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jeksterslab · Apr 10, 2024 · c126d3b · c126d3b
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Showing 63 changed files with 28 additions and 8,481 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.github/linters/.lintr b/.github/linters/.lintr
diff --git a/.setup/build/cTMed.pdf b/.setup/build/cTMed.pdf
diff --git a/.setup/build/cTMed_0.0.0.9000.tar.gz b/.setup/build/cTMed_0.0.0.9000.tar.gz
diff --git a/.setup/cpp/cTMed-direct-vec.cpp b/.setup/cpp/cTMed-direct-vec.cpp
@@ -6,8 +6,7 @@
 #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);

diff --git a/.setup/cpp/cTMed-direct.cpp b/.setup/cpp/cTMed-direct.cpp
@@ -6,8 +6,7 @@
 #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;

diff --git a/.setup/cpp/cTMed-indirect-vec.cpp b/.setup/cpp/cTMed-indirect-vec.cpp
@@ -6,8 +6,7 @@
 #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

diff --git a/.setup/cpp/cTMed-indirect.cpp b/.setup/cpp/cTMed-indirect.cpp
@@ -6,8 +6,7 @@
 #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);

diff --git a/.setup/cpp/cTMed-mc-med.cpp b/.setup/cpp/cTMed-mc-med.cpp
@@ -6,9 +6,7 @@
 #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;

diff --git a/.setup/cpp/cTMed-mc-phi-i.cpp b/.setup/cpp/cTMed-mc-phi-i.cpp
@@ -6,8 +6,7 @@
 #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);

diff --git a/.setup/cpp/cTMed-mc-phi.cpp b/.setup/cpp/cTMed-mc-phi.cpp
@@ -6,8 +6,7 @@
 #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;

diff --git a/.setup/cpp/cTMed-med-s.cpp b/.setup/cpp/cTMed-med-s.cpp
@@ -6,8 +6,7 @@
 #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;

diff --git a/.setup/cpp/cTMed-med-vec.cpp b/.setup/cpp/cTMed-med-vec.cpp
@@ -6,9 +6,7 @@
 #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);

diff --git a/.setup/cpp/cTMed-med.cpp b/.setup/cpp/cTMed-med.cpp
@@ -6,8 +6,7 @@
 #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

diff --git a/.setup/latex/bib/quarto.bib b/.setup/latex/bib/quarto.bib
diff --git a/.setup/lint/.lintr b/.setup/lint/.lintr
diff --git a/CITATION.cff b/CITATION.cff
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,4 +30,3 @@ Suggests:
     testthat,
     simStateSpace,
     expm
-RoxygenNote: 7.3.1
diff --git a/LICENSE b/LICENSE
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/RcppExports.R b/R/RcppExports.R