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removed unused rcpp::exports and added better plotting tests

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+210

-3162

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12 files changed

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`‎R/RcppExports.R‎`

Lines changed: 104 additions & 294 deletions

Large diffs are not rendered by default.

`‎src/Calc_Repeated.cpp‎`

Lines changed: 26 additions & 29 deletions

Large diffs are not rendered by default.

`‎src/Main_Bound.cpp‎`

Lines changed: 6 additions & 6 deletions

Original file line number	Diff line number	Diff line change
`@@ -73,7 +73,7 @@ void visit_lambda(const Mat& m, const Func& f) {`
`73`	`73`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`74`	`74`	`//' @noRd`
`75`	`75`	`//'`
`76`		`-// [[Rcpp::export]]`
	`76`	`+//`
`77`	`77`	ListLogLik_Cox_PH_Omnibus_Log_Bound(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double mult) {
`78`	`78`	`//`
`79`	`79`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -495,7 +495,7 @@ List LogLik_Cox_PH_Omnibus_Log_Bound(IntegerVector term_n, StringVector tform, N`
`495`	`495`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`496`	`496`	`//' @noRd`
`497`	`497`	`//'`
`498`		`-// [[Rcpp::export]]`
	`498`	`+//`
`499`	`499`	ListLogLik_Cox_PH_Omnibus_Log_Bound_Search(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double mult) {
`500`	`500`	`//`
`501`	`501`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -1368,7 +1368,7 @@ List LogLik_Cox_PH_Omnibus_Log_Bound_Search(IntegerVector term_n, StringVector t`
`1368`	`1368`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`1369`	`1369`	`//' @noRd`
`1370`	`1370`	`//'`
`1371`		`-// [[Rcpp::export]]`
	`1371`	`+//`
`1372`	`1372`	ListLogLik_Poisson_Omnibus_Log_Bound(const MatrixXd& PyrC,const MatrixXd& dfs, IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double mult) {
`1373`	`1373`	`//`
`1374`	`1374`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -1768,7 +1768,7 @@ List LogLik_Poisson_Omnibus_Log_Bound(const MatrixXd& PyrC, const MatrixXd& dfs,`
`1768`	`1768`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`1769`	`1769`	`//' @noRd`
`1770`	`1770`	`//'`
`1771`		`-// [[Rcpp::export]]`
	`1771`	`+//`
`1772`	`1772`	ListLogLik_Poisson_Omnibus_Log_Bound_Search(const MatrixXd& PyrC,const MatrixXd& dfs, IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double mult) {
`1773`	`1773`	`//`
`1774`	`1774`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -2602,7 +2602,7 @@ List LogLik_Poisson_Omnibus_Log_Bound_Search(const MatrixXd& PyrC, const MatrixX`
`2602`	`2602`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`2603`	`2603`	`//' @noRd`
`2604`	`2604`	`//'`
`2605`		`-// [[Rcpp::export]]`
	`2605`	`+//`
`2606`	`2606`	ListLogLik_Cox_PH_Omnibus_Log_Bound_CurveSearch(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double step_size) {
`2607`	`2607`	`//`
`2608`	`2608`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -3060,7 +3060,7 @@ List LogLik_Cox_PH_Omnibus_Log_Bound_CurveSearch(IntegerVector term_n, StringVec`
`3060`	`3060`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`3061`	`3061`	`//' @noRd`
`3062`	`3062`	`//'`
`3063`		`-// [[Rcpp::export]]`
	`3063`	`+//`
`3064`	`3064`	ListLogLik_Poisson_Omnibus_Log_Bound_CurveSearch(const MatrixXd& PyrC,const MatrixXd& dfs, IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res,double qchi,int para_number,int maxstep,double step_size) {
`3065`	`3065`	`//`
`3066`	`3066`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`

`‎src/Main_Functions.cpp‎`

Lines changed: 5 additions & 5 deletions

Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,7 @@ void visit_lambda(const Mat& m, const Func& f) {`
`76`	`76`	`//' @return True for viable point, False for negative error`
`77`	`77`	`//' @noRd`
`78`	`78`	`//'`
`79`		`-// [[Rcpp::export]]`
	`79`	`+//`
`80`	`80`	`boolCheck_Risk(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads,constdouble gmix_theta,const IntegerVector gmix_term) {`
`81`	`81`	`//`
`82`	`82`	`List temp_list =List::create(_["Status"] ="FAILED");// used as a dummy return value for code checking`
`@@ -132,7 +132,7 @@ bool Check_Risk(IntegerVector term_n, StringVector tform, NumericVector a_n, Num`
`132`	`132`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`133`	`133`	`//' @noRd`
`134`	`134`	`//'`
`135`		`-// [[Rcpp::export]]`
	`135`	`+//`
`136`	`136`	ListLogLik_Cox_PH_Omnibus(IntegerVector term_n, StringVector tform, NumericMatrix& a_ns, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`137`	`137`	`//`
`138`	`138`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -728,7 +728,7 @@ List LogLik_Cox_PH_Omnibus(IntegerVector term_n, StringVector tform, NumericMatr`
`728`	`728`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`729`	`729`	`//' @noRd`
`730`	`730`	`//'`
`731`		`-// [[Rcpp::export]]`
	`731`	`+//`
`732`	`732`	ListLogLik_Pois_Omnibus(const MatrixXd& PyrC, IntegerVector term_n, StringVector tform, NumericMatrix& a_ns, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads,const MatrixXd& dfs, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`733`	`733`	`//`
`734`	`734`	`List temp_list =List::create(_["Status"] ="FAILED");// used as a dummy return value for code checking`
`@@ -1276,7 +1276,7 @@ List LogLik_Pois_Omnibus(const MatrixXd& PyrC, IntegerVector term_n, StringVecto`
`1276`	`1276`	`//' @return only if it works`
`1277`	`1277`	`//' @noRd`
`1278`	`1278`	`//'`
`1279`		`-// [[Rcpp::export]]`
	`1279`	`+//`
`1280`	`1280`	ListLogLik_CaseCon_Omnibus(IntegerVector term_n, StringVector tform, NumericMatrix& a_ns, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`1281`	`1281`	`//`
`1282`	`1282`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -2107,7 +2107,7 @@ List LogLik_CaseCon_Omnibus(IntegerVector term_n, StringVector tform, NumericMat`
`2107`	`2107`	`//' @return List of final results: Log-likelihood of optimum, first derivative of log-likelihood, second derivative matrix, parameter list, standard deviation estimate, AIC, model information`
`2108`	`2108`	`//' @noRd`
`2109`	`2109`	`//'`
`2110`		`-// [[Rcpp::export]]`
	`2110`	`+//`
`2111`	`2111`	ListLogLik_Logist_Omnibus(const MatrixXd& CountEvent, IntegerVector term_n, StringVector tform, NumericMatrix& a_ns, NumericMatrix& x_all, IntegerVector dfc,int fir, string modelform,double lr, List optim_para, NumericVector maxiters,int guesses,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`2112`	`2112`	`//`
`2113`	`2113`	`List temp_list =List::create(_["Status"] ="FAILED");// used as a dummy return value for code checking`

`‎src/Main_Multi.cpp‎`

Lines changed: 4 additions & 4 deletions

Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,7 @@ void visit_lambda(const Mat& m, const Func& f) {`
`76`	`76`	`//' @return List of final results: Log-likelihood of optimum, standard error, and convergence for each realization`
`77`	`77`	`//' @noRd`
`78`	`78`	`//'`
`79`		`-// [[Rcpp::export]]`
	`79`	`+//`
`80`	`80`	ListLogLik_Cox_PH_Multidose_Omnibus_Serial(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, NumericMatrix& dose_all, IntegerMatrix dose_cols, IntegerVector dose_index, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`81`	`81`	`//`
`82`	`82`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -583,7 +583,7 @@ List LogLik_Cox_PH_Multidose_Omnibus_Serial(IntegerVector term_n, StringVector t`
`583`	`583`	`//' @return List of final results: standard cox outputs for the integrated solution`
`584`	`584`	`//' @noRd`
`585`	`585`	`//'`
`586`		`-// [[Rcpp::export]]`
	`586`	`+//`
`587`	`587`	ListLogLik_Cox_PH_Multidose_Omnibus_Integrated(IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, NumericMatrix& dose_all, IntegerMatrix dose_cols, IntegerVector dose_index, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon, NumericMatrix df_groups, NumericVector tu,int verbose, IntegerVector KeepConstant,int term_tot, string ties_method,int nthreads, NumericVector& Strata_vals,const VectorXd& cens_weight, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`588`	`588`	`//`
`589`	`589`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -1189,7 +1189,7 @@ List LogLik_Cox_PH_Multidose_Omnibus_Integrated(IntegerVector term_n, StringVect`
`1189`	`1189`	`//' @return List of final results: Log-likelihood of optimum, standard error, and convergence for each realization`
`1190`	`1190`	`//' @noRd`
`1191`	`1191`	`//'`
`1192`		`-// [[Rcpp::export]]`
	`1192`	`+//`
`1193`	`1193`	ListLogLik_Pois_PH_Multidose_Omnibus_Serial(const MatrixXd& PyrC, IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, NumericMatrix& dose_all, IntegerMatrix dose_cols, IntegerVector dose_index, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,const MatrixXd& dfs,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`1194`	`1194`	`//`
`1195`	`1195`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`
`@@ -1593,7 +1593,7 @@ List LogLik_Pois_PH_Multidose_Omnibus_Serial(const MatrixXd& PyrC, IntegerVector`
`1593`	`1593`	`//' @return List of final results: standard cox outputs for the integrated solution`
`1594`	`1594`	`//' @noRd`
`1595`	`1595`	`//'`
`1596`		`-// [[Rcpp::export]]`
	`1596`	`+//`
`1597`	`1597`	ListLogLik_Pois_PH_Multidose_Omnibus_Integrated(const MatrixXd& PyrC, IntegerVector term_n, StringVector tform, NumericVector a_n, NumericMatrix& x_all, NumericMatrix& dose_all, IntegerMatrix dose_cols, IntegerVector dose_index, IntegerVector dfc,int fir, string modelform,double lr, List optim_para,int maxiter,int halfmax,double epsilon,double step_max,double thres_step_max,double deriv_epsilon,const MatrixXd& dfs,int verbose, IntegerVector KeepConstant,int term_tot,int nthreads, List model_bool,constdouble gmix_theta,const IntegerVector gmix_term,const MatrixXd Lin_Sys,const VectorXd Lin_Res) {
`1598`	`1598`	`//`
`1599`	`1599`	`List temp_list =List::create(_["Status"] ="TEMP");// used as a dummy return value for code checking`

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Commitd53af52

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12 files changed

12 files changed

`‎R/RcppExports.R‎`

`‎src/Calc_Repeated.cpp‎`

`‎src/Main_Bound.cpp‎`

`‎src/Main_Functions.cpp‎`

`‎src/Main_Multi.cpp‎`

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