==3520640== Memcheck, a memory error detector ==3520640== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==3520640== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info ==3520640== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla ==3520640== R Under development (unstable) (2026-04-27 r89967) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "glmmrBase" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('glmmrBase') Loading required package: Matrix > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("Covariance") > ### * Covariance > > flush(stderr()); flush(stdout()) > > ### Name: Covariance > ### Title: R6 Class representing a covariance function and data > ### Aliases: Covariance > > ### ** Examples > > > ## ------------------------------------------------ > ## Method `Covariance$new` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(5)*t(5)) > ind(5)) > cov <- Covariance$new(formula = ~(1|gr(cl)*ar0(t)), + parameters = c(0.05,0.7), + data= df) > > ## ------------------------------------------------ > ## Method `Covariance$print` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(5)*t(5)) > ind(5)) > Covariance$new(formula = ~(1|gr(cl)*ar0(t)), + parameters = c(0.05,0.8), + data= df) ⯈ Covariance ⮡ Terms: (1|gr(cl)*ar0(t)) ⮡ Parameters: 0.05 0.8 > > ## ------------------------------------------------ > ## Method `Covariance$subset` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(10)*t(5)) > ind(10)) > cov <- Covariance$new(formula = ~(1|gr(cl)*ar0(t)), + parameters = c(0.05,0.8), + data= df) > cov$subset(1:100) > > > > cleanEx() > nameEx("MeanFunction") > ### * MeanFunction > > flush(stderr()); flush(stdout()) > > ### Name: MeanFunction > ### Title: For the generalised linear mixed model > ### Aliases: MeanFunction > > ### ** Examples > > > ## ------------------------------------------------ > ## Method `MeanFunction$n` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(4)*t(5)) > ind(5)) > df$int <- 0 > df[df$cl <= 2, 'int'] <- 1 > mf1 <- MeanFunction$new(formula = ~ int , + data=df, + parameters = c(-1,1) + ) > mf1$n() [1] 100 > > ## ------------------------------------------------ > ## Method `MeanFunction$new` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(4)*t(5)) > ind(5)) > df$int <- 0 > df[df$cl <= 2, 'int'] <- 1 > mf1 <- MeanFunction$new(formula = ~ int , + data=df, + parameters = c(-1,1), + ) > > ## ------------------------------------------------ > ## Method `MeanFunction$colnames` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(4)*t(5)) > ind(5)) > df$int <- 0 > df[df$cl <= 5, 'int'] <- 1 > mf1 <- MeanFunction$new(formula = ~ int , + data=df, + parameters = c(-1,1) + ) > mf1$colnames(c("cluster","time","individual","treatment")) > mf1$colnames() [1] "cluster" "time" "individual" "treatment" > > ## ------------------------------------------------ > ## Method `MeanFunction$subset_rows` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(4)*t(5)) > ind(5)) > df$int <- 0 > df[df$cl <= 5, 'int'] <- 1 > mf1 <- MeanFunction$new(formula = ~ int , + data=df, + parameters = c(-1,1) + ) > mf1$subset_rows(1:20) > > > > cleanEx() > nameEx("Model") > ### * Model > > flush(stderr()); flush(stdout()) > > ### Name: Model > ### Title: A GLMM Model > ### Aliases: Model > > ### ** Examples > > > ## ------------------------------------------------ > ## Method `Model$new` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) > ## End(Don't show) > # For more examples, see the examples for MCML. > > #create a data frame describing a cross-sectional parallel cluster > #randomised trial > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df$int <- 0 > df[df$cl > 5, 'int'] <- 1 > mod <- Model$new( + formula = ~ factor(t) + int - 1 + (1|gr(cl)) + (1|gr(cl,t)), + data = df, + family = stats::gaussian() + ) > > # We can also include the outcome data in the model initialisation. > # For example, simulating data and creating a new object: > df$y <- mod$sim_data() > > mod <- Model$new( + formula = y ~ factor(t) + int - 1 + (1|gr(cl)) + (1|gr(cl,t)), + data = df, + family = stats::gaussian() + ) > > # Here we will specify a cohort study > df <- nelder(~ind(20) * t(6)) > df$int <- 0 > df[df$t > 3, 'int'] <- 1 > > des <- Model$new( + formula = ~ int + (1|gr(ind)), + data = df, + family = stats::poisson() + ) > > # or with parameter values specified > > des <- Model$new( + formula = ~ int + (1|gr(ind)), + covariance = c(0.05), + mean = c(1,0.5), + data = df, + family = stats::poisson() + ) > > #an example of a spatial grid with two time points > > df <- nelder(~ (x(10)*y(10))*t(2)) > spt_design <- Model$new(formula = ~ 1 + (1|ar0(t)*fexp(x,y)), + data = df, + family = stats::gaussian()) > > ## ------------------------------------------------ > ## Method `Model$sim_data` > ## ------------------------------------------------ > > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df$int <- 0 > df[df$cl > 5, 'int'] <- 1 > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > des <- Model$new( + formula = ~ factor(t) + int - 1 + (1|gr(cl)*ar0(t)), + covariance = c(0.05,0.8), + mean = c(rep(0,5),0.6), + data = df, + family = stats::binomial() + ) > ysim <- des$sim_data() > > ## ------------------------------------------------ > ## Method `Model$update_parameters` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df$int <- 0 > df[df$cl > 5, 'int'] <- 1 > des <- Model$new( + formula = ~ factor(t) + int - 1 + (1|gr(cl)*ar0(t)), + data = df, + family = stats::binomial() + ) > des$update_parameters(cov.pars = c(0.1,0.9)) > > ## ------------------------------------------------ > ## Method `Model$power` > ## ------------------------------------------------ > > ## Don't show: > setParallel(FALSE) # for the CRAN check > ## End(Don't show) > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df$int <- 0 > df[df$cl > 5, 'int'] <- 1 > des <- Model$new( + formula = ~ factor(t) + int - 1 + (1|gr(cl)) + (1|gr(cl,t)), + covariance = c(0.05,0.1), + mean = c(rep(0,5),0.6), + data = df, + family = stats::gaussian(), + var_par = 1 + ) > des$power() #power of 0.90 for the int parameter ==3520640== Invalid read of size 16 ==3520640== at 0x1E411E26: _mm_mul_pd (/usr/lib/gcc/x86_64-redhat-linux/14/include/emmintrin.h:275) ==3520640== by 0x1E411E26: pmul<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:347) ==3520640== by 0x1E411E26: packetOp<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:83) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:790) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1430) ==3520640== by 0x1E411E26: assignPacket<16, 16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:681) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:437) ==3520640== by 0x1E411E26: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411E26: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411E26: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411E26: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411E26: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E41682C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:245) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x4F955C: do_set (svn/R-devel/src/main/eval.c:3579) ==3520640== Address 0x18dd0bd0 is 0 bytes inside a block of size 480 free'd ==3520640== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3520640== by 0x1E31D1D0: aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:203) ==3520640== by 0x1E31D1D0: conditional_aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:259) ==3520640== by 0x1E31D1D0: conditional_aligned_delete_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:446) ==3520640== by 0x1E31D1D0: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:637) ==3520640== by 0x1E31D1D0: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411DFE: resize_if_allowed, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411DFE: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411DFE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411DFE: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411DFE: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411DFE: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411DFE: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E41682C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:245) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== Block was alloc'd at ==3520640== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3520640== by 0x1E308318: Eigen::internal::aligned_malloc(unsigned long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:182) ==3520640== by 0x1E31D205: conditional_aligned_malloc (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:241) ==3520640== by 0x1E31D205: conditional_aligned_new_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:404) ==3520640== by 0x1E31D205: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639) ==3520640== by 0x1E31D205: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411D68: resize_if_allowed, Eigen::ArrayWrapper >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411D68: call_dense_assignment_loop, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411D68: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411D68: call_assignment_no_alias, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411D68: _set > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411D68: operator= > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411D68: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:61) ==3520640== by 0x1E41682C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:245) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== Value SE Power b_t1 0.0 0.08697363 0.0250000 b_t2 0.0 0.07541870 0.0250000 b_t3 0.0 0.07504544 0.0250000 b_t4 0.0 0.07637034 0.0250000 b_t5 0.0 0.07823686 0.0250000 b_int 0.6 0.09020891 0.9999986 > > ## ------------------------------------------------ > ## Method `Model$fit` > ## ------------------------------------------------ > > # Simulated trial data example using REML > set.seed(123) > data(SimTrial,package = "glmmrBase") > fit1 <- Model$new( + formula = y ~ int + factor(t) - 1 + (1|grlog(cl)*ar0log(t)), + data = SimTrial, + family = gaussian() + )$fit(reml = TRUE) ==3520640== Invalid read of size 16 ==3520640== at 0x1E411E26: _mm_mul_pd (/usr/lib/gcc/x86_64-redhat-linux/14/include/emmintrin.h:275) ==3520640== by 0x1E411E26: pmul<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:347) ==3520640== by 0x1E411E26: packetOp<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:83) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:790) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1430) ==3520640== by 0x1E411E26: assignPacket<16, 16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:681) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:437) ==3520640== by 0x1E411E26: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411E26: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411E26: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411E26: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411E26: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E2F21FE: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1143) ==3520640== by 0x1E2F21FE: __invoke_impl, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F21FE: __invoke, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:96) ==3520640== by 0x1E2F21FE: __visit_invoke (/usr/include/c++/14/variant:1060) ==3520640== by 0x1E2F21FE: __do_visit, overloaded, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F21FE: visit, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1882) ==3520640== by 0x1E2F21FE: Model__update_W(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1145) ==3520640== by 0x1E2A4986: _glmmrBase_Model__update_W (packages/tests-vg/glmmrBase/src/RcppExports.cpp:673) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x4F7F84: do_begin (svn/R-devel/src/main/eval.c:2990) ==3520640== by 0x4F48D2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3520640== Address 0x20369870 is 0 bytes inside a block of size 560 free'd ==3520640== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3520640== by 0x1E31D1D0: aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:203) ==3520640== by 0x1E31D1D0: conditional_aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:259) ==3520640== by 0x1E31D1D0: conditional_aligned_delete_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:446) ==3520640== by 0x1E31D1D0: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:637) ==3520640== by 0x1E31D1D0: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411DFE: resize_if_allowed, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411DFE: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411DFE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411DFE: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411DFE: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411DFE: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411DFE: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E2F21FE: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1143) ==3520640== by 0x1E2F21FE: __invoke_impl, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F21FE: __invoke, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:96) ==3520640== by 0x1E2F21FE: __visit_invoke (/usr/include/c++/14/variant:1060) ==3520640== by 0x1E2F21FE: __do_visit, overloaded, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F21FE: visit, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1882) ==3520640== by 0x1E2F21FE: Model__update_W(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1145) ==3520640== by 0x1E2A4986: _glmmrBase_Model__update_W (packages/tests-vg/glmmrBase/src/RcppExports.cpp:673) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== Block was alloc'd at ==3520640== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3520640== by 0x1E308318: Eigen::internal::aligned_malloc(unsigned long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:182) ==3520640== by 0x1E31D205: conditional_aligned_malloc (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:241) ==3520640== by 0x1E31D205: conditional_aligned_new_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:404) ==3520640== by 0x1E31D205: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639) ==3520640== by 0x1E31D205: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411D68: resize_if_allowed, Eigen::ArrayWrapper >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411D68: call_dense_assignment_loop, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411D68: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411D68: call_assignment_no_alias, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411D68: _set > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411D68: operator= > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411D68: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:61) ==3520640== by 0x1E2F21FE: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1143) ==3520640== by 0x1E2F21FE: __invoke_impl, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F21FE: __invoke, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:96) ==3520640== by 0x1E2F21FE: __visit_invoke (/usr/include/c++/14/variant:1060) ==3520640== by 0x1E2F21FE: __do_visit, overloaded, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F21FE: visit, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1882) ==3520640== by 0x1E2F21FE: Model__update_W(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1145) ==3520640== by 0x1E2A4986: _glmmrBase_Model__update_W (packages/tests-vg/glmmrBase/src/RcppExports.cpp:673) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== > > # Salamanders data example > data(Salamanders,package="glmmrBase") > model <- Model$new( + mating~fpop:mpop-1+(1|grlog(mnum))+(1|grlog(fnum)), + data = Salamanders, + family = binomial() + ) > set.seed(125) > fit2 <- model$fit() ==3520640== Invalid read of size 16 ==3520640== at 0x1E411E26: _mm_mul_pd (/usr/lib/gcc/x86_64-redhat-linux/14/include/emmintrin.h:275) ==3520640== by 0x1E411E26: pmul<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:347) ==3520640== by 0x1E411E26: packetOp<__vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:83) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:790) ==3520640== by 0x1E411E26: packet<16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1430) ==3520640== by 0x1E411E26: assignPacket<16, 16, __vector(2) double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:681) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:437) ==3520640== by 0x1E411E26: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3520640== by 0x1E411E26: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411E26: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411E26: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411E26: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411E26: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411E26: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E4292C5: glmmr::ModelMatrix >::ave_information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:346) ==3520640== by 0x1E2F039F: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1435) ==3520640== by 0x1E2F039F: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F039F: __invoke, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2F039F: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2F039F: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F039F: visit, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2F039F: Model__ave_information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1437) ==3520640== by 0x1E2A6482: _glmmrBase_Model__ave_information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:928) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x4F955C: do_set (svn/R-devel/src/main/eval.c:3579) ==3520640== Address 0x12473bc0 is 0 bytes inside a block of size 160 free'd ==3520640== at 0x4846B83: free (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:989) ==3520640== by 0x1E31D1D0: aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:203) ==3520640== by 0x1E31D1D0: conditional_aligned_free (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:259) ==3520640== by 0x1E31D1D0: conditional_aligned_delete_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:446) ==3520640== by 0x1E31D1D0: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:637) ==3520640== by 0x1E31D1D0: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411DFE: resize_if_allowed, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411DFE: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411DFE: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411DFE: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411DFE: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411DFE: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411DFE: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411DFE: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E4292C5: glmmr::ModelMatrix >::ave_information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:346) ==3520640== by 0x1E2F039F: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1435) ==3520640== by 0x1E2F039F: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F039F: __invoke, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2F039F: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2F039F: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F039F: visit, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2F039F: Model__ave_information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1437) ==3520640== by 0x1E2A6482: _glmmrBase_Model__ave_information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:928) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== Block was alloc'd at ==3520640== at 0x4843866: malloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:446) ==3520640== by 0x1E308318: Eigen::internal::aligned_malloc(unsigned long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:182) ==3520640== by 0x1E31D205: conditional_aligned_malloc (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:241) ==3520640== by 0x1E31D205: conditional_aligned_new_auto (R-devel/site-library/RcppEigen/include/Eigen/src/Core/util/Memory.h:404) ==3520640== by 0x1E31D205: resize (R-devel/site-library/RcppEigen/include/Eigen/src/Core/DenseStorage.h:639) ==3520640== by 0x1E31D205: Eigen::PlainObjectBase >::resize(long, long) (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:285) ==3520640== by 0x1E411D68: resize_if_allowed, Eigen::ArrayWrapper >, double, double> (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:764) ==3520640== by 0x1E411D68: call_dense_assignment_loop, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:778) ==3520640== by 0x1E411D68: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411D68: call_assignment_no_alias, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411D68: call_assignment, Eigen::ArrayWrapper > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411D68: _set > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411D68: operator= > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411D68: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:61) ==3520640== by 0x1E4292C5: glmmr::ModelMatrix >::ave_information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:346) ==3520640== by 0x1E2F039F: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1435) ==3520640== by 0x1E2F039F: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F039F: __invoke, Model__ave_information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2F039F: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2F039F: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F039F: visit, Model__ave_information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2F039F: Model__ave_information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1437) ==3520640== by 0x1E2A6482: _glmmrBase_Model__ave_information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:928) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== ==3520640== Conditional jump or move depends on uninitialised value(s) ==3520640== at 0x5C04AB: real_mean (svn/R-devel/src/main/summary.c:488) ==3520640== by 0x5C11AF: do_summary (svn/R-devel/src/main/summary.c:552) ==3520640== by 0x4E630C: bcEval_loop (svn/R-devel/src/main/eval.c:8144) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F7BC8: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x53FA2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3520640== by 0x54002E: Rf_usemethod (svn/R-devel/src/main/objects.c:523) ==3520640== by 0x5402C2: do_usemethod (svn/R-devel/src/main/objects.c:579) ==3520640== by 0x4E5FF1: bcEval_loop (svn/R-devel/src/main/eval.c:8164) ==3520640== Uninitialised value was created by a client request ==3520640== at 0x538FF8: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2986) ==3520640== by 0x53A818: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3520640== by 0x53A818: R_alloc (svn/R-devel/src/main/memory.c:2332) ==3520640== by 0x48CECB: R_decompress1 (svn/R-devel/src/main/connections.c:6637) ==3520640== by 0x59C804: do_lazyLoadDBfetch (svn/R-devel/src/main/serialize.c:3332) ==3520640== by 0x4E630C: bcEval_loop (svn/R-devel/src/main/eval.c:8144) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x596392: CallHook (svn/R-devel/src/main/serialize.c:2595) ==3520640== by 0x598D2F: PersistentRestore (svn/R-devel/src/main/serialize.c:843) ==3520640== by 0x598D2F: ReadItem_Recursive (svn/R-devel/src/main/serialize.c:1912) ==3520640== ==3520640== Conditional jump or move depends on uninitialised value(s) ==3520640== at 0x5C0509: real_mean (svn/R-devel/src/main/summary.c:508) ==3520640== by 0x5C11AF: do_summary (svn/R-devel/src/main/summary.c:552) ==3520640== by 0x4E630C: bcEval_loop (svn/R-devel/src/main/eval.c:8144) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F7BC8: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x53FA2B: dispatchMethod (svn/R-devel/src/main/objects.c:473) ==3520640== by 0x54002E: Rf_usemethod (svn/R-devel/src/main/objects.c:523) ==3520640== by 0x5402C2: do_usemethod (svn/R-devel/src/main/objects.c:579) ==3520640== by 0x4E5FF1: bcEval_loop (svn/R-devel/src/main/eval.c:8164) ==3520640== Uninitialised value was created by a client request ==3520640== at 0x538FF8: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2986) ==3520640== by 0x53A818: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:609) ==3520640== by 0x53A818: R_alloc (svn/R-devel/src/main/memory.c:2332) ==3520640== by 0x48CECB: R_decompress1 (svn/R-devel/src/main/connections.c:6637) ==3520640== by 0x59C804: do_lazyLoadDBfetch (svn/R-devel/src/main/serialize.c:3332) ==3520640== by 0x4E630C: bcEval_loop (svn/R-devel/src/main/eval.c:8144) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x596392: CallHook (svn/R-devel/src/main/serialize.c:2595) ==3520640== by 0x598D2F: PersistentRestore (svn/R-devel/src/main/serialize.c:843) ==3520640== by 0x598D2F: ReadItem_Recursive (svn/R-devel/src/main/serialize.c:1912) ==3520640== > > # Example using simulated data > #create example data with six clusters, five time periods, and five people per cluster-period > df <- nelder(~(cl(20)*t(10)) > ind(5)) > # parallel trial design intervention indicator > df$int <- 0 > df[df$cl > 10, 'int'] <- 1 > # specify parameter values in the call for the data simulation below > des <- Model$new( + formula= ~ factor(t) + int - 1 +(1|grlog(cl)*ar0log(t)), + covariance = log(c(0.15,0.7)), + mean = c(rep(0,10),0.2), + data = df, + family = binomial() + ) > ysim <- des$sim_data() # simulate some data from the model > des$update_y(ysim) > set.seed(123) > fit2 <- des$fit() > > # use of Gaussian process approximations > # simulate some data - binomial observation on [-1,1] x [-1,1] > set.seed(123) > df <- data.frame( + x = runif(100, -1, 1), + y = runif(100, -1, 1)) > df$z <- rnorm(100) > > df$outcome <- Model$new( + ~ z + (1|matern1log(x, y)), + data = df, + family = binomial(), + mean = c(1, 0.1), + covariance = c(log(2), log(0.3)), + trials = rep(10, nrow(df)) + )$sim_data() > > # we can fit the SPDE approximation using a mesh built by fmesher > df_pred <- expand.grid(x= seq(-1,1,by=0.05), y = seq(-1,1,by=0.05)) > df_pred$z <- 0 > mesh_data <- mesh_helper(unique(df[,1:2]), df_pred[,1:2], c(0.15, 0.75), 0.075, c(0.1,0.3)) Loading required namespace: fmesher > > mod <- Model$new( + outcome ~ z + (1|spde_matern1log(x, y)), + data = df, + family = binomial(), + trials = rep(10, nrow(df)), + mesh = mesh_data[["data"]], + covariance = log(c(0.5, 0.3)) + ) > set.seed(123) > fit1 <- mod$fit(niter = 50) > > #generate predictions > pred1 <- mod$predict(newdata = df_pred,mesh_A = mesh_data[["A_pred"]]) > > #' # Non-linear model fitting example using the example provided by nlmer in lme4 > data(Orange, package = "datasets") > > # the lme4 example: > startvec <- c(Asym = 200, xmid = 725, scal = 350) > (nm1 <- lme4::nlmer(circumference ~ SSlogis(age, Asym, xmid, scal) ~ Asym|Tree, + Orange, start = startvec)) Nonlinear mixed model fit by maximum likelihood ['nlmerMod'] Formula: circumference ~ SSlogis(age, Asym, xmid, scal) ~ Asym | Tree Data: Orange AIC BIC logLik -2*log(L) df.resid 273.1438 280.9205 -131.5719 263.1438 30 Random effects: Groups Name Std.Dev. Tree Asym 31.646 Residual 7.843 Number of obs: 35, groups: Tree, 5 Fixed Effects: Asym xmid scal 192.1 727.9 348.1 > > Orange <- as.data.frame(Orange) > Orange$Tree <- as.numeric(Orange$Tree) > > # Here we can specify the model as a function. > > model <- Model$new( + circumference ~ Asym/(1 + exp((xmid - (age))/scal)) - 1 + (Asym|grlog(Tree)), + data = Orange, + family = gaussian(), + mean = c(200,725,350), + covariance = log(c(500)), + var_par = 50 + ) > set.seed(123) > nfit <- model$fit(niter = 100) ==3520640== Invalid read of size 8 ==3520640== at 0x1E411E60: operator() (R-devel/site-library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:80) ==3520640== by 0x1E411E60: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:775) ==3520640== by 0x1E411E60: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1404) ==3520640== by 0x1E411E60: assignCoeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:660) ==3520640== by 0x1E411E60: run >, Eigen::internal::evaluator, const Eigen::ArrayWrapper >, const Eigen::Array > > >, Eigen::internal::assign_op, 0> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:411) ==3520640== by 0x1E411E60: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:439) ==3520640== by 0x1E411E60: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3520640== by 0x1E411E60: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411E60: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411E60: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411E60: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411E60: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411E60: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411E60: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E41682C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:245) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x4F955C: do_set (svn/R-devel/src/main/eval.c:3579) ==3520640== Address 0x220d56e0 is 16 bytes before a block of size 16 free'd ==3520640== at 0x4847BB8: operator delete(void*, unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:1181) ==3520640== by 0x1E316AF2: deallocate (/usr/include/c++/14/bits/new_allocator.h:172) ==3520640== by 0x1E316AF2: deallocate (/usr/include/c++/14/bits/alloc_traits.h:513) ==3520640== by 0x1E316AF2: ~_Guard (/usr/include/c++/14/bits/vector.tcc:616) ==3520640== by 0x1E316AF2: void std::vector >::_M_realloc_append(double const&) (/usr/include/c++/14/bits/vector.tcc:688) ==3520640== by 0x1E344973: push_back (/usr/include/c++/14/bits/stl_vector.h:1294) ==3520640== by 0x1E344973: void glmmr::operation<(Do)23>(glmmr::calcData&, glmmr::calculator const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:279) ==3520640== by 0x1E3BF487: std::vector > glmmr::calculator::calculate<(glmmr::CalcDyDx)1>(int, int, int, double) const (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1386) ==3520640== by 0x1E3C13D2: jacobian (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1224) ==3520640== by 0x1E3C13D2: glmmr::LinearPredictor::X() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/linearpredictor.hpp:186) ==3520640== by 0x1E34A686: glmmr::Covariance::Z_updater() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:605) ==3520640== by 0x1E34EBFA: glmmr::Covariance::ZL_sparse_new() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:855) ==3520640== by 0x1E31A60E: glmmr::Covariance::ZLu(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:870) ==3520640== by 0x1E3CEA0F: glmmr::ModelMatrix >::posterior_u_samples(int, bool, bool, bool) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:1642) ==3520640== by 0x1E3D1564: optim > const&), BOBYQA>::fn<&glmmr::ModelOptim >::log_likelihood_beta, glmmr::ModelOptim >, void>(glmmr::ModelOptim >*)::{lambda(long, double const*, void*)#1}::_FUN(long, double const*, void*) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modeloptim.hpp:426) ==3520640== by 0x1E2F81C6: bobyqb(long, long, double (*)(long, double const*, void*), void*, double*, double const*, double const*, double, double, long, long, double*, double*, double*, double*, double*, double*, double*, double*, double*, long, double*, double*, double*, double*, double*, double*, double*) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/bobyqa_general.h:884) ==3520640== by 0x1E327518: bobyqa (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/bobyqa_general.h:344) ==3520640== by 0x1E327518: optim > const&), BOBYQA>::minimise() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/optim.h:174) ==3520640== Block was alloc'd at ==3520640== at 0x4843FEC: operator new(unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:487) ==3520640== by 0x1E316A7D: allocate (/usr/include/c++/14/bits/new_allocator.h:151) ==3520640== by 0x1E316A7D: allocate (/usr/include/c++/14/bits/alloc_traits.h:478) ==3520640== by 0x1E316A7D: _M_allocate (/usr/include/c++/14/bits/stl_vector.h:380) ==3520640== by 0x1E316A7D: void std::vector >::_M_realloc_append(double const&) (/usr/include/c++/14/bits/vector.tcc:596) ==3520640== by 0x1E344973: push_back (/usr/include/c++/14/bits/stl_vector.h:1294) ==3520640== by 0x1E344973: void glmmr::operation<(Do)23>(glmmr::calcData&, glmmr::calculator const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:279) ==3520640== by 0x1E3BF487: std::vector > glmmr::calculator::calculate<(glmmr::CalcDyDx)1>(int, int, int, double) const (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1386) ==3520640== by 0x1E3C13D2: jacobian (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1224) ==3520640== by 0x1E3C13D2: glmmr::LinearPredictor::X() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/linearpredictor.hpp:186) ==3520640== by 0x1E34A686: glmmr::Covariance::Z_updater() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:605) ==3520640== by 0x1E34EBFA: glmmr::Covariance::ZL_sparse_new() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:855) ==3520640== by 0x1E31A60E: glmmr::Covariance::ZLu(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:870) ==3520640== by 0x1E3CEA0F: glmmr::ModelMatrix >::posterior_u_samples(int, bool, bool, bool) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:1642) ==3520640== by 0x1E3D1564: optim > const&), BOBYQA>::fn<&glmmr::ModelOptim >::log_likelihood_beta, glmmr::ModelOptim >, void>(glmmr::ModelOptim >*)::{lambda(long, double const*, void*)#1}::_FUN(long, double const*, void*) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modeloptim.hpp:426) ==3520640== by 0x1E2F81C6: bobyqb(long, long, double (*)(long, double const*, void*), void*, double*, double const*, double const*, double, double, long, long, double*, double*, double*, double*, double*, double*, double*, double*, double*, long, double*, double*, double*, double*, double*, double*, double*) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/bobyqa_general.h:884) ==3520640== by 0x1E327518: bobyqa (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/bobyqa_general.h:344) ==3520640== by 0x1E327518: optim > const&), BOBYQA>::minimise() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/optim/optim.h:174) ==3520640== ==3520640== Invalid read of size 8 ==3520640== at 0x1E411E60: operator() (R-devel/site-library/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:80) ==3520640== by 0x1E411E60: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:775) ==3520640== by 0x1E411E60: coeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1404) ==3520640== by 0x1E411E60: assignCoeff (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:660) ==3520640== by 0x1E411E60: run >, Eigen::internal::evaluator, const Eigen::ArrayWrapper >, const Eigen::Array > > >, Eigen::internal::assign_op, 0> > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:411) ==3520640== by 0x1E411E60: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:439) ==3520640== by 0x1E411E60: call_dense_assignment_loop, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:785) ==3520640== by 0x1E411E60: run (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954) ==3520640== by 0x1E411E60: call_assignment_no_alias, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890) ==3520640== by 0x1E411E60: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > >, Eigen::internal::assign_op > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858) ==3520640== by 0x1E411E60: call_assignment, Eigen::MatrixWrapper, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836) ==3520640== by 0x1E411E60: _set, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779) ==3520640== by 0x1E411E60: operator=, const Eigen::ArrayWrapper >, const Eigen::Array > > > (R-devel/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:225) ==3520640== by 0x1E411E60: glmmr::MatrixW >::update(Eigen::Matrix const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/matrixw.hpp:62) ==3520640== by 0x1E2F21FE: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1143) ==3520640== by 0x1E2F21FE: __invoke_impl, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2F21FE: __invoke, Model__update_W(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:96) ==3520640== by 0x1E2F21FE: __visit_invoke (/usr/include/c++/14/variant:1060) ==3520640== by 0x1E2F21FE: __do_visit, overloaded, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2F21FE: visit, Model__update_W(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1882) ==3520640== by 0x1E2F21FE: Model__update_W(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1145) ==3520640== by 0x1E2A4986: _glmmrBase_Model__update_W (packages/tests-vg/glmmrBase/src/RcppExports.cpp:673) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== by 0x4E41C3: bcEval_loop (svn/R-devel/src/main/eval.c:8694) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7527) ==3520640== by 0x4F4237: bcEval (svn/R-devel/src/main/eval.c:7512) ==3520640== by 0x4F456A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3520640== by 0x4F64FD: R_execClosure (svn/R-devel/src/main/eval.c:2387) ==3520640== by 0x4F71C6: applyClosure_core (svn/R-devel/src/main/eval.c:2300) ==3520640== by 0x4F4677: Rf_applyClosure (svn/R-devel/src/main/eval.c:2322) ==3520640== by 0x4F4677: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3520640== by 0x4F7F84: do_begin (svn/R-devel/src/main/eval.c:2990) ==3520640== by 0x4F48D2: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3520640== Address 0x1dee9b80 is 0 bytes after a block of size 32 free'd ==3520640== at 0x4847BB8: operator delete(void*, unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:1181) ==3520640== by 0x1E3448F6: ~vector (/usr/include/c++/14/bits/stl_vector.h:738) ==3520640== by 0x1E3448F6: void glmmr::operation<(Do)23>(glmmr::calcData&, glmmr::calculator const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:310) ==3520640== by 0x1E3BF487: std::vector > glmmr::calculator::calculate<(glmmr::CalcDyDx)1>(int, int, int, double) const (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1386) ==3520640== by 0x1E3C13D2: jacobian (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1224) ==3520640== by 0x1E3C13D2: glmmr::LinearPredictor::X() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/linearpredictor.hpp:186) ==3520640== by 0x1E34A686: glmmr::Covariance::Z_updater() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:605) ==3520640== by 0x1E34EBFA: glmmr::Covariance::ZL_sparse_new() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:855) ==3520640== by 0x1E387C4B: ZL (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:865) ==3520640== by 0x1E387C4B: glmmr::ModelMatrix >::sigma_block(int, bool) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:532) ==3520640== by 0x1E3C15BC: glmmr::ModelMatrix >::information_matrix_by_block(int) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:152) ==3520640== by 0x1E41688C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:248) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== by 0x4A9169: R_doDotCall (svn/R-devel/src/main/dotcode.c:757) ==3520640== Block was alloc'd at ==3520640== at 0x4843FEC: operator new(unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:487) ==3520640== by 0x1E316A7D: allocate (/usr/include/c++/14/bits/new_allocator.h:151) ==3520640== by 0x1E316A7D: allocate (/usr/include/c++/14/bits/alloc_traits.h:478) ==3520640== by 0x1E316A7D: _M_allocate (/usr/include/c++/14/bits/stl_vector.h:380) ==3520640== by 0x1E316A7D: void std::vector >::_M_realloc_append(double const&) (/usr/include/c++/14/bits/vector.tcc:596) ==3520640== by 0x1E3449EE: push_back (/usr/include/c++/14/bits/stl_vector.h:1294) ==3520640== by 0x1E3449EE: void glmmr::operation<(Do)23>(glmmr::calcData&, glmmr::calculator const&) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:281) ==3520640== by 0x1E3BF487: std::vector > glmmr::calculator::calculate<(glmmr::CalcDyDx)1>(int, int, int, double) const (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1386) ==3520640== by 0x1E3C13D2: jacobian (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/calculator.hpp:1224) ==3520640== by 0x1E3C13D2: glmmr::LinearPredictor::X() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/linearpredictor.hpp:186) ==3520640== by 0x1E34A686: glmmr::Covariance::Z_updater() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:605) ==3520640== by 0x1E34EBFA: glmmr::Covariance::ZL_sparse_new() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:855) ==3520640== by 0x1E387C4B: ZL (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/covariance.hpp:865) ==3520640== by 0x1E387C4B: glmmr::ModelMatrix >::sigma_block(int, bool) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:532) ==3520640== by 0x1E3C15BC: glmmr::ModelMatrix >::information_matrix_by_block(int) (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:152) ==3520640== by 0x1E41688C: glmmr::ModelMatrix >::information_matrix() (packages/tests-vg/glmmrBase/src/../inst/include/glmmr/modelmatrix.hpp:248) ==3520640== by 0x1E2EFDBF: operator() > > > (packages/tests-vg/glmmrBase/src/model_module.cpp:1424) ==3520640== by 0x1E2EFDBF: __invoke_impl, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair >, overloaded, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:61) ==3520640== by 0x1E2EFDBF: __invoke, Model__information_matrix(SEXP, int):: >&, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>&> (/usr/include/c++/14/bits/invoke.h:97) ==3520640== by 0x1E2EFDBF: __visit_invoke (/usr/include/c++/14/variant:1062) ==3520640== by 0x1E2EFDBF: __do_visit, Eigen::Array, Eigen::Matrix, std::vector >, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::vector >, VectorMatrix, MatrixMatrix, CorrectionData<(glmmr::SE)1>, CorrectionData<(glmmr::SE)4>, CorrectionData<(glmmr::SE)6>, CorrectionData<(glmmr::SE)5>, std::vector, std::allocator > >, std::pair, BoxResults, std::pair > >, overloaded, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1820) ==3520640== by 0x1E2EFDBF: visit, Model__information_matrix(SEXP, int):: >&, std::variant >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false>, Rcpp::XPtr >, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer > >, false> >&> (/usr/include/c++/14/variant:1884) ==3520640== by 0x1E2EFDBF: Model__information_matrix(SEXPREC*, int) (packages/tests-vg/glmmrBase/src/model_module.cpp:1426) ==3520640== by 0x1E2A62F2: _glmmrBase_Model__information_matrix (packages/tests-vg/glmmrBase/src/RcppExports.cpp:916) ==3520640== > > summary(nfit) Markov chain Monte Carlo Maximum Likelihood Estimation Algorithm: Markov Chain Newton-Raphson Fixed effects formula : Asym/(1+exp((xmid-(age))/scal))-1+(Asym|grlog(Tree)) Covariance function formula: (Asym|grlog(Tree)) Family: gaussian , Link function: identity Standard error: GLS Number of Monte Carlo simulations per iteration: 1 with tolerance 1e-06 Random effects: Estimate Std. Err. grlog(Tree) 6.9151 0.6452 sigma 61.6906 0.2582 Fixed effects: Estimate Std. Err. z value p value 2.5% CI 97.5% CI Asym 192.6876 13.8182 13.9445 0 165.6044 219.7708 xmid 728.7564 4.3002 169.4721 0 720.3283 737.1846 scal 353.5337 4.4399 79.6273 0 344.8317 362.2356 cAIC: 573.1907 Approximate R-squared: Conditional: 0 Marginal: 0 Log-likelihood: -260.6252 Random effects estimates Estimate 2.5% CI 97.5% CI 1 5.57 2.37 7.87 > suppressWarnings(summary(nm1)) # lme4 reports Hessian warnings Nonlinear mixed model fit by maximum likelihood ['nlmerMod'] Formula: circumference ~ SSlogis(age, Asym, xmid, scal) ~ Asym | Tree Data: Orange AIC BIC logLik -2*log(L) df.resid 273.1 280.9 -131.6 263.1 30 Scaled residuals: Min 1Q Median 3Q Max -1.9170 -0.5421 0.1754 0.7116 1.6820 Random effects: Groups Name Variance Std.Dev. Tree Asym 1001.49 31.646 Residual 61.51 7.843 Number of obs: 35, groups: Tree, 5 Fixed effects: Estimate Std. Error t value Asym 192.05 15.58 12.32 xmid 727.90 34.44 21.14 scal 348.07 26.31 13.23 Correlation of Fixed Effects: Asym xmid xmid 0.384 scal 0.362 0.762 > > > > cleanEx() > nameEx("SimGeospat") > ### * SimGeospat > > flush(stderr()); flush(stdout()) > > ### Name: SimGeospat > ### Title: Simulated data from a geospatial study with continuous outcomes > ### Aliases: SimGeospat > > ### ** Examples > > #Data were generated with the following code: > n <- 600 > SimGeospat <- data.frame(x = runif(n,-1,1), y = runif(n,-1,1)) > > sim_model <- Model$new( + formula = ~ (1|fexp(x,y)), + data = SimGeospat, + covariance = c(0.25,0.8), + mean = c(0), + family = gaussian() + ) > > SimGeospat$y <- sim_model$sim_data() > > > > cleanEx() > nameEx("SimTrial") > ### * SimTrial > > flush(stderr()); flush(stdout()) > > ### Name: SimTrial > ### Title: Simulated data from a stepped-wedge cluster trial > ### Aliases: SimTrial > > ### ** Examples > > #Data were generated with the following code: > SimTrial <- nelder(~ (cl(10)*t(7))>i(10)) > SimTrial$int <- 0 > SimTrial[SimTrial$t > SimTrial$cl,'int'] <- 1 > > model <- Model$new( + formula = ~ int + factor(t) - 1 + (1|gr(cl)*ar1(t)), + covariance = c(0.05,0.8), + mean = rep(0,8), + data = SimTrial, + family = gaussian() + ) > > SimTrial$y <- model$sim_data() > > > > cleanEx() > nameEx("cross_df") > ### * cross_df > > flush(stderr()); flush(stdout()) > > ### Name: cross_df > ### Title: Generate crossed block structure > ### Aliases: cross_df > > ### ** Examples > > cross_df(data.frame(t=1:4),data.frame(cl=1:3)) t cl 1 1 1 2 1 2 3 1 3 4 2 1 5 2 2 6 2 3 7 3 1 8 3 2 9 3 3 10 4 1 11 4 2 12 4 3 > > > > cleanEx() > nameEx("hessian_from_formula") > ### * hessian_from_formula > > flush(stderr()); flush(stdout()) > > ### Name: hessian_from_formula > ### Title: Automatic differentiation of formulae > ### Aliases: hessian_from_formula > > ### ** Examples > > # obtain the Jacobian and Hessian of the log-binomial model log-likelihood. > # The model is of data from an intervention and control group > # with n1 and n0 participants, respectively, with y1 and y0 the number of events in each group. > # The mean is exp(alpha) in the control > # group and exp(alpha + beta) in the intervention group, so that beta is the log relative risk. > hessian_from_formula( + form_ = "(y1)*(a+b)+((n1)-(y1))*log((1-exp(a+b)))+(y0)*a+((n0)-(y0))*log((1-exp(a)))", + data_ = matrix(c(10,100,20,100), nrow = 1), + colnames_ = c("y1","n1","y0","n0"), + parameters_ = c(log(0.1),log(0.5))) $vec [1] 16.374269 5.263158 $mat [,1] [,2] [1,] -14.86269 -4.98615 [2,] -4.98615 -4.98615 > > > > cleanEx() > nameEx("hsgp_rescale") > ### * hsgp_rescale > > flush(stderr()); flush(stdout()) > > ### Name: hsgp_rescale > ### Title: Rescales data to [-1,1] > ### Aliases: hsgp_rescale > > ### ** Examples > > df <- data.frame(x = runif(100,0,2), y = runif(100, -2,2)) > df <- hsgp_rescale(df, 1:2) > > > > cleanEx() > nameEx("lme4_to_glmmr") > ### * lme4_to_glmmr > > flush(stderr()); flush(stdout()) > > ### Name: lme4_to_glmmr > ### Title: Map lme4 formula to glmmrBase formula > ### Aliases: lme4_to_glmmr > > ### ** Examples > > df <- data.frame(cl = 1:3, t = 4:6) > f1 <- lme4_to_glmmr(y ~ x + (1|cl/t),colnames(df)) > > > > cleanEx() > nameEx("match_rows") > ### * match_rows > > flush(stderr()); flush(stdout()) > > ### Name: match_rows > ### Title: Generate matrix mapping between data frames > ### Aliases: match_rows > > ### ** Examples > > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df_unique <- df[!duplicated(df[,c('cl','t')]),] > match_rows(df,df_unique,c('cl','t')) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [2,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [3,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [4,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [5,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [6,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [7,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [8,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [9,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [10,] 1 0 0 0 0 0 0 0 0 0 0 0 0 [11,] 0 1 0 0 0 0 0 0 0 0 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[68,] 0 [69,] 0 [70,] 0 [71,] 0 [72,] 0 [73,] 0 [74,] 0 [75,] 0 [76,] 0 [77,] 0 [78,] 0 [79,] 0 [80,] 0 [81,] 0 [82,] 0 [83,] 0 [84,] 0 [85,] 0 [86,] 0 [87,] 0 [88,] 0 [89,] 0 [90,] 0 [91,] 0 [92,] 0 [93,] 0 [94,] 0 [95,] 0 [96,] 0 [97,] 0 [98,] 0 [99,] 0 [100,] 0 [101,] 0 [102,] 0 [103,] 0 [104,] 0 [105,] 0 [106,] 0 [107,] 0 [108,] 0 [109,] 0 [110,] 0 [111,] 0 [112,] 0 [113,] 0 [114,] 0 [115,] 0 [116,] 0 [117,] 0 [118,] 0 [119,] 0 [120,] 0 [121,] 0 [122,] 0 [123,] 0 [124,] 0 [125,] 0 [126,] 0 [127,] 0 [128,] 0 [129,] 0 [130,] 0 [131,] 0 [132,] 0 [133,] 0 [134,] 0 [135,] 0 [136,] 0 [137,] 0 [138,] 0 [139,] 0 [140,] 0 [141,] 0 [142,] 0 [143,] 0 [144,] 0 [145,] 0 [146,] 0 [147,] 0 [148,] 0 [149,] 0 [150,] 0 [151,] 0 [152,] 0 [153,] 0 [154,] 0 [155,] 0 [156,] 0 [157,] 0 [158,] 0 [159,] 0 [160,] 0 [161,] 0 [162,] 0 [163,] 0 [164,] 0 [165,] 0 [166,] 0 [167,] 0 [168,] 0 [169,] 0 [170,] 0 [171,] 0 [172,] 0 [173,] 0 [174,] 0 [175,] 0 [176,] 0 [177,] 0 [178,] 0 [179,] 0 [180,] 0 [181,] 0 [182,] 0 [183,] 0 [184,] 0 [185,] 0 [186,] 0 [187,] 0 [188,] 0 [189,] 0 [190,] 0 [191,] 0 [192,] 0 [193,] 0 [194,] 0 [195,] 0 [196,] 0 [197,] 0 [198,] 0 [199,] 0 [200,] 0 [201,] 0 [202,] 0 [203,] 0 [204,] 0 [205,] 0 [206,] 0 [207,] 0 [208,] 0 [209,] 0 [210,] 0 [211,] 0 [212,] 0 [213,] 0 [214,] 0 [215,] 0 [216,] 0 [217,] 0 [218,] 0 [219,] 0 [220,] 0 [221,] 0 [222,] 0 [223,] 0 [224,] 0 [225,] 0 [226,] 0 [227,] 0 [228,] 0 [229,] 0 [230,] 0 [231,] 0 [232,] 0 [233,] 0 [234,] 0 [235,] 0 [236,] 0 [237,] 0 [238,] 0 [239,] 0 [240,] 0 [241,] 0 [242,] 0 [243,] 0 [244,] 0 [245,] 0 [246,] 0 [247,] 0 [248,] 0 [249,] 0 [250,] 0 [251,] 0 [252,] 0 [253,] 0 [254,] 0 [255,] 0 [256,] 0 [257,] 0 [258,] 0 [259,] 0 [260,] 0 [261,] 0 [262,] 0 [263,] 0 [264,] 0 [265,] 0 [266,] 0 [267,] 0 [268,] 0 [269,] 0 [270,] 0 [271,] 0 [272,] 0 [273,] 0 [274,] 0 [275,] 0 [276,] 0 [277,] 0 [278,] 0 [279,] 0 [280,] 0 [281,] 0 [282,] 0 [283,] 0 [284,] 0 [285,] 0 [286,] 0 [287,] 0 [288,] 0 [289,] 0 [290,] 0 [291,] 0 [292,] 0 [293,] 0 [294,] 0 [295,] 0 [296,] 0 [297,] 0 [298,] 0 [299,] 0 [300,] 0 [301,] 0 [302,] 0 [303,] 0 [304,] 0 [305,] 0 [306,] 0 [307,] 0 [308,] 0 [309,] 0 [310,] 0 [311,] 0 [312,] 0 [313,] 0 [314,] 0 [315,] 0 [316,] 0 [317,] 0 [318,] 0 [319,] 0 [320,] 0 [321,] 0 [322,] 0 [323,] 0 [324,] 0 [325,] 0 [326,] 0 [327,] 0 [328,] 0 [329,] 0 [330,] 0 [331,] 0 [332,] 0 [333,] 0 [334,] 0 [335,] 0 [336,] 0 [337,] 0 [338,] 0 [339,] 0 [340,] 0 [341,] 0 [342,] 0 [343,] 0 [344,] 0 [345,] 0 [346,] 0 [347,] 0 [348,] 0 [349,] 0 [350,] 0 [351,] 0 [352,] 0 [353,] 0 [354,] 0 [355,] 0 [356,] 0 [357,] 0 [358,] 0 [359,] 0 [360,] 0 [361,] 0 [362,] 0 [363,] 0 [364,] 0 [365,] 0 [366,] 0 [367,] 0 [368,] 0 [369,] 0 [370,] 0 [371,] 0 [372,] 0 [373,] 0 [374,] 0 [375,] 0 [376,] 0 [377,] 0 [378,] 0 [379,] 0 [380,] 0 [381,] 0 [382,] 0 [383,] 0 [384,] 0 [385,] 0 [386,] 0 [387,] 0 [388,] 0 [389,] 0 [390,] 0 [391,] 0 [392,] 0 [393,] 0 [394,] 0 [395,] 0 [396,] 0 [397,] 0 [398,] 0 [399,] 0 [400,] 0 [401,] 0 [402,] 0 [403,] 0 [404,] 0 [405,] 0 [406,] 0 [407,] 0 [408,] 0 [409,] 0 [410,] 0 [411,] 0 [412,] 0 [413,] 0 [414,] 0 [415,] 0 [416,] 0 [417,] 0 [418,] 0 [419,] 0 [420,] 0 [421,] 0 [422,] 0 [423,] 0 [424,] 0 [425,] 0 [426,] 0 [427,] 0 [428,] 0 [429,] 0 [430,] 0 [431,] 0 [432,] 0 [433,] 0 [434,] 0 [435,] 0 [436,] 0 [437,] 0 [438,] 0 [439,] 0 [440,] 0 [441,] 0 [442,] 0 [443,] 0 [444,] 0 [445,] 0 [446,] 0 [447,] 0 [448,] 0 [449,] 0 [450,] 0 [451,] 0 [452,] 0 [453,] 0 [454,] 0 [455,] 0 [456,] 0 [457,] 0 [458,] 0 [459,] 0 [460,] 0 [461,] 0 [462,] 0 [463,] 0 [464,] 0 [465,] 0 [466,] 0 [467,] 0 [468,] 0 [469,] 0 [470,] 0 [471,] 0 [472,] 0 [473,] 0 [474,] 0 [475,] 0 [476,] 0 [477,] 0 [478,] 0 [479,] 0 [480,] 0 [481,] 0 [482,] 0 [483,] 0 [484,] 0 [485,] 0 [486,] 0 [487,] 0 [488,] 0 [489,] 0 [490,] 0 [491,] 1 [492,] 1 [493,] 1 [494,] 1 [495,] 1 [496,] 1 [497,] 1 [498,] 1 [499,] 1 [500,] 1 > > > > cleanEx() > nameEx("mcml_glmer") > ### * mcml_glmer > > flush(stderr()); flush(stdout()) > > ### Name: mcml_glmer > ### Title: lme4 style generlized linear mixed model > ### Aliases: mcml_glmer > > ### ** Examples > > #create a data frame describing a cross-sectional parallel cluster > data(Salamanders, package = "glmmrBase") > ## Not run: > ##D glm0 <- mcml_glmer(mating~fpop:mpop-1+(1|mnum)+(1|fnum), > ##D data=Salamanders,family=binomial(),reml=FALSE) > ##D glm1 <- mcml_glmer(mating~fpop:mpop-1+(1|mnum)+(1|fnum), > ##D data =Salamanders, family=binomial(),reml=TRUE) > ## End(Not run) > > > > cleanEx() > nameEx("mcml_lmer") > ### * mcml_lmer > > flush(stderr()); flush(stdout()) > > ### Name: mcml_lmer > ### Title: lme4 style linear mixed model > ### Aliases: mcml_lmer > > ### ** Examples > > #create a data frame describing a cross-sectional parallel cluster > #randomised trial > df <- nelder(~(cl(10)*t(5)) > ind(10)) > df$int <- 0 > df[df$cl > 5, 'int'] <- 1 > # simulate data using the Model class > df$y <- Model$new( + formula = ~ factor(t) + int - 1 + (1|gr(cl)) + (1|gr(cl,t)), + data = df, + family = stats::gaussian() + )$sim_data() > ## Not run: > ##D fit <- mcml_lmer(y ~ factor(t) + int - 1 + (1|cl/t), data = df) > ## End(Not run) > > > > cleanEx() > nameEx("mesh_helper") > ### * mesh_helper > > flush(stderr()); flush(stdout()) > > ### Name: mesh_helper > ### Title: Generates the required mesh data from fmesher for SPDE > ### approximations > ### Aliases: mesh_helper > > ### ** Examples > > df <- data.frame( + x = runif(100, -1, 1), + y = runif(100, -1, 1)) > mesh <- mesh_helper(df, max_edge = c(0.15, 0.75), cutoff = 0.075, offset = c(0.1,0.3)) > > > > cleanEx() > nameEx("nelder") > ### * nelder > > flush(stderr()); flush(stdout()) > > ### Name: nelder > ### Title: Generates a block experimental structure using Nelder's formula > ### Aliases: nelder > > ### ** Examples > > nelder(~(j(4) * t(5)) > i(5)) j t i 1 1 1 1 2 1 1 2 3 1 1 3 4 1 1 4 5 1 1 5 6 1 2 6 7 1 2 7 8 1 2 8 9 1 2 9 10 1 2 10 11 1 3 11 12 1 3 12 13 1 3 13 14 1 3 14 15 1 3 15 16 1 4 16 17 1 4 17 18 1 4 18 19 1 4 19 20 1 4 20 21 1 5 21 22 1 5 22 23 1 5 23 24 1 5 24 25 1 5 25 26 2 1 26 27 2 1 27 28 2 1 28 29 2 1 29 30 2 1 30 31 2 2 31 32 2 2 32 33 2 2 33 34 2 2 34 35 2 2 35 36 2 3 36 37 2 3 37 38 2 3 38 39 2 3 39 40 2 3 40 41 2 4 41 42 2 4 42 43 2 4 43 44 2 4 44 45 2 4 45 46 2 5 46 47 2 5 47 48 2 5 48 49 2 5 49 50 2 5 50 51 3 1 51 52 3 1 52 53 3 1 53 54 3 1 54 55 3 1 55 56 3 2 56 57 3 2 57 58 3 2 58 59 3 2 59 60 3 2 60 61 3 3 61 62 3 3 62 63 3 3 63 64 3 3 64 65 3 3 65 66 3 4 66 67 3 4 67 68 3 4 68 69 3 4 69 70 3 4 70 71 3 5 71 72 3 5 72 73 3 5 73 74 3 5 74 75 3 5 75 76 4 1 76 77 4 1 77 78 4 1 78 79 4 1 79 80 4 1 80 81 4 2 81 82 4 2 82 83 4 2 83 84 4 2 84 85 4 2 85 86 4 3 86 87 4 3 87 88 4 3 88 89 4 3 89 90 4 3 90 91 4 4 91 92 4 4 92 93 4 4 93 94 4 4 94 95 4 4 95 96 4 5 96 97 4 5 97 98 4 5 98 99 4 5 99 100 4 5 100 > nelder(~person(5) * time(10)) person time 1 1 1 2 1 2 3 1 3 4 1 4 5 1 5 6 1 6 7 1 7 8 1 8 9 1 9 10 1 10 11 2 1 12 2 2 13 2 3 14 2 4 15 2 5 16 2 6 17 2 7 18 2 8 19 2 9 20 2 10 21 3 1 22 3 2 23 3 3 24 3 4 25 3 5 26 3 6 27 3 7 28 3 8 29 3 9 30 3 10 31 4 1 32 4 2 33 4 3 34 4 4 35 4 5 36 4 6 37 4 7 38 4 8 39 4 9 40 4 10 41 5 1 42 5 2 43 5 3 44 5 4 45 5 5 46 5 6 47 5 7 48 5 8 49 5 9 50 5 10 > > > > cleanEx() > nameEx("nest_df") > ### * nest_df > > flush(stderr()); flush(stdout()) > > ### Name: nest_df > ### Title: Generate nested block structure > ### Aliases: nest_df > > ### ** Examples > > nest_df(data.frame(t=1:4),data.frame(cl=1:3)) t cl 1 1 1 2 1 2 3 1 3 4 2 4 5 2 5 6 2 6 7 3 7 8 3 8 9 3 9 10 4 10 11 4 11 12 4 12 > > > > cleanEx() > nameEx("progress_bar") > ### * progress_bar > > flush(stderr()); flush(stdout()) > > ### Name: progress_bar > ### Title: Generates a progress bar > ### Aliases: progress_bar > > ### ** Examples > > progress_bar(10,100) [1] "|=== | 10%" > > > > ### *