Merge branch 'master' of github.com:lme4/lme4

.Rbuildignore

@@ -37,4 +37,4 @@ src/mcmcsamp\.cpp$
 revdep/
 Rplots.pdf
 R/scaleX.R
-
+\.Rout

.github/workflows/rhub.yaml

@@ -60,10 +60,37 @@ jobs:
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
+      - uses: teatimeguest/setup-texlive-action@v3
+        with:
+          packages: >-
+             scheme-basic
+             inputenc
+             graphicx
+             array
+             colortbl
+             multirow
+             hhline
+             calc
+             tabularx
+             threeparttable
+             wrapfig
+             url
+             hyperref
+             fancyvrb
+             natbib
+             xcolor
+             etoolbox
+             caption
+             adjustbox
+             thumbpdf
+             framed
+             blkarray
       - uses: r-hub/rhub2/actions/rhub-run-check@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
+          build_args: 'c("--compact-vignettes=both")'
+
 
   other-platforms:
     needs: setup
@@ -90,7 +117,6 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
       - uses: teatimeguest/setup-texlive-action@v3
-        if: runner.os != 'Linux'
         with:
           packages: >-
              scheme-basic
@@ -115,11 +141,8 @@ jobs:
              thumbpdf
              framed
              blkarray
-      - name: Install LaTeX etc.
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get install texlive texlive-science texlive-latex-base texlive-latex-extra texlive-bibtex-extra
       - uses: r-hub/rhub2/actions/rhub-run-check@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
+          build_args: 'c("--compact-vignettes=both")'

inst/NEWS.Rd

@@ -7,7 +7,7 @@
 \section{CHANGES IN VERSION 1.1-35.3}{
   \subsection{BUG FIXES}{
     \itemize{
-      bug-fix for ASAN/memory access problem in CholmodDecomposition,
+      \item bug-fix for ASAN/memory access problem in CholmodDecomposition,
       (Mikael Jagan)
     }
   } % bug fixes

misc/lme4_bigpred.R

@@ -0,0 +1,40 @@
+library(lme4)
+print(packageVersion("Matrix"))
+m1 <- lmer(Reaction 1~ Days + (Days|Subject), data = sleepstudy)
+predict(m1, newdata = sleepstudy, se.fit = TRUE)
+simulate(~Days + (Days|Subject),
+         newdata = sleepstudy,
+         newparams = list(beta = c(250, 1),
+                          theta = c(1, 1, 1),
+                          sigma = 1),
+         family = gaussian)
+
+set.seed(101)
+dd <- expand.grid(id = factor(1:1000), year = 1:15)
+d_age <- data.frame(id = factor(1:1000),
+                    age0 = sample(20:50, size = 1000, replace= TRUE))
+dd2 <- merge(dd, d_age, by = "id") |>
+    transform(age = age0 + year,
+              score = sample(1:50, size = nrow(dd), replace = TRUE))
+form <- adl~I(year^2)+score*year + age*year + (1+year|id)
+colnames(X <- model.matrix(nobars(form[-2]), data = dd2))
+beta_vec <- c(20, 0.1, 0.5, 1, 1, 0.5, 0.5)
+stopifnot(ncol(X) == length(beta_vec))
+dd2$adl <- simulate(form[-2],
+                    newdata = dd2,
+                    newparams = list(beta = beta_vec,
+                                     theta = c(2, 0.1, 0),
+                                     sigma = 1),
+                    family = gaussian)[[1]]
+
+fit <- lmer(form, data = dd2)
+
+pred.dd <- expand.grid(age = 50:100, year = 1:15,
+                       score = seq(min(dd2$score), max(dd2$score), length.out=100), 
+                       id = sample(dd2$id, size = 10, replace = FALSE))
+
+pred <- predict(fit, newdata = pred.dd) ## OK
+pred <- predict(fit, newdata = pred.dd, se.fit = TRUE)
+
+pred <- predict(fit, newdata = pred.dd[sample(nrow(pred.dd), size = 1000,
+                                            replace = FALSE),], se.fit = TRUE)

src/lme4CholmodDecomposition.h

@@ -75,38 +75,7 @@ namespace lme4 {
 
     template<typename T>
     SEXP Eigen_cholmod_wrap(const lme4CholmodDecomposition<Eigen::SparseMatrix<T> >& obj) {
-        typedef T* Tpt;
-        const cholmod_factor* f = obj.factor();
-        if (f->minor < f->n)
-            throw std::runtime_error("CHOLMOD factorization was unsuccessful");
-
-        //FIXME: Should extend this selection according to T
-        ::Rcpp::S4 ans(std::string(f->is_super ? "dCHMsuper" : "dCHMsimpl"));
-        ::Rcpp::IntegerVector  dd(2);
-        dd[0] = dd[1] = f->n;
-        ans.slot("Dim") = dd;
-        ans.slot("perm") = ::Rcpp::wrap((int*)f->Perm, (int*)f->Perm + f->n);
-        ans.slot("colcount") = ::Rcpp::wrap((int*)f->ColCount, (int*)f->ColCount + f->n);
-        ::Rcpp::IntegerVector tt(f->is_super ? 6 : 4);
-        tt[0] = f->ordering; tt[1] = f->is_ll;
-        tt[2] = f->is_super; tt[3] = f->is_monotonic;
-        ans.slot("type") = tt;
-        if (f->is_super) {
-            tt[4] = f->maxcsize; tt[5] = f->maxesize;
-            ans.slot("super") = ::Rcpp::wrap((int*)f->super, ((int*)f->super) + f->nsuper + 1);
-            ans.slot("pi")    = ::Rcpp::wrap((int*)f->pi, ((int*)f->pi) + f->nsuper + 1);
-            ans.slot("px")    = ::Rcpp::wrap((int*)f->px, ((int*)f->px) + f->nsuper + 1);
-            ans.slot("s")     = ::Rcpp::wrap((int*)f->s, ((int*)f->s) + f->ssize);
-            ans.slot("x")     = ::Rcpp::wrap((Tpt)f->x, ((T*)f->x) + f->xsize);
-        } else {
-            ans.slot("i")     = ::Rcpp::wrap((int*)f->i, ((int*)f->i) + f->nzmax);
-            ans.slot("p")     = ::Rcpp::wrap((int*)f->p, ((int*)f->p) + f->n + 1);
-            ans.slot("x")     = ::Rcpp::wrap((Tpt)f->x, ((T*)f->x) + f->nzmax);
-            ans.slot("nz")    = ::Rcpp::wrap((int*)f->nz, ((int*)f->nz) + f->n);
-            ans.slot("nxt")   = ::Rcpp::wrap((int*)f->next, ((int*)f->next) + f->n + 2);
-            ans.slot("prv")   = ::Rcpp::wrap((int*)f->prev, ((int*)f->prev) + f->n + 2);
-        }
-        return ::Rcpp::wrap(ans);
+        return M_chm_factor_to_SEXP(obj.factor(), 0);
     }
 
 } // namespace lme4