version 1.0-1

DESCRIPTION

@@ -2,8 +2,8 @@ Package: vcrpart
 Type: Package
 Title: Tree-Based Varying Coefficient Regression for Generalized Linear
         and Ordinal Mixed Models
-Version: 1.0-0
-Date: 2017-08-21
+Version: 1.0-1
+Date: 2017-10-17
 Authors@R: c(
   person("Reto", "Buergin", role = c("aut", "cre", "cph"), email = "rbuergin@gmx.ch"),
   person("Gilbert", "Ritschard", role = c("ctb", "ths"),
@@ -16,8 +16,8 @@ Imports: stats, grid, graphics, methods, nlme (>= 3.1-123), rpart,
         formula.tools, numDeriv, ucminf, zoo, sandwich, strucchange
 LazyLoad: yes
 NeedsCompilation: yes
-Packaged: 2017-08-21 21:04:26 UTC; reto
+Packaged: 2017-10-17 20:47:15 UTC; reto
 Author: Reto Buergin [aut, cre, cph],
   Gilbert Ritschard [ctb, ths]
 Repository: CRAN
-Date/Publication: 2017-08-22 15:35:07 UTC
+Date/Publication: 2017-10-17 21:42:31 UTC

MD5

@@ -1,6 +1,6 @@
-6f97001bc9307a6c61fc6c2dec447ede *DESCRIPTION
+00fa11f453239d83c49a391f1d7dd2b2 *DESCRIPTION
 88f2a7e8732471db378d8c7ad4d414b7 *NAMESPACE
-db2354e4a737b45a2d4e1f9416f8752a *NEWS
+ef76328b52cdee76b9eb87f36c8d18c4 *NEWS
 8b40e51cf24df0eb99503a7070b84a93 *R/AAA.R
 160b81f4ae1117bfe2f84236b2d2af0f *R/AllGeneric.R
 594f5359a79fc4cd908512f91da3f439 *R/fvcm.R
@@ -12,7 +12,7 @@ db2354e4a737b45a2d4e1f9416f8752a *NEWS
 0d61b66e97dd63d12acc811055982b13 *R/tvcm-cv.R
 a56eb3ce150852b6e0f89bae76045145 *R/tvcm-methods.R
 773603a317d64e5674e7257c9a857409 *R/tvcm-plot.R
-9da6909d2a597d6d4d64de42c05b593b *R/tvcm-utils.R
+6b7a6de9c4bf75d4c88e81c11df5124b *R/tvcm-utils.R
 86cd70f18d32eb1b9a58ff4e7d0b4338 *R/tvcm.R
 9d40db38c5fd987f14b5716ed08da2b1 *R/utils.R
 60387778eacc623d54ae76f33d4de60c *ToDo
@@ -26,8 +26,8 @@ ea62be4e5d10df5bc683725a7f7935f6 *data/schizo.RData
 cb803decf95c39567f648e1e5e0ddb45 *data/vcrpart_2.RData
 3ddf5ac69dc37253946b83c5bfd5fca7 *data/vcrpart_3.RData
 073dbc46eee3af9fc409b395fef38eaa *inst/CITATION
-596630a3792956eede699a719233bae1 *inst/doc/vcrpart.Rnw
-3a6075206932b1be8110c82c31679adb *inst/doc/vcrpart.pdf
+2cc6e45ac533eb0551eab45747d2b613 *inst/doc/vcrpart.Rnw
+6ad00ccbe8d06fe5532c01aa1632c940 *inst/doc/vcrpart.pdf
 38f1299f8a057cb18bbe99fb630249f3 *man/PL.Rd
 ef7899f341e4dd14895e0f20af9ff4bf *man/contr-wsum.Rd
 d019d09b94cae8c5342c3b4bb42838da *man/fvcm-methods.Rd
@@ -53,7 +53,7 @@ c77bcd03b4cb28c5a91036575b93d716 *man/tvcolmm.Rd
 873a11355678ee053f51b38089f893f4 *man/vcrpart-formula.Rd
 2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
 bdcec3746d75f6748e912f41ccab8baa *src/init.c
-35966357c5a95456455ed60954652fb3 *src/olmm.c
+405cbdb2b8f51375ddec28bfdff553a0 *src/olmm.c
 79ee30a544c9bd2e26891000e3bb2a59 *src/olmm.h
 0af72621bd0a3d74afc3a3a0220f92c4 *src/tvcm.c
 e8b96835ed09462a3fef4b1f581279cd *src/tvcm.h
@@ -70,4 +70,4 @@ dca495b2e307300047257c547e9795ed *vignettes/Figures/jss2564-school-fig-tree.pdf
 31aee9b5f0da739c73a2117f48a42c67 *vignettes/Figures/jss2564-ucba-fig-cv.pdf
 287d69566937f6e73e6f421d1a9b4bb9 *vignettes/Figures/jss2564-ucba-fig-vcm.pdf
 fd41663f2eacaabf3a9ebf47b94eac4d *vignettes/Figures/jss2564-ucba-fig-vcmL.pdf
-596630a3792956eede699a719233bae1 *vignettes/vcrpart.Rnw
+2cc6e45ac533eb0551eab45747d2b613 *vignettes/vcrpart.Rnw

NEWS

@@ -1,3 +1,14 @@
+Changes in Version 1.0-1
+
+    o   Internal modification for the 'singular.ok' argument of future
+        R versions.
+
+    o   Replaced 'memcpy' calls in C-code with 'for' loops because they
+        were used for small objects.
+
+    o   Improve R-Code for 'alloca' calls (adding 'R_CheckStack()'
+        after calls)
+
 Changes in Version 1.0-0
 
     o    Added vignette.

R/tvcm-utils.R

@@ -51,6 +51,8 @@
 ## tvcm_grow_splitpath:      creates a 'splitpath.tvcm' object
 ##
 ## Last modifications:
+## 2017-10-16: add argument 'singular.ok' for 'glm.doNotFit', see mail
+##             of Martin Maechler, 2017-09-30
 ## 2017-08-21: - rename arguments for 'tvcm_get_terms'.
 ##             - bug fix for 'tvcm_get_estimates' for situations where
 ##               'fe' terms include factor variables or operators
@@ -574,7 +576,8 @@ tvcm_grow <- function(object, subset = NULL, weights = NULL) {
 glm.doNotFit <- function(x, y, weights = NULL, start = NULL,
                          etastart = NULL,
                          mustart = NULL, offset = NULL, family = gaussian(),
-                         control = list(), intercept = TRUE) {
+                         control = list(), intercept = TRUE,
+                         singular.ok = TRUE) {
     coefficients <- rep.int(0, NCOL(x))
     names(coefficients) <- colnames(x)
     if (is.null(weights)) weights <- rep.int(1.0, NROW(x))

inst/doc/vcrpart.Rnw

@@ -53,7 +53,8 @@ empirical applications.
   E-mail: \email{Gilbert.Ritschard@unige.ch}
 }
 
-\usepackage[utf8x]{inputenc}
+\usepackage[utf8]{inputenc} % 2017-08-23
+%\usepackage[utf8x]{inputenc}
 %\usepackage{Sweave.sty}
 % \usepackage{Sweave}
 % \SweaveOpts{eps=TRUE}

src/olmm.c

@@ -143,12 +143,15 @@ SEXP olmm_setPar(SEXP x, SEXP par) {
   const double zero = 0.0, one = 1.0; /* for matrix manipulations */
 
   /* overwrite coefficients slot */
-  Memcpy(coefficients, newPar, nPar);
-
+  for (int i = 0; i < nPar; i++)
+    coefficients[i] = newPar[i];
+
   /* overwrite fixed effect parameter slot */
   for (int i = 0; i < nEta; i++) {
-    Memcpy(fixef + i * pEta, newPar + i * pCe, pCe);
-    Memcpy(fixef + i * pEta + pCe, newPar + pCe*nEta, pGe);
+    for (int j = 0; j < pCe; j++)
+      fixef[i * pEta + j] = newPar[i * pCe + j];
+    for (int j = 0; j < pGe; j++)
+      fixef[i * pEta + pCe + j] = newPar[pCe * nEta + j];
   }
 
   /* set predictor-invariant fixed effects of adjacent-category model 
@@ -163,9 +166,12 @@ SEXP olmm_setPar(SEXP x, SEXP par) {
   }
 
   /* overwrite (cholesky decompositioned) random effect parameters */
-  double *vRanefCholFac = Memcpy(Alloca(lenVRanefCholFac, double), 
-				 newPar + p, lenVRanefCholFac);
-
+  double *vRanefCholFac = Alloca(lenVRanefCholFac, double);
+  R_CheckStack();
+
+  for (int i = 0; i < lenVRanefCholFac; i++)
+    vRanefCholFac[i] = newPar[p + i];
+
   F77_CALL(dgemv)("T", /* multiply with l. t. elimination matrix */ 
 		  &lenVRanefCholFac, &lenVecRanefCholFac,
   		  &one, ranefElMat, 
@@ -177,7 +183,7 @@ SEXP olmm_setPar(SEXP x, SEXP par) {
   SET_VECTOR_ELT(rvalR, 1, vecRanefCholFacR);
   SET_VECTOR_ELT(rvalR, 2, coefficientsR);
   SET_VECTOR_ELT(rvalR, 3, ranefElMatR);
-  
+
   UNPROTECT(5);
   return rvalR;
 }
@@ -201,7 +207,8 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
   /* get subject slot */  
   int *subject =
     INTEGER(coerceVector(getListElement(x, "subject"), INTSXP));
-
+  R_CheckStack();
+
   /* integer valued slots */
   int *dims = DIMS_SLOT(x);
 
@@ -231,9 +238,7 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
     *score_sbj = REAL(score_sbjR),
     *score = REAL(scoreR),
     *info = REAL(infoR);
-
-  R_CheckStack();
-
+
   /* set constants (dimensions of vectors etc.) */
   const int n = dims[n_POS], N = dims[N_POS], 
     p = dims[p_POS], pEta = dims[pEta_POS],
@@ -249,9 +254,8 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
 
   /* get response variable */
   int *yI = INTEGER(coerceVector(getListElement(x, "y"), INTSXP));
-  /* double *yD = REAL(coerceVector(getListElement(x, "y"), REALSXP));xs */ 
   R_CheckStack();
-
+  
   /* variables for matrix operations etc. */
   int i1 = 1, tmpJ, subsTmp; 
   double one = 1.0, zero = 0.0, 
@@ -354,8 +358,10 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
 
     /* ranefVec (vector) to ranef (matrix) */
     for (int i = 0; i < nEta; i++) {
-      Memcpy(ranef + i * qEta, ranefVec + i * qCe, qCe);
-      Memcpy(ranef + i*qEta + qCe, ranefVec + qCe*nEta, qGe);
+      for (int j = 0; j < qCe; j++)
+      	ranef[i * qEta + j] = ranefVec[i * qCe + j];
+      for (int j = 0; j < qGe; j++)
+      	ranef[i * qEta + qCe + j] = ranefVec[qCe * nEta + j];
     }
 
     /* set predictor-invariant random effects of adjacent-category models 
@@ -614,7 +620,9 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
   if (numHess == 0) {
 
     AllocVal(info, nPar * nPar, zero); /* reset info matrix*/
-    double *hDerVec = Alloca(nPar, double), hInv2;
+    double *hDerVec = Alloca(nPar, double),
+      hInv2;
+    R_CheckStack();
 
     for (int i = 0; i < N; i++) {    
       hInv2 = - weights_sbj[i] / (logLik_sbj[i] * logLik_sbj[i]);
@@ -692,8 +700,10 @@ SEXP olmm_update_marg(SEXP x, SEXP par) {
 SEXP olmm_update_u(SEXP x) {
 
   /* get subject slot */  
-  int *subject = INTEGER(coerceVector(getListElement(x, "subject"), INTSXP));
-
+  int *subject =
+    INTEGER(coerceVector(getListElement(x, "subject"), INTSXP));
+  R_CheckStack();
+
   /* integer valued slots */
   int *dims = DIMS_SLOT(x);
 
@@ -722,7 +732,6 @@ SEXP olmm_update_u(SEXP x) {
 
   /* get response variable */
   int *yI = INTEGER(coerceVector(getListElement(x, "y"), INTSXP));
-  /* double *yD = REAL(coerceVector(getListElement(x, "y"), REALSXP)); */ 
   R_CheckStack();
 
   /* variables for matrix operations */
@@ -764,7 +773,8 @@ SEXP olmm_update_u(SEXP x) {
     *ranef = Alloca(q, double),
     *logLikCond_obs = Calloc(n, double),
     *logLikCond_sbj = Calloc(N, double);
-
+  R_CheckStack();
+
   for (int k = 0; k < nQP; k++) {
 
     /* clear temporary objects */
@@ -785,8 +795,10 @@ SEXP olmm_update_u(SEXP x) {
 
     /* ranefVec (vector) to ranef (matrix) */
     for (int i = 0; i < nEta; i++) {
-      Memcpy(ranef + i * qEta, ranefVec + i * qCe, qCe);
-      Memcpy(ranef + i*qEta + qCe, ranefVec + qCe*nEta, qGe);
+      for (int j = 0; j < qCe; j++)
+      	ranef[i * qEta + j] = ranefVec[i * qCe + j];
+      for (int j = 0; j < qGe; j++)
+      	ranef[i * qEta + qCe + j] = ranefVec[qCe * nEta + j];
     }
 
     /* set predictor-invariant random effects of adjacent-category model 
@@ -860,9 +872,7 @@ SEXP olmm_update_u(SEXP x) {
   if (family == 1) Free(etaCLM);
   if (family == 1) Free(etaRanefCLM);
   if ((family == 2) | (family == 3)) Free(sumBL);
-
-  UNPROTECT(1);
-
+  UNPROTECT(1);  
   return uR;
 }
 
@@ -938,8 +948,10 @@ SEXP olmm_pred_marg(SEXP x, SEXP eta, SEXP W, SEXP n, SEXP pred) {
 
     /* ranefVec (vector) to ranef (matrix) */
     for (int i = 0; i < nEta; i++) {
-      Memcpy(ranef + i * qEta, ranefVec + i * qCe, qCe);
-      Memcpy(ranef + i*qEta + qCe, ranefVec + qCe*nEta, qGe);
+      for (int j = 0; j < qCe; j++)
+      	ranef[i * qEta + j] = ranefVec[i * qCe + j];
+      for (int j = 0; j < qGe; j++)
+      	ranef[i * qEta + qCe + j] = ranefVec[qCe * nEta + j];
     }
 
     /* set predictor-invariant random effects of adjacent-category models 
@@ -987,6 +999,7 @@ SEXP olmm_pred_marg(SEXP x, SEXP eta, SEXP W, SEXP n, SEXP pred) {
 
     gq_weight = 1; /* reset integration weight */
   }
+
   Free(etaRanef);
   Free(predCond);  
   UNPROTECT(1); 
@@ -1006,16 +1019,17 @@ SEXP olmm_pred_margNew(SEXP x, SEXP etaNew, SEXP WNew, SEXP subjectNew,
   const int rnNew = INTEGER(nNew)[0];
 
   /* get subject slot */
-  int *subject = INTEGER(coerceVector(getListElement(x, "subject"), INTSXP));
-
+  int *subject =
+    INTEGER(coerceVector(getListElement(x, "subject"), INTSXP));
+  R_CheckStack();
+
   /* integer valued slots */
   int *dims = DIMS_SLOT(x);
 
   /* numeric valued objects */
   double *ranefCholFac = RANEFCHOLFAC_SLOT(x),
     *ghw = GHW_SLOT(x), *ghx = GHX_SLOT(x), *eta = ETA_SLOT(x),
     *W = W_SLOT(x), *logLik_sbj = LOGLIKSBJ_SLOT(x);
-  R_CheckStack();
 
   /* set constants (dimensions of vectors etc.) */
   const int q = dims[q_POS], qEta = dims[qEta_POS], 
@@ -1026,7 +1040,6 @@ SEXP olmm_pred_margNew(SEXP x, SEXP etaNew, SEXP WNew, SEXP subjectNew,
 
   /* get response variable */
   int *yI = INTEGER(coerceVector(getListElement(x, "y"), INTSXP));
-  /* double *yD = REAL(coerceVector(getListElement(x, "y"), REALSXP)); */ 
   R_CheckStack();
 
   /* variables for matrix operations etc. */
@@ -1065,10 +1078,13 @@ SEXP olmm_pred_margNew(SEXP x, SEXP etaNew, SEXP WNew, SEXP subjectNew,
 
     /* ranefVec (vector) to ranef (matrix) */
     for (int i = 0; i < nEta; i++) {
-      Memcpy(ranef + i * qEta, ranefVec + i * qCe, qCe);
-      Memcpy(ranef + i*qEta + qCe, ranefVec + qCe*nEta, qGe);
+      for (int j = 0; j < qCe; j++)
+      	ranef[i * qEta + j] = ranefVec[i * qCe + j];
+      for (int j = 0; j < qGe; j++)
+      	ranef[i * qEta + qCe + j] = ranefVec[qCe * nEta + j];
     }
 
+
     /* set predictor-invariant random effects of adjacent-category models 
        to use the Likelihood of the baseline-category model */
     if (family == 3) {

vignettes/vcrpart.Rnw

@@ -53,7 +53,8 @@ empirical applications.
   E-mail: \email{Gilbert.Ritschard@unige.ch}
 }
 
-\usepackage[utf8x]{inputenc}
+\usepackage[utf8]{inputenc} % 2017-08-23
+%\usepackage[utf8x]{inputenc}
 %\usepackage{Sweave.sty}
 % \usepackage{Sweave}
 % \SweaveOpts{eps=TRUE}