version 1.1.6

cran · Oct 27, 2022 · 5e496db · 5e496db
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: repeated
-Version: 1.1.5
+Version: 1.1.6
 Title: Non-Normal Repeated Measurements Models
 Authors@R: c(
     person("Bruce", "Swihart", email="bruce.swihart@gmail.com", role=c("cre", "aut")),
@@ -34,7 +34,7 @@ Encoding: UTF-8
 LazyLoad: true
 RoxygenNote: 7.1.2
 NeedsCompilation: yes
-Packaged: 2022-03-01 04:40:04 UTC; swihartbj
+Packaged: 2022-10-27 18:27:05 UTC; swihartbj
 Author: Bruce Swihart [cre, aut],
   Jim Lindsey [aut] (Jim created this package, Bruce is maintaining the
     CRAN version),
@@ -48,4 +48,4 @@ Author: Bruce Swihart [cre, aut],
   Euginia Zharichenko [ctb, cph] (Wrote logitord.f.)
 Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
 Repository: CRAN
-Date/Publication: 2022-03-01 10:10:02 UTC
+Date/Publication: 2022-10-27 23:42:39 UTC
diff --git a/MD5 b/MD5
@@ -1,7 +1,7 @@
 ad4652e2dcfd4a0ecf91a2c01a7defd5 *COPYING
-196e33f9397967d1c8262d4e47b9565b *DESCRIPTION
+971e34c3183421e087b54aa72e28ca81 *DESCRIPTION
 fba233ff25d8cbc4cf1daa9261662f5c *NAMESPACE
-e4c576fa207e060942496944ef6535ef *NEWS.md
+ec67d7f48464ddbdaa557fbaf22c2410 *NEWS.md
 023f9a154fa58c9a8ade2f230bcaa609 *R/binnest.r
 7f7e23c08b633bf337bf4df41a960c41 *R/bivbetab.r
 08f383919987272fb0d1bb761a643570 *R/bivbinom.r
@@ -57,7 +57,7 @@ fd6402b5ca818411a437833f22a1b63f *src/chidden.f
 17b9883568d316efe771b524b68394d5 *src/cphidden.f
 56be3da0a27ad554ac2b456af1cd58c9 *src/cutil.c
 dec0bfcc01ab69b25ed9121cf66652c0 *src/defs.h
-374d0366926b8694a9afb8c88f10ede0 *src/dist.c
+a0548a77c75486186ab6f15c90828dc2 *src/dist.c
 dccd5a32702ff168ef068262881d710c *src/dist.h
 86525d463916de7bbdb23ec868bc2032 *src/eigen.f
 b9c96a37979accae8a8baa5cd7e81448 *src/gaps.c

diff --git a/NEWS.md b/NEWS.md
@@ -1,26 +1,32 @@
-#------------------------------------------------------------------------------
-#version 1.1.5
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.6
+------------------------------------------------------------------------------
+
+  * Corrected clang15 warnings and news.md formatting
+
+------------------------------------------------------------------------------
+version 1.1.5
+------------------------------------------------------------------------------
 
   * Corrected license back to original:  GPL>=2
 
-#------------------------------------------------------------------------------
-#version 1.1.4
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.4
+------------------------------------------------------------------------------
 
   * Corrected the LTO issues by correcting registration in repeated_init.c
 
-#------------------------------------------------------------------------------
-#version 1.1.3
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.3
+------------------------------------------------------------------------------
 
   * https://github.com/swihart/repeated/issues/16
   * `call_R()` be gone!
   * rewrite the C-code of romberg integration in gnlmix to have entry .Call
 
-#------------------------------------------------------------------------------
-#version 1.1.2
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.2
+------------------------------------------------------------------------------
 
   * https://github.com/swihart/repeated/issues/15
   * `repeated` was flagged for LTO mismatches using gcc9 and subsequently taken off CRAN.
@@ -32,21 +38,21 @@
   In addition I've embellished the DESCRIPTION with information about models and citations   to JK
   Lindsey's textbooks.
 
-#------------------------------------------------------------------------------
-#version 1.1.1
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.1
+------------------------------------------------------------------------------
 
   * https://github.com/swihart/repeated/issues/14
   * Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’) Fix
   * abs --> fabs in gar.c
   * comment out plevy .C calls because we just import from rmutil all along
   * Corrected failure: length > 1 in coercion to logical errors
 
-#------------------------------------------------------------------------------
-#version 1.1.0
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.1.0
+------------------------------------------------------------------------------
 
-## Major changes ##
+Major changes 
 
 Passed CRAN checks and is back on CRAN.  Please see github page 
 https://github.com/swihart/repeated to see the changes required 
@@ -61,9 +67,9 @@ https://github.com/swihart/repeated/issues.
 **Below this line corresponds to [changes.txt](https://www.commanster.eu/rcode/changes.txt), which was Jim Lindsey's file for
 detailing changes across the v1.0 packages `rmutil`, `repeated`, `gnlm`, `growth`, `event`, `stable` on his homepage**
 
-#------------------------------------------------------------------------------
-#version 1.0
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 1.0
+------------------------------------------------------------------------------
 
 30.11.10 (growth)
 
@@ -369,9 +375,9 @@ diagonal constant
       added check that double Poisson, multiplicative Poisson, gamma
       count, and logarithmic data are not censored
 
-#------------------------------------------------------------------------------
-#version 0.9
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.9
+------------------------------------------------------------------------------
 
 28.4.02
 
@@ -927,9 +933,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
   * gausscop: multivariate Gaussian copula with arbitrary marginals
   * elliptic.r: several typing errors corrected
 
-#------------------------------------------------------------------------------
-#version 0.8
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.8
+------------------------------------------------------------------------------
 
 17.10.00
 
@@ -1136,9 +1142,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
 	    Osman Buyukisk)
   * restovec: responses can have more than one type class
 
-#------------------------------------------------------------------------------
-#version 0.7
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.7
+------------------------------------------------------------------------------
 
 3.1.2000
 
@@ -1330,9 +1336,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
 
   * ordglm.r: generalized linear ordinal regression
 
-#------------------------------------------------------------------------------
-#version 0.6
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.6
+------------------------------------------------------------------------------
 
 21.9.99
 
@@ -1374,9 +1380,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
   * binnest.f: modified comments to compile with standard Fortran (thanks
 	to Martin Maechler)
 
-#------------------------------------------------------------------------------
-#version 0.5
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.5
+------------------------------------------------------------------------------
 
 29.6.99
 
@@ -1507,9 +1513,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
   * carma.r: corrected predicted values when response is transformed
   * gar.r, kalseries.r: changed handling of transformed responses
 
-#------------------------------------------------------------------------------
-#version 0.4
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.4
+------------------------------------------------------------------------------
 
 12.4.99
 
@@ -1692,9 +1698,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
 	agree with kalsurv.r
   * elliptic.r: use var(y) to get initial estimate of variance
 
-#------------------------------------------------------------------------------
-#version 0.3
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.3
+------------------------------------------------------------------------------
 
 14.1.99
 
@@ -1791,9 +1797,9 @@ gar: added loglog link for binomial data (corrected cloglog which was,
 
   * carmasub.f and survkit.f: changes for compatibility with g77
 
-#------------------------------------------------------------------------------
-#version 0.2
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.2
+------------------------------------------------------------------------------
 
 2.11.98
 
@@ -1971,6 +1977,6 @@ bessel.r: added docs
 
   * gar.r Corrected predictions for transformed responses
 
-#------------------------------------------------------------------------------
-#version 0.1
-#------------------------------------------------------------------------------
+------------------------------------------------------------------------------
+version 0.1
+------------------------------------------------------------------------------
diff --git a/src/dist.c b/src/dist.c
@@ -243,45 +243,45 @@ static void interp(double x[], double fx[], int pts, double tab1[],
     *df=2*ni<(pts-j-3)?tab1[ni+1]:tab2[ni--];
     *f+=*df;}}
 
-static void evalfn(void fcn(), double a[], double b[], int n,
-		   int len, double sum[], double tmpsum[], double zz[],
-		   double pnt1[], double pnt2[], double arg1[],
-		   double arg2[], double arg3[], double x[])
-{
-  int i,j,k,nn;
-
-  if(n==1){
-    for(k=0;k<len;k++)zz[k]=0.5*(a[k]+b[k]);
-    fcn(zz,arg1,arg2,arg3,len,x);
-    for(k=0;k<len;k++)sum[k]=(b[k]-a[k])*x[k];
-    return;}
-  else {
-    for(i=1,j=1;j<n-1;j++) i*=3;
-    nn=i;
-    for(k=0;k<len;k++){
-      pnt1[k]=(b[k]-a[k])/(3.0*nn);
-      pnt2[k]=2.0*pnt1[k];
-      zz[k]=a[k]+0.5*pnt1[k];
-      tmpsum[k]=0.0;}
-    for(j=1;j<=i;j++){
-      fcn(zz,arg1,arg2,arg3,len,x);
-      for(k=0;k<len;k++){
-	tmpsum[k]+=x[k];
-	zz[k]+=pnt2[k];}
-      fcn(zz,arg1,arg2,arg3,len,x);
-      for(k=0;k<len;k++){
-	tmpsum[k]+=x[k];
-	zz[k]+=pnt1[k];}}
-    for(k=0;k<len;k++)sum[k]=(sum[k]+(b[k]-a[k])*tmpsum[k]/nn)/3.0;
-    return;}}
+static void evalfn(void (*fcn)(double*, double*, double*, double*, int, double*), double a[], double b[], int n,
+                       int len, double sum[], double tmpsum[], double zz[],
+                                                                        double pnt1[], double pnt2[], double arg1[],
+                                                                                                                 double arg2[], double arg3[], double x[])
+    {
+      int i,j,k,nn;
+      
+      if(n==1){
+        for(k=0;k<len;k++)zz[k]=0.5*(a[k]+b[k]);
+        fcn(zz,arg1,arg2,arg3,len,x);
+        for(k=0;k<len;k++)sum[k]=(b[k]-a[k])*x[k];
+        return;}
+      else {
+        for(i=1,j=1;j<n-1;j++) i*=3;
+        nn=i;
+        for(k=0;k<len;k++){
+          pnt1[k]=(b[k]-a[k])/(3.0*nn);
+          pnt2[k]=2.0*pnt1[k];
+          zz[k]=a[k]+0.5*pnt1[k];
+          tmpsum[k]=0.0;}
+        for(j=1;j<=i;j++){
+          fcn(zz,arg1,arg2,arg3,len,x);
+          for(k=0;k<len;k++){
+            tmpsum[k]+=x[k];
+            zz[k]+=pnt2[k];}
+          fcn(zz,arg1,arg2,arg3,len,x);
+          for(k=0;k<len;k++){
+            tmpsum[k]+=x[k];
+            zz[k]+=pnt1[k];}}
+        for(k=0;k<len;k++)sum[k]=(sum[k]+(b[k]-a[k])*tmpsum[k]/nn)/3.0;
+        return;}}
 
-static void romberg2(void fcn(), double *a, double *b, int len,
-		    double *arg1, double *arg2, double *arg3, double eps,
-		    int pts, int max, int *err, double sumlen[])
+static void romberg2(void (*fcn)(double*, double*, double*, double*, int, double*), double *a, double *b, int len,
+                     double *arg1, double *arg2, double *arg3, double eps,
+                     int pts, int max, int *err, double sumlen[])
 {
   int i,j,j1,finish;
   double errsum,*tab1,*tab2,*x,*fx,*sum,*tmpsum,*zz,*pnt1,*pnt2,*y;
-
+  
   x=(double*)R_alloc((size_t)(max*len),sizeof(double));
   fx=(double*)R_alloc((size_t)(max*len),sizeof(double));
   sum=(double*)R_alloc((size_t)len,sizeof(double));
@@ -304,9 +304,9 @@ static void romberg2(void fcn(), double *a, double *b, int len,
     for(i=0;i<len;i++){
       fx[j+i*max]=sum[i];
       if(j1>=pts){
-	interp(&x[j1-pts+i*max],&fx[j1-pts+i*max],pts,tab1,tab2,&sumlen[i],&errsum,err);
-	if(*err)return;
-	if(fabs(errsum)>eps*fabs(sumlen[i]))finish=0;}
+        interp(&x[j1-pts+i*max],&fx[j1-pts+i*max],pts,tab1,tab2,&sumlen[i],&errsum,err);
+        if(*err)return;
+        if(fabs(errsum)>eps*fabs(sumlen[i]))finish=0;}
       x[j1+i*max]=x[j+i*max]/9.0;
       fx[j1+i*max]=fx[j+i*max];}
     if(finish)return;}