imbroglio-dc / concrete / #17

Committed 08 Sep 2023 04:21AM UTC coverage: 23.74% (-55.2%) from 78.898%

Build # #17

Build Type

push

travis-pro

Committed by

imbroglio-dc

Commit Message

CRAN compatibilty + R Journal paper

Run Details

832 of 832 new or added lines in 7 files covered. (100.0%)

325 of 1369 relevant lines covered (23.74%)

0.68 hits per line

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0.0

/src/rcpp_getCleverCovariate.cpp

// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
//
// we only include RcppArmadillo.h which pulls Rcpp.h in for us
#include "RcppArmadillo.h"
// via the depends attribute we tell Rcpp to create hooks for
// RcppArmadillo so that the build process will know what to do
//
// [[Rcpp::depends(RcppArmadillo)]]
//
// via the exports attribute we tell Rcpp to make this function
// available from R
//
// [[Rcpp::export]]
arma::dmat getCleverCovariate(arma::dvec GStar, 
                              arma::dmat NuisanceWeight, 
                              arma::dmat hFS, 
                              int LeqJ) {
    for (arma::uword i = 0; i < NuisanceWeight.n_cols; ++i) {
        NuisanceWeight.col(i) = GStar(i) * NuisanceWeight.col(i);
    }
    return NuisanceWeight % (LeqJ - hFS);
}

// [[Rcpp::export]]
arma::dmat getHazLS(arma::dvec T_Tilde,
                    arma::dvec EvalTimes,
                    arma::dmat HazL) {
    for (arma::uword i = 0; i < HazL.n_cols; ++i) {
        HazL.col(i) = (EvalTimes <= T_Tilde(i)) % HazL.col(i);
    }
    return HazL;
}

// Needs Debugging
// // [[Rcpp::export]]
// arma::cube updateHazardsCpp(arma::dvec J,
//                             arma::dvec TargetTimes,
//                             arma::dvec L, 
//                             arma::cube Hazards, 
//                             arma::dmat TotalSurv,
//                             arma::dvec EvalTimes,
//                             arma::dvec GStar, 
//                             arma::dmat NuisanceWeight,  
//                             arma::dvec PnEIC, 
//                             double StepSize) {
//     arma::cube UpdatedHaz(size(Hazards), arma::fill::zeros);
//     for (arma::uword l = 0; l < Hazards.n_slices; l++) {
//         for (arma::uword j = 0; j < J.size(); j++) {
//             int LeqJ = L(l) == J(j);
//             arma::dmat Fjt = Hazards.slice( arma::as_scalar(arma::find(L == J(j))) ) % TotalSurv;
//             Fjt = arma::cumsum(Fjt, 0);
//             for (arma::uword k = 0; k < TargetTimes.size(); k++) {
//                 arma::dmat hFS(Fjt.n_rows, Fjt.n_cols, arma::fill::zeros);
//                 arma::uword RowK = arma::as_scalar(arma::find(EvalTimes == TargetTimes(k)));
//                 hFS.rows(0, RowK) = arma::repmat(arma::dmat(Fjt.row(RowK)), RowK+1, 1);
//                 hFS.rows(0, RowK) = (hFS.rows(0, RowK) - Fjt.rows(0, RowK)) % TotalSurv.rows(0, RowK);
//                 arma::dmat hG(hFS.n_rows, hFS.n_cols, arma::fill::zeros);
//                 arma::vec TLeqTk(hG.n_rows, arma::fill::zeros);
//                 TLeqTk.head(RowK+1).ones();
//                 for (arma::uword i = 0; i < NuisanceWeight.n_cols; i++) {
//                     hG.col(i) = GStar(i) * TLeqTk % NuisanceWeight.col(i);
//                 }
//                 UpdatedHaz.slice(l) = UpdatedHaz.slice(l) + hG % (LeqJ - hFS) * PnEIC(j*TargetTimes.size() + k);
//             }
//         }
//     }
//     for (arma::uword m=0; m < UpdatedHaz.n_slices; m++) {
//         UpdatedHaz.slice(m) = Hazards.slice(m) % arma::exp(UpdatedHaz.slice(m) * StepSize);
//     }
//     return UpdatedHaz;
// }

1	// -- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; --
2	//
3	// we only include RcppArmadillo.h which pulls Rcpp.h in for us
4	#include "RcppArmadillo.h"
5	// via the depends attribute we tell Rcpp to create hooks for
6	// RcppArmadillo so that the build process will know what to do
7	//
8	// [[Rcpp::depends(RcppArmadillo)]]
9	//
10	// via the exports attribute we tell Rcpp to make this function
11	// available from R
12	//
13	// [[Rcpp::export]]
14	arma::dmat getCleverCovariate(arma::dvec GStar,	×
15	arma::dmat NuisanceWeight,
16	arma::dmat hFS,
17	int LeqJ) {
18	for (arma::uword i = 0; i < NuisanceWeight.n_cols; ++i) {	×
19	NuisanceWeight.col(i) = GStar(i) * NuisanceWeight.col(i);	×
20	}
21	return NuisanceWeight % (LeqJ - hFS);	×
22	}
23
24	// [[Rcpp::export]]
25	arma::dmat getHazLS(arma::dvec T_Tilde,	×
26	arma::dvec EvalTimes,
27	arma::dmat HazL) {
28	for (arma::uword i = 0; i < HazL.n_cols; ++i) {	×
29	HazL.col(i) = (EvalTimes <= T_Tilde(i)) % HazL.col(i);	×
30	}
31	return HazL;	×
32	}
33
34	// Needs Debugging
35	// // [[Rcpp::export]]
36	// arma::cube updateHazardsCpp(arma::dvec J,
37	// arma::dvec TargetTimes,
38	// arma::dvec L,
39	// arma::cube Hazards,
40	// arma::dmat TotalSurv,
41	// arma::dvec EvalTimes,
42	// arma::dvec GStar,
43	// arma::dmat NuisanceWeight,
44	// arma::dvec PnEIC,
45	// double StepSize) {
46	// arma::cube UpdatedHaz(size(Hazards), arma::fill::zeros);
47	// for (arma::uword l = 0; l < Hazards.n_slices; l++) {
48	// for (arma::uword j = 0; j < J.size(); j++) {
49	// int LeqJ = L(l) == J(j);
50	// arma::dmat Fjt = Hazards.slice( arma::as_scalar(arma::find(L == J(j))) ) % TotalSurv;
51	// Fjt = arma::cumsum(Fjt, 0);
52	// for (arma::uword k = 0; k < TargetTimes.size(); k++) {
53	// arma::dmat hFS(Fjt.n_rows, Fjt.n_cols, arma::fill::zeros);
54	// arma::uword RowK = arma::as_scalar(arma::find(EvalTimes == TargetTimes(k)));
55	// hFS.rows(0, RowK) = arma::repmat(arma::dmat(Fjt.row(RowK)), RowK+1, 1);
56	// hFS.rows(0, RowK) = (hFS.rows(0, RowK) - Fjt.rows(0, RowK)) % TotalSurv.rows(0, RowK);
57	// arma::dmat hG(hFS.n_rows, hFS.n_cols, arma::fill::zeros);
58	// arma::vec TLeqTk(hG.n_rows, arma::fill::zeros);
59	// TLeqTk.head(RowK+1).ones();
60	// for (arma::uword i = 0; i < NuisanceWeight.n_cols; i++) {
61	// hG.col(i) = GStar(i) * TLeqTk % NuisanceWeight.col(i);
62	// }
63	// UpdatedHaz.slice(l) = UpdatedHaz.slice(l) + hG % (LeqJ - hFS) * PnEIC(j*TargetTimes.size() + k);
64	// }
65	// }
66	// }
67	// for (arma::uword m=0; m < UpdatedHaz.n_slices; m++) {
68	// UpdatedHaz.slice(m) = Hazards.slice(m) % arma::exp(UpdatedHaz.slice(m) * StepSize);
69	// }
70	// return UpdatedHaz;
71	// }

imbroglio-dc / concrete / #17

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