Automated build.

Files changed:
A	.Rbuildignore
A	.github/linters/.lintr
A	.setup/build/betaMC.pdf
A	.setup/build/betaMC_1.3.1.tar.gz
A	.setup/data-raw/benchmark.Rds
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-acov-hc-dot.R
A	R/betaSandwich-acov-sem-inverse-dot.R
A	R/betaSandwich-cov-hc-dot.R
A	R/betaSandwich-gamma-hc-dot.R
A	R/betaSandwich-q-mat-dot.R
A	R/dataSets-nas1982.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-pinv-of-d-mat-dot.R
A	R/linearAlgebra-positive-definite-2-test-dot.R
A	R/linearAlgebra-positive-definite-test-dot.R
A	R/linearAlgebra-sym-of-vech-dot.R
A	R/linearAlgebra-vec-dot.R
A	R/linearAlgebra-vech-dot.R
A	R/linearAlgebra-vech-names-dot.R
A	R/miHelper-ariv-dot.R
A	R/miHelper-mi-combine-dot.R
A	R/miHelper-total-adj-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/processLM-dif-dot.R
A	R/processLM-process-lm-dot.R
A	R/randomGaussian-location-dot.R
A	R/randomGaussian-random-gaussian-chol-dot.R
A	R/randomGaussian-random-gaussian-eigen-dot.R
A	R/randomGaussian-random-gaussian-svd-dot.R
A	R/randomGaussian-random-gaussian-z-dot.R
A	R/rhoMatrix-rho-of-sigma-dot.R
A	R/semmcci-theta-hat-star-dot.R
A	R/strRegression-beta-star-dot.R
A	R/strRegression-beta-star-of-rho-dot.R
A	R/strRegression-jacobian-vech-sigma-wrt-theta-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/strRegression-sigma-y-sq-dot.R
A	R/strRegression-sigma-yx-dot.R
A	R/strRegression-theta-index-dot.R
A	README.md
M	data/nas1982.rda
A	man/BetaMC.Rd
A	man/DeltaRSqMC.Rd
A	man/DiffBetaMC.Rd
A	man/MC.Rd
A	man/MCMI.Rd
A	man/PCorMC.Rd
A	man/RSqMC.Rd
A	man/SCorMC.Rd
A	man/betaMC-package.Rd
A	man/coef.betamc.Rd
A	man/confint.betamc.Rd
A	man/nas1982.Rd
A	man/print.betamc.Rd
A	man/print.mc.Rd
A	man/summary.betamc.Rd
A	man/summary.mc.Rd
A	man/vcov.betamc.Rd
M	project.Rproj
A	vignettes/benchmark.Rmd
A	vignettes/fig-vignettes-benchmark-unnamed-chunk-15-1.png
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 "betaMC" in publications use:'
+type: software
+license: MIT
+title: 'betaMC: Monte Carlo for Regression Effect Sizes'
+version: 1.3.1
+doi: 10.3758/s13428-023-02114-4
+abstract: Generates Monte Carlo confidence intervals 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(). 'betaMC' combines ideas from
+  Monte Carlo confidence intervals for the indirect effect (Pesigan and Cheung, 2023
+  <doi:10.3758/s13428-023-02114-4>) and the sampling covariance matrix of regression
+  coefficients (Dudgeon, 2017 <doi:10.1007/s11336-017-9563-z>) to generate confidence
+  intervals effect sizes in regression.
+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: Monte Carlo confidence intervals for the indirect effect with missing data
+  authors:
+  - family-names: Pesigan
+    given-names: Ivan Jacob Agaloos
+    email: r.jeksterslab@gmail.com
+    orcid: https://orcid.org/0000-0003-4818-8420
+  - family-names: Cheung
+    given-names: Shu Fai
+    email: shufai.cheung@gmail.com
+    orcid: https://orcid.org/0000-0002-9871-9448
+  year: '2023'
+  doi: 10.3758/s13428-023-02114-4
+  journal: Behavior Research Methods
+  notes: R package version 1.3.1
+repository: https://packagemanager.rstudio.com/all/__linux__/jammy/latest/
+repository-code: https://github.com/jeksterslab/betaMC
+url: https://jeksterslab.github.io/betaMC/
+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
+- monte-carlo
+- r
+- r-package
+- regression-effect-sizes
+- standardized-regression-coefficients

DESCRIPTION

@@ -35,3 +35,4 @@ Suggests:
     MASS,
     mice,
     Amelia
+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,betamc)
+S3method(confint,betamc)
+S3method(print,betamc)
+S3method(print,mc)
+S3method(summary,betamc)
+S3method(summary,mc)
+S3method(vcov,betamc)
+export(BetaMC)
+export(DeltaRSqMC)
+export(DiffBetaMC)
+export(MC)
+export(MCMI)
+export(PCorMC)
+export(RSqMC)
+export(SCorMC)

R/betaSandwich-acov-hc-dot.R

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+#' Asymptotic Covariance Matrix of the
+#' Standardized Parameter Vector
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param jcap Numeric matrix.
+#'   Jacobian matrix of the half-vectorization
+#'   of the model-implied covariance matrix
+#'   with respect to the standardized parameter vector.
+#' @param gammacap Numeric matrix.
+#'   Adjusted asymptotic covariance matrix.
+#' @param gammacap_mvn Numeric matrix.
+#'   Asymptotic covariance matrix of the sample covariance matrix
+#'   assuming multivariate normal distribution.
+#'
+#' @family Beta Sandwich Functions
+#' @keywords betaSandwich acov internal
+#' @noRd
+.ACovHC <- function(jcap,
+                    gammacap,
+                    gammacap_mvn) {
+  inversemvn <- chol2inv(
+    chol(gammacap_mvn)
+  )
+  tjcapinversemvn <- t(jcap) %*% inversemvn
+  bread <- chol2inv(
+    chol(tjcapinversemvn %*% jcap)
+  )
+  meat <- tjcapinversemvn %*% gammacap %*% inversemvn %*% jcap
+  return(
+    bread %*% meat %*% bread
+  )
+}

R/betaSandwich-acov-sem-inverse-dot.R

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+#' Inverse of The Asymptotic Covariance Matrix of the
+#' Standardized Parameter Vector
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param jcap Numeric matrix.
+#'   Jacobian matrix of the half-vectorization
+#'   of the model-implied covariance matrix
+#'   with respect to the standardized parameter vector.
+#' @param acov Numeric matrix.
+#'   Asymptotic covariance matrix of the sample covariance matrix.
+#'
+#' @family Beta Sandwich Functions
+#' @keywords betaSandwich acov internal
+#' @noRd
+.ACovSEMInverse <- function(jcap,
+                            acov) {
+  return(
+    t(jcap) %*% chol2inv(
+      chol(acov)
+    ) %*% jcap
+  )
+}

R/betaSandwich-cov-hc-dot.R

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+#' Sampling Covariance Matrix of the Standardized Parameter Vector
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param acov Numeric matrix.
+#'   Asymptotic covariance matrix of the standardized parameter vector.
+#' @param type Character string.
+#'   Correction type.
+#'   Possible values are
+#'   `"hc0"`,
+#'   `"hc1"`,
+#'   `"hc2"`,
+#'   `"hc3"`,
+#'   `"hc4"`,
+#'   `"hc4m"`, and
+#'   `"hc5"`.
+#' @param n Integer.
+#'   Sample size.
+#' @param df Integer.
+#'   Degrees of freedom.
+#'
+#' @family Beta Sandwich Functions
+#' @keywords betaSandwich cov internal
+#' @noRd
+.CovHC <- function(acov,
+                   type,
+                   n,
+                   df) {
+  nstar <- ((n - 1)^2) / n
+  out <- (1 / nstar) * acov
+  if (type == "hc1") {
+    out <- (n / df) * out
+  }
+  return(
+    out
+  )
+}

R/betaSandwich-gamma-hc-dot.R

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+#' Asymptotic Covariance Matrix of the Sample Covariance Matrix
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param d Numeric matrix.
+#'   Centered data.
+#' @param sigmacap Numeric matrix.
+#'   Covariance matrix of \eqn{Y, X_1, \dots, X_p}.
+#' @param qcap Numeric vector
+#'   Leverage adjustment.
+#' @param n Integer.
+#'   Sample size.
+#'
+#' @family BetaSandwich Functions
+#' @keywords betaSandwich gamma internal
+#' @noRd
+.GammaHC <- function(d,
+                     sigmacap,
+                     qcap,
+                     n) {
+  return(
+    (
+      1 / n
+    ) * Reduce(
+      f = "+",
+      x = lapply(
+        X = seq_len(n),
+        FUN = function(i) {
+          qcap[i] * tcrossprod(
+            .Vech(
+              tcrossprod(
+                d[i, ]
+              ) - sigmacap
+            )
+          )
+        }
+      )
+    )
+  )
+}