@@ -2,7 +2,7 @@ Package: epistasisGA

 Type: Package

 Title: An R package to identify multi-snp effects in nuclear family studies 

     using the GADGETS method

-Version: 1.1.2

+Version: 1.1.3

 Authors@R: c(person("Michael", "Nodzenski", 

     email = "[email protected]",role = c("aut", "cre")), 

     person("Juno", "Krahn", role = "ctb"))

@@ -1173,7 +1173,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

     if (!E_pd){

         arma::vec sum_dif_vecs(chrom_size, fill::ones);

-        arma::vec beta_exposure_prob_disease(x_orig.n_cols, fill::zeros);

+        arma::vec beta_prob_disease(x_orig.n_cols, fill::zeros);

         List res;

         res = List::create(Named("fitness_score") =  pow(10, -10),

@@ -1182,7 +1182,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                            Named("wald_stat") = pow(10, -10), 

                            Named("risk_set_alleles") = sum_diffs, 

                            Named("beta_exposure_prob_disease") = 

-                               beta_exposure_prob_disease.t());

+                               beta_prob_disease.t());

         return(res);

     } else {

@@ -1193,7 +1193,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

         arma::vec prob_disease(mom_target.n_rows);

         //nominate risk alleles

-        arma::mat pred_means = x_orig*beta_full;

+        //arma::mat pred_means = x_orig*beta_full;

         for (unsigned int i = 0; i < mom_target.n_rows; i++){

             arma::vec risk_geno_probs(mom_target.n_cols);

@@ -1208,11 +1208,11 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                     // zero out predicted mean difference vector for inconsistencies

                     // with nominated risk alleles

-                    if (pred_means(i, j) <= 0){

-                        

-                        pred_means(i, j) = 0.0;

-                        

-                    }

+                    // if (pred_means(i, j) <= 0){

+                    //     

+                    //     pred_means(i, j) = 0.0;

+                    //     

+                    // }

                     if (mom_geno == 2.0 | dad_geno == 2.0){

@@ -1236,11 +1236,11 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                     // zero out predicted mean difference vector for inconsistencies

                     // with nominated risk alleles

-                    if (pred_means(i, j) > 0){

-                        

-                        pred_means(i, j) = 0.0;

-                        

-                    }

+                    // if (pred_means(i, j) > 0){

+                    //     

+                    //     pred_means(i, j) = 0.0;

+                    //     

+                    // }

                     if (mom_geno == 0.0 | dad_geno == 0.0){

@@ -1270,53 +1270,53 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

         }

         // get the lengths of the predicted mean vecs

-        arma::vec mean_vec_lengths = arma::sqrt(arma::sum(arma::square(pred_means), 1));

+        // arma::vec mean_vec_lengths = arma::sqrt(arma::sum(arma::square(pred_means), 1));

         // make sure we have unique values (possible for all to be zero)    

-        arma::vec unique_vec_lengths = arma::unique(mean_vec_lengths);

-        

-        // return small value if only one predicted mean 

-        if (unique_vec_lengths.n_elem == 1){

-            

-            arma::vec sum_dif_vecs(chrom_size, fill::ones);

-            arma::vec beta_exposure_prob_disease(x_orig.n_cols, fill::zeros);

-            List res = List::create(Named("fitness_score") =  pow(10, -10),

-                                    Named("sum_dif_vecs") = sum_dif_vecs.t(),

-                                    Named("ht_trace") = pow(10, -10),

-                                    Named("wald_stat") = pow(10, -10), 

-                                    Named("risk_set_alleles") = sum_diffs, 

-                                    Named("beta_exposure_prob_disease") = 

-                                        beta_exposure_prob_disease.t());

-            return(res);

-            

-            

-        }

+        // arma::vec unique_vec_lengths = arma::unique(mean_vec_lengths);

+        // 

+        // // return small value if only one predicted mean 

+        // if (unique_vec_lengths.n_elem == 1){

+        //     

+        //     arma::vec sum_dif_vecs(chrom_size, fill::ones);

+        //     arma::vec beta_exposure_prob_disease(x_orig.n_cols, fill::zeros);

+        //     List res = List::create(Named("fitness_score") =  pow(10, -10),

+        //                             Named("sum_dif_vecs") = sum_dif_vecs.t(),

+        //                             Named("ht_trace") = pow(10, -10),

+        //                             Named("wald_stat") = pow(10, -10), 

+        //                             Named("risk_set_alleles") = sum_diffs, 

+        //                             Named("beta_exposure_prob_disease") = 

+        //                                 beta_exposure_prob_disease.t());

+        //     return(res);

+        //     

+        //     

+        // }

-        arma::mat x_vec_lengths = join_rows(x0_orig, mean_vec_lengths);

-        arma::vec beta_prob_disease = solve(x_vec_lengths, prob_disease, solve_opts::fast);

-        arma::vec beta_exposure_prob_disease = solve(x_orig, prob_disease, solve_opts::fast);

+        // arma::mat x_vec_lengths = join_rows(x0_orig, mean_vec_lengths);

+        // arma::vec beta_prob_disease = solve(x_vec_lengths, prob_disease, solve_opts::fast);

+        arma::vec beta_prob_disease = solve(x_orig, prob_disease, solve_opts::fast);

         // make sure association is positive 

-        bool pos_assoc = beta_prob_disease(1) > 0;

-        if (! pos_assoc){

-            

-            arma::vec sum_dif_vecs(chrom_size, fill::ones);

-            List res = List::create(Named("fitness_score") =  pow(10, -10),

-                                    Named("sum_dif_vecs") = sum_dif_vecs.t(),

-                                    Named("ht_trace") = pow(10, -10),

-                                    Named("wald_stat") = pow(10, -10), 

-                                    Named("risk_set_alleles") = sum_diffs, 

-                                    Named("beta_exposure_prob_disease") = 

-                                        beta_exposure_prob_disease.t());

-            

-            return(res);

-            

-        }

+        // bool pos_assoc = beta_prob_disease(1) > 0;

+        // if (! pos_assoc){

+        //     

+        //     arma::vec sum_dif_vecs(chrom_size, fill::ones);

+        //     List res = List::create(Named("fitness_score") =  pow(10, -10),

+        //                             Named("sum_dif_vecs") = sum_dif_vecs.t(),

+        //                             Named("ht_trace") = pow(10, -10),

+        //                             Named("wald_stat") = pow(10, -10), 

+        //                             Named("risk_set_alleles") = sum_diffs, 

+        //                             Named("beta_exposure_prob_disease") = 

+        //                                 beta_exposure_prob_disease.t());

+        //     

+        //     return(res);

+        //     

+        // }

-        arma::colvec resid_prob_disease = prob_disease - x_vec_lengths*beta_prob_disease;

+        arma::colvec resid_prob_disease = prob_disease - x_orig*beta_prob_disease;

         double sig2 = arma::as_scalar(arma::trans(resid_prob_disease)*resid_prob_disease/

-                                      (x_vec_lengths.n_rows - x_vec_lengths.n_cols));

-        arma::mat vcov_beta_prob_disease = sig2 * arma::pinv(arma::trans(x_vec_lengths)*x_vec_lengths);

+                                      (x_orig.n_rows - x_orig.n_cols));

+        arma::mat vcov_beta_prob_disease = sig2 * arma::pinv(arma::trans(x_orig)*x_orig);

         // make sure cov is positive definite and return small score if not

         bool vcov_beta_prob_disease_pd = vcov_beta_prob_disease.is_sympd();

@@ -1331,7 +1331,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                                     Named("wald_stat") = pow(10, -10), 

                                     Named("risk_set_alleles") = sum_diffs, 

                                     Named("beta_exposure_prob_disease") = 

-                                        beta_exposure_prob_disease.t());

+                                        beta_prob_disease.t());

             return(res);

@@ -1364,7 +1364,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                                Named("wald_stat") = wald_test, 

                                Named("risk_set_alleles") = sum_diffs, 

                                Named("beta_exposure_prob_disease") = 

-                                   beta_exposure_prob_disease.t());

+                                   beta_prob_disease.t());

             return(res);

         } else {

@@ -1391,7 +1391,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

                                Named("wald_stat") = wald_test, 

                                Named("risk_set_alleles") = sum_diffs, 

                                Named("beta_exposure_prob_disease") = 

-                                   beta_exposure_prob_disease.t());

+                                   beta_prob_disease.t());

             return(res);

         }