Automated build.

Files changed:
A	.Rbuildignore
A	.github/linters/.lintr
A	.setup/build/betaNB.pdf
A	.setup/build/betaNB_1.0.2.9000.tar.gz
A	.setup/latex/bib/quarto.bib
A	.setup/lint/.lintr
A	CITATION.cff
M	DESCRIPTION
A	LICENSE
A	LICENSE.md
A	NAMESPACE
A	R/dataSets-nas1982.R
A	R/linearAlgebra-d-mat-dot.R
A	R/linearAlgebra-pinv-of-d-mat-dot.R
A	R/linearAlgebra-vec-dot.R
A	R/linearAlgebra-vech-dot.R
A	R/nBootstrap-acceleration-dot.R
A	R/nBootstrap-bc-ci-dot.R
A	R/nBootstrap-bc-probs-dot.R
A	R/nBootstrap-bca-ci-dot.R
A	R/nBootstrap-bca-probs-dot.R
A	R/nBootstrap-ci-format-dot.R
A	R/nBootstrap-pc-ci-dot.R
A	R/nBootstrap-pc-probs-dot.R
A	R/nBootstrap-z0-dot.R
A	R/nBootstrap-z1-dot.R
A	R/processLM-dif-dot.R
A	R/processLM-process-lm-dot.R
A	R/rhoMatrix-rho-of-sigma-dot.R
A	R/strRegression-beta-star-of-rho-dot.R
A	R/strRegression-beta-star-of-sigma-dot.R
A	R/strRegression-p-cor-sq-dot.R
A	R/strRegression-r-sq-bar-dot.R
A	R/strRegression-r-sq-of-sigma-dot.R
A	R/strRegression-s-p-cor-dot.R
A	README.md
M	data/nas1982.rda
A	man/BetaNB.Rd
A	man/DeltaRSqNB.Rd
A	man/DiffBetaNB.Rd
A	man/NB.Rd
A	man/PCorNB.Rd
A	man/RSqNB.Rd
A	man/SCorNB.Rd
A	man/betaNB-package.Rd
A	man/coef.betanb.Rd
A	man/confint.betanb.Rd
A	man/nas1982.Rd
A	man/print.betanb.Rd
A	man/print.nb.Rd
A	man/summary.betanb.Rd
A	man/vcov.betanb.Rd
M	project.Rproj
A	vignettes/vignettes.bib

.Rbuildignore

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+.*\.Rcheck$
+.*\.Rproj$
+^CITATION\.cff$
+^LICENSE\.md$
+^Makefile$
+^README\.Rmd$
+^README\.md$
+^\.Rproj\.user$
+^\.devcontainer$
+^\.git.*$
+^\.library$
+^\.setup$
+^\.sim$
+^detritus$
+^index\.qmd$
+^pkgdown$
+^quarto$
+^scripts$
+^vignettes$

.github/linters/.lintr

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+linters: lintr::linters_with_defaults(lintr::object_name_linter(styles = c("CamelCase", "snake_case", "symbols")))
+exclusions: list("R/RcppExports.R")
+exclude: "# Exclude Linting"
+exclude_start: "# Begin Exclude Linting"
+exclude_end: "# End Exclude Linting"
+

.setup/latex/bib/quarto.bib

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+@Article{Wright-1918,
+  author = {Sewall Wright},
+  date = {1918-07},
+  journaltitle = {Genetics},
+  title = {On the nature of size factors},
+  doi = {10.1093/genetics/3.4.367},
+  number = {4},
+  pages = {367--374},
+  volume = {3},
+  publisher = {Oxford University Press ({OUP})},
+}

.setup/lint/.lintr

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+linters: lintr::linters_with_defaults(lintr::object_name_linter(styles = c("CamelCase", "snake_case", "symbols")))
+exclusions: list("R/RcppExports.R")
+exclude: "# Exclude Linting"
+exclude_start: "# Begin Exclude Linting"
+exclude_end: "# End Exclude Linting"
+

CITATION.cff

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+# -----------------------------------------------------------
+# CITATION file created with {cffr} R package, v0.5.0
+# See also: https://docs.ropensci.org/cffr/
+# -----------------------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "betaNB" in publications use:'
+type: software
+license: MIT
+title: 'betaNB: Bootstrap for Regression Effect Sizes'
+version: 1.0.2.9000
+abstract: 'Generates nonparametric bootstrap confidence intervals (Efron & Tibshirani,
+  1993: <doi:10.1201/9780429246593>) for standardized regression coefficients (beta)
+  and other effect sizes, including multiple correlation, semipartial correlations,
+  improvement in R-squared, squared partial correlations, and differences in standardized
+  regression coefficients, for models fitted by lm().'
+authors:
+- family-names: Pesigan
+  given-names: Ivan Jacob Agaloos
+  email: r.jeksterslab@gmail.com
+  orcid: https://orcid.org/0000-0003-4818-8420
+preferred-citation:
+  type: thesis
+  title: 'Confidence intervals for standardized coefficients: Applied to regression
+    coefficients in primary studies and indirect effects in meta-analytic structural
+    equation modeling'
+  authors:
+  - family-names: Pesigan
+    given-names: Ivan Jacob Agaloos
+    email: r.jeksterslab@gmail.com
+    orcid: https://orcid.org/0000-0003-4818-8420
+  year: '2022'
+  institution:
+    name: University of Macau
+  thesis-type: PhD Thesis
+repository: https://packagemanager.rstudio.com/all/__linux__/jammy/latest/
+repository-code: https://github.com/jeksterslab/betaNB
+url: https://jeksterslab.github.io/betaNB/
+contact:
+- family-names: Pesigan
+  given-names: Ivan Jacob Agaloos
+  email: r.jeksterslab@gmail.com
+  orcid: https://orcid.org/0000-0003-4818-8420
+keywords:
+- confidence-intervals
+- nonparametric-bootstrap
+- r
+- r-package
+- regression-effect-sizes
+- standardized-regression-coefficients
+references:
+- type: manual
+  title: 'betaNB: Bootstrap for Regression Effect Sizes'
+  authors:
+  - family-names: Pesigan
+    given-names: Ivan Jacob Agaloos
+    email: r.jeksterslab@gmail.com
+    orcid: https://orcid.org/0000-0003-4818-8420
+  year: '2023'
+  notes: R package version 1.0.2.9000

DESCRIPTION

@@ -28,3 +28,4 @@ Suggests:
     knitr,
     rmarkdown,
     testthat
+RoxygenNote: 7.2.3

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: Ivan Jacob Agaloos Pesigan

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 Ivan Jacob Agaloos Pesigan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method(coef,betanb)
+S3method(confint,betanb)
+S3method(print,betanb)
+S3method(print,nb)
+S3method(summary,betanb)
+S3method(vcov,betanb)
+export(BetaNB)
+export(DeltaRSqNB)
+export(DiffBetaNB)
+export(NB)
+export(PCorNB)
+export(RSqNB)
+export(SCorNB)

R/dataSets-nas1982.R

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+#' 1982 National Academy of Sciences Doctoral Programs Data
+#'
+#' @format Ratings of 46 doctoral programs in psychology in the USA
+#'   with the following variables:
+#'   \describe{
+#'     \item{QUALITY}{Program quality ratings.}
+#'     \item{NFACUL}{Number of faculty members in the program.}
+#'     \item{NGRADS}{Number of program graduates.}
+#'     \item{PCTSUPP}{Percentage of program graduates who received support.}
+#'     \item{PCTGRT}{Percent of faculty members holding research grants.}
+#'     \item{NARTIC}{Number of published articles
+#'                   attributed to program faculty member.}
+#'     \item{PCTPUB}{Percent of faculty with one or more published article.}
+#'   }
+#' @references
+#' National Research Council. (1982).
+#' *An assessment of research-doctorate programs in the United States:
+#' Social and behavioral sciences*.
+#' \doi{10.17226/9781}.
+#' Reproduced with permission from the National Academy of Sciences,
+#' Courtesy of the National Academies Press, Washington, D.C.
+#' @keywords data
+"nas1982"

R/linearAlgebra-d-mat-dot.R

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+#' The Duplication Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param k Positive integer.
+#'   Dimension of the `k` by `k` matrix.
+#'
+#' @return Returns a matrix.
+#'
+#' @family Symmetric Functions
+#' @keywords linearAlgebra symmetric internal
+#' @noRd
+.DMat <- function(k) {
+  sym <- matrix(
+    0,
+    nrow = k,
+    ncol = k
+  )
+  q <- seq_len(
+    0.5 * k * (k + 1)
+  )
+  sym[lower.tri(sym, diag = TRUE)] <- q
+  sym[upper.tri(sym)] <- t(sym)[upper.tri(sym)]
+  return(
+    outer(
+      X = .Vec(sym),
+      Y = q,
+      FUN = function(x, y) {
+        ifelse(
+          test = x == y,
+          yes = 1,
+          no = 0
+        )
+      }
+    )
+  )
+}

R/linearAlgebra-pinv-of-d-mat-dot.R

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+#' The Moore-Penrose Inverse of the Duplication Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param d Numeric matrix.
+#'   Duplication matrix.
+#'
+#' @return Returns a matrix.
+#'
+#' @family Symmetric Functions
+#' @keywords linearAlgebra symmetric internal
+#' @noRd
+.PInvDmat <- function(d) {
+  return(
+    tcrossprod(
+      chol2inv(
+        chol(
+          crossprod(d)
+        )
+      ),
+      d
+    )
+  )
+}

R/linearAlgebra-vec-dot.R

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+#' Vectorize a Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @return Returns a vector.
+#'
+#' @param x Matrix.
+#'
+#' @family Vectorization Functions
+#' @keywords linearAlgebra vectorization internal
+#' @noRd
+.Vec <- function(x) {
+  dim(x) <- NULL
+  return(x)
+}

R/linearAlgebra-vech-dot.R

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+#' Half-Vectorize a Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param x Matrix.
+#'
+#' @return Returns a vector.
+#'
+#' @family Vectorization Functions
+#' @keywords linearAlgebra vectorization internal
+#' @noRd
+.Vech <- function(x) {
+  return(
+    x[
+      lower.tri(
+        x = x,
+        diag = TRUE
+      )
+    ]
+  )
+}

R/nBootstrap-acceleration-dot.R

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+#' Acceleration
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param jackknife Numeric vector.
+#'   Jackknife estimates.
+#'
+#' @return Returns a numeric vector of length one.
+#'
+#' @family Confidence Intervals Functions
+#' @keywords nBootstrap ci internal
+#' @noRd
+.Acceleration <- function(jackknife) {
+  parenthesis <- mean(jackknife) - jackknife
+  numerator <- sum(parenthesis^3)
+  denominator <- 6 * ((sum(parenthesis^2))^(3 / 2))
+  return(
+    numerator / denominator
+  )
+}

R/nBootstrap-bc-ci-dot.R

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+#' Bias Corrected Confidence Intervals
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param thetahatstar Numeric vector.
+#'   Sampling distribution.
+#' @param thetahat Numeric.
+#'   Parameter estimate.
+#' @param probs Numeric vector.
+#'   Vector of probabilities.
+#' @param z0 Numeric.
+#' @param z1 Numeric vector
+#'   with length equal to two times the length of alpha.
+#' @return Returns a matrix of estimates, standard errors,
+#'   number of replications, and confidence intervals.
+#'
+#' @family Confidence Intervals Functions
+#' @keywords nBootstrap ci internal
+#' @noRd
+.BCCI <- function(thetahatstar,
+                  thetahat,
+                  probs,
+                  z0,
+                  z1) {
+  thetahatstar <- as.vector(thetahatstar)
+  thetahatstar <- thetahatstar[stats::complete.cases(thetahatstar)]
+  ci <- stats::quantile(
+    x = thetahatstar,
+    probs = .BCProbs(
+      z0 = z0,
+      z1 = z1
+    ),
+    names = FALSE
+  )
+  return(
+    .CIFormat(
+      thetahatstar = thetahatstar,
+      thetahat = thetahat,
+      probs = probs,
+      ci = ci
+    )
+  )
+}

R/nBootstrap-bc-probs-dot.R

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+#' Bias Corrected Probablities
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param z0 Numeric.
+#' @param z1 Numeric vector
+#'   with length equal to two times the length of alpha.
+#' @return Returns a vector of prababilities.
+#'
+#' @family Confidence Intervals Functions
+#' @keywords nBootstrap ci internal
+#' @noRd
+.BCProbs <- function(z0,
+                     z1) {
+  return(
+    stats::pnorm(
+      q = 2 * z0 + z1
+    )
+  )
+}