Automated build.

Files changed:
A	.Rbuildignore
A	.github/linters/.lintr
A	.setup/build/cTMed.pdf
A	.setup/build/cTMed_0.0.0.9000.tar.gz
M	.setup/cpp/cTMed-direct-vec.cpp
M	.setup/cpp/cTMed-direct.cpp
M	.setup/cpp/cTMed-indirect-vec.cpp
M	.setup/cpp/cTMed-indirect.cpp
M	.setup/cpp/cTMed-mc-med.cpp
M	.setup/cpp/cTMed-mc-phi-i.cpp
M	.setup/cpp/cTMed-mc-phi.cpp
M	.setup/cpp/cTMed-med-s.cpp
M	.setup/cpp/cTMed-med-vec.cpp
M	.setup/cpp/cTMed-med.cpp
A	.setup/data-raw/deboeck2015.Rds
A	.setup/data-raw/deboeck2015_na.Rds
A	.setup/data-raw/deboeck2015_ou_ctsem.Rds
A	.setup/data-raw/deboeck2015_ou_dynr.Rds
A	.setup/data-raw/deboeck2015_ssm.Rds
A	.setup/data-raw/deboeck2015phi.Rds
A	.setup/data-raw/delta.Rds
A	.setup/data-raw/mc.Rds
A	.setup/data-raw/posterior.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/RcppExports.R
A	R/nBootstrap-ci-format-dot.R
A	R/nBootstrap-pc-ci-dot.R
A	R/nBootstrap-pc-probs-dot.R
A	R/wald-ci-wald-dot.R
A	R/wald-probs-of-alpha-dot.R
A	README.md
M	data/deboeck2015.rda
M	data/deboeck2015phi.rda
A	man/DeltaMed.Rd
A	man/Direct.Rd
A	man/Indirect.Rd
A	man/MCMed.Rd
A	man/MCPhi.Rd
A	man/Med.Rd
A	man/PosteriorMed.Rd
A	man/TestPhi.Rd
A	man/TestStable.Rd
A	man/Total.Rd
A	man/cTMed-package.Rd
A	man/confint.ctmeddelta.Rd
A	man/confint.ctmedmc.Rd
A	man/deboeck2015.Rd
A	man/deboeck2015phi.Rd
A	man/plot.ctmeddelta.Rd
A	man/plot.ctmedmc.Rd
A	man/plot.ctmedmed.Rd
A	man/print.ctmeddelta.Rd
A	man/print.ctmedeffect.Rd
A	man/print.ctmedmc.Rd
A	man/print.ctmedmcphi.Rd
A	man/print.ctmedmed.Rd
A	man/summary.ctmeddelta.Rd
A	man/summary.ctmedmc.Rd
A	man/summary.ctmedmed.Rd
M	project.Rproj
A	src/Makevars
A	src/Makevars.win
A	src/RcppExports.cpp
A	src/source.cpp
A	vignettes/data.Rmd
A	vignettes/delta.Rmd
A	vignettes/fig-vignettes-data-error-1.png
A	vignettes/fig-vignettes-data-error-2.png
A	vignettes/fig-vignettes-data-error-3.png
A	vignettes/fig-vignettes-data-no-error-1.png
A	vignettes/fig-vignettes-data-no-error-2.png
A	vignettes/fig-vignettes-data-no-error-3.png
A	vignettes/fig-vignettes-delta-ctsem-delta-1.png
A	vignettes/fig-vignettes-delta-ctsem-delta-2-1.png
A	vignettes/fig-vignettes-delta-ctsem-delta-2-2.png
A	vignettes/fig-vignettes-delta-ctsem-delta-2-3.png
A	vignettes/fig-vignettes-delta-ctsem-delta-2.png
A	vignettes/fig-vignettes-delta-ctsem-delta-3.png
A	vignettes/fig-vignettes-delta-ctsem-med-1.png
A	vignettes/fig-vignettes-delta-dynr-delta-1.png
A	vignettes/fig-vignettes-delta-dynr-delta-2.png
A	vignettes/fig-vignettes-delta-dynr-delta-3.png
A	vignettes/fig-vignettes-delta-dynr-med-1.png
A	vignettes/fig-vignettes-mc-ctsem-mc-1.png
A	vignettes/fig-vignettes-mc-ctsem-mc-2-1.png
A	vignettes/fig-vignettes-mc-ctsem-mc-2-2.png
A	vignettes/fig-vignettes-mc-ctsem-mc-2-3.png
A	vignettes/fig-vignettes-mc-ctsem-mc-2.png
A	vignettes/fig-vignettes-mc-ctsem-mc-3.png
A	vignettes/fig-vignettes-mc-ctsem-med-1.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-1.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-2-1.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-2-2.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-2-3.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-2.png
A	vignettes/fig-vignettes-mc-ctsem-posterior-3.png
A	vignettes/fig-vignettes-mc-dynr-mc-1.png
A	vignettes/fig-vignettes-mc-dynr-mc-2.png
A	vignettes/fig-vignettes-mc-dynr-mc-3.png
A	vignettes/fig-vignettes-mc-dynr-med-1.png
A	vignettes/fig-vignettes-ou-model-1.png
A	vignettes/mc.Rmd
A	vignettes/ou.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

@@ -0,0 +1,6 @@
+linters: lintr::linters_with_defaults(lintr::object_name_linter(styles = c("CamelCase", "snake_case", "symbols")))
+exclusions: list("R/RcppExports.R", "R/methods.R")
+exclude: "# Exclude Linting"
+exclude_start: "# Begin Exclude Linting"
+exclude_end: "# End Exclude Linting"
+

.setup/cpp/cTMed-direct-vec.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.DirectVec)]]
-double DirectVec(const arma::vec& phi_vec, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+double DirectVec(const arma::vec& phi_vec, const double& delta_t,
+                 const int& from, const int& to, const arma::vec& med) {
   int p = std::sqrt(phi_vec.n_elem);
   arma::mat phi = arma::reshape(phi_vec, p, p);
   arma::mat d = arma::eye(p, p);

.setup/cpp/cTMed-direct.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.Direct)]]
-double Direct(const arma::mat& phi, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+double Direct(const arma::mat& phi, const double& delta_t, const int& from,
+              const int& to, const arma::vec& med) {
   int p = phi.n_rows;
   arma::mat d = arma::eye(p, p);
   int m = med.n_elem;

.setup/cpp/cTMed-indirect-vec.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.IndirectVec)]]
-double IndirectVec(const arma::vec& phi_vec, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+double IndirectVec(const arma::vec& phi_vec, const double& delta_t,
+                   const int& from, const int& to, const arma::vec& med) {
   int p = std::sqrt(phi_vec.n_elem);
   arma::mat phi = arma::reshape(phi_vec, p, p);
   // total effect

.setup/cpp/cTMed-indirect.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.Indirect)]]
-double Indirect(const arma::mat& phi, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+double Indirect(const arma::mat& phi, const double& delta_t, const int& from,
+                const int& to, const arma::vec& med) {
   int p = phi.n_rows;
   // total effect
   arma::mat total = arma::expmat(delta_t * phi);

.setup/cpp/cTMed-mc-med.cpp

@@ -6,7 +6,9 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.MCMed)]]
-arma::mat MCMed(const arma::mat& phi, const arma::mat& vcov_phi_vec_l, const double& delta_t, const int& from, const int& to, const arma::vec& med, const int& R, bool test_phi = true) {
+arma::mat MCMed(const arma::mat& phi, const arma::mat& vcov_phi_vec_l,
+                const double& delta_t, const int& from, const int& to,
+                const arma::vec& med, const int& R, bool test_phi = true) {
   arma::mat output(R, 4);
   int p = phi.n_rows;
   int q = p * p;

.setup/cpp/cTMed-mc-phi-i.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.MCPhiI)]]
-arma::mat MCPhiI(const arma::mat& phi, const arma::mat& vcov_phi_vec_l, bool test_phi = true) {
+arma::mat MCPhiI(const arma::mat& phi, const arma::mat& vcov_phi_vec_l,
+                 bool test_phi = true) {
   int p = phi.n_rows;
   int q = p * p;
   arma::mat phi_i = arma::mat(p, p);

.setup/cpp/cTMed-mc-phi.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.MCPhi)]]
-Rcpp::List MCPhi(const arma::mat& phi, const arma::mat& vcov_phi_vec_l, const int& R, bool test_phi = true) {
+Rcpp::List MCPhi(const arma::mat& phi, const arma::mat& vcov_phi_vec_l,
+                 const int& R, bool test_phi = true) {
   Rcpp::List output(R);
   int p = phi.n_rows;
   int q = p * p;

.setup/cpp/cTMed-med-s.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.Meds)]]
-const arma::mat Meds(const arma::mat& phi, const arma::vec& delta_t, const int& from, const int& to, const arma::vec& med) {
+const arma::mat Meds(const arma::mat& phi, const arma::vec& delta_t,
+                     const int& from, const int& to, const arma::vec& med) {
   int t = delta_t.n_rows;
   arma::mat output = arma::mat(t, 4);
   int p = phi.n_rows;

.setup/cpp/cTMed-med-vec.cpp

@@ -6,7 +6,9 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.MedVec)]]
-Rcpp::NumericVector MedVec(const arma::vec& phi_vec, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+Rcpp::NumericVector MedVec(const arma::vec& phi_vec, const double& delta_t,
+                           const int& from, const int& to,
+                           const arma::vec& med) {
   Rcpp::NumericVector output(3);
   int p = std::sqrt(phi_vec.n_elem);
   arma::mat phi = arma::reshape(phi_vec, p, p);

.setup/cpp/cTMed-med.cpp

@@ -6,7 +6,8 @@
 #include <RcppArmadillo.h>
 // [[Rcpp::depends(RcppArmadillo)]]
 // [[Rcpp::export(.Med)]]
-Rcpp::NumericVector Med(const arma::mat& phi, const double& delta_t, const int& from, const int& to, const arma::vec& med) {
+Rcpp::NumericVector Med(const arma::mat& phi, const double& delta_t,
+                        const int& from, const int& to, const arma::vec& med) {
   Rcpp::NumericVector output(4);
   int p = phi.n_rows;
   // total effect

.setup/latex/bib/quarto.bib

@@ -0,0 +1,11 @@
+@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

@@ -0,0 +1,6 @@
+linters: lintr::linters_with_defaults(lintr::object_name_linter(styles = c("CamelCase", "snake_case", "symbols")))
+exclusions: list("R/RcppExports.R", "R/methods.R")
+exclude: "# Exclude Linting"
+exclude_start: "# Begin Exclude Linting"
+exclude_end: "# End Exclude Linting"
+

CITATION.cff

@@ -0,0 +1,35 @@
+# -----------------------------------------------------------
+# CITATION file created with {cffr} R package, v1.0.0
+# See also: https://docs.ropensci.org/cffr/
+# -----------------------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "cTMed" in publications use:'
+type: software
+license: MIT
+title: 'cTMed: Continuous Time Mediation'
+version: 0.0.0.9000
+abstract: Calculates standard errors and confidence intervals for the indirect effect
+  in continuous time mediation models.
+authors:
+- family-names: Pesigan
+  given-names: Ivan Jacob Agaloos
+  email: [email protected]
+  orcid: https://orcid.org/0000-0003-4818-8420
+preferred-citation:
+  type: manual
+  title: 'cTMed: Continuous Time Mediation'
+  authors:
+  - family-names: Pesigan
+    given-names: Ivan Jacob Agaloos
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4818-8420
+  year: '2024'
+  notes: R package version 0.0.0.9000
+repository-code: https://github.com/jeksterslab/cTMed
+url: https://jeksterslab.github.io/cTMed/
+contact:
+- family-names: Pesigan
+  given-names: Ivan Jacob Agaloos
+  email: [email protected]
+  orcid: https://orcid.org/0000-0003-4818-8420

DESCRIPTION

@@ -29,3 +29,4 @@ Suggests:
     testthat,
     simStateSpace,
     expm
+RoxygenNote: 7.3.1

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: Ivan Jacob Agaloos Pesigan

LICENSE.md

@@ -0,0 +1,21 @@
+# 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 +1,27 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(confint,ctmeddelta)
+S3method(confint,ctmedmc)
+S3method(plot,ctmeddelta)
+S3method(plot,ctmedmc)
+S3method(plot,ctmedmed)
+S3method(print,ctmeddelta)
+S3method(print,ctmedeffect)
+S3method(print,ctmedmc)
+S3method(print,ctmedmcphi)
+S3method(print,ctmedmed)
+S3method(summary,ctmeddelta)
+S3method(summary,ctmedmc)
+S3method(summary,ctmedmed)
+export(DeltaMed)
+export(Direct)
+export(Indirect)
+export(MCMed)
+export(MCPhi)
+export(Med)
+export(PosteriorMed)
+export(TestPhi)
+export(TestStable)
+export(Total)
+importFrom(Rcpp,sourceCpp)
+useDynLib(cTMed, .registration = TRUE)

R/RcppExports.R

@@ -0,0 +1,133 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+.DirectVec <- function(phi_vec, delta_t, from, to, med) {
+    .Call(`_cTMed_DirectVec`, phi_vec, delta_t, from, to, med)
+}
+
+.Direct <- function(phi, delta_t, from, to, med) {
+    .Call(`_cTMed_Direct`, phi, delta_t, from, to, med)
+}
+
+.IndirectVec <- function(phi_vec, delta_t, from, to, med) {
+    .Call(`_cTMed_IndirectVec`, phi_vec, delta_t, from, to, med)
+}
+
+.Indirect <- function(phi, delta_t, from, to, med) {
+    .Call(`_cTMed_Indirect`, phi, delta_t, from, to, med)
+}
+
+.MCMed <- function(phi, vcov_phi_vec_l, delta_t, from, to, med, R, test_phi = TRUE) {
+    .Call(`_cTMed_MCMed`, phi, vcov_phi_vec_l, delta_t, from, to, med, R, test_phi)
+}
+
+.MCPhiI <- function(phi, vcov_phi_vec_l, test_phi = TRUE) {
+    .Call(`_cTMed_MCPhiI`, phi, vcov_phi_vec_l, test_phi)
+}
+
+.MCPhi <- function(phi, vcov_phi_vec_l, R, test_phi = TRUE) {
+    .Call(`_cTMed_MCPhi`, phi, vcov_phi_vec_l, R, test_phi)
+}
+
+.Meds <- function(phi, delta_t, from, to, med) {
+    .Call(`_cTMed_Meds`, phi, delta_t, from, to, med)
+}
+
+.MedVec <- function(phi_vec, delta_t, from, to, med) {
+    .Call(`_cTMed_MedVec`, phi_vec, delta_t, from, to, med)
+}
+
+.Med <- function(phi, delta_t, from, to, med) {
+    .Call(`_cTMed_Med`, phi, delta_t, from, to, med)
+}
+
+#' Test the Drift Matrix
+#'
+#' Both have to be true for the function to return `TRUE`.
+#'   - Test that the real part of all eigenvalues of \eqn{\boldsymbol{\Phi}}
+#'     is less than zero.
+#'   - Test that the diagonal values of \eqn{\boldsymbol{\Phi}}
+#'     are between 0 to negative inifinity.
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param phi Numeric matrix.
+#'   The drift matrix (\eqn{\boldsymbol{\Phi}}).
+#'
+#' @examples
+#' phi <- matrix(
+#'   data = c(
+#'     -0.357, 0.771, -0.450,
+#'     0.0, -0.511, 0.729,
+#'     0, 0, -0.693
+#'   ),
+#'   nrow = 3
+#' )
+#' colnames(phi) <- rownames(phi) <- c("x", "m", "y")
+#' TestPhi(phi = phi)
+#' phi <- matrix(
+#'   data = c(
+#'     -6, 5.5, 0, 0,
+#'     1.25, -2.5, 5.9, -7.3,
+#'     0, 0, -6, 2.5,
+#'     5, 0, 0, -6
+#'   ),
+#'   nrow = 4
+#' )
+#' colnames(phi) <- rownames(phi) <- paste0("y", 1:4)
+#' TestPhi(phi = phi)
+#'
+#' @family Continuous Time Mediation Functions
+#' @keywords cTMed test
+#' @export
+TestPhi <- function(phi) {
+    .Call(`_cTMed_TestPhi`, phi)
+}
+
+#' Test Stability
+#'
+#' The function computes the eigenvalues of the input matrix `x`.
+#' It checks if the real part of all eigenvalues is negative.
+#' If all eigenvalues have negative real parts,
+#' the system is considered stable.
+#'
+#' @author Ivan Jacob Agaloos Pesigan
+#'
+#' @param x Numeric matrix.
+#'
+#' @examples
+#' x <- matrix(
+#'   data = c(
+#'     -0.357, 0.771, -0.450,
+#'     0.0, -0.511, 0.729,
+#'     0, 0, -0.693
+#'   ),
+#'   nrow = 3
+#' )
+#' TestStable(x)
+#' x <- matrix(
+#'   data = c(
+#'     -6, 5.5, 0, 0,
+#'     1.25, -2.5, 5.9, -7.3,
+#'     0, 0, -6, 2.5,
+#'     5, 0, 0, -6
+#'   ),
+#'   nrow = 4
+#' )
+#' TestStable(x)
+#'
+#' @family Continuous Time Mediation Functions
+#' @keywords cTMed test
+#' @export
+TestStable <- function(x) {
+    .Call(`_cTMed_TestStable`, x)
+}
+
+.TotalVec <- function(phi_vec, delta_t) {
+    .Call(`_cTMed_TotalVec`, phi_vec, delta_t)
+}
+
+.Total <- function(phi, delta_t) {
+    .Call(`_cTMed_Total`, phi, delta_t)
+}
+