Automated build.

Files changed:
A	.Rbuildignore
A	.github/linters/.lintr
A	.setup/build/betaDelta.pdf
A	.setup/build/betaDelta_1.0.3.9000.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/betaSandwich-jacobian-diff-beta-star-wrt-beta-star-dot.R
A	R/dataSets-nas1982.R
A	R/deltaMethod-acov-delta.R
A	R/deltaMethod-delta-generic.R
A	R/gammaADF-gamma-adf-consistent-dot.R
A	R/gammaADF-gamma-adf-unbiased-dot.R
A	R/gammaN-gamma-mvn-dot.R
A	R/linearAlgebra-d-mat-dot.R
A	R/linearAlgebra-d-of-mat-dot.R
A	R/linearAlgebra-diag-of-vech-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/linearAlgebra-vech-names-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-jacobian-beta-star-wrt-vech-sigma-dot.R
A	R/strRegression-moments-index-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	R/wald-ci-wald-dot.R
A	R/wald-probs-of-alpha-dot.R
A	README.md
M	data/nas1982.rda
A	man/BetaDelta.Rd
A	man/DeltaGeneric.Rd
A	man/DiffBetaDelta.Rd
A	man/betaDelta-package.Rd
A	man/coef.betadelta.Rd
A	man/coef.diffbetadelta.Rd
A	man/confint.betadelta.Rd
A	man/confint.diffbetadelta.Rd
A	man/nas1982.Rd
A	man/print.betadelta.Rd
A	man/print.diffbetadelta.Rd
A	man/summary.betadelta.Rd
A	man/summary.diffbetadelta.Rd
A	man/vcov.betadelta.Rd
A	man/vcov.diffbetadelta.Rd
M	project.Rproj
A	vignettes/example_beta_delta.Rmd
A	vignettes/example_diff_beta_delta.Rmd
A	vignettes/vignettes.bib

.Rbuildignore

@@ -0,0 +1,19 @@
+.*\.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 "betaDelta" in publications use:'
+type: software
+license: MIT
+title: 'betaDelta: Confidence Intervals for Standardized Regression Coefficients'
+version: 1.0.3.9000
+doi: 10.1080/00273171.2023.2201277
+abstract: Generates confidence intervals for standardized regression coefficients
+  using delta method standard errors for models fitted by lm() as described in Yuan
+  and Chan (2011) <doi:10.1007/s11336-011-9224-6> and Jones and Waller (2015) <doi:10.1007/s11336-013-9380-y>.
+  A description of the package and code examples are presented in Pesigan, Sun, and
+  Cheung (2023) <doi:10.1080/00273171.2023.2201277>.
+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: article
+  title: 'betaDelta and betaSandwich: Confidence intervals for standardized regression
+    coefficients in R'
+  authors:
+  - family-names: Pesigan
+    given-names: Ivan Jacob Agaloos
+    email: r.jeksterslab@gmail.com
+    orcid: https://orcid.org/0000-0003-4818-8420
+  - family-names: Sun
+    given-names: Rongwei
+    email: irissun_s@hotmail.com
+    orcid: https://orcid.org/0000-0003-0034-1422
+  - family-names: Cheung
+    given-names: Shu Fai
+    email: shufai.cheung@gmail.com
+    orcid: https://orcid.org/0000-0002-9871-9448
+  year: '2023'
+  doi: 10.1080/00273171.2023.2201277
+  journal: Multivariate Behavioral Research
+  notes: R package version 1.0.3.9000
+repository: https://packagemanager.rstudio.com/all/__linux__/jammy/latest/
+repository-code: https://github.com/jeksterslab/betaDelta
+url: https://jeksterslab.github.io/betaDelta/
+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
+- delta-method-standard-errors
+- r
+- r-package
+- standardized-regression-coefficients

DESCRIPTION

@@ -27,3 +27,4 @@ Suggests:
     rmarkdown,
     testthat,
     betaSandwich
+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

@@ -0,0 +1,16 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(coef,betadelta)
+S3method(coef,diffbetadelta)
+S3method(confint,betadelta)
+S3method(confint,diffbetadelta)
+S3method(print,betadelta)
+S3method(print,diffbetadelta)
+S3method(summary,betadelta)
+S3method(summary,diffbetadelta)
+S3method(vcov,betadelta)
+S3method(vcov,diffbetadelta)
+export(BetaDelta)
+export(DeltaGeneric)
+export(DiffBetaDelta)
+importFrom(numDeriv,jacobian)

R/betaSandwich-jacobian-diff-beta-star-wrt-beta-star-dot.R

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+#' Jacobian Matrix of Differences of Standardized Regression Slopes
+#' with Respect to the Standardized Regression Slopes
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param p positive integer.
+#'   Number of regressors.
+#'
+#' @family Beta Sandwich Functions
+#' @keywords betaSandwich derivatives internal
+#' @noRd
+.JacobianDiffBetaStar <- function(p) {
+  idx <- utils::combn(seq_len(p), 2)
+  q <- dim(idx)[2]
+  out <- matrix(
+    data = 0,
+    nrow = q,
+    ncol = p
+  )
+  for (i in seq_len(q)) {
+    j <- idx[, i]
+    out[i, j[1]] <- 1
+    out[i, j[2]] <- -1
+  }
+  return(out)
+}

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/deltaMethod-acov-delta.R

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+#' Delta Method Asymptotic Covariance Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param jcap Numeric matrix.
+#'   Jacobian matrix.
+#' @param acov Numeric matrix.
+#'   Asymptotic covariance matrix.
+#' @family Delta Method Functions
+#' @keywords deltaMethod acov internal
+#' @noRd
+.ACovDelta <- function(jcap,
+                       acov) {
+  return(
+    jcap %*% tcrossprod(
+      acov,
+      jcap
+    )
+  )
+}

R/deltaMethod-delta-generic.R

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+#' Delta Method Confidence Intervals (Generic)
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @return Returns a numeric matrix with the following variables:
+#'   \describe{
+#'     \item{est}{Estimates}
+#'     \item{se}{Standard errors}
+#'     \item{t or z}{Test statistics}
+#'     \item{p}{p value}
+#'     \item{ci}{Confidence intervals}
+#'   }
+#'   Note that if `test = TRUE`, the `ci` columns are omitted.
+#'
+#' @param func An R function the input of which is `mu`.
+#'   The function should return a vector of any length.
+#'
+#' @param mu Numeric vector.
+#'   Input of `func`.
+#' @param sigmacap Numeric vector or matrix.
+#'   Asymptotic covariance matrix of `mu`.
+#' @param n Sample size.
+#' @param theta Numeric vector.
+#'   Parameter values when the null hypothesis is true.
+#' @param alpha Numeric vector.
+#'   Significance level/s.
+#' @param z Logical.
+#'   If `z = TRUE`,
+#'   use the standard normal distribution.
+#'   If `z = FALSE`,
+#'   use the t distribution.
+#' @param df Numeric.
+#'   Degrees of freedom if `z = FALSE`.
+#' @param test Logical.
+#'   If `TRUE`,
+#'   return only the results of hypothesis tests.
+#'   If `FALSE`,
+#'   return both results of hypothesis tests and confidence intervals.
+#'
+#' @examples
+#' g <- function(x) {
+#'   1 / x
+#' }
+#' mu <- 100
+#' sigmasq <- 225
+#' n <- 30
+#' DeltaGeneric(
+#'   func = g,
+#'   mu = mu,
+#'   sigmacap = sigmasq,
+#'   n = n
+#' )
+#' @importFrom numDeriv jacobian
+#' @export
+#' @family Delta Method Functions
+#' @keywords deltaMethod
+DeltaGeneric <- function(func,
+                         mu,
+                         sigmacap,
+                         n,
+                         theta = 0,
+                         alpha = c(0.05, 0.01, 0.001),
+                         z = TRUE,
+                         df,
+                         test = FALSE) {
+  stopifnot(
+    is.vector(mu)
+  )
+  stopifnot(
+    is.vector(sigmacap) | is.matrix(sigmacap)
+  )
+  k <- length(mu)
+  j <- numDeriv::jacobian(
+    func = func,
+    x = mu
+  )
+  if (k == 1) {
+    # univariate
+    sigmacap <- as.vector(sigmacap)
+    stopifnot(length(sigmacap) == 1)
+    vcov <- j^2 * (sigmacap / n)
+    se <- as.vector(sqrt(vcov))
+  } else {
+    # multivariate
+    stopifnot(
+      sigmacap == t(sigmacap),
+      dim(sigmacap)[1] == k
+    )
+    vcov <- j %*% (sigmacap / n) %*% t(j)
+    se <- as.vector(sqrt(diag(vcov)))
+  }
+  est <- func(mu)
+  return(
+    .CIWald(
+      est = est,
+      se = se,
+      theta = theta,
+      alpha = alpha,
+      z = z,
+      df = df,
+      test = test
+    )
+  )
+}

R/gammaADF-gamma-adf-consistent-dot.R

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+#' Asymptotic Covariance Matrix of the Sample Covariance Matrix
+#' (Asymptotic Distribution Free - Consistent)
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param d Numeric matrix.
+#'   Deviation scores.
+#' @param vechsigmacap_consistent Numeric vector.
+#'   Half-vectorization of the consistent covariance matrix.
+#' @param n Integer.
+#'   Sample size.
+#'
+#' @family gammaADF Functions
+#' @keywords gammaADF gamma internal
+#' @noRd
+.GammaADFConsistent <- function(d,
+                                vechsigmacap_consistent,
+                                n) {
+  return(
+    (
+      (1 / n) * (
+        Reduce(
+          f = `+`,
+          x = lapply(
+            X = 1:n,
+            FUN = function(i,
+                           d) {
+              tcrossprod(
+                .Vech(
+                  tcrossprod(d[i, ])
+                )
+              )
+            },
+            d = d
+          )
+        )
+      )
+    ) - tcrossprod(
+      vechsigmacap_consistent
+    )
+  )
+}