1. COMPASS
  2. src
  3. COMPASS_init.c
Browse code

MH sampler with improved priors should lead to better convergence

Greg Finak authored on 27/01/2021 19:11:59
Showing 1 changed files
src/COMPASS_init.c
History View file @ ec34eb3
... ... 
@@ -1,4 +1,3 @@
1 
-// Copyright [2014] <Fred Hutchinson Cancer Research Center>
2 1 
 // This file was automatically generated by Kmisc::registerFunctions()
3 2
4 3 
 #include <R.h>
... ... 
@@ -34,6 +33,15 @@ SEXP updatealphas_Exp(SEXP alphast,
34 33 
                       SEXP var_2,
35 34 
                       SEXP p_var,
36 35 
                       SEXP ttt);
36 
+SEXP updatealphas_Exp_MH(SEXP alphast,
37 
+                         SEXP n_s,
38 
+                         SEXP K,
39 
+                         SEXP I,
40 
+                         SEXP lambda_s,
41 
+                         SEXP gammat,
42 
+                         SEXP var_1,
43 
+                         SEXP var_2,
44 
+                         SEXP p_var);
37 45 
 SEXP updatealphau_noPu_Exp(SEXP alphaut,
38 46 
                            SEXP n_s,
39 47 
                            SEXP n_u,
... ... 
@@ -43,6 +51,14 @@ SEXP updatealphau_noPu_Exp(SEXP alphaut,
43 51 
                            SEXP var_p,
44 52 
                            SEXP ttt,
45 53 
                            SEXP gammat);
54 
+SEXP updatealphau_noPu_Exp_MH(SEXP alphaut,
55 
+                              SEXP n_s,
56 
+                              SEXP n_u,
57 
+                              SEXP I,
58 
+                              SEXP K,
59 
+                              SEXP lambda_u,
60 
+                              SEXP var_p,
61 
+                              SEXP gammat);
46 62 
 SEXP updategammak_noPu(SEXP n_s,
47 63 
                        SEXP n_u,
48 64 
                        SEXP gammat,
... ... 
@@ -69,7 +85,9 @@ R_CallMethodDef callMethods[] = {
69 85 
     {"C_COMPASS_CellCounts", (DL_FUNC) & _COMPASS_CellCounts, 2},
70 86 
     {"C_samplePuPs", (DL_FUNC) & samplePuPs, 9},
71 87 
     {"C_updatealphas_Exp", (DL_FUNC) & updatealphas_Exp, 10},
88 
+    {"C_updatealphas_Exp_MH", (DL_FUNC) & updatealphas_Exp_MH, 9},
72 89 
     {"C_updatealphau_noPu_Exp", (DL_FUNC) & updatealphau_noPu_Exp, 9},
90 
+    {"C_updatealphau_noPu_Exp_MH", (DL_FUNC) & updatealphau_noPu_Exp_MH, 8},
73 91 
     {"C_updategammak_noPu", (DL_FUNC) & updategammak_noPu, 16},
74 92 
     {NULL, NULL, 0}};
75 93
Browse code

C code cleanup

Greg Finak authored on 26/01/2021 17:15:43
Showing 1 changed files
src/COMPASS_init.c
History View file @ 3dd3307
... ... 
@@ -1,3 +1,4 @@
1 
+// Copyright [2014] <Fred Hutchinson Cancer Research Center>
1 2 
 // This file was automatically generated by Kmisc::registerFunctions()
2 3
3 4 
 #include <R.h>
Browse code

Merge branch 'master' into trunk

Greg Finak authored on 25/08/2017 00:01:30
Showing 0 changed files
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit(s).

Commit information:

Commit id: 060940bf9d25ab794e641134f5113e73a9235dae
Commit message:
Re-format
Committed by Kevin Ushey <kevinushey at gmail.com>
Commit date: 2014-05-01T21:10:15-07:00

From: Bioconductor Git-SVN Bridge <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@89817 bc3139a8-67e5-0310-9ffc-ced21a209358

k.ushey authored on 02/05/2014 04:10:32
Showing 1 changed files
src/COMPASS_init.c
History View file @ a241239
... ... 
@@ -5,31 +5,74 @@
5 5
6 6 
 #include <R_ext/Rdynload.h>
7 7
8 
-SEXP melt_dataframe( SEXP x, SEXP id_ind_, SEXP val_ind_, SEXP variable_name, SEXP value_name );
9 
-SEXP melt_matrix( SEXP x );
8 
+SEXP melt_dataframe(SEXP x,
9 
+                    SEXP id_ind_,
10 
+                    SEXP val_ind_,
11 
+                    SEXP variable_name,
12 
+                    SEXP value_name);
13 
+SEXP melt_matrix(SEXP x);
10 14 
 SEXP transpose_list(SEXP x);
11 15 
 SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
12 16 
 SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
13 
-SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
14 
-SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
15 
-SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
16 
-SEXP updategammak_noPu(SEXP n_s,SEXP n_u, SEXP gammat, SEXP I, SEXP K, SEXP SS, SEXP alphau, SEXP alphas, SEXP alpha, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP indi);
17 
+SEXP samplePuPs(SEXP alphau,
18 
+                SEXP alphas,
19 
+                SEXP gammat,
20 
+                SEXP T,
21 
+                SEXP K,
22 
+                SEXP nsi,
23 
+                SEXP nui,
24 
+                SEXP d,
25 
+                SEXP M);
26 
+SEXP updatealphas_Exp(SEXP alphast,
27 
+                      SEXP n_s,
28 
+                      SEXP K,
29 
+                      SEXP I,
30 
+                      SEXP lambda_s,
31 
+                      SEXP gammat,
32 
+                      SEXP var_1,
33 
+                      SEXP var_2,
34 
+                      SEXP p_var,
35 
+                      SEXP ttt);
36 
+SEXP updatealphau_noPu_Exp(SEXP alphaut,
37 
+                           SEXP n_s,
38 
+                           SEXP n_u,
39 
+                           SEXP I,
40 
+                           SEXP K,
41 
+                           SEXP lambda_u,
42 
+                           SEXP var_p,
43 
+                           SEXP ttt,
44 
+                           SEXP gammat);
45 
+SEXP updategammak_noPu(SEXP n_s,
46 
+                       SEXP n_u,
47 
+                       SEXP gammat,
48 
+                       SEXP I,
49 
+                       SEXP K,
50 
+                       SEXP SS,
51 
+                       SEXP alphau,
52 
+                       SEXP alphas,
53 
+                       SEXP alpha,
54 
+                       SEXP mk,
55 
+                       SEXP Istar,
56 
+                       SEXP mKstar,
57 
+                       SEXP pp,
58 
+                       SEXP pb1,
59 
+                       SEXP pb2,
60 
+                       SEXP indi);
17 61
18 
-R_CallMethodDef callMethods[]  = {
19 
-  {"C_melt_dataframe", (DL_FUNC) &melt_dataframe, 5},
20 
-  {"C_melt_matrix", (DL_FUNC) &melt_matrix, 1},
21 
-  {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
22 
-  {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
23 
-  {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
24 
-  {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
25 
-  {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
26 
-  {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
27 
-  {"C_updategammak_noPu", (DL_FUNC) &updategammak_noPu, 16},
28 
-  {NULL, NULL, 0}
29 
-};
62 
+R_CallMethodDef callMethods[] = {
63 
+    {"C_melt_dataframe", (DL_FUNC) & melt_dataframe, 5},
64 
+    {"C_melt_matrix", (DL_FUNC) & melt_matrix, 1},
65 
+    {"C_transpose_list", (DL_FUNC) & transpose_list, 1},
66 
+    {"C_COMPASS_CellCounts_character", (DL_FUNC) & COMPASS_CellCounts_character,
67 
+     2},
68 
+    {"C_COMPASS_CellCounts", (DL_FUNC) & COMPASS_CellCounts, 2},
69 
+    {"C_samplePuPs", (DL_FUNC) & samplePuPs, 9},
70 
+    {"C_updatealphas_Exp", (DL_FUNC) & updatealphas_Exp, 10},
71 
+    {"C_updatealphau_noPu_Exp", (DL_FUNC) & updatealphau_noPu_Exp, 9},
72 
+    {"C_updategammak_noPu", (DL_FUNC) & updategammak_noPu, 16},
73 
+    {NULL, NULL, 0}};
30 74
31 
-void R_init_COMPASS(DllInfo *info) {
75 
+void R_init_COMPASS(DllInfo* info) {
32 76 
   R_registerRoutines(info, NULL, callMethods, NULL, NULL);
33 77 
   R_useDynamicSymbols(info, FALSE);
34 78 
 }
35 
-
Browse code

Re-format

Kevin Ushey authored on 02/05/2014 04:10:15
Showing 1 changed files
src/COMPASS_init.c
History View file @ 060940b
... ... 
@@ -5,31 +5,74 @@
5 5
6 6 
 #include <R_ext/Rdynload.h>
7 7
8 
-SEXP melt_dataframe( SEXP x, SEXP id_ind_, SEXP val_ind_, SEXP variable_name, SEXP value_name );
9 
-SEXP melt_matrix( SEXP x );
8 
+SEXP melt_dataframe(SEXP x,
9 
+                    SEXP id_ind_,
10 
+                    SEXP val_ind_,
11 
+                    SEXP variable_name,
12 
+                    SEXP value_name);
13 
+SEXP melt_matrix(SEXP x);
10 14 
 SEXP transpose_list(SEXP x);
11 15 
 SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
12 16 
 SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
13 
-SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
14 
-SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
15 
-SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
16 
-SEXP updategammak_noPu(SEXP n_s,SEXP n_u, SEXP gammat, SEXP I, SEXP K, SEXP SS, SEXP alphau, SEXP alphas, SEXP alpha, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP indi);
17 
+SEXP samplePuPs(SEXP alphau,
18 
+                SEXP alphas,
19 
+                SEXP gammat,
20 
+                SEXP T,
21 
+                SEXP K,
22 
+                SEXP nsi,
23 
+                SEXP nui,
24 
+                SEXP d,
25 
+                SEXP M);
26 
+SEXP updatealphas_Exp(SEXP alphast,
27 
+                      SEXP n_s,
28 
+                      SEXP K,
29 
+                      SEXP I,
30 
+                      SEXP lambda_s,
31 
+                      SEXP gammat,
32 
+                      SEXP var_1,
33 
+                      SEXP var_2,
34 
+                      SEXP p_var,
35 
+                      SEXP ttt);
36 
+SEXP updatealphau_noPu_Exp(SEXP alphaut,
37 
+                           SEXP n_s,
38 
+                           SEXP n_u,
39 
+                           SEXP I,
40 
+                           SEXP K,
41 
+                           SEXP lambda_u,
42 
+                           SEXP var_p,
43 
+                           SEXP ttt,
44 
+                           SEXP gammat);
45 
+SEXP updategammak_noPu(SEXP n_s,
46 
+                       SEXP n_u,
47 
+                       SEXP gammat,
48 
+                       SEXP I,
49 
+                       SEXP K,
50 
+                       SEXP SS,
51 
+                       SEXP alphau,
52 
+                       SEXP alphas,
53 
+                       SEXP alpha,
54 
+                       SEXP mk,
55 
+                       SEXP Istar,
56 
+                       SEXP mKstar,
57 
+                       SEXP pp,
58 
+                       SEXP pb1,
59 
+                       SEXP pb2,
60 
+                       SEXP indi);
17 61
18 
-R_CallMethodDef callMethods[]  = {
19 
-  {"C_melt_dataframe", (DL_FUNC) &melt_dataframe, 5},
20 
-  {"C_melt_matrix", (DL_FUNC) &melt_matrix, 1},
21 
-  {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
22 
-  {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
23 
-  {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
24 
-  {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
25 
-  {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
26 
-  {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
27 
-  {"C_updategammak_noPu", (DL_FUNC) &updategammak_noPu, 16},
28 
-  {NULL, NULL, 0}
29 
-};
62 
+R_CallMethodDef callMethods[] = {
63 
+    {"C_melt_dataframe", (DL_FUNC) & melt_dataframe, 5},
64 
+    {"C_melt_matrix", (DL_FUNC) & melt_matrix, 1},
65 
+    {"C_transpose_list", (DL_FUNC) & transpose_list, 1},
66 
+    {"C_COMPASS_CellCounts_character", (DL_FUNC) & COMPASS_CellCounts_character,
67 
+     2},
68 
+    {"C_COMPASS_CellCounts", (DL_FUNC) & COMPASS_CellCounts, 2},
69 
+    {"C_samplePuPs", (DL_FUNC) & samplePuPs, 9},
70 
+    {"C_updatealphas_Exp", (DL_FUNC) & updatealphas_Exp, 10},
71 
+    {"C_updatealphau_noPu_Exp", (DL_FUNC) & updatealphau_noPu_Exp, 9},
72 
+    {"C_updategammak_noPu", (DL_FUNC) & updategammak_noPu, 16},
73 
+    {NULL, NULL, 0}};
30 74
31 
-void R_init_COMPASS(DllInfo *info) {
75 
+void R_init_COMPASS(DllInfo* info) {
32 76 
   R_registerRoutines(info, NULL, callMethods, NULL, NULL);
33 77 
   R_useDynamicSymbols(info, FALSE);
34 78 
 }
35 
-
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 2 commit(s).

Commit information:

Commit id: a77bbd32f9b1665bb3a0c7e4ed2c8d92509b4864
Commit message:
One more unit test
Committed by kevinushey <kevinushey at gmail.com>
Commit date: 2014-04-04T12:33:29-07:00

Commit id: b7396ae1d8ab4e3ce8701225feacde97215fb529
Commit message:
Clean out the continuous model files (not used)
Committed by kevinushey <kevinushey at gmail.com>
Commit date: 2014-04-04T12:33:29-07:00

From: Bioconductor Git-SVN Bridge <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@88439 bc3139a8-67e5-0310-9ffc-ced21a209358

k.ushey authored on 04/04/2014 19:33:48
Showing 1 changed files
src/COMPASS_init.c
History View file @ dcf8e59
... ... 
@@ -10,7 +10,6 @@ SEXP melt_matrix( SEXP x );
10 10 
 SEXP transpose_list(SEXP x);
11 11 
 SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
12 12 
 SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
13 
-SEXP model(SEXP T, SEXP I, SEXP K, SEXP M, SEXP ttt, SEXP SS, SEXP alpha_u, SEXP alpha_s, SEXP mu_u, SEXP mu_s, SEXP alpha, SEXP beta, SEXP gamma, SEXP n_s, SEXP n_u, SEXP varp_u, SEXP lambda_u,SEXP indi, SEXP d, SEXP ybar_s, SEXP ybar_u, SEXP ys2_s, SEXP ys2_u, SEXP a, SEXP b, SEXP lambda, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP lambda_s,SEXP var_1, SEXP var_2, SEXP p_var, SEXP p_vars, SEXP var_1s, SEXP var_2s, SEXP m_s,SEXP Sigma_s, SEXP p_varu, SEXP var_1u,SEXP var_2u, SEXP m_u, SEXP Sigma_u, SEXP p_vara, SEXP var_1a, SEXP var_2a, SEXP sig_alpha1, SEXP alpha1, SEXP p_varb, SEXP var_1b, SEXP var_2b, SEXP sig_beta1, SEXP beta1, SEXP A_alphau, SEXP A_alphas, SEXP A_gm, SEXP A_mus, SEXP A_muu, SEXP A_alpha, SEXP A_beta, SEXP Tune, SEXP pgamma);
14 13 
 SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
15 14 
 SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
16 15 
 SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
... ... 
@@ -22,7 +21,6 @@ R_CallMethodDef callMethods[]  = {
22 21 
   {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
23 22 
   {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
24 23 
   {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
25 
-  {"C_model", (DL_FUNC) &model, 65},
26 24 
   {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
27 25 
   {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
28 26 
   {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
Browse code

Clean out the continuous model files (not used)

kevinushey authored on 04/04/2014 19:33:21
Showing 1 changed files
src/COMPASS_init.c
History View file @ b7396ae
... ... 
@@ -10,7 +10,6 @@ SEXP melt_matrix( SEXP x );
10 10 
 SEXP transpose_list(SEXP x);
11 11 
 SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
12 12 
 SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
13 
-SEXP model(SEXP T, SEXP I, SEXP K, SEXP M, SEXP ttt, SEXP SS, SEXP alpha_u, SEXP alpha_s, SEXP mu_u, SEXP mu_s, SEXP alpha, SEXP beta, SEXP gamma, SEXP n_s, SEXP n_u, SEXP varp_u, SEXP lambda_u,SEXP indi, SEXP d, SEXP ybar_s, SEXP ybar_u, SEXP ys2_s, SEXP ys2_u, SEXP a, SEXP b, SEXP lambda, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP lambda_s,SEXP var_1, SEXP var_2, SEXP p_var, SEXP p_vars, SEXP var_1s, SEXP var_2s, SEXP m_s,SEXP Sigma_s, SEXP p_varu, SEXP var_1u,SEXP var_2u, SEXP m_u, SEXP Sigma_u, SEXP p_vara, SEXP var_1a, SEXP var_2a, SEXP sig_alpha1, SEXP alpha1, SEXP p_varb, SEXP var_1b, SEXP var_2b, SEXP sig_beta1, SEXP beta1, SEXP A_alphau, SEXP A_alphas, SEXP A_gm, SEXP A_mus, SEXP A_muu, SEXP A_alpha, SEXP A_beta, SEXP Tune, SEXP pgamma);
14 13 
 SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
15 14 
 SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
16 15 
 SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
... ... 
@@ -22,7 +21,6 @@ R_CallMethodDef callMethods[]  = {
22 21 
   {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
23 22 
   {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
24 23 
   {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
25 
-  {"C_model", (DL_FUNC) &model, 65},
26 24 
   {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
27 25 
   {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
28 26 
   {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
Browse code

version bump

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@86807 bc3139a8-67e5-0310-9ffc-ced21a209358

k.ushey authored on 25/02/2014 22:41:09
Showing 1 changed files
src/COMPASS_init.c
History View file @ e7fb642
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,37 @@
1 
+// This file was automatically generated by Kmisc::registerFunctions()
2 
+
3 
+#include <R.h>
4 
+#include <Rinternals.h>
5 
+
6 
+#include <R_ext/Rdynload.h>
7 
+
8 
+SEXP melt_dataframe( SEXP x, SEXP id_ind_, SEXP val_ind_, SEXP variable_name, SEXP value_name );
9 
+SEXP melt_matrix( SEXP x );
10 
+SEXP transpose_list(SEXP x);
11 
+SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
12 
+SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
13 
+SEXP model(SEXP T, SEXP I, SEXP K, SEXP M, SEXP ttt, SEXP SS, SEXP alpha_u, SEXP alpha_s, SEXP mu_u, SEXP mu_s, SEXP alpha, SEXP beta, SEXP gamma, SEXP n_s, SEXP n_u, SEXP varp_u, SEXP lambda_u,SEXP indi, SEXP d, SEXP ybar_s, SEXP ybar_u, SEXP ys2_s, SEXP ys2_u, SEXP a, SEXP b, SEXP lambda, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP lambda_s,SEXP var_1, SEXP var_2, SEXP p_var, SEXP p_vars, SEXP var_1s, SEXP var_2s, SEXP m_s,SEXP Sigma_s, SEXP p_varu, SEXP var_1u,SEXP var_2u, SEXP m_u, SEXP Sigma_u, SEXP p_vara, SEXP var_1a, SEXP var_2a, SEXP sig_alpha1, SEXP alpha1, SEXP p_varb, SEXP var_1b, SEXP var_2b, SEXP sig_beta1, SEXP beta1, SEXP A_alphau, SEXP A_alphas, SEXP A_gm, SEXP A_mus, SEXP A_muu, SEXP A_alpha, SEXP A_beta, SEXP Tune, SEXP pgamma);
14 
+SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
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+SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
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+SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
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+SEXP updategammak_noPu(SEXP n_s,SEXP n_u, SEXP gammat, SEXP I, SEXP K, SEXP SS, SEXP alphau, SEXP alphas, SEXP alpha, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP indi);
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+
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+R_CallMethodDef callMethods[]  = {
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+  {"C_melt_dataframe", (DL_FUNC) &melt_dataframe, 5},
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+  {"C_melt_matrix", (DL_FUNC) &melt_matrix, 1},
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+  {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
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+  {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
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+  {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
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+  {"C_model", (DL_FUNC) &model, 65},
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+  {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
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+  {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
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+  {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
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+  {"C_updategammak_noPu", (DL_FUNC) &updategammak_noPu, 16},
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+  {NULL, NULL, 0}
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+};
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+
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+void R_init_COMPASS(DllInfo *info) {
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+  R_registerRoutines(info, NULL, callMethods, NULL, NULL);
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+  R_useDynamicSymbols(info, FALSE);
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+}
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+
Browse code

Adds COMPASS/ GSCA/ CopyNumber450k/ sangerseqR/ unifiedWMWqPCR/ to the repos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS@86791 bc3139a8-67e5-0310-9ffc-ced21a209358

m.carlson authored on 25/02/2014 18:56:48
Showing 1 changed files
src/COMPASS_init.c
History View file @ c75adc5
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new file mode 100644
... ... 
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+// This file was automatically generated by Kmisc::registerFunctions()
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+
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+#include <R.h>
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+#include <Rinternals.h>
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+
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+#include <R_ext/Rdynload.h>
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+
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+SEXP melt_dataframe( SEXP x, SEXP id_ind_, SEXP val_ind_, SEXP variable_name, SEXP value_name );
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+SEXP melt_matrix( SEXP x );
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+SEXP transpose_list(SEXP x);
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+SEXP COMPASS_CellCounts_character(SEXP dataSEXP, SEXP combinationsSEXP);
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+SEXP COMPASS_CellCounts(SEXP xSEXP, SEXP combosSEXP);
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+SEXP model(SEXP T, SEXP I, SEXP K, SEXP M, SEXP ttt, SEXP SS, SEXP alpha_u, SEXP alpha_s, SEXP mu_u, SEXP mu_s, SEXP alpha, SEXP beta, SEXP gamma, SEXP n_s, SEXP n_u, SEXP varp_u, SEXP lambda_u,SEXP indi, SEXP d, SEXP ybar_s, SEXP ybar_u, SEXP ys2_s, SEXP ys2_u, SEXP a, SEXP b, SEXP lambda, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP lambda_s,SEXP var_1, SEXP var_2, SEXP p_var, SEXP p_vars, SEXP var_1s, SEXP var_2s, SEXP m_s,SEXP Sigma_s, SEXP p_varu, SEXP var_1u,SEXP var_2u, SEXP m_u, SEXP Sigma_u, SEXP p_vara, SEXP var_1a, SEXP var_2a, SEXP sig_alpha1, SEXP alpha1, SEXP p_varb, SEXP var_1b, SEXP var_2b, SEXP sig_beta1, SEXP beta1, SEXP A_alphau, SEXP A_alphas, SEXP A_gm, SEXP A_mus, SEXP A_muu, SEXP A_alpha, SEXP A_beta, SEXP Tune, SEXP pgamma);
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+SEXP samplePuPs(SEXP alphau, SEXP alphas, SEXP gammat, SEXP T, SEXP K , SEXP nsi, SEXP nui, SEXP d, SEXP M);
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+SEXP updatealphas_Exp(SEXP alphast,SEXP n_s, SEXP K, SEXP I, SEXP lambda_s, SEXP gammat, SEXP var_1,SEXP var_2, SEXP p_var, SEXP ttt);
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+SEXP updatealphau_noPu_Exp(SEXP alphaut, SEXP n_s, SEXP n_u, SEXP I, SEXP K, SEXP lambda_u, SEXP var_p, SEXP ttt, SEXP gammat);
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+SEXP updategammak_noPu(SEXP n_s,SEXP n_u, SEXP gammat, SEXP I, SEXP K, SEXP SS, SEXP alphau, SEXP alphas, SEXP alpha, SEXP mk, SEXP Istar, SEXP mKstar, SEXP pp, SEXP pb1, SEXP pb2, SEXP indi);
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+
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+R_CallMethodDef callMethods[]  = {
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+  {"C_melt_dataframe", (DL_FUNC) &melt_dataframe, 5},
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+  {"C_melt_matrix", (DL_FUNC) &melt_matrix, 1},
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+  {"C_transpose_list", (DL_FUNC) &transpose_list, 1},
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+  {"C_COMPASS_CellCounts_character", (DL_FUNC) &COMPASS_CellCounts_character, 2},
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+  {"C_COMPASS_CellCounts", (DL_FUNC) &COMPASS_CellCounts, 2},
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+  {"C_model", (DL_FUNC) &model, 65},
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+  {"C_samplePuPs", (DL_FUNC) &samplePuPs, 9},
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+  {"C_updatealphas_Exp", (DL_FUNC) &updatealphas_Exp, 10},
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+  {"C_updatealphau_noPu_Exp", (DL_FUNC) &updatealphau_noPu_Exp, 9},
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+  {"C_updategammak_noPu", (DL_FUNC) &updategammak_noPu, 16},
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+  {NULL, NULL, 0}
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+};
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+
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+void R_init_COMPASS(DllInfo *info) {
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+  R_registerRoutines(info, NULL, callMethods, NULL, NULL);
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+  R_useDynamicSymbols(info, FALSE);
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+}
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+