::element_blank())
   }
 
   if (color) {
     base_plot <-
       base_plot +
-      ggplot2::aes_string(color = "row") +
+      eval(substitute(ggplot2::aes(color = CLR), list(CLR = as.name("row")))) +
       ggplot2::theme(legend.title = ggplot2::element_blank())
   }
 

R/cp_diagnostics.R

@@ -4,23 +4,24 @@
 #'
 #' @return
 #' \code{cp_value} returns the ordinate on the control polygon line segment for
-#' the abscissae \code{x} given.  \code{x} could be a control vertex or on a
+#' the abscissa \code{x} given.  \code{x} could be a control vertex or on a
 #' line segment defined by two control vertices of the control polygon
 #' provided.
 #'
 #' \code{cp_diff} returns the absolute vertical distance between the control
 #' vertices of cp1 to the control polygon cp2.
 #'
-#' @export
-#' @rdname cp_diagnostics
-#' @param x absicissa at which to determine the ordinate on control polygon cp
+#' @param x abscissa at which to determine the ordinate on control polygon cp
 #' @param obj a cpr_cp object or \code{data.frame} where the first column is the
 #' abscissa and the second column is the ordinate for the control polygon vertices.
+#'
+#' @export
+#' @rdname cp_diagnostics
 cp_value <- function(obj, x) {
   UseMethod("cp_value")
 }
 
-#' @method cp_value cpr_cp
+#' @export
 cp_value.cpr_cp <- function(obj, x) {
   xi_star <- obj$xi_star
   theta   <- obj$theta
@@ -30,7 +31,7 @@ cp_value.cpr_cp <- function(obj, x) {
   unname((theta[idx] - theta[idx - 1L]) / (xi_star[idx] - xi_star[idx - 1L]) * (x - xi_star[idx]) + theta[idx])
 }
 
-#' @method cp_value default
+#' @export
 cp_value.default <- function(obj, x) {
   xi_star <- obj[[1]]
   theta   <- obj[[2]]